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Sample records for investigate microbial metabolism

  1. Summer investigations into the metabolic diversity of the microbial world

    Energy Technology Data Exchange (ETDEWEB)

    Breznak, J.; Dworkin, M.

    1993-05-17

    The philosophy of the course described here is to underscore the essence of microbiology which is diversity>: diversity of morphology and cellular development, behavior, and metabolic and physiological functions. Emphasis is on microbes other than those customarily covered in conventional microbiology courses and includes: the archaebacteria, extremophiles, and array of obligate anaerobes, various phototrophs, and those microbes exhibiting complex developmental cycles. Also included are microbes carrying out a variety of transformations of organic and inorganic compounds, as well as those which normally occur in symbiotic association with other microbes or with higher forms of life.

  2. Noninvasive analysis of metabolic changes following nutrient input into diverse fish species, as investigated by metabolic and microbial profiling approaches

    Directory of Open Access Journals (Sweden)

    Taiga Asakura

    2014-10-01

    Full Text Available An NMR-based metabolomic approach in aquatic ecosystems is valuable for studying the environmental effects of pharmaceuticals and other chemicals on fish. This technique has also contributed to new information in numerous research areas, such as basic physiology and development, disease, and water pollution. We evaluated the microbial diversity in various fish species collected from Japan’s coastal waters using next-generation sequencing, followed by evaluation of the effects of feed type on co-metabolic modulations in fish-microbial symbiotic ecosystems in laboratory-scale experiments. Intestinal bacteria of fish in their natural environment were characterized (using 16S rRNA genes for trophic level using pyrosequencing and noninvasive sampling procedures developed to study the metabolism of intestinal symbiotic ecosystems in fish reared in their environment. Metabolites in feces were compared, and intestinal contents and feed were annotated based on HSQC and TOCSY using SpinAssign and network analysis. Feces were characterized by species and varied greatly depending on the feeding types. In addition, feces samples demonstrated a response to changes in the time series of feeding. The potential of this approach as a non-invasive inspection technique in aquaculture is suggested.

  3. Investigations into the metabolic diversity of microorganisms as part of microbial diversity

    Energy Technology Data Exchange (ETDEWEB)

    Leadbetter, Jared [California Inst. of Technology (CalTech), Pasadena, CA (United States)

    2016-07-25

    DOE funds supported a key portion of the MBL Microbial Diversity (Woods Hole) program across 6 complete summers. The initial 4 years of the funded period were overseen by two co-Directors, Daniel Buckley (Cornell) and Steve Zinder (Cornell), who then completed their term. The final 2 summers were overseen by 2 new co-Directors, Jared R. Leadbetter (Caltech) and Dianne Newman (Caltech). The 6 funded summer iterations of the course included the incorporation of new themes such as single cell approaches applied to natural microbial communities (cell separation and sorting, genome amplification from single cells, and the use of Nano-SIMS to examine assimilation of carbon and nitrogen from isotopically labeled substrates into single cells), genetics and genomics on bacteria freshly isolated during the course of the programs, quantitative systems biology, and modern quantitative light microscopy.

  4. Thermodynamic Driving Force of Hydrogen on Rumen Microbial Metabolism: A Theoretical Investigation.

    Science.gov (United States)

    van Lingen, Henk J; Plugge, Caroline M; Fadel, James G; Kebreab, Ermias; Bannink, André; Dijkstra, Jan

    2016-01-01

    Hydrogen is a key product of rumen fermentation and has been suggested to thermodynamically control the production of the various volatile fatty acids (VFA). Previous studies, however, have not accounted for the fact that only thermodynamic near-equilibrium conditions control the magnitude of reaction rate. Furthermore, the role of NAD, which is affected by hydrogen partial pressure (PH2), has often not been considered. The aim of this study was to quantify the control of PH2 on reaction rates of specific fermentation pathways, methanogenesis and NADH oxidation in rumen microbes. The control of PH2 was quantified using the thermodynamic potential factor (FT), which is a dimensionless factor that corrects a predicted kinetic reaction rate for the thermodynamic control exerted. Unity FT was calculated for all glucose fermentation pathways considered, indicating no inhibition of PH2 on the production of a specific type of VFA (e.g., acetate, propionate and butyrate) in the rumen. For NADH oxidation without ferredoxin oxidation, increasing PH2 within the rumen physiological range decreased FT from unity to zero for different NAD+ to NADH ratios and pH of 6.2 and 7.0, which indicates thermodynamic control of PH2. For NADH oxidation with ferredoxin oxidation, increasing PH2 within the rumen physiological range decreased FT from unity at pH of 7.0 only. For the acetate to propionate conversion, FT increased from 0.65 to unity with increasing PH2, which indicates thermodynamic control. For propionate to acetate and butyrate to acetate conversions, FT decreased to zero below the rumen range of PH2, indicating full thermodynamic suppression. For methanogenesis by archaea without cytochromes, FT differed from unity only below the rumen range of PH2, indicating no thermodynamic control. This theoretical investigation shows that thermodynamic control of PH2 on individual VFA produced and associated yield of hydrogen and methane cannot be explained without considering NADH

  5. Microbial Metabolism in Serpentinite Fluids

    Science.gov (United States)

    Crespo-Medina, M.; Brazelton, W. J.; Twing, K. I.; Kubo, M.; Hoehler, T. M.; Schrenk, M. O.

    2013-12-01

    Serpentinization is the process in which ultramafic rocks, characteristic of the upper mantle, react with water liberating mantle carbon and reducing power to potenially support chemosynthetic microbial communities. These communities may be important mediators of carbon and energy exchange between the deep Earth and the surface biosphere. Our work focuses on the Coast Range Ophiolite Microbial Observatory (CROMO) in Northern California where subsurface fluids are accessible through a series of wells. Preliminary analyses indicate that the highly basic fluids (pH 9-12) have low microbial diversity, but there is limited knowledge about the metabolic capabilities of these communties. Metagenomic data from similar serpentine environments [1] have identified Betaproteobacteria belonging to the order Burkholderiales and Gram-positive bacteria from the order Clostridiales as key components of the serpentine microbiome. In an effort to better characterize the microbial community, metabolism, and geochemistry at CROMO, fluids from two representative wells (N08B and CSWold) were sampled during recent field campaigns. Geochemical characterization of the fluids includes measurements of dissolved gases (H2, CO, CH4), dissolved inorganic and organic carbon, volatile fatty acids, and nutrients. The wells selected can be differentiated in that N08B had higher pH (10-11), lower dissolved oxygen, and cell counts ranging from 105-106 cells mL-1 of fluid, with an abundance of the betaproteobacterium Hydrogenophaga. In contrast, fluids from CSWold have slightly lower pH (9-9.5), DO, and conductivity, as well as higher TDN and TDP. CSWold fluid is also characterized for having lower cell counts (~103 cells mL-1) and an abundance of Dethiobacter, a taxon within the phylum Clostridiales. Microcosm experiments were conducted with the purpose of monitoring carbon fixation, methanotrophy and metabolism of small organic compounds, such as acetate and formate, while tracing changes in fluid

  6. Microbial Metabolism in Permafrost and Ice

    Science.gov (United States)

    Price, P. B.; Bramall, N.; Bay, R. C.

    2003-12-01

    Metabolic rates of microbial communities at low temperature have not been systematically studied, despite discoveries of microbes that survive with very little nutrient in ice, permafrost, and deep open-ocean sites, and despite interest in possible life on Mars and Europa. We investigated the temperature-dependence of growth rates kg, maintenance rates km, and survival rates ks, using existing data on kg(T) for permafrost bacteria, on km(T) using radiotracers, and on ks(T) using geochemical methods. Data were collected for temperatures from 28° C to -40° C. The rates for the three modes are consistent with a single activation energy U ≈ 100-110 kJ/mol, and they scale as kg(T):km(T):ks(T) ≈ 107:104:1. The rate ks(T) for survival of a dormant microbial community is found to be roughly that required solely for repairing molecular damage due to amino acid racemization + DNA depurination. We conclude that for living microbes the rate of molecular repair equals the rate of molecular damage. There is no indication of a threshold temperature for metabolism, at least down to -40° C. To assay microbial life in the coldest terrestrial environments (down to -55° C) and in future to search for present or past life on Mars, we have designed a miniaturized biospectral logger that will fit into a 4-cm borehole in ice, permafrost and rock. The logger will use side-directed laser beams at wavelengths 224 and 370 nm to detect autofluorescence of biomolecules and discriminate against mineral autofluorescence. Six channels will map fluorescence spectra and a seventh channel will measure light scattered from dust (in ice) or rock (in permafrost). Fluorescent biomolecules of interest include tryptophan, tyrosine, NADH, FAD, F420, chlorophyll, bacteriorhodopsin, porphyrins, pyoverdin, PAHs, humic acid, and fulvic acid. The logger will be able to detect microbial concentrations as low as 1 cell cm-3 in clean ice.

  7. Methylobacterium genome sequences: a reference blueprint to investigate microbial metabolism of C1 compounds from natural and industrial sources.

    Directory of Open Access Journals (Sweden)

    Stéphane Vuilleumier

    Full Text Available Methylotrophy describes the ability of organisms to grow on reduced organic compounds without carbon-carbon bonds. The genomes of two pink-pigmented facultative methylotrophic bacteria of the Alpha-proteobacterial genus Methylobacterium, the reference species Methylobacterium extorquens strain AM1 and the dichloromethane-degrading strain DM4, were compared.The 6.88 Mb genome of strain AM1 comprises a 5.51 Mb chromosome, a 1.26 Mb megaplasmid and three plasmids, while the 6.12 Mb genome of strain DM4 features a 5.94 Mb chromosome and two plasmids. The chromosomes are highly syntenic and share a large majority of genes, while plasmids are mostly strain-specific, with the exception of a 130 kb region of the strain AM1 megaplasmid which is syntenic to a chromosomal region of strain DM4. Both genomes contain large sets of insertion elements, many of them strain-specific, suggesting an important potential for genomic plasticity. Most of the genomic determinants associated with methylotrophy are nearly identical, with two exceptions that illustrate the metabolic and genomic versatility of Methylobacterium. A 126 kb dichloromethane utilization (dcm gene cluster is essential for the ability of strain DM4 to use DCM as the sole carbon and energy source for growth and is unique to strain DM4. The methylamine utilization (mau gene cluster is only found in strain AM1, indicating that strain DM4 employs an alternative system for growth with methylamine. The dcm and mau clusters represent two of the chromosomal genomic islands (AM1: 28; DM4: 17 that were defined. The mau cluster is flanked by mobile elements, but the dcm cluster disrupts a gene annotated as chelatase and for which we propose the name "island integration determinant" (iid.These two genome sequences provide a platform for intra- and interspecies genomic comparisons in the genus Methylobacterium, and for investigations of the adaptive mechanisms which allow bacterial lineages to acquire

  8. Controlling fluxes for microbial metabolic engineering

    OpenAIRE

    Sachdeva, Gairik

    2014-01-01

    This thesis presents novel synthetic biology tools and design principles usable for microbial metabolic engineering. Controlling metabolic fluxes is essential for biological manufacturing of fuels, materials, and high value chemicals. Insulating the flow of metabolites is a successful natural strategy for metabolic flux regulation. Recently, approaches using scaffolds, both in vitro and in vivo, to spatially co-localize enzymes have reported significant gains in product yields. RNA is suitabl...

  9. Summer investigations into the metabolic diversity of the microbial world. Progress report, May 5, 1992--April 30, 1993

    Energy Technology Data Exchange (ETDEWEB)

    Breznak, J.; Dworkin, M.

    1993-05-17

    The philosophy of the course described here is to underscore the essence of microbiology which is diversity>: diversity of morphology and cellular development, behavior, and metabolic and physiological functions. Emphasis is on microbes other than those customarily covered in conventional microbiology courses and includes: the archaebacteria, extremophiles, and array of obligate anaerobes, various phototrophs, and those microbes exhibiting complex developmental cycles. Also included are microbes carrying out a variety of transformations of organic and inorganic compounds, as well as those which normally occur in symbiotic association with other microbes or with higher forms of life.

  10. Multidimensional optimality of microbial metabolism

    NARCIS (Netherlands)

    Schuetz, Robert; Zamboni, Nicola; Zampieri, Mattia; Heinemann, Matthias; Sauer, Uwe

    2012-01-01

    Although the network topology of metabolism is well known, understanding the principles that govern the distribution of fluxes through metabolism lags behind. Experimentally, these fluxes can be measured by (13)C-flux analysis, and there has been a long-standing interest in understanding this

  11. Enhancing microbial production of biofuels by expanding microbial metabolic pathways.

    Science.gov (United States)

    Yu, Ping; Chen, Xingge; Li, Peng

    2017-09-01

    Fatty acid, isoprenoid, and alcohol pathways have been successfully engineered to produce biofuels. By introducing three genes, atfA, adhE, and pdc, into Escherichia coli to expand fatty acid pathway, up to 1.28 g/L of fatty acid ethyl esters can be achieved. The isoprenoid pathway can be expanded to produce bisabolene with a high titer of 900 mg/L in Saccharomyces cerevisiae. Short- and long-chain alcohols can also be effectively biosynthesized by extending the carbon chain of ketoacids with an engineered "+1" alcohol pathway. Thus, it can be concluded that expanding microbial metabolic pathways has enormous potential for enhancing microbial production of biofuels for future industrial applications. However, some major challenges for microbial production of biofuels should be overcome to compete with traditional fossil fuels: lowering production costs, reducing the time required to construct genetic elements and to increase their predictability and reliability, and creating reusable parts with useful and predictable behavior. To address these challenges, several aspects should be further considered in future: mining and transformation of genetic elements related to metabolic pathways, assembling biofuel elements and coordinating their functions, enhancing the tolerance of host cells to biofuels, and creating modular subpathways that can be easily interconnected. © 2016 International Union of Biochemistry and Molecular Biology, Inc.

  12. EVA Suit Microbial Leakage Investigation

    Data.gov (United States)

    National Aeronautics and Space Administration — The objective of this project is to collect microbial samples from various EVA suits to determine how much microbial contamination is typically released during...

  13. Coupling spatiotemporal community assembly processes to changes in microbial metabolism

    Directory of Open Access Journals (Sweden)

    Emily B. Graham

    2016-12-01

    Full Text Available Community assembly processes generate shifts in species abundances that influence ecosystem cycling of carbon and nutrients, yet our understanding of assembly remains largely separate from ecosystem-level functioning. Here, we investigate relationships between assembly and changes in microbial metabolism across space and time in hyporheic microbial communities. We pair sampling of two habitat types (i.e., attached and planktonic through seasonal and sub-hourly hydrologic fluctuation with null modeling and temporally-explicit multivariate statistics. We demonstrate that multiple selective pressures—imposed by sediment and porewater physicochemistry—integrate to generate changes in microbial community composition at distinct timescales among habitat types. These changes in composition are reflective of contrasting associations of Betaproteobacteria and Thaumarchaeota with ecological selection and with seasonal changes in microbial metabolism. We present a conceptual model based on our results in which metabolism increases when oscillating selective pressures oppose temporally-stable selective pressures. Our conceptual model is pertinent to both macrobial and microbial systems experiencing multiple selective pressures and presents an avenue for assimilating community assembly processes into predictions of ecosystem-level functioning.

  14. Microbial nitrogen metabolism: response to warming and resource supply

    Science.gov (United States)

    Buckeridge, K. M.; Min, K.; Lehmeier, C.; Ballantyne, F.; Billings, S. A.

    2013-12-01

    Ecosystem nitrogen (N) dynamics are dependent on microbial metabolic responses to a changing climate. Most studies that investigate soil microbial N dynamics in response to temperature employ measurements reflective of many interacting and confounding phenomena, as altering soil temperature can simultaneously alter moisture regime, substrate availability, and competitive dynamics between microbial populations. As a result, it is difficult to discern how temperature alone can alter patterns of microbial N metabolism using whole soils. Without that knowledge, it is impossible to parse temperature effects on soil N fluxes from other drivers. We address this issue by exploring the sensitivity of microbial partitioning of N between assimilation (growing biomass) and dissimilation (releasing N to the environment) in response to changes in temperature and quality (C:N ratio) of substrate, using a chemostat approach in which a microbial population is maintained at steady state. We perform our experiments using a Gram-negative bacterium (Pseudomonas fluorescens), ubiquitous in soils and dependent on organic compounds to satisfy its resource demand. Individual chemostat runs, all conducted at similar microbial growth rates, generate data describing microbial biomass N, solution N pools and microbial biomass and solution d15N. With these data we can calculate d15N enrichment (d15N microbial biomass - d15N nutrient solution) a proxy for microbial N partitioning. From a recently published model of microbial biomass d15N drivers, fractionation of N occurs with both uptake and excretion of NH3+ so that microbes with a net dissimilation become 15N enriched relative to their source. Because a related study has demonstrated increased microbial C demand with temperature, we predict that in a warming environment microorganisms will become relatively C limited. Accordingly, we hypothesize that warming will enhance microbial dissimilation, and that this N release will be exacerbated as

  15. Investigation of metabolic encephalopathy

    African Journals Online (AJOL)

    , and. Table 1. Confirmed IMD cases associated with metabolic encephalopathy diagnosed at Red Cross Children's Hospital Metabolic Disease. Laboratory, 2006 - 2012. Name of disorder. Number of cases. Glutaric aciduria type 1 (GA1)*. 23.

  16. Metabolic modeling to understand and redesign microbial systems

    NARCIS (Netherlands)

    Heck, van Ruben G.A.

    2017-01-01

    The goals of this thesis are to increase the understanding of microbial metabolism and to functionally (re-)design microbial systems using Genome- Scale Metabolic models (GSMs). GSMs are species-specific knowledge repositories that can be used to predict metabolic activities for wildtype and

  17. Microbial community assembly and metabolic function during mammalian corpse decomposition

    Energy Technology Data Exchange (ETDEWEB)

    Metcalf, J. L.; Xu, Z. Z.; Weiss, S.; Lax, S.; Van Treuren, W.; Hyde, E. R.; Song, S. J.; Amir, A.; Larsen, P.; Sangwan, N.; Haarmann, D.; Humphrey, G. C.; Ackermann, G.; Thompson, L. R.; Lauber, C.; Bibat, A.; Nicholas, C.; Gebert, M. J.; Petrosino, J. F.; Reed, S. C.; Gilbert, J. A.; Lynne, A. M.; Bucheli, S. R.; Carter, D. O.; Knight, R.

    2015-12-10

    Vertebrate corpse decomposition provides an important stage in nutrient cycling in most terrestrial habitats, yet microbially mediated processes are poorly understood. Here we combine deep microbial community characterization, community-level metabolic reconstruction, and soil biogeochemical assessment to understand the principles governing microbial community assembly during decomposition of mouse and human corpses on different soil substrates. We find a suite of bacterial and fungal groups that contribute to nitrogen cycling and a reproducible network of decomposers that emerge on predictable time scales. Our results show that this decomposer community is derived primarily from bulk soil, but key decomposers are ubiquitous in low abundance. Soil type was not a dominant factor driving community development, and the process of decomposition is sufficiently reproducible to offer new opportunities for forensic investigations.

  18. Effects of introducing heterologous pathways on microbial metabolism with respect to metabolic optimality

    DEFF Research Database (Denmark)

    Kim, Hyun Uk; Kim, Byoungjin; Seung, Do Young

    2014-01-01

    Although optimality of microbial metabolism under genetic and environmental perturbations is well studied, the effects of introducing heterologous reactions on the overall metabolism are not well understood. This point is important in the field of metabolic engineering because heterologous reacti...

  19. Gut Microbial Glycerol Metabolism as an Endogenous Acrolein Source

    Directory of Open Access Journals (Sweden)

    Jianbo Zhang

    2018-01-01

    Full Text Available Acrolein is a highly reactive electrophile causing toxic effects, such as DNA and protein adduction, oxidative stress, endoplasmic reticulum stress, immune dysfunction, and membrane damage. This Opinion/Hypothesis provides an overview of endogenous and exogenous acrolein sources, acrolein’s mode of action, and its metabolic fate. Recent reports underpin the finding that gut microbial glycerol metabolism leading to the formation of reuterin is an additional source of endogenous acrolein. Reuterin is an antimicrobial multicomponent system consisting of 3-hydroxypropionaldehyde, its dimer and hydrate, and also acrolein. The major conclusion is that gut microbes can metabolize glycerol to reuterin and that this transformation occurs in vivo. Given the known toxicity of acrolein, the observation that acrolein is formed in the gut necessitates further investigations on functional relevance for gut microbiota and the host.

  20. Metaproteomics: extracting and mining proteome information to characterize metabolic activities in microbial communities

    Energy Technology Data Exchange (ETDEWEB)

    Abraham, Paul E [ORNL; Giannone, Richard J [ORNL; Xiong, Weili [ORNL; Hettich, Robert {Bob} L [ORNL

    2014-01-01

    Contemporary microbial ecology studies usually employ one or more omics approaches to investigate the structure and function of microbial communities. Among these, metaproteomics aims to characterize the metabolic activities of the microbial membership, providing a direct link between the genetic potential and functional metabolism. The successful deployment of metaproteomics research depends on the integration of high-quality experimental and bioinformatic techniques for uncovering the metabolic activities of a microbial community in a way that is complementary to other meta-omic approaches. The essential, quality-defining informatics steps in metaproteomics investigations are: (1) construction of the metagenome, (2) functional annotation of predicted protein-coding genes, (3) protein database searching, (4) protein inference, and (5) extraction of metabolic information. In this article, we provide an overview of current bioinformatic approaches and software implementations in metaproteome studies in order to highlight the key considerations needed for successful implementation of this powerful community-biology tool.

  1. Unravelling core microbial metabolisms in the hypersaline microbial mats of Shark Bay using high-throughput metagenomics

    Energy Technology Data Exchange (ETDEWEB)

    Ruvindy, Rendy; White III, Richard Allen; Neilan, Brett Anthony; Burns, Brendan Paul

    2015-05-29

    Modern microbial mats are potential analogues of some of Earth’s earliest ecosystems. Excellent examples can be found in Shark Bay, Australia, with mats of various morphologies. To further our understanding of the functional genetic potential of these complex microbial ecosystems, we conducted for the first time shotgun metagenomic analyses. We assembled metagenomic nextgeneration sequencing data to classify the taxonomic and metabolic potential across diverse morphologies of marine mats in Shark Bay. The microbial community across taxonomic classifications using protein-coding and small subunit rRNA genes directly extracted from the metagenomes suggests that three phyla Proteobacteria, Cyanobacteria and Bacteriodetes dominate all marine mats. However, the microbial community structure between Shark Bay and Highbourne Cay (Bahamas) marine systems appears to be distinct from each other. The metabolic potential (based on SEED subsystem classifications) of the Shark Bay and Highbourne Cay microbial communities were also distinct. Shark Bay metagenomes have a metabolic pathway profile consisting of both heterotrophic and photosynthetic pathways, whereas Highbourne Cay appears to be dominated almost exclusively by photosynthetic pathways. Alternative non-rubisco-based carbon metabolism including reductive TCA cycle and 3-hydroxypropionate/4-hydroxybutyrate pathways is highly represented in Shark Bay metagenomes while not represented in Highbourne Cay microbial mats or any other mat forming ecosystems investigated to date. Potentially novel aspects of nitrogen cycling were also observed, as well as putative heavy metal cycling (arsenic, mercury, copper and cadmium). Finally, archaea are highly represented in Shark Bay and may have critical roles in overall ecosystem function in these modern microbial mats.

  2. Microbial heterotrophic metabolic rates constrain the microbial carbon pump

    Digital Repository Service at National Institute of Oceanography (India)

    Robinson, C.; Ramaiah, N.

    (2008). 10. P.A. del Giorgio, J. J. Cole, in MicrobialEcologyoftheOceans D. L. Kirchman Ed. (JohnWiley & Sons, Inc. NewYork ed. 1. 2000),pp. 289–325. 11. A. B. Burd etal., DeepSeaRes.II 57, 1557 (2010). 12. S. Martinez-García, E. Fernández, M.... R.A. Straza, D. L. Kirchman, Aquat.Microb.Ecol. 62, 267(2011). 16. O. Hoegh-Guldberg, J. F. Bruno, Science 328,1523 (2010). 17. J. Piontek, M. Lunau, N. Handel, C. Borchard, M.Wurst,A. Engel, Biogeosciences 7, 1615 (2010). 18. J. K.Apple, P.A. del...

  3. Microbial Metabolism and Inhibition Studies of Phenobarbital

    African Journals Online (AJOL)

    Erah

    characterize the pharmacokinetics of potential drugs in man. This type of work requires selective ..... of diclofenac. Saudi. Pharm. J. 1996; 4: 165-. 169. 17. Diez D, Sanchez JM, Rodilla JM, Rocha PM, Mendes. RS, Paulino C, Marcos IS, Basabe P, Urones. JG. Microbial hydroxylation of sclarelol by. Rhizopus stolonifer.

  4. Microbial dark matter investigations: how microbial studies transform biological knowledge and empirically sketch a logic of scientific discovery.

    Science.gov (United States)

    Bernard, Guillaume; Pathmanathan, Jananan S; Lannes, Romain; Lopez, Philippe; Bapteste, Eric

    2018-02-05

    Microbes are the oldest and most widespread, phylogenetically and metabolically diverse life forms on Earth. However, they have been discovered only 334 years ago, and their diversity started to become seriously investigated even later. For these reasons, microbial studies that unveil novel microbial lineages and processes affecting or involving microbes deeply (and repeatedly) transform knowledge in biology. Considering the quantitative prevalence of taxonomically and functionally unassigned sequences in environmental genomics datasets, and that of uncultured microbes on the planet, we propose that unraveling the microbial dark matter should be identified as a central priority for biologists. Based on former empirical findings of microbial studies, we sketch a logic of discovery with the potential to further highlight the microbial unknowns. © The Author(s) 2018. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  5. Microbial Dark Matter Investigations: How Microbial Studies Transform Biological Knowledge and Empirically Sketch a Logic of Scientific Discovery

    Science.gov (United States)

    Bernard, Guillaume; Pathmanathan, Jananan S; Lannes, Romain; Lopez, Philippe; Bapteste, Eric

    2018-01-01

    Abstract Microbes are the oldest and most widespread, phylogenetically and metabolically diverse life forms on Earth. However, they have been discovered only 334 years ago, and their diversity started to become seriously investigated even later. For these reasons, microbial studies that unveil novel microbial lineages and processes affecting or involving microbes deeply (and repeatedly) transform knowledge in biology. Considering the quantitative prevalence of taxonomically and functionally unassigned sequences in environmental genomics data sets, and that of uncultured microbes on the planet, we propose that unraveling the microbial dark matter should be identified as a central priority for biologists. Based on former empirical findings of microbial studies, we sketch a logic of discovery with the potential to further highlight the microbial unknowns. PMID:29420719

  6. Gut Microbial Glycerol Metabolism as an Endogenous Acrolein Source

    OpenAIRE

    Zhang, Jianbo; Sturla, Shana; Lacroix, Christophe; Schwab, Clarissa

    2018-01-01

    ABSTRACT Acrolein is a highly reactive electrophile causing toxic effects, such as DNA and protein adduction, oxidative stress, endoplasmic reticulum stress, immune dysfunction, and membrane damage. This Opinion/Hypothesis provides an overview of endogenous and exogenous acrolein sources, acrolein’s mode of action, and its metabolic fate. Recent reports underpin the finding that gut microbial glycerol metabolism leading to the formation of reuterin is an additional source of endogenous acrole...

  7. Microbial diversity and metabolic networks in acid mine drainage habitats.

    Science.gov (United States)

    Méndez-García, Celia; Peláez, Ana I; Mesa, Victoria; Sánchez, Jesús; Golyshina, Olga V; Ferrer, Manuel

    2015-01-01

    Acid mine drainage (AMD) emplacements are low-complexity natural systems. Low-pH conditions appear to be the main factor underlying the limited diversity of the microbial populations thriving in these environments, although temperature, ionic composition, total organic carbon, and dissolved oxygen are also considered to significantly influence their microbial life. This natural reduction in diversity driven by extreme conditions was reflected in several studies on the microbial populations inhabiting the various micro-environments present in such ecosystems. Early studies based on the physiology of the autochthonous microbiota and the growing success of omics-based methodologies have enabled a better understanding of microbial ecology and function in low-pH mine outflows; however, complementary omics-derived data should be included to completely describe their microbial ecology. Furthermore, recent updates on the distribution of eukaryotes and archaea recovered through sterile filtering (herein referred to as filterable fraction) in these environments demand their inclusion in the microbial characterization of AMD systems. In this review, we present a complete overview of the bacterial, archaeal (including filterable fraction), and eukaryotic diversity in these ecosystems, and include a thorough depiction of the metabolism and element cycling in AMD habitats. We also review different metabolic network structures at the organismal level, which is necessary to disentangle the role of each member of the AMD communities described thus far.

  8. [Microbial metabolism in typical flooded paddy soils ].

    Science.gov (United States)

    Cai, Yuanfeng; Wu, Yucheng; Wang, Shuwei; Yan, Xiaoyuan; Zhu, Yongguan; Jia, Zhongjun

    2014-09-04

    [OBJECTIVE] The object of this study is to reveal the composition of active microorganism and their metabolic activities in flooded paddy soils with long-term fertilization ( Mineral nitrogen, phosphorus, and potassium, NPK) and without fertilizer (Control check, CK) by environmental transcriptomics. [METHODS] Flooded soil microcosms were incubated in the laboratory for two weeks, then total RNA were extracted from the soil for transcriptome sequencing. Resulting fastq files were uploaded to the Metagenomics Analysis Server (MG-RAST) for taxonomic analysis, gene annotation and function classification. [RESULTS] Transcripts from diverse active microorganism, including bacteria ( > 95% ) , archaea, eukaryotes and viruses, were detected in both flooded paddy soils of CK and NPK treatments. Most of the transcripts (active genes) of bacteria and archaea were derived from Proteobacteria (more than 50% of total bacterial transcripts) and Thaumarchaaeota (about 70% of total archaeal transcripts ) respectively in both treatments. Transcriptional activity of Acidobacteria in NPK treatment paddy soil was significantly higher than that in CK treatment paddy soil. As for other phyla of bacteria and archaea, there were no significant differences of transcriptional activity of them between CK and NPK treatment paddy soils. The highest expressed gene in both CK and NPK treatment paddy soils is ABC transporter encoding gene which related to the transmembrane transport of substances. Based on gene function category of COG (Clusters of Orthologous Genes), Subsystem and KEGG (Kyoto Encyclopedia of Genes and Genomes) database, we found that the main metabolic activities of microorganisms in both CK and NPK treatment paddy soils were related to energy production and conversion, carbohydrate metabolism, protein metabolism and amino acid metabolism, and the dominant KEGG pathways were oxidative phosphorylation and aminoacyl-tRNA biosynthesis. [ CONCLUSION] Composition of active

  9. Deep-Sea Hydrothermal Vent Viruses Compensate for Microbial Metabolism in Virus-Host Interactions.

    Science.gov (United States)

    He, Tianliang; Li, Hongyun; Zhang, Xiaobo

    2017-07-11

    Viruses are believed to be responsible for the mortality of host organisms. However, some recent investigations reveal that viruses may be essential for host survival. To date, it remains unclear whether viruses are beneficial or harmful to their hosts. To reveal the roles of viruses in the virus-host interactions, viromes and microbiomes of sediment samples from three deep-sea hydrothermal vents were explored in this study. To exclude the influence of exogenous DNAs on viromes, the virus particles were purified with nuclease (DNase I and RNase A) treatments and cesium chloride density gradient centrifugation. The metagenomic analysis of viromes without exogenous DNA contamination and microbiomes of vent samples indicated that viruses had compensation effects on the metabolisms of their host microorganisms. Viral genes not only participated in most of the microbial metabolic pathways but also formed branched pathways in microbial metabolisms, including pyrimidine metabolism; alanine, aspartate, and glutamate metabolism; nitrogen metabolism and assimilation pathways of the two-component system; selenocompound metabolism; aminoacyl-tRNA biosynthesis; and amino sugar and nucleotide sugar metabolism. As is well known, deep-sea hydrothermal vent ecosystems exist in relatively isolated environments which are barely influenced by other ecosystems. The metabolic compensation of hosts mediated by viruses might represent a very important aspect of virus-host interactions. IMPORTANCE Viruses are the most abundant biological entities in the oceans and have very important roles in regulating microbial community structure and biogeochemical cycles. The relationship between virus and host microbes is broadly thought to be that of predator and prey. Viruses can lyse host cells to control microbial population sizes and affect community structures of hosts by killing specific microbes. However, viruses also influence their hosts through manipulation of bacterial metabolism. We found

  10. Microbial Metabolism and Inhibition Studies of Phenobarbital ...

    African Journals Online (AJOL)

    Purpose: Screening scale studies were performed with eight cultures for their ability to metabolize phenobarbital, an antiepileptic, sedative, hypnotic and substrate for CYP 2C9 and 2C19. Methods: The transformation of phenobarbital was confirmed and characterized by fermentation techniques, high performance liquid ...

  11. Arsenic and selenium in microbial metabolism

    Science.gov (United States)

    Stolz, John F.; Basu, Partha; Santini, Joanne M.; Oremland, Ronald S.

    2006-01-01

    Arsenic and selenium are readily metabolized by prokaryotes, participating in a full range of metabolic functions including assimilation, methylation, detoxification, and anaerobic respiration. Arsenic speciation and mobility is affected by microbes through oxidation/reduction reactions as part of resistance and respiratory processes. A robust arsenic cycle has been demonstrated in diverse environments. Respiratory arsenate reductases, arsenic methyltransferases, and new components in arsenic resistance have been recently described. The requirement for selenium stems primarily from its incorporation into selenocysteine and its function in selenoenzymes. Selenium oxyanions can serve as an electron acceptor in anaerobic respiration, forming distinct nanoparticles of elemental selenium that may be enriched in (76)Se. The biogenesis of selenoproteins has been elucidated, and selenium methyltransferases and a respiratory selenate reductase have also been described. This review highlights recent advances in ecology, biochemistry, and molecular biology and provides a prelude to the impact of genomics studies.

  12. Metabolic models to investigate energy limited anaerobic ecosystems.

    Science.gov (United States)

    Rodríguez, J; Premier, G C; Guwy, A J; Dinsdale, R; Kleerebezem, R

    2009-01-01

    Anaerobic wastewater treatment is shifting from a philosophy of solely pollutants removal to a philosophy of combined resource recovery and waste treatment. Simultaneous wastewater treatment with energy recovery in the form of energy rich products, brings renewed interest to non-methanogenic anaerobic bioprocesses such as the anaerobic production of hydrogen, ethanol, solvents, VFAs, bioplastics and even electricity from microbial fuel cells. The existing kinetic-based modelling approaches, widely used in aerobic and methanogenic wastewater treatment processes, do not seem adequate in investigating such energy limited microbial ecosystems. The great diversity of similar microbial species, which share many of the fermentative reaction pathways, makes quantify microbial groups very difficult and causes identifiability problems. A modelling approach based on the consideration of metabolic reaction networks instead of on separated microbial groups is suggested as an alternative to describe anaerobic microbial ecosystems and in particular for the prediction of product formation as a function of environmental conditions imposed. The limited number of existing relevant fermentative pathways in conjunction with the fact that anaerobic reactions proceed very close to thermodynamic equilibrium reduces the complexity of such approach and the degrees of freedom in terms of product formation fluxes. In addition, energy limitation in these anaerobic microbial ecosystems makes plausible that selective forces associated with energy further define the system activity by favouring those conversions/microorganisms which provide the most energy for growth under the conditions imposed.

  13. Metabolic modeling of a mutualistic microbial community

    Energy Technology Data Exchange (ETDEWEB)

    Stolyar, Sergey; Van Dien, Steve; Hillesland, Kristina Linnea; Pinel, Nicolas; Lie, Thomas J.; Leigh, John A.; Stahl, David A.

    2007-03-13

    The rate of production of methane in many environmentsdepends upon mutualistic interactions between sulfate-reducing bacteriaand methanogens. To enhance our understanding of these relationships, wetook advantage of the fully sequenced genomes of Desulfovibrio vulgarisand Methanococcus maripaludis to produce and analyze the firstmultispecies stoichiometric metabolic model. Model results were comparedto data on growth of the co-culture on lactate in the absence of sulfate.The model accurately predicted several ecologically relevantcharacteristics, including the flux of metabolites and the ratio of D.vulgaris to M. maripaludis cells during growth. In addition, the modeland our data suggested that it was possible to eliminate formate as aninterspecies electron shuttle, but hydrogen transfer was essential forsyntrophic growth. Our work demonstrated that reconstructed metabolicnetworks and stoichiometric models can serve not only to predictmetabolic fluxes and growth phenotypes of single organisms, but also tocapture growth parameters and community composition of simple bacterialcommunities.

  14. Microbial metabolism of alkyl and condensed thiophenes: Final report

    Energy Technology Data Exchange (ETDEWEB)

    Fedorak, P.M.

    1992-01-01

    This study was conducted to gain a better understanding of the metabolic pathways used by aerobic microorganisms for the biodegradation or biotransformation of organosulfur compounds found in petroleum. The study used alkyl-substituted thiophenes, benzothiophene and alkyl-substituted benzothiophenes and alkyl-substituted dibenzothiophenes. The results provide information relevant to environmental matters, aspects of microbial transformations in petroleum reservoirs and further assessment of the feasibility of biodesulfurization.

  15. Characterization of proton production and consumption associated with microbial metabolism

    Directory of Open Access Journals (Sweden)

    Mahadevan Radhakrishnan

    2010-01-01

    Full Text Available Abstract Background Production or consumption of protons in growth medium during microbial metabolism plays an important role in determining the pH of the environment. Such pH changes resulting from microbial metabolism may influence the geochemical speciation of many elements in subsurface environments. Protons produced or consumed during microbial growth were measured by determining the amount of acid or base added in a 5 L batch bioreactor equipped with pH control for different species including Escherichia coli, Geobacter sulfurreducens, and Geobacter metallireducens. Results An in silico model was used to predict the proton secretion or consumption rates and the results were compared with the data. The data was found to confirm predictions of proton consumption during aerobic growth of E. coli with acetate as the carbon source. However, in contrast to proton consumption observed during aerobic growth of E. coli with acetate, proton secretion was observed during growth of Geobacter species with acetate as the donor and Fe(III as the extracellular electron acceptor. Conclusions In this study, we have also shown that the final pH of the medium can be either acidic or basic depending on the choice of the electron acceptor for the same electron donor. In all cases, the in silico model could predict qualitatively the proton production/consumption rates obtained from the experimental data. Therefore, measurements of pH equivalents generated or consumed during growth can help characterize the microbial physiology further and can be valuable for optimizing practical applications such as microbial fuel cells, where growth associated pH changes can limit current generation rates.

  16. Investigating the impact of microbial interactions with geologic media on geophysical properties

    Science.gov (United States)

    Davis, Caroline Ann

    The goals of this study were to investigate the effect of: (1) microbial metabolic byproducts, microbial growth, and biofilm formation on the low frequency electrical properties of porous media, (2) biofilm formation on acoustic wave properties, and (3) the natural electrical (self-potential) signatures associated with an in-situ biological permeable reactive barrier (PRB). The results suggest: (1) increases in electrolytic conductivity are consistent with increased concentrations of organic acids and biosurfactants; (2) mineral weathering promoted by organic acids causes increases in electrolytic conductivity, concomitant with increases in major cation concentrations; (3) interfacial conductivity generally parallels microbial cell concentrations and biofilm formation; (4) variations in microbial growth and biofilms causes spatiotemporal heterogeneity in the elastic properties of porous media; (5) SP signatures associated with the injection of groundwater into an in-situ biological PRB are dominated by diffusion potentials induced by the injections. The results suggest that electrolytic conductivity may be useful as an indicator of metabolism, while interfacial conductivity may be used as proxy indicator for microbial growth and biofilm formation in porous media. In addition, acoustic measurements may provide diagnostic spatiotemporal data for the validation of bioclogging models/simulations. Collectively, this study provides further evidence that geophysical measurements are sensitive to microbial-induced changes to geologic media, and may be useful for the detection and monitoring of subsurface microbial growth, activity, and distribution such as in microbial enhanced oil recovery, assessing biofilm barriers used for contaminant remediation, or as sealants for reservoirs in CO2 sequestration studies.

  17. EVA Suit Microbial Leakage Investigation Project

    Science.gov (United States)

    Falker, Jay; Baker, Christopher; Clayton, Ronald; Rucker, Michelle

    2016-01-01

    The objective of this project is to collect microbial samples from various EVA suits to determine how much microbial contamination is typically released during simulated planetary exploration activities. Data will be released to the planetary protection and science communities, and advanced EVA system designers. In the best case scenario, we will discover that very little microbial contamination leaks from our current or prototype suit designs, in the worst case scenario, we will identify leak paths, learn more about what affects leakage--and we'll have a new, flight-certified swab tool for our EVA toolbox.

  18. Genome-scale metabolic model in guiding metabolic engineering of microbial improvement.

    Science.gov (United States)

    Xu, Chuan; Liu, Lili; Zhang, Zhao; Jin, Danfeng; Qiu, Juanping; Chen, Ming

    2013-01-01

    In the past few decades, despite all the significant achievements in industrial microbial improvement, the approaches of traditional random mutation and selection as well as the rational metabolic engineering based on the local knowledge cannot meet today's needs. With rapid reconstructions and accurate in silico simulations, genome-scale metabolic model (GSMM) has become an indispensable tool to study the microbial metabolism and design strain improvements. In this review, we highlight the application of GSMM in guiding microbial improvements focusing on a systematic strategy and its achievements in different industrial fields. This strategy includes a repetitive process with four steps: essential data acquisition, GSMM reconstruction, constraints-based optimizing simulation, and experimental validation, in which the second and third steps are the centerpiece. The achievements presented here belong to different industrial application fields, including food and nutrients, biopharmaceuticals, biopolymers, microbial biofuel, and bioremediation. This strategy and its achievements demonstrate a momentous guidance of GSMM for metabolic engineering breeding of industrial microbes. More efforts are required to extend this kind of study in the meantime.

  19. Investigations on abundance and activity of microbial sponge symbionts using quantitative real - time PCR

    DEFF Research Database (Denmark)

    Kumala, Lars; Hentschel, Ute; Bayer, Kristina

    Marine sponges are hosts to dense and diverse microbial consortia that are likely to play a key role in the metabolic processes of the host sponge due to their enormous abundance. Common symbioses between nitrogen transforming microorganisms and sponges indicate complex nitrogen cycling within...... the host. Of particular interest is determining the community structure and function of microbial symbionts in order to gain deeper insight into host-symbiont interactions. We investigated the abundance and activity of microbial symbionts in two Mediterranean sponge species using quantitative real-time PCR....... An absolute quantification of functional genes and transcripts in archaeal and bacterial symbionts was conducted to determine their involvement in nitrification and denitrification, comparing the low microbial abundance (LMA) sponge Dysidea avara with the high microbial abundance (HMA) representative Aplysina...

  20. BiomeNet: a Bayesian model for inference of metabolic divergence among microbial communities.

    OpenAIRE

    Mahdi Shafiei; Katherine A Dunn; Hugh Chipman; Hong Gu; Joseph P Bielawski

    2014-01-01

    Metagenomics yields enormous numbers of microbial sequences that can be assigned a metabolic function. Using such data to infer community-level metabolic divergence is hindered by the lack of a suitable statistical framework. Here, we describe a novel hierarchical Bayesian model, called BiomeNet (Bayesian inference of metabolic networks), for inferring differential prevalence of metabolic subnetworks among microbial communities. To infer the structure of community-level metabolic interactions...

  1. Coupling Spatiotemporal Community Assembly Processes to Changes in Microbial Metabolism

    Energy Technology Data Exchange (ETDEWEB)

    Graham, Emily B.; Crump, Alex R.; Resch, Charles T.; Fansler, Sarah; Arntzen, Evan; Kennedy, David W.; Fredrickson, Jim K.; Stegen, James C.

    2016-12-16

    Community assembly processes govern shifts in species abundances in response to environmental change, yet our understanding of assembly remains largely decoupled from ecosystem function. Here, we test hypotheses regarding assembly and function across space and time using hyporheic microbial communities as a model system. We pair sampling of two habitat types through hydrologic fluctuation with null modeling and multivariate statistics. We demonstrate that dual selective pressures assimilate to generate compositional changes at distinct timescales among habitat types, resulting in contrasting associations of Betaproteobacteria and Thaumarchaeota with selection and with seasonal changes in aerobic metabolism. Our results culminate in a conceptual model in which selection from contrasting environments regulates taxon abundance and ecosystem function through time, with increases in function when oscillating selection opposes stable selective pressures. Our model is applicable within both macrobial and microbial ecology and presents an avenue for assimilating community assembly processes into predictions of ecosystem function.

  2. Mechanistic links between gut microbial community dynamics, microbial functions and metabolic health

    Science.gov (United States)

    Ha, Connie WY; Lam, Yan Y; Holmes, Andrew J

    2014-01-01

    Gut microbes comprise a high density, biologically active community that lies at the interface of an animal with its nutritional environment. Consequently their activity profoundly influences many aspects of the physiology and metabolism of the host animal. A range of microbial structural components and metabolites directly interact with host intestinal cells and tissues to influence nutrient uptake and epithelial health. Endocrine, neuronal and lymphoid cells in the gut also integrate signals from these microbial factors to influence systemic responses. Dysregulation of these host-microbe interactions is now recognised as a major risk factor in the development of metabolic dysfunction. This is a two-way process and understanding the factors that tip host-microbiome homeostasis over to dysbiosis requires greater appreciation of the host feedbacks that contribute to regulation of microbial community composition. To date, numerous studies have employed taxonomic profiling approaches to explore the links between microbial composition and host outcomes (especially obesity and its comorbidities), but inconsistent host-microbe associations have been reported. Available data indicates multiple factors have contributed to discrepancies between studies. These include the high level of functional redundancy in host-microbiome interactions combined with individual variation in microbiome composition; differences in study design, diet composition and host system between studies; and inherent limitations to the resolution of rRNA-based community profiling. Accounting for these factors allows for recognition of the common microbial and host factors driving community composition and development of dysbiosis on high fat diets. New therapeutic intervention options are now emerging. PMID:25469018

  3. Modelling microbial metabolic rewiring during growth in a complex medium.

    Science.gov (United States)

    Fondi, Marco; Bosi, Emanuele; Presta, Luana; Natoli, Diletta; Fani, Renato

    2016-11-24

    In their natural environment, bacteria face a wide range of environmental conditions that change over time and that impose continuous rearrangements at all the cellular levels (e.g. gene expression, metabolism). When facing a nutritionally rich environment, for example, microbes first use the preferred compound(s) and only later start metabolizing the other one(s). A systemic re-organization of the overall microbial metabolic network in response to a variation in the composition/concentration of the surrounding nutrients has been suggested, although the range and the entity of such modifications in organisms other than a few model microbes has been scarcely described up to now. We used multi-step constraint-based metabolic modelling to simulate the growth in a complex medium over several time steps of the Antarctic model organism Pseudoalteromonas haloplanktis TAC125. As each of these phases is characterized by a specific set of amino acids to be used as carbon and energy source our modelling framework describes the major consequences of nutrients switching at the system level. The model predicts that a deep metabolic reprogramming might be required to achieve optimal biomass production in different stages of growth (different medium composition), with at least half of the cellular metabolic network involved (more than 50% of the metabolic genes). Additionally, we show that our modelling framework is able to capture metabolic functional association and/or common regulatory features of the genes embedded in our reconstruction (e.g. the presence of common regulatory motifs). Finally, to explore the possibility of a sub-optimal biomass objective function (i.e. that cells use resources in alternative metabolic processes at the expense of optimal growth) we have implemented a MOMA-based approach (called nutritional-MOMA) and compared the outcomes with those obtained with Flux Balance Analysis (FBA). Growth simulations under this scenario revealed the deep impact of

  4. Metabolic modelling of polyhydroxyalkanoate copolymers production by mixed microbial cultures

    Directory of Open Access Journals (Sweden)

    Reis Maria AM

    2008-07-01

    Full Text Available Abstract Background This paper presents a metabolic model describing the production of polyhydroxyalkanoate (PHA copolymers in mixed microbial cultures, using mixtures of acetic and propionic acid as carbon source material. Material and energetic balances were established on the basis of previously elucidated metabolic pathways. Equations were derived for the theoretical yields for cell growth and PHA production on mixtures of acetic and propionic acid as functions of the oxidative phosphorylation efficiency, P/O ratio. The oxidative phosphorylation efficiency was estimated from rate measurements, which in turn allowed the estimation of the theoretical yield coefficients. Results The model was validated with experimental data collected in a sequencing batch reactor (SBR operated under varying feeding conditions: feeding of acetic and propionic acid separately (control experiments, and the feeding of acetic and propionic acid simultaneously. Two different feast and famine culture enrichment strategies were studied: (i either with acetate or (ii with propionate as carbon source material. Metabolic flux analysis (MFA was performed for the different feeding conditions and culture enrichment strategies. Flux balance analysis (FBA was used to calculate optimal feeding scenarios for high quality PHA polymers production, where it was found that a suitable polymer would be obtained when acetate is fed in excess and the feeding rate of propionate is limited to ~0.17 C-mol/(C-mol.h. The results were compared with published pure culture metabolic studies. Conclusion Acetate was more conducive toward the enrichment of a microbial culture with higher PHA storage fluxes and yields as compared to propionate. The P/O ratio was not only influenced by the selected microbial culture, but also by the carbon substrate fed to each culture, where higher P/O ratio values were consistently observed for acetate than propionate. MFA studies suggest that when mixtures of

  5. Microbial production of antioxidant food ingredients via metabolic engineering.

    Science.gov (United States)

    Lin, Yuheng; Jain, Rachit; Yan, Yajun

    2014-04-01

    Antioxidants are biological molecules with the ability to protect vital metabolites from harmful oxidation. Due to this fascinating role, their beneficial effects on human health are of paramount importance. Traditional approaches using solvent-based extraction from food/non-food sources and chemical synthesis are often expensive, exhaustive, and detrimental to the environment. With the advent of metabolic engineering tools, the successful reconstitution of heterologous pathways in Escherichia coli and other microorganisms provides a more exciting and amenable alternative to meet the increasing demand of natural antioxidants. In this review, we elucidate the recent progress in metabolic engineering efforts for the microbial production of antioxidant food ingredients - polyphenols, carotenoids, and antioxidant vitamins. Copyright © 2013 Elsevier Ltd. All rights reserved.

  6. Marine Metagenomics: New Tools for the Study and Exploitation of Marine Microbial Metabolism

    Directory of Open Access Journals (Sweden)

    Alan D. W. Dobson

    2010-03-01

    Full Text Available The marine environment is extremely diverse, with huge variations in pressure and temperature. Nevertheless, life, especially microbial life, thrives throughout the marine biosphere and microbes have adapted to all the divergent environments present. Large scale DNA sequence based approaches have recently been used to investigate the marine environment and these studies have revealed that the oceans harbor unprecedented microbial diversity. Novel gene families with representatives only within such metagenomic datasets represent a large proportion of the ocean metagenome. The presence of so many new gene families from these uncultured and highly diverse microbial populations represents a challenge for the understanding of and exploitation of the biology and biochemistry of the ocean environment. The application of new metagenomic and single cell genomics tools offers new ways to explore the complete metabolic diversity of the marine biome.

  7. Metabolism of microbial nitrogen in ruminants with special reference to nucleic acids.

    Science.gov (United States)

    Fujihara, Tsutomu; Shem, Martin N

    2011-04-01

    Characteristically the metabolism of microbial nitrogen (N) compounds in ruminants involves the degradation of dietary N and synthesis of microbial protein (MP), compounds including a small amount of peptides and free amino acids, which may account for 75-85% of total N and the remainder are nucleic acids (NA: DNA and RNA). Generally rumen microbes contain 10-25% NA-N of the total N while 70-80% is in the form of RNA. This paper describes the degradation and synthesis of NA in the rumen and their fate in the lower digestive tracts. Their physiological and nutritional significance in different types of ruminant animals is also discussed. The research works on NA metabolism in ruminants has been mainly on metabolism of purines after rumen microbial digestion and absorption in the lower gut. Subsequently, the fate of absorbed purines has been intensively investigated to assess the extent of MP synthesis in the rumen. The method for predicting ruminal synthesized MP and subsequently digested MP has been proposed using urinary purine derivative (PD) excretion in sheep and cattle fed on ordinary feed. The latter approach has now been adopted for calculation of protein supply in some feeding standards, although there are still difficulties in predicting representative samples of rumen microbes, and also uncertainties in variations of non-renal and endogenous purine losses. © 2011 The Authors. Journal compilation © 2011 Japanese Society of Animal Science.

  8. Influence of Wastewater Discharge on the Metabolic Potential of the Microbial Community in River Sediments

    KAUST Repository

    Li, Dong

    2015-09-24

    To reveal the variation of microbial community functions during water filtration process in river sediments, which has been utilized widely in natural water treatment systems, this study investigates the influence of municipal wastewater discharge to streams on the phylotype and metabolic potential of the microbiome in upstream and particularly various depths of downstream river sediments. Cluster analyses based on both microbial phylogenetic and functional data collectively revealed that shallow upstream sediments grouped with those from deeper subsurface downstream regions. These sediment samples were distinct from those found in shallow downstream sediments. Functional genes associated with carbohydrate, xenobiotic, and certain amino acid metabolisms were overrepresented in upstream and deep downstream samples. In contrast, the more immediate contact with wastewater discharge in shallow downstream samples resulted in an increase in the relative abundance of genes associated with nitrogen, sulfur, purine and pyrimidine metabolisms, as well as restriction–modification systems. More diverse bacterial phyla were associated with upstream and deep downstream sediments, mainly including Actinobacteria, Planctomycetes, and Firmicutes. In contrast, in shallow downstream sediments, genera affiliated with Betaproteobacteria and Gammaproteobacteria were enriched with putative functions that included ammonia and sulfur oxidation, polyphosphate accumulation, and methylotrophic bacteria. Collectively, these results highlight the enhanced capabilities of microbial communities residing in deeper stream sediments for the transformation of water contaminants and thus provide a foundation for better design of natural water treatment systems to further improve the removal of contaminants. © 2015, Springer Science+Business Media New York.

  9. An algorithm for designing minimal microbial communities with desired metabolic capacities.

    Science.gov (United States)

    Eng, Alexander; Borenstein, Elhanan

    2016-07-01

    Recent efforts to manipulate various microbial communities, such as fecal microbiota transplant and bioreactor systems' optimization, suggest a promising route for microbial community engineering with numerous medical, environmental and industrial applications. However, such applications are currently restricted in scale and often rely on mimicking or enhancing natural communities, calling for the development of tools for designing synthetic communities with specific, tailored, desired metabolic capacities. Here, we present a first step toward this goal, introducing a novel algorithm for identifying minimal sets of microbial species that collectively provide the enzymatic capacity required to synthesize a set of desired target product metabolites from a predefined set of available substrates. Our method integrates a graph theoretic representation of network flow with the set cover problem in an integer linear programming (ILP) framework to simultaneously identify possible metabolic paths from substrates to products while minimizing the number of species required to catalyze these metabolic reactions. We apply our algorithm to successfully identify minimal communities both in a set of simple toy problems and in more complex, realistic settings, and to investigate metabolic capacities in the gut microbiome. Our framework adds to the growing toolset for supporting informed microbial community engineering and for ultimately realizing the full potential of such engineering efforts. The algorithm source code, compilation, usage instructions and examples are available under a non-commercial research use only license at https://github.com/borenstein-lab/CoMiDA CONTACT: elbo@uw.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  10. Impact of metabolism and growth phase on the hydrogen isotopic composition of microbial fatty acids

    Science.gov (United States)

    Heinzelmann, Sandra M.; Villanueva, Laura; Sinke-Schoen, Danielle; Sinninghe Damsté, Jaap S.; Schouten, Stefan; van der Meer, Marcel T. J.

    2015-01-01

    Microorganisms are involved in all elemental cycles and therefore it is important to study their metabolism in the natural environment. A recent technique to investigate this is the hydrogen isotopic composition of microbial fatty acids, i.e., heterotrophic microorganisms produce fatty acids enriched in deuterium (D) while photoautotrophic and chemoautotrophic microorganisms produce fatty acids depleted in D compared to the water in the culture medium (growth water). However, the impact of factors other than metabolism have not been investigated. Here, we evaluate the impact of growth phase compared to metabolism on the hydrogen isotopic composition of fatty acids of different environmentally relevant microorganisms with heterotrophic, photoautotrophic and chemoautotrophic metabolisms. Fatty acids produced by heterotrophs are enriched in D compared to growth water with εlipid/water between 82 and 359‰ when grown on glucose or acetate, respectively. Photoautotrophs (εlipid/water between −149 and −264‰) and chemoautotrophs (εlipid/water between −217 and −275‰) produce fatty acids depleted in D. Fatty acids become, in general, enriched by between 4 and 46‰ with growth phase which is minor compared to the influence of metabolisms. Therefore, the D/H ratio of fatty acids is a promising tool to investigate community metabolisms in nature. PMID:26005437

  11. Shifts in coastal sediment oxygenation cause pronounced changes in microbial community composition and associated metabolism.

    Science.gov (United States)

    Broman, Elias; Sjöstedt, Johanna; Pinhassi, Jarone; Dopson, Mark

    2017-08-09

    A key characteristic of eutrophication in coastal seas is the expansion of hypoxic bottom waters, often referred to as 'dead zones'. One proposed remediation strategy for coastal dead zones in the Baltic Sea is to mix the water column using pump stations, circulating oxygenated water to the sea bottom. Although microbial metabolism in the sediment surface is recognized as key in regulating bulk chemical fluxes, it remains unknown how the microbial community and its metabolic processes are influenced by shifts in oxygen availability. Here, coastal Baltic Sea sediments sampled from oxic and anoxic sites, plus an intermediate area subjected to episodic oxygenation, were experimentally exposed to oxygen shifts. Chemical, 16S rRNA gene, metagenomic, and metatranscriptomic analyses were conducted to investigate changes in chemistry fluxes, microbial community structure, and metabolic functions in the sediment surface. Compared to anoxic controls, oxygenation of anoxic sediment resulted in a proliferation of bacterial populations in the facultative anaerobic genus Sulfurovum that are capable of oxidizing toxic sulfide. Furthermore, the oxygenated sediment had higher amounts of RNA transcripts annotated as sqr, fccB, and dsrA involved in sulfide oxidation. In addition, the importance of cryptic sulfur cycling was highlighted by the oxidative genes listed above as well as dsvA, ttrB, dmsA, and ddhAB that encode reductive processes being identified in anoxic and intermediate sediments turned oxic. In particular, the intermediate site sediments responded differently upon oxygenation compared to the anoxic and oxic site sediments. This included a microbial community composition with more habitat generalists, lower amounts of RNA transcripts attributed to methane oxidation, and a reduced rate of organic matter degradation. These novel data emphasize that genetic expression analyses has the power to identify key molecular mechanisms that regulate microbial community responses

  12. Investigation of Chemical and Microbial Leaching of Iron ore in ...

    African Journals Online (AJOL)

    Investigations on the chemical and microbial leaching of a Nigerian Iron-ore in sulphuric acid have been carried out. The influence of physico-chemical parameters such as acid concentration, temperature, particle size and stirring speed on the chemical dissolution of the ore was investigated. The dissolution rates are ...

  13. MbT-Tool: An open-access tool based on Thermodynamic Electron Equivalents Model to obtain microbial-metabolic reactions to be used in biotechnological process

    Directory of Open Access Journals (Sweden)

    Pablo Araujo Granda

    2016-01-01

    Full Text Available Modelling cellular metabolism is a strategic factor in investigating microbial behaviour and interactions, especially for bio-technological processes. A key factor for modelling microbial activity is the calculation of nutrient amounts and products generated as a result of the microbial metabolism. Representing metabolic pathways through balanced reactions is a complex and time-consuming task for biologists, ecologists, modellers and engineers. A new computational tool to represent microbial pathways through microbial metabolic reactions (MMRs using the approach of the Thermodynamic Electron Equivalents Model has been designed and implemented in the open-access framework NetLogo. This computational tool, called MbT-Tool (Metabolism based on Thermodynamics can write MMRs for different microbial functional groups, such as aerobic heterotrophs, nitrifiers, denitrifiers, methanogens, sulphate reducers, sulphide oxidizers and fermenters. The MbT-Tool's code contains eighteen organic and twenty inorganic reduction-half-reactions, four N-sources (NH4+, NO3−, NO2−, N2 to biomass synthesis and twenty-four microbial empirical formulas, one of which can be determined by the user (CnHaObNc. MbT-Tool is an open-source program capable of writing MMRs based on thermodynamic concepts, which are applicable in a wide range of academic research interested in designing, optimizing and modelling microbial activity without any extensive chemical, microbiological and programing experience.

  14. Rumen microbial communities influence metabolic phenotypes in lambs

    Directory of Open Access Journals (Sweden)

    Diego P. Morgavi

    2015-10-01

    Full Text Available The rumen microbiota is an essential part of ruminants forging their nutrition and health. Despite its importance, it is not fully understood how various groups of rumen microbes affect host-microbe relationships and functions. The aim of the study was to simultaneously explore the rumen microbiota and the metabolic phenotype of lambs for identifying host-microbe associations and potential biomarkers of digestive functions. Twin lambs, separated in two groups after birth were exposed to practices (isolation and gavage with rumen fluid with protozoa or protozoa-depleted that differentially restricted the acquisition of microbes. Rumen microbiota, fermentation parameters, digestibility and growth were monitored for up to 31 weeks of age. Microbiota assembled in isolation from other ruminants lacked protozoa and had low bacterial and archaeal diversity whereas digestibility was not affected. Exposure to adult sheep microbiota increased bacterial and archaeal diversity independently of protozoa presence. For archaea, Methanomassiliicoccales displaced Methanosphaera. Notwithstanding, protozoa induced differences in functional traits such as digestibility and significantly shaped bacterial community structure, notably Ruminococcaceae and Lachnospiraceae lower up to 6 folds, Prevotellaceae lower by ~40%, and Clostridiaceae and Veillonellaceae higher up to 10 folds compared to microbiota without protozoa. An orthogonal partial least squares-discriminant analysis of urinary metabolome matched differences in microbiota structure. Discriminant metabolites were mainly involved in amino acids and protein metabolic pathways while a negative interaction was observed between methylotrophic methanogens Methanomassiliicoccales and trimethylamine N-oxide. These results stress the influence of gut microbes on animal phenotype and show the potential of metabolomics for monitoring rumen microbial functions.

  15. Compartmentalized metabolic network reconstruction of microbial communities to determine the effect of agricultural intervention on soils.

    Science.gov (United States)

    Alvarez-Silva, María Camila; Álvarez-Yela, Astrid Catalina; Gómez-Cano, Fabio; Zambrano, María Mercedes; Husserl, Johana; Danies, Giovanna; Restrepo, Silvia; González-Barrios, Andrés Fernando

    2017-01-01

    Soil microbial communities are responsible for a wide range of ecological processes and have an important economic impact in agriculture. Determining the metabolic processes performed by microbial communities is crucial for understanding and managing ecosystem properties. Metagenomic approaches allow the elucidation of the main metabolic processes that determine the performance of microbial communities under different environmental conditions and perturbations. Here we present the first compartmentalized metabolic reconstruction at a metagenomics scale of a microbial ecosystem. This systematic approach conceives a meta-organism without boundaries between individual organisms and allows the in silico evaluation of the effect of agricultural intervention on soils at a metagenomics level. To characterize the microbial ecosystems, topological properties, taxonomic and metabolic profiles, as well as a Flux Balance Analysis (FBA) were considered. Furthermore, topological and optimization algorithms were implemented to carry out the curation of the models, to ensure the continuity of the fluxes between the metabolic pathways, and to confirm the metabolite exchange between subcellular compartments. The proposed models provide specific information about ecosystems that are generally overlooked in non-compartmentalized or non-curated networks, like the influence of transport reactions in the metabolic processes, especially the important effect on mitochondrial processes, as well as provide more accurate results of the fluxes used to optimize the metabolic processes within the microbial community.

  16. Compartmentalized metabolic network reconstruction of microbial communities to determine the effect of agricultural intervention on soils.

    Directory of Open Access Journals (Sweden)

    María Camila Alvarez-Silva

    Full Text Available Soil microbial communities are responsible for a wide range of ecological processes and have an important economic impact in agriculture. Determining the metabolic processes performed by microbial communities is crucial for understanding and managing ecosystem properties. Metagenomic approaches allow the elucidation of the main metabolic processes that determine the performance of microbial communities under different environmental conditions and perturbations. Here we present the first compartmentalized metabolic reconstruction at a metagenomics scale of a microbial ecosystem. This systematic approach conceives a meta-organism without boundaries between individual organisms and allows the in silico evaluation of the effect of agricultural intervention on soils at a metagenomics level. To characterize the microbial ecosystems, topological properties, taxonomic and metabolic profiles, as well as a Flux Balance Analysis (FBA were considered. Furthermore, topological and optimization algorithms were implemented to carry out the curation of the models, to ensure the continuity of the fluxes between the metabolic pathways, and to confirm the metabolite exchange between subcellular compartments. The proposed models provide specific information about ecosystems that are generally overlooked in non-compartmentalized or non-curated networks, like the influence of transport reactions in the metabolic processes, especially the important effect on mitochondrial processes, as well as provide more accurate results of the fluxes used to optimize the metabolic processes within the microbial community.

  17. [Carbon sources metabolic characteristics of airborne microbial communities in constructed wetlands].

    Science.gov (United States)

    Song, Zhi-Wen; Wang, Lin; Xu, Ai-Ling; Wu, Deng-Deng; Xia, Yan

    2015-02-01

    Using BIOLOG-GN plates, this article describes the carbon sources metabolic characteristics of airborne microbial communities in a free surface-flow constructed wetland in different seasons and clarify the correlation between airborne microbial metabolic functions and environmental factors. The average well color development (AWCD), carbon metabolic profiles and McIntosh values of airborne microbial communities in different seasons were quite different. Analysis of the variations showed that AWCD in spring and summer differed significantly from that in autumn and winter (P carbon by airborne microbes was different. Summer had a significant difference from other seasons (P carbon metabolic characteristics of airborne microbial community in autumn were similar to those in winter but different from those in spring and summer. The characteristics of carbon metabolism revealed differences between summer and spring, autumn, or winter. These differences were mainly caused by amines or amides while the differences between spring and autumn or winter were mainly caused by carboxylic acids. Environmental factors, including changes in wind speed, temperature, and humidity acted to influence the carbon sources metabolic properties of airborne microbial community. The dominant environmental factors that acted to influence the carbon sources metabolic properties of airborne microbial community varied between different seasons.

  18. Integrative investigation of metabolic and transcriptomic data

    Directory of Open Access Journals (Sweden)

    Önsan Z İlsen

    2006-04-01

    Full Text Available Abstract Background New analysis methods are being developed to integrate data from transcriptome, proteome, interactome, metabolome, and other investigative approaches. At the same time, existing methods are being modified to serve the objectives of systems biology and permit the interpretation of the huge datasets currently being generated by high-throughput methods. Results Transcriptomic and metabolic data from chemostat fermentors were collected with the aim of investigating the relationship between these two data sets. The variation in transcriptome data in response to three physiological or genetic perturbations (medium composition, growth rate, and specific gene deletions was investigated using linear modelling, and open reading-frames (ORFs whose expression changed significantly in response to these perturbations were identified. Assuming that the metabolic profile is a function of the transcriptome profile, expression levels of the different ORFs were used to model the metabolic variables via Partial Least Squares (Projection to Latent Structures – PLS using PLS toolbox in Matlab. Conclusion The experimental design allowed the analyses to discriminate between the effects which the growth medium, dilution rate, and the deletion of specific genes had on the transcriptome and metabolite profiles. Metabolite data were modelled as a function of the transcriptome to determine their congruence. The genes that are involved in central carbon metabolism of yeast cells were found to be the ORFs with the most significant contribution to the model.

  19. Microbial functional genes elucidate environmental drivers of biofilm metabolism in glacier-fed streams.

    Science.gov (United States)

    Ren, Ze; Gao, Hongkai; Elser, James J; Zhao, Qiudong

    2017-10-04

    Benthic biofilms in glacier-fed streams harbor diverse microorganisms driving biogeochemical cycles and, consequently, influencing ecosystem-level processes. Benthic biofilms are vulnerable to glacial retreat induced by climate change. To investigate microbial functions of benthic biofilms in glacier-fed streams, we predicted metagenomes from 16s rRNA gene sequence data using PICRUSt and identified functional genes associated with nitrogen and sulfur metabolisms based on KEGG database and explored the relationships between metabolic pathways and abiotic factors in glacier-fed streams in the Tianshan Mountains in Central Asia. Results showed that the distribution of functional genes was mainly associated with glacier area proportion, glacier source proportion, total nitrogen, dissolved organic carbon, and pH. For nitrogen metabolism, the relative abundance of functional genes associated with dissimilatory pathways was higher than those for assimilatory pathways. The relative abundance of functional genes associated with assimilatory sulfate reduction was higher than those involved with the sulfur oxidation system and dissimilatory sulfate reduction. Hydrological factors had more significant correlations with nitrogen metabolism than physicochemical factors and anammox was the most sensitive nitrogen cycling pathway responding to variation of the abiotic environment in these glacial-fed streams. In contrast, sulfur metabolism pathways were not sensitive to variations of abiotic factors in these systems.

  20. Metabolism of microbial communities in the environment : A compound-specific stable hydrogen isotope approach

    NARCIS (Netherlands)

    Heinzelmann, S.M.

    2015-01-01

    Microorganisms are key players in all elemental cycles, their metabolic activity and potential impacts the environment on a local and global scale. In order to understand this significant role in the environment, microbial communities, their diversity and metabolic activity have to be studied in

  1. Microbial population heterogeneity versus bioreactor heterogeneity: evaluation of Redox Sensor Green as an exogenous metabolic biosensor

    DEFF Research Database (Denmark)

    Baert, Jonathan; Delepierre, Anissa; Telek, Samuel

    2016-01-01

    Microbial heterogeneity in metabolic performances has attracted a lot of attention, considering its potential impact on industrial bioprocesses. However, little is known about the impact of extracellular perturbations (i.e. bioreactor heterogeneity) on cell-to-cell variability in metabolic perfor...

  2. Water type and irrigation time effects on microbial metabolism of a soil cultivated with Bermuda-grass Tifton 85

    Directory of Open Access Journals (Sweden)

    Sandra Furlan Nogueira

    2011-06-01

    Full Text Available This study investigated the microbial metabolism in Bermuda-grass Tifton 85 areas after potable-water and effluent irrigation treatments. The experiment was carried out in Lins/SP with samples taken in the rainy and dry seasons (2006 after one year and three years of irrigation management, and set up on an entirely randomized block design with four treatments: C (control, without irrigation or fertilization, PW (potable water + 520 kg of N ha-1 year-1; TE3 and TE0 (treated effluent + 520 kg of N ha-1 year-1 for three years and one year, respectively. The parameters determined were: microbial biomass carbon, microbial activity, and metabolic quotient. Irrigation with wastewater after three years indicated no alteration in soil quality for C and ET3; for PW, a negative impact on soil quality (microbial biomass decrease suggested that water-potable irrigation in Lins is not an adequate option. Microbial activity alterations observed in TE0 characterize a priming effect.

  3. Metabolic Network Modeling of Microbial Interactions in Natural and Engineered Environmental Systems

    Science.gov (United States)

    Perez-Garcia, Octavio; Lear, Gavin; Singhal, Naresh

    2016-01-01

    We review approaches to characterize metabolic interactions within microbial communities using Stoichiometric Metabolic Network (SMN) models for applications in environmental and industrial biotechnology. SMN models are computational tools used to evaluate the metabolic engineering potential of various organisms. They have successfully been applied to design and optimize the microbial production of antibiotics, alcohols and amino acids by single strains. To date however, such models have been rarely applied to analyze and control the metabolism of more complex microbial communities. This is largely attributed to the diversity of microbial community functions, metabolisms, and interactions. Here, we firstly review different types of microbial interaction and describe their relevance for natural and engineered environmental processes. Next, we provide a general description of the essential methods of the SMN modeling workflow including the steps of network reconstruction, simulation through Flux Balance Analysis (FBA), experimental data gathering, and model calibration. Then we broadly describe and compare four approaches to model microbial interactions using metabolic networks, i.e., (i) lumped networks, (ii) compartment per guild networks, (iii) bi-level optimization simulations, and (iv) dynamic-SMN methods. These approaches can be used to integrate and analyze diverse microbial physiology, ecology and molecular community data. All of them (except the lumped approach) are suitable for incorporating species abundance data but so far they have been used only to model simple communities of two to eight different species. Interactions based on substrate exchange and competition can be directly modeled using the above approaches. However, interactions based on metabolic feedbacks, such as product inhibition and synthropy require extensions to current models, incorporating gene regulation and compounding accumulation mechanisms. SMN models of microbial interactions can

  4. Metabolic Network Modeling of Microbial Interactions in Natural and Engineered Environmental Systems.

    Science.gov (United States)

    Perez-Garcia, Octavio; Lear, Gavin; Singhal, Naresh

    2016-01-01

    We review approaches to characterize metabolic interactions within microbial communities using Stoichiometric Metabolic Network (SMN) models for applications in environmental and industrial biotechnology. SMN models are computational tools used to evaluate the metabolic engineering potential of various organisms. They have successfully been applied to design and optimize the microbial production of antibiotics, alcohols and amino acids by single strains. To date however, such models have been rarely applied to analyze and control the metabolism of more complex microbial communities. This is largely attributed to the diversity of microbial community functions, metabolisms, and interactions. Here, we firstly review different types of microbial interaction and describe their relevance for natural and engineered environmental processes. Next, we provide a general description of the essential methods of the SMN modeling workflow including the steps of network reconstruction, simulation through Flux Balance Analysis (FBA), experimental data gathering, and model calibration. Then we broadly describe and compare four approaches to model microbial interactions using metabolic networks, i.e., (i) lumped networks, (ii) compartment per guild networks, (iii) bi-level optimization simulations, and (iv) dynamic-SMN methods. These approaches can be used to integrate and analyze diverse microbial physiology, ecology and molecular community data. All of them (except the lumped approach) are suitable for incorporating species abundance data but so far they have been used only to model simple communities of two to eight different species. Interactions based on substrate exchange and competition can be directly modeled using the above approaches. However, interactions based on metabolic feedbacks, such as product inhibition and synthropy require extensions to current models, incorporating gene regulation and compounding accumulation mechanisms. SMN models of microbial interactions can

  5. Metabolic network modeling of microbial interactions in natural and engineered environmental systems

    Directory of Open Access Journals (Sweden)

    Octavio ePerez-Garcia

    2016-05-01

    Full Text Available We review approaches to characterize metabolic interactions within microbial communities using Stoichiometric Metabolic Network (SMN models for applications in environmental and industrial biotechnology. SMN models are computational tools used to evaluate the metabolic engineering potential of various organisms. They have successfully been applied to design and optimize the microbial production of antibiotics, alcohols and amino acids by single strains. To date however, such models have been rarely applied to analyze and control the metabolism of more complex microbial communities. This is largely attributed to the diversity of microbial community functions, metabolisms and interactions. Here, we firstly review different types of microbial interaction and describe their relevance for natural and engineered environmental processes. Next, we provide a general description of the essential methods of the SMN modeling workflow including the steps of network reconstruction, simulation through Flux Balance Analysis (FBA, experimental data gathering, and model calibration. Then we broadly describe and compare four approaches to model microbial interactions using metabolic networks, i.e. i lumped networks, ii compartment per guild networks, iii bi-level optimization simulations and iv dynamic-SMN methods. These approaches can be used to integrate and analyze diverse microbial physiology, ecology and molecular community data. All of them (except the lumped approach are suitable for incorporating species abundance data but so far they have been used only to model simple communities of two to eight different species. Interactions based on substrate exchange and competition can be directly modeled using the above approaches. However, interactions based on metabolic feedbacks, such as product inhibition and synthropy require extensions to current models, incorporating gene regulation and compounding accumulation mechanisms. SMN models of microbial

  6. Transmissible microbial and metabolomic remodeling by soluble dietary fiber improves metabolic homeostasis.

    Science.gov (United States)

    He, Baokun; Nohara, Kazunari; Ajami, Nadim J; Michalek, Ryan D; Tian, Xiangjun; Wong, Matthew; Losee-Olson, Susan H; Petrosino, Joseph F; Yoo, Seung-Hee; Shimomura, Kazuhiro; Chen, Zheng

    2015-06-04

    Dietary fibers are increasingly appreciated as beneficial nutritional components. However, a requisite role of gut microbiota in fiber function and the overall impact of fibers on metabolomic flux remain unclear. We herein showed enhancing effects of a soluble resistant maltodextrin (RM) on glucose homeostasis in mouse metabolic disease models. Remarkably, fecal microbiota transplantation (FMT) caused pronounced and time-dependent improvement in glucose tolerance in RM recipient mice, indicating a causal relationship between microbial remodeling and metabolic efficacy. Microbial 16S sequencing revealed transmissible taxonomic changes correlated with improved metabolism, notably enrichment of probiotics and reduction of Alistipes and Bacteroides known to associate with high fat/protein diets. Metabolomic profiling further illustrated broad changes, including enrichment of phenylpropionates and decreases in key intermediates of glucose utilization, cholesterol biosynthesis and amino acid fermentation. These studies elucidate beneficial roles of RM-dependent microbial remodeling in metabolic homeostasis, and showcase prevalent health-promoting potentials of dietary fibers.

  7. GENOME-BASED MODELING AND DESIGN OF METABOLIC INTERACTIONS IN MICROBIAL COMMUNITIES

    Directory of Open Access Journals (Sweden)

    Radhakrishnan Mahadevan

    2012-10-01

    With the advent of genome sequencing, omics technologies, bioinformatics and genome-scale modeling, researchers now have unprecedented capabilities to analyze and engineer the metabolism of microbial communities. The goal of this review is to summarize recent applications of genome-scale metabolic modeling to microbial communities. A brief introduction to lumped community models is used to motivate the need for genome-level descriptions of individual species and their metabolic interactions. The review of genome-scale models begins with static modeling approaches, which are appropriate for communities where the extracellular environment can be assumed to be time invariant or slowly varying. Dynamic extensions of the static modeling approach are described, and then applications of genome-scale models for design of synthetic microbial communities are reviewed. The review concludes with a summary of metagenomic tools for analyzing community metabolism and an outlook for future research.

  8. Maternal obesity is associated with gut microbial metabolic potential in offspring during infancy.

    Science.gov (United States)

    Cerdó, Tomás; Ruiz, Alicia; Jáuregui, Ruy; Azaryah, Hatim; Torres-Espínola, Francisco José; García-Valdés, Luz; Teresa Segura, M; Suárez, Antonio; Campoy, Cristina

    2018-02-01

    Children born to obese mothers are at increased risk for obesity, but the mechanisms behind this association are not fully understood. Our study aimed to investigate differences in the functions encoded by the microbiome of infants at 18 months of age when the transition from early infant-feeding to solid family foods is established. To investigate the impact of maternal prepregnancy body mass index on infants' gut microbiome, faecal samples from infants born to normoweight (n = 21) and obese mothers (n = 18) were analysed by 16S rRNA gene sequencing and a functional-inference-based microbiome analysis. Our results indicated that Firmicutes was significantly enriched in infants born to normoweight mothers whereas Bacteroidetes was significantly enriched in infants born to obese women. In both microbiomes, the greatest number of genes (>50%) that were assigned a function encoded for proteins involved in "metabolism" among tier 1 KEGG Orthology (KO) categories. At lower KO functional categories, the microbiome of infants born to normoweight mothers was characterized by a significant enrichment in the abundances of "pentose phosphate pathway" (p = 0.037), "lysine biosynthesis" (p = 0.043), "glycerolipid metabolism" (p = 0.042), and "C5-branched dibasic acid metabolism" (p = 0.045). Notably, the microbiome of infants born to obese mothers was significantly enriched in "streptomycin biosynthesis" (p = 0.047), "sulphur metabolism" (p = 0.041), "taurine and hypotaurine metabolism" (p = 0.036), and "lipopolysaccharide biosynthesis" (p = 0.043). In summary, our study showed that maternal prepregnancy obesity may imprint a selective gut microbial composition during late infancy with distinct functional performances.

  9. Investigating Microbial Biofilm Formations on Crustal Rock Substrates

    Science.gov (United States)

    Weiser, M.; D'Angelo, T.; Carr, S. A.; Orcutt, B.

    2017-12-01

    Ocean crust hosts microbial life that, in some cases, alter the component rocks as a means of obtaining energy. Variations in crust lithology, included trace metal and mineral content, as well as the chemistry of the fluids circulating through them, provide substrates for some microbes to metabolize, leading to formation of biofilm community structures. Microbes have different parameters for the situations in which they will form biofilms, but they must have some source of energy in excess at the site of biofilm formation for them to become stationary and form the carbohydrate-rich structures connecting the cells to one another and the substrate. Generally, the requirements for microbes to form biofilms on crustal minerals are unclear. We designed two experiments to test (1) mineral preference and biofilm formation rates by natural seawater microbial communities, and (2) biofilm development as a function of phosphate availability for an organism isolated from subseafloor ocean crust. In Experiment 1, we observed that phyric basalt groundmass is preferentially colonized over aphyric basalt or metal sulfides in a shallow water and oxic seawater environment. In experiment 2, tests of the anaerobic heterotroph Thalassospira bacteria isolated from oceanic crustal fluids showed that they preferentially form biofilms, lose motility, and increase exponentially in number over time in higher-PO4 treatments (50 micromolar), including with phosphate-doped basalts, than in treatments with low phosphate concentrations (0.5 micromolar) often found in crustal fluids. These observations suggest phosphate as a main driver of biofilm formation in subsurface crust. Overall, these data suggest that the drivers of microbial biofilm formation on crustal substrates are selective to the substrate conditions, which has important implications for estimating the global biomass of life harbored in oceanic crust.

  10. Towards the understanding of microbial metabolism in relation to microbial enhanced oil recovery

    DEFF Research Database (Denmark)

    Halim, Amalia Yunita; Nielsen, Sidsel Marie; Nielsen, Kristian Fog

    2017-01-01

    In this study, Bacillus licheniformis 421 was used as a model organism to understand the effects of microbial cell growth and metabolite production under anaerobic conditions in relation to microbial enhanced oil recovery. The bacterium was able to grow anaerobically on different carbon compounds...

  11. Kinetic modeling of microbially-driven redox chemistry of radionuclides in subsurface environments: Coupling transport, microbial metabolism and geochemistry

    International Nuclear Information System (INIS)

    Wang, Yifeng; Papenguth, Hans W.

    2000-01-01

    Microbial degradation of organic matter is a driving force in many subsurface geochemical systems, and therefore may have significant impacts on the fate of radionuclides released into subsurface environments. In this paper, the authors present a general reaction-transport model for microbial metabolism, redox chemistry, and radionuclide migration in subsurface systems. The model explicitly accounts for biomass accumulation and the coupling of radionuclide redox reactions with major biogeochemical processes. Based on the consideration that the biomass accumulation in subsurface environments is likely to achieve a quasi-steady state, they have accordingly modified the traditional microbial growth kinetic equation. They justified the use of the biogeochemical models without the explicit representation of biomass accumulation, if the interest of modeling is in the net impact of microbial reactions on geochemical processes. They then applied their model to a scenario in which an oxic water flow containing both uranium and completing organic ligands is recharged into an oxic aquifer in a carbonate formation. The model simulation shows that uranium can be reduced and therefore immobilized in the anoxic zone created by microbial degradation

  12. An integrated study to analyze soil microbial community structure and metabolic potential in two forest types.

    Directory of Open Access Journals (Sweden)

    Yuguang Zhang

    Full Text Available Soil microbial metabolic potential and ecosystem function have received little attention owing to difficulties in methodology. In this study, we selected natural mature forest and natural secondary forest and analyzed the soil microbial community and metabolic potential combing the high-throughput sequencing and GeoChip technologies. Phylogenetic analysis based on 16S rRNA sequencing showed that one known archaeal phylum and 15 known bacterial phyla as well as unclassified phylotypes were presented in these forest soils, and Acidobacteria, Protecobacteria, and Actinobacteria were three of most abundant phyla. The detected microbial functional gene groups were related to different biogeochemical processes, including carbon degradation, carbon fixation, methane metabolism, nitrogen cycling, phosphorus utilization, sulfur cycling, etc. The Shannon index for detected functional gene probes was significantly higher (P<0.05 at natural secondary forest site. The regression analysis showed that a strong positive (P<0.05 correlation was existed between the soil microbial functional gene diversity and phylogenetic diversity. Mantel test showed that soil oxidizable organic carbon, soil total nitrogen and cellulose, glucanase, and amylase activities were significantly linked (P<0.05 to the relative abundance of corresponded functional gene groups. Variance partitioning analysis showed that a total of 81.58% of the variation in community structure was explained by soil chemical factors, soil temperature, and plant diversity. Therefore, the positive link of soil microbial structure and composition to functional activity related to ecosystem functioning was existed, and the natural secondary forest soil may occur the high microbial metabolic potential. Although the results can't directly reflect the actual microbial populations and functional activities, this study provides insight into the potential activity of the microbial community and associated feedback

  13. An integrated study to analyze soil microbial community structure and metabolic potential in two forest types.

    Science.gov (United States)

    Zhang, Yuguang; Cong, Jing; Lu, Hui; Yang, Caiyun; Yang, Yunfeng; Zhou, Jizhong; Li, Diqiang

    2014-01-01

    Soil microbial metabolic potential and ecosystem function have received little attention owing to difficulties in methodology. In this study, we selected natural mature forest and natural secondary forest and analyzed the soil microbial community and metabolic potential combing the high-throughput sequencing and GeoChip technologies. Phylogenetic analysis based on 16S rRNA sequencing showed that one known archaeal phylum and 15 known bacterial phyla as well as unclassified phylotypes were presented in these forest soils, and Acidobacteria, Protecobacteria, and Actinobacteria were three of most abundant phyla. The detected microbial functional gene groups were related to different biogeochemical processes, including carbon degradation, carbon fixation, methane metabolism, nitrogen cycling, phosphorus utilization, sulfur cycling, etc. The Shannon index for detected functional gene probes was significantly higher (PThe regression analysis showed that a strong positive (Pthe soil microbial functional gene diversity and phylogenetic diversity. Mantel test showed that soil oxidizable organic carbon, soil total nitrogen and cellulose, glucanase, and amylase activities were significantly linked (Pthe relative abundance of corresponded functional gene groups. Variance partitioning analysis showed that a total of 81.58% of the variation in community structure was explained by soil chemical factors, soil temperature, and plant diversity. Therefore, the positive link of soil microbial structure and composition to functional activity related to ecosystem functioning was existed, and the natural secondary forest soil may occur the high microbial metabolic potential. Although the results can't directly reflect the actual microbial populations and functional activities, this study provides insight into the potential activity of the microbial community and associated feedback responses of the terrestrial ecosystem to environmental changes.

  14. Nanoscale zero-valent iron/persulfate enhanced upflow anaerobic sludge blanket reactor for dye removal: Insight into microbial metabolism and microbial community

    Science.gov (United States)

    Pan, Fei; Zhong, Xiaohan; Xia, Dongsheng; Yin, Xianze; Li, Fan; Zhao, Dongye; Ji, Haodong; Liu, Wen

    2017-01-01

    This study investigated the efficiency of nanoscale zero-valent iron combined with persulfate (NZVI/PS) for enhanced degradation of brilliant red X-3B in an upflow anaerobic sludge blanket (UASB) reactor, and examined the effects of NZVI/PS on anaerobic microbial communities during the treatment process. The addition of NZVI (0.5 g/L) greatly enhanced the decolourization rate of X-3B from 63.8% to 98.4%. The Biolog EcoPlateTM technique was utilized to examine microbial metabolism in the reactor, and the Illumina MiSeq high-throughput sequencing revealed 22 phyla and 88 genera of the bacteria. The largest genera (Lactococcus) decreased from 33.03% to 7.94%, while the Akkermansia genera increased from 1.69% to 20.23% according to the abundance in the presence of 0.2 g/L NZVI during the biological treatment process. Meanwhile, three strains were isolated from the sludge in the UASB reactors and identified by 16 S rRNA analysis. The distribution of three strains was consistent with the results from the Illumina MiSeq high throughput sequencing. The X-ray photoelectron spectroscopy results indicated that Fe(0) was transformed into Fe(II)/Fe(III) during the treatment process, which are beneficial for the microorganism growth, and thus promoting their metabolic processes and microbial community. PMID:28300176

  15. Nanoscale zero-valent iron/persulfate enhanced upflow anaerobic sludge blanket reactor for dye removal: Insight into microbial metabolism and microbial community

    Science.gov (United States)

    Pan, Fei; Zhong, Xiaohan; Xia, Dongsheng; Yin, Xianze; Li, Fan; Zhao, Dongye; Ji, Haodong; Liu, Wen

    2017-03-01

    This study investigated the efficiency of nanoscale zero-valent iron combined with persulfate (NZVI/PS) for enhanced degradation of brilliant red X-3B in an upflow anaerobic sludge blanket (UASB) reactor, and examined the effects of NZVI/PS on anaerobic microbial communities during the treatment process. The addition of NZVI (0.5 g/L) greatly enhanced the decolourization rate of X-3B from 63.8% to 98.4%. The Biolog EcoPlateTM technique was utilized to examine microbial metabolism in the reactor, and the Illumina MiSeq high-throughput sequencing revealed 22 phyla and 88 genera of the bacteria. The largest genera (Lactococcus) decreased from 33.03% to 7.94%, while the Akkermansia genera increased from 1.69% to 20.23% according to the abundance in the presence of 0.2 g/L NZVI during the biological treatment process. Meanwhile, three strains were isolated from the sludge in the UASB reactors and identified by 16 S rRNA analysis. The distribution of three strains was consistent with the results from the Illumina MiSeq high throughput sequencing. The X-ray photoelectron spectroscopy results indicated that Fe(0) was transformed into Fe(II)/Fe(III) during the treatment process, which are beneficial for the microorganism growth, and thus promoting their metabolic processes and microbial community.

  16. Dietary Gut Microbial Metabolites, Short-chain Fatty Acids, and Host Metabolic Regulation

    Directory of Open Access Journals (Sweden)

    Mayu Kasubuchi

    2015-04-01

    Full Text Available During feeding, the gut microbiota contributes to the host energy acquisition and metabolic regulation thereby influencing the development of metabolic disorders such as obesity and diabetes. Short-chain fatty acids (SCFAs such as acetate, butyrate, and propionate, which are produced by gut microbial fermentation of dietary fiber, are recognized as essential host energy sources and act as signal transduction molecules via G-protein coupled receptors (FFAR2, FFAR3, OLFR78, GPR109A and as epigenetic regulators of gene expression by the inhibition of histone deacetylase (HDAC. Recent evidence suggests that dietary fiber and the gut microbial-derived SCFAs exert multiple beneficial effects on the host energy metabolism not only by improving the intestinal environment, but also by directly affecting various host peripheral tissues. In this review, we summarize the roles of gut microbial SCFAs in the host energy regulation and present an overview of the current understanding of its physiological functions.

  17. Nitrification-driven forms of nitrogen metabolism in microbial mat communities thriving along an ammonium-enriched subsurface geothermal stream

    Science.gov (United States)

    Nishizawa, Manabu; Koba, Keisuke; Makabe, Akiko; Yoshida, Naohiro; Kaneko, Masanori; Hirao, Shingo; Ishibashi, Jun-ichiro; Yamanaka, Toshiro; Shibuya, Takazo; Kikuchi, Tohru; Hirai, Miho; Miyazaki, Junichi; Nunoura, Takuro; Takai, Ken

    2013-07-01

    We report here the concurrence and interaction among forms of nitrogen metabolism in thermophilic microbial mat communities that developed in an ammonium-abundant subsurface geothermal stream. First, the physical and chemical conditions of the stream water at several representative microbial mat habitats (including upper, middle and downstream sites) were characterized. A thermodynamic calculation using these physical and chemical conditions predicted that nitrification consisting of ammonia and nitrite oxidations would provide one of the largest energy yields of chemolithotrophic metabolisms. Second, near-complete prokaryotic 16S rRNA gene clone analysis was conducted for representative microbial mat communities at the upper, middle and downstream sites. The results indicated a dynamic shift in the 16S rRNA gene phylotype composition through physical and chemical variations of the stream water. The predominant prokaryotic components varied from phylotypes related to hydrogeno (H2)- and thio (S)-trophic Aquificales, thermophilic methanotrophs and putative ammonia-oxidizing Archaea (AOA) located upstream (72 °C) to the phylotypes affiliated with putative AOA and nitrite-oxidizing bacteria (NOB) located at the middle and downstream sites (65 and 57 °C, respectively). In addition, the potential in situ metabolic activities of different forms of nitrogen metabolism were estimated through laboratory experiments using bulk microbial mat communities. Finally, the compositional and isotopic variation in nitrogen compounds was investigated in the stream water flowing over the microbial mats and in the interstitial water inside the mats. Although the stream water was characterized by a gradual decrease in the total ammonia concentration (ΣNH3: the sum of ammonia and ammonium concentrations) and a gradual increase in the total concentration of nitrite and nitrate (NO2- + NO3-), the total inorganic nitrogen concentration (TIN: the sum of ΣNH3, NO2- and NO3- concentrations

  18. Organic chemistry of basal ice - presence of labile, low molecular weight compounds available for microbial metabolism

    Science.gov (United States)

    Lis, Grzegorz P.; Wadham, Jemma L.; Lawson, Emily; Stibal, Marek; Telling, Jon

    2010-05-01

    Recent studies show that subglacial environments previously thought to be devoid of life contain a host of active microbial organisms. Presence of liquid water due to overburden pressure, the release of nutrients from chemical erosion of bedrock, and the potential carbon sources in overridden sediments facilitate life in this extreme environment. However, little is still known of concentrations and diversity of labile organic compounds essential for sustaining microbial metabolism in subglacial environments. Three subglacial ecosystems that considerably differ in range and amount of available organic compounds were selected for this study 1-Engabreen, northern Norway, overlying high-grade metamorphic rocks with low organic carbon content; 2-Finsterwalderbreen, Svalbard, overriding ancient black shales with a relatively high carbon content yet recalcitrant to microbiological consumption; and 3-Russell Glacier in western Greenland with recently overridden quaternary organic rich paleosols. Basal and pressure ridge ice samples were collected and subsequently analysed for low molecular weight organic compounds, with the emphasis on volatile fatty acids, carbohydrates and amino acids. The highest concentration of labile organic compounds in Greenland basal ice suggest that recently overridden paleosols have the greatest potential for sustaining microbial populations present within and underneath basal ice. The high concentration of "ancient" organic carbon in basal ice from Finsterwalderbreen, Svalbard, doesn't correlate with the presence of labile organic compounds. This indicates the inability of microbes to digest recalcitrant kerogen carbon in cold temperatures. In all three investigated environments, concentrations of labile organic compounds are elevated in basal ice with a high debris content. Until recently, most models of the global carbon cycle tend to neglect the pool of subglacial organic carbon as little is known about the range and concentrations of

  19. Total microbial biomass and metabolic state of microorganisms in a typical chernozem of Moldova

    Science.gov (United States)

    Frunze, N. I.

    2013-04-01

    New data on the total microbial biomass and its metabolic state in a typical chernozem of Moldova were obtained. The carbon content of the microbial biomass in the arable chernozems varied from 419 to 1033 μg/g soil and from 1002 to 1432 μg C/g soil under the shelterbelts. The contents of the microbial biomass under the shelter belts was by 2.1-2.9, 1.6-2.2, and 1.2-1.3 times higher than that in the unfertilized and fertilized with mineral and organic nutrients chernozems, respectively. Crop rotations with and without lucerne were examined. The functional activity of the microbial communities in the chernozem was determined by their metabolic diversity, the ability to use alternative metabolic reactions, and the domination of r-strategists. The content of the active part of the microbial community in the natural ecosystems constituted approximately 1/3 (29.1% on the average) of the total microbial community; in the arable soils, it as lower (9.8-21.8%).

  20. Host-microbial interactions in the metabolism of therapeutic and diet-derived xenobiotics

    Science.gov (United States)

    Carmody, Rachel N.; Turnbaugh, Peter J.

    2014-01-01

    Our associated microbial communities play a critical role in human health and predisposition to disease, but the degree to which they also shape therapeutic interventions is not well understood. Here, we integrate results from classic and current studies of the direct and indirect impacts of the gut microbiome on the metabolism of therapeutic drugs and diet-derived bioactive compounds. We pay particular attention to microbial influences on host responses to xenobiotics, adding to the growing consensus that treatment outcomes reflect our intimate partnership with the microbial world, and providing an initial framework from which to consider a more comprehensive view of pharmacology and nutrition. PMID:25105361

  1. The Importance of Transition Metals in the Expanding Network of Microbial Metabolism in the Archean Eon

    Science.gov (United States)

    Moore, E. K.; Jelen, B. I.; Giovannelli, D.; Prabhu, A.; Raanan, H.; Falkowski, P. G.

    2017-12-01

    Deep time changes in Earth surface redox conditions, particularly due to global oxygenation, has impacted the availability of different metals and substrates that are central in biology. Oxidoreductase proteins are molecular nanomachines responsible for all biological electron transfer processes across the tree of life. These enzymes largely contain transition metals in their active sites. Microbial metabolic pathways form a global network of electron transfer, which expanded throughout the Archean eon. Older metabolisms (sulfur reduction, methanogenesis, anoxygenic photosynthesis) accessed negative redox potentials, while later evolving metabolisms (oxygenic photosynthesis, nitrification/denitrification, aerobic respiration) accessed positive redox potentials. The incorporation of different transition metals facilitated biological innovation and the expansion of the network of microbial metabolism. Network analysis was used to examine the connections between microbial taxa, metabolic pathways, crucial metallocofactors, and substrates in deep time by incorporating biosignatures preserved in the geologic record. Nitrogen fixation and aerobic respiration have the highest level of betweenness among metabolisms in the network, indicating that the oldest metabolisms are not the most central. Fe has by far the highest betweenness among metals. Clustering analysis largely separates High Metal Bacteria (HMB), Low Metal Bacteria (LMB), and Archaea showing that simple un-weighted links between taxa, metabolism, and metals have phylogenetic relevance. On average HMB have the highest betweenness among taxa, followed by Archaea and LMB. There is a correlation between the number of metallocofactors and metabolic pathways in representative bacterial taxa, but Archaea do not follow this trend. In many cases older and more recently evolved metabolisms were clustered together supporting previous findings that proliferation of metabolic pathways is not necessarily chronological.

  2. Microbial metabolism fuels ecosystem-scale organic matter transformations: an integrated biological and chemical perspective

    Science.gov (United States)

    Wrighton, K. C.; Narrowe, A. B.; Angle, J.; Stefanik, K. S.; Daly, R. A.; Johnston, M.; Miller, C. S.

    2014-12-01

    Freshwater saturated sediments and soils represent vital ecosystems due to their nutrient cycling capacities and their prominent contribution to global greenhouse gas emissions. However, the diversity of microorganisms and metabolic pathways involved in carbon cycling, and the impacts of these processes on other biogeochemical cycles remain poorly understood. Major advances in DNA sequencing have helped forge linkages between the previously disconnected biological and chemical components of these systems. Here, we present data on the use of assembly-based metagenomics to generate hypotheses on microbial carbon degradation and biogeochemical cycling in waterlogged sediments and soils. DNA sequencing from a fresh water aquifer adjacent to the Colorado River in Rifle, CO yielded extensive genome recovery from multiple previously unknown bacterial lineages. Fermentative metabolisms encoded by these genomes drive nitrogen, hydrogen, and sulfur cycling in this subsurface system. We are also applying a similar approach to identify microbial processes in a freshwater wetland on Lake Erie, OH. Given the increased diversity (increased richness, decreased evenness, and strain variation) of wetland sediment microbial communities, we modified methods for specialized assembly of long taxonomic marker gene amplicons (EMIRGE) to create a biogeographical map of Fungi, Archaea, and Bacteria along depth and hydrological transects. This map reveals that the microbial community associated with the top two depths (>7 cm) is significantly different from bottom depths (7-40 cm). Dissolved organic matter (DOM) molecular weight and the presence of oxidized terminal electron acceptors best predict differences in microbial community structure. Laboratory mesocosms amended with pore-water DOM, in situ soil communities, and variable oxygen conditions link DOM composition and redox to microbial metabolic networks, biogeochemical cycles, and green house gas emission. Organism identities from

  3. Rumen microbial communities influence metabolic phenotypes in lambs

    DEFF Research Database (Denmark)

    Morgavi, Diego P.; Rahahao-Paris, Estelle; Popova, Milka

    2015-01-01

    in microbiota structure. Discriminant metabolites were mainly involved in amino acids and protein metabolic pathways while a negative interaction was observed between methylotrophic methanogens Methanomassiliicoccales and trimethylamine N-oxide. These results stress the influence of gut microbes on animal...

  4. A biocompatible alkene hydrogenation merges organic synthesis with microbial metabolism.

    Science.gov (United States)

    Sirasani, Gopal; Tong, Liuchuan; Balskus, Emily P

    2014-07-21

    Organic chemists and metabolic engineers use orthogonal technologies to construct essential small molecules such as pharmaceuticals and commodity chemicals. While chemists have leveraged the unique capabilities of biological catalysts for small-molecule production, metabolic engineers have not likewise integrated reactions from organic synthesis with the metabolism of living organisms. Reported herein is a method for alkene hydrogenation which utilizes a palladium catalyst and hydrogen gas generated directly by a living microorganism. This biocompatible transformation, which requires both catalyst and microbe, and can be used on a preparative scale, represents a new strategy for chemical synthesis that combines organic chemistry and metabolic engineering. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Metabolic engineering of microbial competitive advantage for industrial fermentation processes.

    Science.gov (United States)

    Shaw, A Joe; Lam, Felix H; Hamilton, Maureen; Consiglio, Andrew; MacEwen, Kyle; Brevnova, Elena E; Greenhagen, Emily; LaTouf, W Greg; South, Colin R; van Dijken, Hans; Stephanopoulos, Gregory

    2016-08-05

    Microbial contamination is an obstacle to widespread production of advanced biofuels and chemicals. Current practices such as process sterilization or antibiotic dosage carry excess costs or encourage the development of antibiotic resistance. We engineered Escherichia coli to assimilate melamine, a xenobiotic compound containing nitrogen. After adaptive laboratory evolution to improve pathway efficiency, the engineered strain rapidly outcompeted a control strain when melamine was supplied as the nitrogen source. We additionally engineered the yeasts Saccharomyces cerevisiae and Yarrowia lipolytica to assimilate nitrogen from cyanamide and phosphorus from potassium phosphite, and they outcompeted contaminating strains in several low-cost feedstocks. Supplying essential growth nutrients through xenobiotic or ecologically rare chemicals provides microbial competitive advantage with minimal external risks, given that engineered biocatalysts only have improved fitness within the customized fermentation environment. Copyright © 2016, American Association for the Advancement of Science.

  6. Microbial fuel cells applied to the metabolically based detection of extraterrestrial life.

    Science.gov (United States)

    Abrevaya, Ximena C; Mauas, Pablo J D; Cortón, Eduardo

    2010-12-01

    Since the 1970s, when the Viking spacecrafts carried out experiments to detect microbial metabolism on the surface of Mars, the search for nonspecific methods to detect life in situ has been one of the goals of astrobiology. It is usually required that a methodology detect life independently from its composition or form and that the chosen biological signature point to a feature common to all living systems, such as the presence of metabolism. In this paper, we evaluate the use of microbial fuel cells (MFCs) for the detection of microbial life in situ. MFCs are electrochemical devices originally developed as power electrical sources and can be described as fuel cells in which the anode is submerged in a medium that contains microorganisms. These microorganisms, as part of their metabolic process, oxidize organic material, releasing electrons that contribute to the electric current, which is therefore proportional to metabolic and other redox processes. We show that power and current density values measured in MFCs that use microorganism cultures or soil samples in the anode are much larger than those obtained with a medium free of microorganisms or sterilized soil samples, respectively. In particular, we found that this is true for extremophiles, which have been proposed as potential inhabitants of extraterrestrial environments. Therefore, our results show that MFCs have the potential to be used for in situ detection of microbial life.

  7. Microbial transglutaminase production by Streptoverticillium mobaraense: Analysis of amino acid metabolism using mass balances

    NARCIS (Netherlands)

    Zhu, Y.; Rinzema, A.; Bonarius, H.P.J.; Tramper, J.; Bol, J.

    1998-01-01

    Metabolic flows, especially those of amino acids, were determined and analyzed at different stages of a batch fermentation for microbial transglutaminase production by Streptoverticillium mobaraense. The method is mainly based on mass balances and measurements of amino acids and other metabolites.

  8. Investigation of metabolic encephalopathy | van der Watt ...

    African Journals Online (AJOL)

    Encephalopathy may be a presenting sign in a wide range of medical conditions. This review focuses only on the diagnosis and initial management of those inherited metabolic diseases (IMDs) prevalent in South Africa that may present with encephalopathy in childhood. Metabolic encephalopathy is a medical emergency, ...

  9. Diagnosis of In Situ Metabolic State and Rates of Microbial Metabolism During In Situ Uranium Bioremediation with Molecular Techniques

    Energy Technology Data Exchange (ETDEWEB)

    Lovley, Derek R

    2012-11-28

    The goal of these projects was to develop molecule tools to tract the metabolic activity and physiological status of microorganisms during in situ uranium bioremediation. Such information is important in able to design improved bioremediation strategies. As summarized below, the research was highly successful with new strategies developed for estimating in situ rates of metabolism and diagnosing the physiological status of the predominant subsurface microorganisms. This is a first not only for groundwater bioremediation studies, but also for subsurface microbiology in general. The tools and approaches developed in these studies should be applicable to the study of microbial communities in a diversity of soils and sediments.

  10. Visualization of Metabolic Interaction Networks in Microbial Communities Using VisANT 5.0.

    Directory of Open Access Journals (Sweden)

    Brian R Granger

    2016-04-01

    Full Text Available The complexity of metabolic networks in microbial communities poses an unresolved visualization and interpretation challenge. We address this challenge in the newly expanded version of a software tool for the analysis of biological networks, VisANT 5.0. We focus in particular on facilitating the visual exploration of metabolic interaction between microbes in a community, e.g. as predicted by COMETS (Computation of Microbial Ecosystems in Time and Space, a dynamic stoichiometric modeling framework. Using VisANT's unique metagraph implementation, we show how one can use VisANT 5.0 to explore different time-dependent ecosystem-level metabolic networks. In particular, we analyze the metabolic interaction network between two bacteria previously shown to display an obligate cross-feeding interdependency. In addition, we illustrate how a putative minimal gut microbiome community could be represented in our framework, making it possible to highlight interactions across multiple coexisting species. We envisage that the "symbiotic layout" of VisANT can be employed as a general tool for the analysis of metabolism in complex microbial communities as well as heterogeneous human tissues. VisANT is freely available at: http://visant.bu.edu and COMETS at http://comets.bu.edu.

  11. Functional Gene Diversity and Metabolic Potential of the Microbial Community in an Estuary-Shelf Environment

    Directory of Open Access Journals (Sweden)

    Yu Wang

    2017-06-01

    Full Text Available Microbes play crucial roles in various biogeochemical processes in the ocean, including carbon (C, nitrogen (N, and phosphorus (P cycling. Functional gene diversity and the structure of the microbial community determines its metabolic potential and therefore its ecological function in the marine ecosystem. However, little is known about the functional gene composition and metabolic potential of bacterioplankton in estuary areas. The East China Sea (ECS is a dynamic marginal ecosystem in the western Pacific Ocean that is mainly affected by input from the Changjiang River and the Kuroshio Current. Here, using a high-throughput functional gene microarray (GeoChip, we analyzed the functional gene diversity, composition, structure, and metabolic potential of microbial assemblages in different ECS water masses. Four water masses determined by temperature and salinity relationship showed different patterns of functional gene diversity and composition. Generally, functional gene diversity [Shannon–Weaner’s H and reciprocal of Simpson’s 1/(1-D] in the surface water masses was higher than that in the bottom water masses. The different presence and proportion of functional genes involved in C, N, and P cycling among the bacteria of the different water masses showed different metabolic preferences of the microbial populations in the ECS. Genes involved in starch metabolism (amyA and nplT showed higher proportion in microbial communities of the surface water masses than of the bottom water masses. In contrast, a higher proportion of genes involved in chitin degradation was observed in microorganisms of the bottom water masses. Moreover, we found a higher proportion of nitrogen fixation (nifH, transformation of hydroxylamine to nitrite (hao and ammonification (gdh genes in the microbial communities of the bottom water masses compared with those of the surface water masses. The spatial variation of microbial functional genes was significantly correlated

  12. Functional Gene Diversity and Metabolic Potential of the Microbial Community in an Estuary-Shelf Environment.

    Science.gov (United States)

    Wang, Yu; Zhang, Rui; He, Zhili; Van Nostrand, Joy D; Zheng, Qiang; Zhou, Jizhong; Jiao, Nianzhi

    2017-01-01

    Microbes play crucial roles in various biogeochemical processes in the ocean, including carbon (C), nitrogen (N), and phosphorus (P) cycling. Functional gene diversity and the structure of the microbial community determines its metabolic potential and therefore its ecological function in the marine ecosystem. However, little is known about the functional gene composition and metabolic potential of bacterioplankton in estuary areas. The East China Sea (ECS) is a dynamic marginal ecosystem in the western Pacific Ocean that is mainly affected by input from the Changjiang River and the Kuroshio Current. Here, using a high-throughput functional gene microarray (GeoChip), we analyzed the functional gene diversity, composition, structure, and metabolic potential of microbial assemblages in different ECS water masses. Four water masses determined by temperature and salinity relationship showed different patterns of functional gene diversity and composition. Generally, functional gene diversity [Shannon-Weaner's H and reciprocal of Simpson's 1/(1- D )] in the surface water masses was higher than that in the bottom water masses. The different presence and proportion of functional genes involved in C, N, and P cycling among the bacteria of the different water masses showed different metabolic preferences of the microbial populations in the ECS. Genes involved in starch metabolism ( amyA and nplT ) showed higher proportion in microbial communities of the surface water masses than of the bottom water masses. In contrast, a higher proportion of genes involved in chitin degradation was observed in microorganisms of the bottom water masses. Moreover, we found a higher proportion of nitrogen fixation ( nifH ), transformation of hydroxylamine to nitrite ( hao ) and ammonification ( gdh ) genes in the microbial communities of the bottom water masses compared with those of the surface water masses. The spatial variation of microbial functional genes was significantly correlated with

  13. Influence of excessive exercise on immunity, metabolism, and gut microbial diversity in an overtraining mice model.

    Science.gov (United States)

    Yuan, Xin; Xu, Shijie; Huang, Haiyang; Liang, Jian; Wu, Yayun; Li, Chujie; Yuan, Huiqi; Zhao, Xuejie; Lai, Xiaoping; Hou, Shaozhen

    2018-01-24

    The purpose of this study was to evaluate the negative influence of excessive exercise on immunity, substance and energy metabolism as well as gut microbiota in mice. Firstly, an overtraining model of Male Kunming mice was established by high-intensity swimming exercise for 4 weeks. Then, a series of evaluation indicators, including the routine blood analysis, immune organ coefficient, digestive enzymes, and aquaporins expression levels of small intestine and colon tissue, histological examinations of liver, spleen, small intestine, and colon, were determined based on this model. Furthermore, 16S rRNA gene sequencing was also employed to measure the microbial composition in gut. The results found that immune parameters, substance and energy metabolism of all mice was altered and disturbed after high-intensity swimming for 4 weeks, led to an atrophy of thymus and spleen as well as abnormal structural changes in liver when compared to non-swimming mice. Besides, excessive swimming mice had lower microbial diversity compared to non-swimming mice. However, there was no significant difference in gut microbial taxa between the two groups. The data indicated that excessive exercise exhibits negative impacts on immunity, substance and energy metabolism as well as gut microbial diversity. © 2018 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  14. Microbial arsenic metabolism: New twists on an old poison

    Science.gov (United States)

    Stolz, J.F.; Basu, P.; Oremland, R.S.

    2010-01-01

    Phylogenetically diverse microorganisms metabolize arsenic despite its toxicity and are part of its robust iogeochemical cycle. Respiratory arsenate reductase is a reversible enzyme, functioning in some microbes as an arsenate reductase but in others as an arsenite oxidase. As(III) can serve as an electron donor for anoxygenic photolithoautotrophy and chemolithoautotrophy. Organoarsenicals, such as the feed additive roxarsone, can be used as a source of energy, releasing inorganic arsenic.

  15. Investigating Moorella thermoacetica metabolism with a genome-scale constraint-based metabolic model.

    Science.gov (United States)

    Islam, M Ahsanul; Zengler, Karsten; Edwards, Elizabeth A; Mahadevan, Radhakrishnan; Stephanopoulos, Gregory

    2015-08-01

    Moorella thermoacetica is a strictly anaerobic, endospore-forming, and metabolically versatile acetogenic bacterium capable of conserving energy by both autotrophic (acetogenesis) and heterotrophic (homoacetogenesis) modes of metabolism. Its metabolic diversity and the ability to efficiently convert a wide range of compounds, including syngas (CO + H2) into acetyl-CoA have made this thermophilic bacterium a promising host for industrial biotechnology applications. However, lack of detailed information on M. thermoacetica's metabolism is a major impediment to its use as a microbial cell factory. In order to overcome this issue, a genome-scale constraint-based metabolic model of Moorella thermoacetica, iAI558, has been developed using its genome sequence and physiological data from published literature. The reconstructed metabolic network of M. thermoacetica comprises 558 metabolic genes, 705 biochemical reactions, and 698 metabolites. Of the total 705 model reactions, 680 are gene-associated while the rest are non-gene associated reactions. The model, in addition to simulating both autotrophic and heterotrophic growth of M. thermoacetica, revealed degeneracy in its TCA-cycle, a common characteristic of anaerobic metabolism. Furthermore, the model helped elucidate the poorly understood energy conservation mechanism of M. thermoacetica during autotrophy. Thus, in addition to generating experimentally testable hypotheses regarding its physiology, such a detailed model will facilitate rapid strain designing and metabolic engineering of M. thermoacetica for industrial applications.

  16. Investigating substrate use efficiency across different microbial physiologies in soil-extracted, solubilized organic matter (SESOM)

    Science.gov (United States)

    Cyle, K. T.; Martinez, C. E.

    2017-12-01

    Recent experimental work has elevated the importance of microbial processing for the stabilization of fresh carbon inputs within the soil mineral matrix. Enhancing our understanding of soil carbon and nitrogen dynamics therefore requires a better understanding of how efficiently microbial metabolism can process low molecular weight carbon substrates (carbon use efficiency, CUE) under environmentally relevant conditions. One approach to better understanding microbial uptake rates and CUE is the ecophysiological study of soil isolates in liquid media culture consisting of soil-extracted solubilized organic matter (SESOM). We are using SESOM from an Oa horizon under hemlock hardwood vegetation in upstate New York as liquid media for the growth of 12 isolates from the Oa and B horizon of the same site. Here we seek to test the uptake rates as well as CUE of 5 different low molecular weight substrates spanning compound class and nominal oxidation state (glucose, acetate, formate, glycine, valine) by isolates differing in phylogeny and physiology. The use of a spike of each of the 13C-labeled substrates into SESOM, along with a 0.2 μm filtration step, allows accurate partitioning of labeled carbon between biomass, gaseous CO2 as well as the exometabolome. Coupled UHPLC-MS measurements are being used to identify and determine uptake rates of over 80 potential C substrates present in the extract as well as our labeled substrate of interest along the course of the isolate growth curve. This work seeks to utilize a gradient in substrate class as well as microbial physiologies to inform our understanding of C and N cycling under relevant soil solution conditions. Future experiments may also use labeled biomass from stationary phase to investigate the stabilization potential of anabolic products formed from each substrate with a clay fraction isolated from the same site.

  17. A Status Report on the Global Research in Microbial Metabolic Engineering

    International Nuclear Information System (INIS)

    Joe, Min Ho; Lim, Sang Yong; Kim, Dong Ho

    2008-09-01

    Biotechnology industry is now a global 'Mega-Trend' and metabolic engineering technology has important role is this area. Therefore, many countries has made efforts in this field to produce top value added bio-products efficiently using microorganisms. It has been applied to increase the production of chemicals that are already produced by the host organism, to produce desired chemical substances from less expensive feedstock, and to generate products that are new to the host organism. Recent experimental advances, the so-called '-omics' technologies, mainly functional genomics, proteomics and metabolomics, have enabled wholesale generation of new genomic, transcriptomic, proteomic, and metabolomic data. This report provides the insights of the integrated view of metabolism generated by metabolic engineering for biotechnological applications of microbial metabolic engineering

  18. A Status Report on the Global Research in Microbial Metabolic Engineering

    Energy Technology Data Exchange (ETDEWEB)

    Joe, Min Ho; Lim, Sang Yong; Kim, Dong Ho

    2008-09-15

    Biotechnology industry is now a global 'Mega-Trend' and metabolic engineering technology has important role is this area. Therefore, many countries has made efforts in this field to produce top value added bio-products efficiently using microorganisms. It has been applied to increase the production of chemicals that are already produced by the host organism, to produce desired chemical substances from less expensive feedstock, and to generate products that are new to the host organism. Recent experimental advances, the so-called '-omics' technologies, mainly functional genomics, proteomics and metabolomics, have enabled wholesale generation of new genomic, transcriptomic, proteomic, and metabolomic data. This report provides the insights of the integrated view of metabolism generated by metabolic engineering for biotechnological applications of microbial metabolic engineering.

  19. An expanded role for microbial physiology in metabolic engineering and functional genomics: moving towards systems biology

    DEFF Research Database (Denmark)

    Nielsen, Jens; Olsson, Lisbeth

    2002-01-01

    . With the progress in molecular biology it has become possible to optimize industrial fermentations through introduction of directed genetic modification - an approach referred to as metabolic engineering. Furthermore, as a consequence of large sequencing programs the complete genomic sequence has become available...... for an increasing number of microorganisms. This has resulted in substantial research efforts in assigning function to all identified open reading frames - referred to as functional genomics. In both metabolic engineering and functional genomics there is a trend towards application of a macroscopic view on cell......Microbial physiology has traditionally played a very important role in both fundamental research and in industrial applications of microorganisms. The classical approach in microbial physiology has been to analyze the role of individual components (genes or proteins) in the overall cell function...

  20. Looking at microbial metabolism by high-resolution 2H-NMR spectroscopy

    Directory of Open Access Journals (Sweden)

    Victor P. Kutyshenko

    2013-07-01

    Full Text Available We analyzed the applicability of high-resolution 2H-HMR spectroscopy for the analysis of microbe metabolism in samples of mitochondrion isolated from rat liver and from aqueous extracts of homogenates of rat liver and other organs and tissues in the presence of high D2O contents. Such analysis is possible due to the fast microbe adaptation to life in the heavy water. It is also shown that some enzymatic processes typical for the intact cells are preserved in the homogenized tissue preparations. The microbial and cellular metabolic processes can be differentiated via the strategic use of cell poisons and antibiotics.

  1. Metal availability and the expanding network of microbial metabolisms in the Archaean eon

    Science.gov (United States)

    Moore, Eli K.; Jelen, Benjamin I.; Giovannelli, Donato; Raanan, Hagai; Falkowski, Paul G.

    2017-09-01

    Life is based on energy gained by electron-transfer processes; these processes rely on oxidoreductase enzymes, which often contain transition metals in their structures. The availability of different metals and substrates has changed over the course of Earth's history as a result of secular changes in redox conditions, particularly global oxygenation. New metabolic pathways using different transition metals co-evolved alongside changing redox conditions. Sulfur reduction, sulfate reduction, methanogenesis and anoxygenic photosynthesis appeared between about 3.8 and 3.4 billion years ago. The oxidoreductases responsible for these metabolisms incorporated metals that were readily available in Archaean oceans, chiefly iron and iron-sulfur clusters. Oxygenic photosynthesis appeared between 3.2 and 2.5 billion years ago, as did methane oxidation, nitrogen fixation, nitrification and denitrification. These metabolisms rely on an expanded range of transition metals presumably made available by the build-up of molecular oxygen in soil crusts and marine microbial mats. The appropriation of copper in enzymes before the Great Oxidation Event is particularly important, as copper is key to nitrogen and methane cycling and was later incorporated into numerous aerobic metabolisms. We find that the diversity of metals used in oxidoreductases has increased through time, suggesting that surface redox potential and metal incorporation influenced the evolution of metabolism, biological electron transfer and microbial ecology.

  2. Electronic Nose Technology to Measure Soil Microbial Activity and Classify Soil Metabolic Status

    OpenAIRE

    Fabrizio De Cesare; Elena Di Mattia; Simone Pantalei; Emiliano Zampetti; Vittorio Vinciguerra; Antonella Macagnano

    2011-01-01

    The electronic nose (E-nose) is a sensing technology that has been widely used to monitor environments in the last decade. In the present study, the capability of an E-nose, in combination with biochemical and microbiological techniques, of both detecting the microbial activity and estimating the metabolic status of soil ecosystems, was tested by measuring on one side respiration, enzyme activities and growth of bacteria in natural but simplified soil ecosystems over 23 days of incubation thr...

  3. 2004 Molecular Basis of Microbial One-Carbon Metabolism Gordon Conference - August 1-6, 2004

    Energy Technology Data Exchange (ETDEWEB)

    Joseph A. Krzycki

    2005-09-15

    The Gordon Research Conference (GRC) on 2004 Molecular Basis of Microbial One-Carbon Metabolism Gordon Conference - August 1-6, 2004 was held at Mount Holyoke College, South Hadley, MA from August 1-6, 2004. The Conference was well-attended with 117 participants (attendees list attached). The attendees represented the spectrum of endeavor in this field coming from academia, industry, and government laboratories, both U.S. and foreign scientists, senior researchers, young investigators, and students. In designing the formal speakers program, emphasis was placed on current unpublished research and discussion of the future target areas in this field. There was a conscious effort to stimulate lively discussion about the key issues in the field today. Time for formal presentations was limited in the interest of group discussions. In order that more scientists could communicate their most recent results, poster presentation time was scheduled. Attached is a copy of the formal schedule and speaker program and the poster program. In addition to these formal interactions, 'free time' was scheduled to allow informal discussions. Such discussions are fostering new collaborations and joint efforts in the field.

  4. Changes in Microbial Energy Metabolism Measured by Nanocalorimetry during Growth Phase Transitions

    Science.gov (United States)

    Robador, Alberto; LaRowe, Douglas E.; Finkel, Steven E.; Amend, Jan P.; Nealson, Kenneth H.

    2018-01-01

    Calorimetric measurements of the change in heat due to microbial metabolic activity convey information about the kinetics, as well as the thermodynamics, of all chemical reactions taking place in a cell. Calorimetric measurements of heat production made on bacterial cultures have recorded the energy yields of all co-occurring microbial metabolic reactions, but this is a complex, composite signal that is difficult to interpret. Here we show that nanocalorimetry can be used in combination with enumeration of viable cell counts, oxygen consumption rates, cellular protein content, and thermodynamic calculations to assess catabolic rates of an isolate of Shewanella oneidensis MR-1 and infer what fraction of the chemical energy is assimilated by the culture into biomass and what fraction is dissipated in the form of heat under different limiting conditions. In particular, our results demonstrate that catabolic rates are not necessarily coupled to rates of cell division, but rather, to physiological rearrangements of S. oneidensis MR-1 upon growth phase transitions. In addition, we conclude that the heat released by growing microorganisms can be measured in order to understand the physiochemical nature of the energy transformation and dissipation associated with microbial metabolic activity in conditions approaching those found in natural systems. PMID:29449836

  5. Disposition and Metabolism of Investigational New Drugs.

    Science.gov (United States)

    1982-09-01

    and Trans- fer of Raw Data for Disposition, Metabolic Profile, and Phar- macokinetics of Mefloquine -SC1, WR-142490-EC1 in the Monkey," July 21, 1980...Studies on DL-Erythro-a- (2-Piperidyl)-2,8-Bis (Tri- fluoromethyl)-4-Quinoline Methanol Hydrochloride, Mefloquine - SHC1, WR-142490"HC1 in the Rat...DL-Erythro--(2-Piperidyl)-2,8-Bis (Trifluoro- Umethyl)-4-Quinolinemethanol Hydrochloride, Mefloquine *ld, WR-142490-HCI in the Monkey," July 21, 1980

  6. Metabolomics analysis reveals large effect of roughage types on rumen microbial metabolic profile in dairy cows.

    Science.gov (United States)

    Zhao, S; Zhao, J; Bu, D; Sun, P; Wang, J; Dong, Z

    2014-07-01

    The aim of our study was to determine the effect of diets with different types of roughage on the ruminal microbial metabolite profile in dairy cows. Holstein dairy cows were fed a diet containing either corn stover (CS group) or a mixture of alfalfa hay, Leymus chinensis hay and corn silage (MF group) at 0700 and 1900 h daily. Rumen fluid was sampled from each cow through a ruminal cannula at 0630 and 1030 h, and the mixed ruminal fluid from 3 day in each cow was analysed using nuclear magnetic resonance (NMR) spectroscopy. A multivariate analysis revealed a significant difference between the ruminal metabolome of the CS and MF groups at both time points. The MF group had higher levels of acetate, valerate, hydrocinnamate and methylamine and lower levels of glucose, glycine, propionate and isovalerate than those in the CS group. Our results showed that different types of roughages can significantly influence the ruminal microbial metabolome, especially with regard to organic acids, amines and amino acids. The microbial metabolites in the rumen provide nutritional precursors that are critical for general health and milk production in dairy cows. However, studies of the effect of diet on ruminal microbial metabolism are scant. In our current study, we analysed the ruminal microbial metabolite profile of cows fed different types of roughage. We found that the ruminal microbial metabolite profile of cows fed a mixed-roughage diet differed significantly from that of cows fed a single type of roughage. Certain metabolites, such as acetate, hydrocinnamate and methylamine, were closely correlated with specific types of roughage. Our findings provide insight into the effects of different roughages on ruminal microbial fermentation in dairy cows. © 2014 The Society for Applied Microbiology.

  7. Starter Culture Selection for Making Chinese Sesame-Flavored Liquor Based on Microbial Metabolic Activity in Mixed-Culture Fermentation

    Science.gov (United States)

    Wu, Qun; Ling, Jie

    2014-01-01

    Selection of a starter culture with excellent viability and metabolic activity is important for inoculated fermentation of traditional food. To obtain a suitable starter culture for making Chinese sesame-flavored liquor, the yeast and bacterium community structures were investigated during spontaneous and solid-state fermentations of this type of liquor. Five dominant species in spontaneous fermentation were identified: Saccharomyces cerevisiae, Pichia membranaefaciens, Issatchenkia orientalis, Bacillus licheniformis, and Bacillus amyloliquefaciens. The metabolic activity of each species in mixed and inoculated fermentations of liquor was investigated in 14 different cocultures that used different combinations of these species. The relationships between the microbial species and volatile metabolites were analyzed by partial least-squares (PLS) regression analysis. We found that S. cerevisiae was positively correlated to nonanal, and B. licheniformis was positively associated with 2,3-butanediol, isobutyric acid, guaiacol, and 4-vinyl guaiacol, while I. orientalis was positively correlated to butyric acid, isovaleric acid, hexanoic acid, and 2,3-butanediol. These three species are excellent flavor producers for Chinese liquor. Although P. membranaefaciens and B. amyloliquefaciens were not efficient flavor producers, the addition of them alleviated competition among the other three species and altered their growth rates and flavor production. As a result, the coculture of all five dominant species produced the largest amount of flavor compounds. The result indicates that flavor producers and microbial interaction regulators are important for inoculated fermentation of Chinese sesame-flavored liquor. PMID:24814798

  8. Phylogenetic Structure and Metabolic Properties of Microbial Communities in Arsenic-Rich Waters of Geothermal Origin

    Directory of Open Access Journals (Sweden)

    Simona Crognale

    2017-12-01

    Full Text Available Arsenic (As is a toxic element released in aquatic environments by geogenic processes or anthropic activities. To counteract its toxicity, several microorganisms have developed mechanisms to tolerate and utilize it for respiratory metabolism. However, still little is known about identity and physiological properties of microorganisms exposed to natural high levels of As and the role they play in As transformation and mobilization processes. This work aims to explore the phylogenetic composition and functional properties of aquatic microbial communities in As-rich freshwater environments of geothermal origin and to elucidate the key microbial functional groups that directly or indirectly may influence As-transformations across a natural range of geogenic arsenic contamination. Distinct bacterial communities in terms of composition and metabolisms were found. Members of Proteobacteria, affiliated to Alpha- and Betaproteobacteria were mainly retrieved in groundwaters and surface waters, whereas Gammaproteobacteria were the main component in thermal waters. Most of the OTUs from thermal waters were only distantly related to 16S rRNA gene sequences of known taxa, indicating the occurrence of bacterial biodiversity so far unexplored. Nitrate and sulfate reduction and heterotrophic As(III-oxidization were found as main metabolic traits of the microbial cultivable fraction in such environments. No growth of autotrophic As(III-oxidizers, autotrophic and heterotrophic As(V-reducers, Fe-reducers and oxidizers, Mn-reducers and sulfide oxidizers was observed. The ars genes, involved in As(V detoxifying reduction, were found in all samples whereas aioA [As(III oxidase] and arrA genes [As(V respiratory reductase] were not found. Overall, we found that As detoxification processes prevailed over As metabolic processes, concomitantly with the intriguing occurrence of novel thermophiles able to tolerate high levels of As.

  9. Metatranscriptomic analysis of diverse microbial communities reveals core metabolic pathways and microbiome-specific functionality.

    Science.gov (United States)

    Jiang, Yue; Xiong, Xuejian; Danska, Jayne; Parkinson, John

    2016-01-12

    Metatranscriptomics is emerging as a powerful technology for the functional characterization of complex microbial communities (microbiomes). Use of unbiased RNA-sequencing can reveal both the taxonomic composition and active biochemical functions of a complex microbial community. However, the lack of established reference genomes, computational tools and pipelines make analysis and interpretation of these datasets challenging. Systematic studies that compare data across microbiomes are needed to demonstrate the ability of such pipelines to deliver biologically meaningful insights on microbiome function. Here, we apply a standardized analytical pipeline to perform a comparative analysis of metatranscriptomic data from diverse microbial communities derived from mouse large intestine, cow rumen, kimchi culture, deep-sea thermal vent and permafrost. Sequence similarity searches allowed annotation of 19 to 76% of putative messenger RNA (mRNA) reads, with the highest frequency in the kimchi dataset due to its relatively low complexity and availability of closely related reference genomes. Metatranscriptomic datasets exhibited distinct taxonomic and functional signatures. From a metabolic perspective, we identified a common core of enzymes involved in amino acid, energy and nucleotide metabolism and also identified microbiome-specific pathways such as phosphonate metabolism (deep sea) and glycan degradation pathways (cow rumen). Integrating taxonomic and functional annotations within a novel visualization framework revealed the contribution of different taxa to metabolic pathways, allowing the identification of taxa that contribute unique functions. The application of a single, standard pipeline confirms that the rich taxonomic and functional diversity observed across microbiomes is not simply an artefact of different analysis pipelines but instead reflects distinct environmental influences. At the same time, our findings show how microbiome complexity and availability of

  10. Systems metabolic engineering: the creation of microbial cell factories by rational metabolic design and evolution.

    Science.gov (United States)

    Furusawa, Chikara; Horinouchi, Takaaki; Hirasawa, Takashi; Shimizu, Hiroshi

    2013-01-01

    It is widely acknowledged that in order to establish sustainable societies, production processes should shift from petrochemical-based processes to bioprocesses. Because bioconversion technologies, in which biomass resources are converted to valuable materials, are preferable to processes dependent on fossil resources, the former should be further developed. The following two approaches can be adopted to improve cellular properties and obtain high productivity and production yield of target products: (1) optimization of cellular metabolic pathways involved in various bioprocesses and (2) creation of stress-tolerant cells that can be active even under severe stress conditions in the bioprocesses. Recent progress in omics analyses has facilitated the analysis of microorganisms based on bioinformatics data for molecular breeding and bioprocess development. Systems metabolic engineering is a new area of study, and it has been defined as a methodology in which metabolic engineering and systems biology are integrated to upgrade the designability of industrially useful microorganisms. This chapter discusses multi-omics analyses and rational design methods for molecular breeding. The first is an example of the rational design of metabolic networks for target production by flux balance analysis using genome-scale metabolic models. Recent progress in the development of genome-scale metabolic models and the application of these models to the design of desirable metabolic networks is also described in this example. The second is an example of evolution engineering with omics analyses for the creation of stress-tolerant microorganisms. Long-term culture experiments to obtain the desired phenotypes and omics analyses to identify the phenotypic changes are described here.

  11. Dietary fat content and fiber type modulate hind gut microbial community and metabolic markers in the pig.

    Science.gov (United States)

    Yan, Hui; Potu, Ramesh; Lu, Hang; Vezzoni de Almeida, Vivian; Stewart, Terry; Ragland, Darryl; Armstrong, Arthur; Adeola, Olayiwola; Nakatsu, Cindy H; Ajuwon, Kolapo M

    2013-01-01

    Obesity leads to changes in the gut microbial community which contribute to the metabolic dysregulation in obesity. Dietary fat and fiber affect the caloric density of foods. The impact of dietary fat content and fiber type on the microbial community in the hind gut is unknown. Effect of dietary fat level and fiber type on hindgut microbiota and volatile fatty acid (VFA) profiles was investigated. Expression of metabolic marker genes in the gut, adipose tissue and liver was determined. A 2 × 2 experiment was conducted in pigs fed at two dietary fat levels (5% or 17.5% swine grease) and two fiber types (4% inulin, fermentable fructo-oligosaccharide or 4% solka floc, non-fermentable cellulose). High fat diets (HFD) resulted in a higher (Pfiber type but not the level of dietary fat. Canonical correspondence analysis (CCA) of PCR- DGGE profiles showed that inulin feeding negatively correlated with back fat thickness. This study suggests a strong interplay between dietary fat level and fiber type in determining susceptibility to obesity.

  12. Impact of atmospheric deposition on the metabolism of coastal microbial communities

    Science.gov (United States)

    Martínez-García, Sandra; Arbones, B.; García-Martín, E. E.; Teixeira, I. G.; Serret, P.; Fernández, E.; Figueiras, F. G.; Teira, E.; Álvarez-Salgado, X. A.

    2015-02-01

    The impact of rain water collected at marine, urban and rural sites on coastal phytoplankton biomass, primary production and community composition as well as the effect on microbial plankton metabolism was studied in 3 microcosm experiments conducted under contrasting spring, autumn and winter conditions. The measured responses were highly variable. Rainwater additions increased chlorophyll a (Chl a) concentration (5-68% difference between rainwater treatments relative to the control) in all experiments and reduced or stimulated primary production (PP) depending on the treatment and the experiment (from -10 to +169% relative to the control). Autotrophic stimulation was highest in spring, probably related to the low initial natural nutrient concentrations. Under winter nutrient replete conditions, rainwater inputs changed the phytoplankton community although this change did not promote increases in primary production. Enhancement of net autotrophy (increase of net oxygen production up to 227%) after rainwater inputs were only found during the period of low nutrient availability. Inputs of dissolved organic nitrogen (DON) explained a large fraction of the variability in the response of PP, Chl a, community respiration (CR) and net community production (NCP). Our results suggest that differences in the initial environmental conditions (i.e. nutrient availability), rainwater composition and the ability of the present autotrophic communities to utilize the new nutrients result in substantial changes in the microbial responses and associated biologically-mediated carbon fluxes. As atmospheric nutrient inputs into coastal oceans are increasing rapidly, our results help to understand the effects of different inputs on the metabolism of distinct microbial communities.

  13. The woodrat gut microbiota as an experimental system for understanding microbial metabolism of dietary toxins

    Directory of Open Access Journals (Sweden)

    Kevin D. Kohl

    2016-07-01

    Full Text Available The microbial communities inhabiting the alimentary tracts of mammals, particularly those of herbivores, are estimated to be one of the densest microbial reservoirs on Earth. The significance of these gut microbes in influencing the physiology, ecology and evolution of their hosts is only beginning to be realized. To understand the microbiome of herbivores with a focus on nutritional ecology, while evaluating the roles of host evolution and environment in sculpting microbial diversity, we have developed an experimental system consisting of the microbial communities of several species of herbivorous woodrats (genus Neotoma that naturally feed on a variety of dietary toxins. We designed this system to investigate the long-standing, but experimentally neglected hypothesis that ingestion of toxic diets by herbivores is facilitated by the gut microbiota. Like several other rodent species, the woodrat stomach has a sacculated, nongastric foregut portion. We have documented a dense and diverse community of microbes in the woodrat foregut, with several genera potentially capable of degrading dietary toxins and/or playing a role in stimulating hepatic detoxification enzymes of the host. The biodiversity of these gut microbes appears to be a function of host evolution, ecological experience and diet, such that dietary toxins increase microbial diversity in hosts with experience with these toxins while novel toxins depress microbial diversity. These microbial communities are critical to the ingestion of a toxic diet as reducing the microbial community with antibiotics impairs the host’s ability to feed on dietary toxins. Furthermore, the detoxification capacity of gut microbes can be transferred from Neotoma both intra and interspecifically to naïve animals that lack ecological and evolutionary history with these toxins. In addition to advancing our knowledge of complex host-microbes interactions, this system holds promise for identifying microbes that

  14. Effects of Conservation Tillage on Topsoil Microbial Metabolic Characteristics and Organic Carbon within Aggregates under a Rice (Oryza sativa L.) –Wheat (Triticum aestivum L.) Cropping System in Central China

    Science.gov (United States)

    Liu, Tian-Qi; Cao, Cou-Gui; Li, Cheng-Fang

    2016-01-01

    Investigating microbial metabolic characteristics and soil organic carbon (SOC) within aggregates and their relationships under conservation tillage may be useful in revealing the mechanism of SOC sequestration in conservation tillage systems. However, limited studies have been conducted to investigate the relationship between SOC and microbial metabolic characteristics within aggregate fractions under conservation tillage. We hypothesized that close relationships can exist between SOC and microbial metabolic characteristics within aggregates under conservation tillage. In this study, a field experiment was conducted from June 2011 to June 2013 following a split-plot design of a randomized complete block with tillage practices [conventional intensive tillage (CT) and no tillage (NT)] as main plots and straw returning methods [preceding crop residue returning (S, 2100−2500 kg C ha−1) and removal (NS, 0 kg C ha-1)] as subplots with three replications. The objective of this study was to reveal the effects of tillage practices and residue-returning methods on topsoil microbial metabolic characteristics and organic carbon (SOC) fractions within aggregates and their relationships under a rice–wheat cropping system in central China. Microbial metabolic characteristics investigated using the Biolog system was examined within two aggregate fractions (>0.25 and 0.25 aggregate, and 0.25 mm aggregate (11.3%), and 0.25 mm aggregate, and 0.25 mm aggregate, and tillage (NT and S) increased microbial metabolic activities and Shannon index in >0.25 and directly improved SOC by promoting DOC in >0.25 mm aggregate in the upper (0−5 cm) soil layer under conservation tillage systems, as well as directly and indirectly by promoting DOC and MBC in tillage increased SOC in aggregates in the topsoil by improving microbial metabolic activities. PMID:26731654

  15. Investigation on liver fast metabolism with CT

    International Nuclear Information System (INIS)

    Huebener, K.H.; Schmitt, W.G.H.

    1981-01-01

    Measurements of the density of normal and diffusely diseased liver parenchyma show a significant difference only in fatty liver. A linear relationship between the fat content and physical density has been demonstrated. Computed tomographic densitometry of liver tissue correlates well with physical in vitro measurements of fat content and is sufficiently accurate for clinical use. Other types of liver diseases cannot be differentiated by densitometry, Lipolisis in fatty liver in chronic alcoholism alcohol withdrawal has been investigated. It has been found that a rate of decrease of the fatty degeneration of the liver equals to 1 percent/day. Fatty degeneration of the liver in acute pancreatitis and other diseases have been also investigated. CT densitometry of the liver should be considered as a useful routine clinical method to determine the fat content of liver. (author)

  16. The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism

    DEFF Research Database (Denmark)

    Birkel, Garrett W.; Ghosh, Amit; Kumar, Vinay S.

    2017-01-01

    analysis, new methods for the effective use of the ever more readily available and abundant -omics data (i.e. transcriptomics, proteomics and metabolomics) are urgently needed.Results: The jQMM library presented here provides an open-source, Python-based framework for modeling internal metabolic fluxes...

  17. Soil Metabolome and Metabolic Fate: Microbial Insights into Freshwater Tidal Wetland Redox Biogeochemistry

    Science.gov (United States)

    Roy Chowdhury, T.; Bramer, L.; Hoyt, D. W.; Kim, Y. M.; Metz, T. O.; McCue, L. A.; Jansson, J.; Bailey, V. L.

    2017-12-01

    Earth System Models predict climate extremes that will impact regional and global hydrology. Aquatic-terrestrial transition zones like wetlands will experience the immediate consequence of climate change as shifts in the magnitude and dynamics of hydrologic flow. Such fluctuating hydrology can alter the structure and function of the soil microbial populations that in turn will alter the nature and rate of biogeochemical transformations and significantly impact the carbon balance of the ecosystem. We tested the impacts of shifting hydrology on the soil microbiome and the role of antecedent moisture condition on redox active microbial processes in soils sampled from a tidal freshwater wetland system in the lower Columbia River, WA, USA. Our objectives were to characterize changes in the soil microbial community composition in response to soil moisture legacy effects, and to elucidate relationships between community response, geochemical signatures and metabolite profiles in this soil. The 16S rRNA gene sequencing showed significant decreases in bacterial abundance capable of anaerobic metabolism in response to drying, but quickly recovered to the antecedent moisture condition, as observed by redox processes. Metabolomics and biogeochemical process rates generated evidence for moisture-driven redox conditions as principal controls on the community and metabolic function. Fluctuating redox conditions altered terminal electron acceptor and donor availability and recovery strengths of these pools in soil such that a disproportionate release of carbon dioxide stemmed from alternative anaerobic degradation processes like sulfate and iron reduction in compared to methanogenesis. Our results show that anoxic conditions impact microbial communities in both permanently and temporarily saturated conditions and that rapid change in hydrology can increase substrate availability for both aerobic and anaerobic decomposition processes, including methanogenesis.

  18. Sulfur metabolizing microbes dominate microbial communities in Andesite-hosted shallow-sea hydrothermal systems.

    Science.gov (United States)

    Zhang, Yao; Zhao, Zihao; Chen, Chen-Tung Arthur; Tang, Kai; Su, Jianqiang; Jiao, Nianzhi

    2012-01-01

    To determine microbial community composition, community spatial structure and possible key microbial processes in the shallow-sea hydrothermal vent systems off NE Taiwan's coast, we examined the bacterial and archaeal communities of four samples collected from the water column extending over a redoxocline gradient of a yellow and four from a white hydrothermal vent. Ribosomal tag pyrosequencing based on DNA and RNA showed statistically significant differences between the bacterial and archaeal communities of the different hydrothermal plumes. The bacterial and archaeal communities from the white hydrothermal plume were dominated by sulfur-reducing Nautilia and Thermococcus, whereas the yellow hydrothermal plume and the surface water were dominated by sulfide-oxidizing Thiomicrospira and Euryarchaeota Marine Group II, respectively. Canonical correspondence analyses indicate that methane (CH(4)) concentration was the only statistically significant variable that explains all community cluster patterns. However, the results of pyrosequencing showed an essential absence of methanogens and methanotrophs at the two vent fields, suggesting that CH(4) was less tied to microbial processes in this shallow-sea hydrothermal system. We speculated that mixing between hydrothermal fluids and the sea or meteoric water leads to distinctly different CH(4) concentrations and redox niches between the yellow and white vents, consequently influencing the distribution patterns of the free-living Bacteria and Archaea. We concluded that sulfur-reducing and sulfide-oxidizing chemolithoautotrophs accounted for most of the primary biomass synthesis and that microbial sulfur metabolism fueled microbial energy flow and element cycling in the shallow hydrothermal systems off the coast of NE Taiwan.

  19. Sulfur metabolizing microbes dominate microbial communities in Andesite-hosted shallow-sea hydrothermal systems.

    Directory of Open Access Journals (Sweden)

    Yao Zhang

    Full Text Available To determine microbial community composition, community spatial structure and possible key microbial processes in the shallow-sea hydrothermal vent systems off NE Taiwan's coast, we examined the bacterial and archaeal communities of four samples collected from the water column extending over a redoxocline gradient of a yellow and four from a white hydrothermal vent. Ribosomal tag pyrosequencing based on DNA and RNA showed statistically significant differences between the bacterial and archaeal communities of the different hydrothermal plumes. The bacterial and archaeal communities from the white hydrothermal plume were dominated by sulfur-reducing Nautilia and Thermococcus, whereas the yellow hydrothermal plume and the surface water were dominated by sulfide-oxidizing Thiomicrospira and Euryarchaeota Marine Group II, respectively. Canonical correspondence analyses indicate that methane (CH(4 concentration was the only statistically significant variable that explains all community cluster patterns. However, the results of pyrosequencing showed an essential absence of methanogens and methanotrophs at the two vent fields, suggesting that CH(4 was less tied to microbial processes in this shallow-sea hydrothermal system. We speculated that mixing between hydrothermal fluids and the sea or meteoric water leads to distinctly different CH(4 concentrations and redox niches between the yellow and white vents, consequently influencing the distribution patterns of the free-living Bacteria and Archaea. We concluded that sulfur-reducing and sulfide-oxidizing chemolithoautotrophs accounted for most of the primary biomass synthesis and that microbial sulfur metabolism fueled microbial energy flow and element cycling in the shallow hydrothermal systems off the coast of NE Taiwan.

  20. Investigating a lotic microbial community following a severe detergent spill.

    Science.gov (United States)

    Or, Amitai; Gophna, Uri

    2014-02-01

    A large non-ionic detergent spill affected the Yarqon stream, where water sampling was performed prior to the spill as a part of the stream's routine sampling and during and after the event. Following the spill, a large foam layer was observed for about 3-4 days accompanied by death of all fauna in the stream. Despite a large quantity of freshwater that was introduced to the stream as an emergency measure, a drastic decrease in dissolved oxygen was also observed. A rapid reduction in bacterial diversity and richness, as measured by automated ribosomal intergenic spacer analysis, was also evident, as microbial assemblages changes accompanied pollutant exposure. However, this analysis showed that the microbial assemblages of the stream were quick to recover and became similar to pre-spill communities as early as a week after the spill. These findings suggest that bacterial assemblages are much more robust to large anthropogenic disturbances than expected.

  1. PRELIMINARY INVESTIGATION ON SOIL MICROBIAL DIVERSITY : EFFECT OF PEDOGENIC SUBSTRATE

    Directory of Open Access Journals (Sweden)

    Armando Pignataro

    2011-07-01

    Full Text Available Soil biological functions, in particular linked to the activities of microbial communities, are influenced by the interaction between the species (canopy, quantity and quality of litter, roots and rhizodepositions and the type of soil. The present study focused on the influence of different pedogenic substrates on the composition and the activities of microbial soil communities. Three systems with the same plant cover (Quercus cerris spp. and same topographic conditions but with different pedogenic material (Andosol, Entisol, Inceptisol were chosen. The soils were sampled in June 2009 in three Natural Reserves in the Centre of Italy (Selva di Meana/Monte Peglia, Monte Rufeno, Lago di Vico at 0-20cm in horizon A. Functional diversity was calculated by estimating eight enzyme activities and the Community Level Physiological Profile (CLPP, together with soil chemical characterization.

  2. Characterization of the microbial community composition and the distribution of Fe-metabolizing bacteria in a creek contaminated by acid mine drainage.

    Science.gov (United States)

    Sun, Weimin; Xiao, Enzong; Krumins, Valdis; Dong, Yiran; Xiao, Tangfu; Ning, Zengping; Chen, Haiyan; Xiao, Qingxiang

    2016-10-01

    A small watershed heavily contaminated by long-term acid mine drainage (AMD) from an upstream abandoned coal mine was selected to study the microbial community developed in such extreme system. The watershed consists of AMD-contaminated creek, adjacent contaminated soils, and a small cascade aeration unit constructed downstream, which provide an excellent contaminated site to study the microbial response in diverse extreme AMD-polluted environments. The results showed that the innate microbial communities were dominated by acidophilic bacteria, especially acidophilic Fe-metabolizing bacteria, suggesting that Fe and pH are the primary environmental factors in governing the indigenous microbial communities. The distribution of Fe-metabolizing bacteria showed distinct site-specific patterns. A pronounced shift from diverse communities in the upstream to Proteobacteria-dominated communities in the downstream was observed in the ecosystem. This location-specific trend was more apparent at genus level. In the upstream samples (sampling sites just below the coal mining adit), a number of Fe(II)-oxidizing bacteria such as Alicyclobacillus spp., Metallibacterium spp., and Acidithrix spp. were dominant, while Halomonas spp. were the major Fe(II)-oxidizing bacteria observed in downstream samples. Additionally, Acidiphilium, an Fe(III)-reducing bacterium, was enriched in the upstream samples, while Shewanella spp. were the dominant Fe(III)-reducing bacteria in downstream samples. Further investigation using linear discriminant analysis (LDA) effect size (LEfSe), principal coordinate analysis (PCoA), and unweighted pair group method with arithmetic mean (UPGMA) clustering confirmed the difference of microbial communities between upstream and downstream samples. Canonical correspondence analysis (CCA) and Spearman's rank correlation indicate that total organic carbon (TOC) content is the primary environmental parameter in structuring the indigenous microbial communities

  3. Microbial metabolic profiles in Australian soils with varying crop management strategies

    Science.gov (United States)

    Aldorri, Sind; McMillan, Mary; Pereg, Lily

    2015-04-01

    Cotton production belt in Australia is covering vast areas from subtropical to temperate and grassland. Soil types are mostly different variations of clay with mainly black, grey and red clay soil containing variable proportions of sand in it. Growers often grow cotton in rotation with other crops, such as wheat, beans and corn, and soil fertilization vary with a number of growers using organic amendments as a main or supplementary source of nutrients. We have collected soil samples from farms in different regions and with different crop management strategies and studied the metabolic signature of microbial communities using the Biolog Ecoplate system. The metabolic patterns, supplemented with molecular analysis of the community will further the understanding of the influence of crop and soil management on soil functions carried out by microbes.

  4. Implications of subzero metabolism on long-term microbial survival in ice (Invited)

    Science.gov (United States)

    Christner, B. C.; Amato, P.; Battista, J. R.; Doyle, S. M.

    2010-12-01

    For a microorganism to remain viable over an extended period of frozen dormancy, the macromolecular damage incurred by the cell must not exceed a level where effective repair is no longer possible. Hence, survival over extended timeframes in the absence of metabolism is likely to be limited by chemical (e.g., hydrolysis and oxidation of nucleic acids; racemization of L-amino acids) and ionizing radiation-induced damage to cellular macromolecules. In freshwater and saline ice, various studies have shown that microbial cells are physically located in the aqueous interstitial veins that exist at ice grain boundaries and remain metabolically active under frozen conditions. In an effort to improve estimates for the long term limits of microbial survival in ice, we determined rates of macromolecular synthesis in cold-adapted bacteria at temperatures down to -15°C and examined their sensitivity to controlled doses of ionizing radiation (0 to 450 Gy). The purpose of this experiment was to simulate the damage which would accumulate in a cell population due to ionizing radiation in the absence of metabolic activity, allowing a prediction of cellular survival over extended dormancy versus subsistence in a metabolically active state. In experiments conducted over ≈400 days at -15°C, the rates of bacterial protein and DNA synthesis ranged from dormant population of radiosensitive bacteria would be reduced by 99% after at least 600,000 years in ice. On the other hand, if microorganisms in natural ices are capable of synthesizing DNA at the lowest rates observed in the subzero laboratory experiments, our calculations imply that ionizing radiation from radionuclide decay or cosmic sources places no constraints on longevity over geological time. Hence, if icy subsurface environments are active biomes and biological activity is maintained over geological time, the long term survival of microorganisms under frozen conditions is likely to be limited by factors such as the water

  5. Mechanistic and structural insight into promiscuity based metabolism of cardiac drug digoxin by gut microbial enzyme.

    Science.gov (United States)

    Kumar, Kundan; Jaiswal, Shubham K; Dhoke, Gaurao V; Srivastava, Gopal N; Sharma, Ashok K; Sharma, Vineet K

    2017-12-23

    The recent advances in microbiome studies have revealed the role of gut microbiota in altering the pharmacological properties of oral drugs, which contributes to patient-response variation and undesired effect of the drug molecule. These studies are essential to guide us for achieving the desired efficacy and pharmacological activity of the existing drug molecule or for discovering novel and more effective therapeutics. However, one of the main limitations is the lack of atomistic details on the binding and metabolism of these drug molecules by gut-microbial enzymes. Therefore, in this study, for a well-known and important FDA-approved cardiac glycoside drug, digoxin, we report the atomistic details and energy economics for its binding and metabolism by the Cgr2 protein of Eggerthela lenta DSM 2243. It was observed that the binding pocket of digoxin to Cgr2 primarily involved the negatively charged polar amino acids and a few non-polar hydrophobic residues. The drug digoxin was found to bind Cgr2 at the same binding site as that of fumarate, which is the proposed natural substrate. However, digoxin showed a much lower binding energy (17.75 ±2 Kcal mol -1 ) than the binding energy (42.17 ±2 Kcal mol -1 ) of fumarate. This study provides mechanistic insights into the structural and promiscuity-based metabolism of widely used cardiac drug digoxin and presents a methodology, which could be useful to confirm the promiscuity-based metabolism of other orally administrated drugs by gut microbial enzymes and also help in designing strategies for improving the efficacy of the drugs. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  6. Computational design of auxotrophy-dependent microbial biosensors for combinatorial metabolic engineering experiments.

    Science.gov (United States)

    Tepper, Naama; Shlomi, Tomer

    2011-01-21

    Combinatorial approaches in metabolic engineering work by generating genetic diversity in a microbial population followed by screening for strains with improved phenotypes. One of the most common goals in this field is the generation of a high rate chemical producing strain. A major hurdle with this approach is that many chemicals do not have easy to recognize attributes, making their screening expensive and time consuming. To address this problem, it was previously suggested to use microbial biosensors to facilitate the detection and quantification of chemicals of interest. Here, we present novel computational methods to: (i) rationally design microbial biosensors for chemicals of interest based on substrate auxotrophy that would enable their high-throughput screening; (ii) predict engineering strategies for coupling the synthesis of a chemical of interest with the production of a proxy metabolite for which high-throughput screening is possible via a designed bio-sensor. The biosensor design method is validated based on known genetic modifications in an array of E. coli strains auxotrophic to various amino-acids. Predicted chemical production rates achievable via the biosensor-based approach are shown to potentially improve upon those predicted by current rational strain design approaches. (A Matlab implementation of the biosensor design method is available via http://www.cs.technion.ac.il/~tomersh/tools).

  7. Nanoscale investigation of pathogenic microbial adhesion to a biomaterial.

    Science.gov (United States)

    Emerson, Ray J; Camesano, Terri A

    2004-10-01

    Microbial infections of medical implants occur in more than 2 million surgical cases each year in the United States alone. These increase patient morbidity and mortality, as well as patient cost and recovery time. Many treatments are available, but none are guaranteed to remove the infection. In many cases, the device infections are caused by the adhesion of microbes to the implant, ensuing growth, pathogenesis, and dissemination. The purpose of this work is to examine the initial events in microbial adhesion by simulating the approach and contact between a planktonic cell, immobilized on an atomic force microscope (AFM) cantilever, and a biomaterial or biofilm substrate. The two model microbes used in this study, Candida parapsilosis (ATCC 90018) and Pseudomonas aeruginosa (ATCC 10145), were chosen for both their clinical relevance and their ease of acquisition and handling in the laboratory setting. Attractive interactions exist between C. parapsilosis and both unmodified silicone rubber and P. aeruginosa biofilms. Using C. parapsilosis cells immobilized on AFM cantilevers with a silicone substrate, we have measured attractive forces of 4.3 +/- 0.25 nN in the approach portion of the force cycle. On P. aeruginosa biofilms, the magnitude of the attractive force decreases to 2.0 +/- 0.40 nN and is preceded by a 2.0-nN repulsion at approximately 75 nm from the cell surface. These data suggest that C. parapsilosis may adhere to both silicone rubber and P. aeruginosa biofilms, possibly contributing to patient morbidity and mortality. Characterization of cell-biomaterial and cell-cell interactions allows for a quantitative link between the physicomechanical and physicochemical properties of implant materials and the nanoscale interactions leading to microbial colonization and infection.

  8. Investigating the Swimming of Microbial Pathogens Using Digital Holography.

    Science.gov (United States)

    Thornton, K L; Findlay, R C; Walrad, P B; Wilson, L G

    2016-01-01

    To understand much of the behaviour of microbial pathogens, it is necessary to image living cells, their interactions with each other and with host cells. Species such as Escherichia coli are difficult subjects to image: they are typically microscopic, colourless and transparent. Traditional cell visualisation techniques such as fluorescent tagging or phase-contrast microscopy give excellent information on cell behaviour in two dimensions, but no information about cells moving in three dimensions. We review the use of digital holographic microscopy for three-dimensional imaging at high speeds, and demonstrate its use for capturing the shape and swimming behaviour of three important model pathogens: E. coli, Plasmodium spp. and Leishmania spp.

  9. Effect of Temperature on Precipitation Rate of Calcium Carbonate Produced through Microbial Metabolic Process of Bio Materials

    Directory of Open Access Journals (Sweden)

    Prima Yane Putri

    2016-09-01

    Full Text Available Concrete is the most widely used construction material in civil engineering. But plain concrete is a brittle material and has little resistance to cracking. The cracking in concrete promotes deterioration such as the corrosion of reinforcing rebar, therefore, repair in filling the crack is often carried out. Recently, repair methods using bio-based materials associated with microbial metabolic processes leading to precipitation of calcium carbonate have been intensively studied. In this study, influencing factors on the precipitation rate depending on the constituents of bio-based material comprising yeast, glucose and calcium acetate mixed in tris buffer solution was examined for improving the rate of initial reactions. In addition, effect of temperature change on the amount of calcium carbonate precipitation was also investigated. The precipitates were identified by X-ray diffraction. It was shown that the increase of temperature lead to a change on calcium carbonate precipitation and caused the pH decrease under 7.0.

  10. Microbial metaproteomics for characterizing the range of metabolic functions and activities of human gut microbiota.

    Science.gov (United States)

    Xiong, Weili; Abraham, Paul E; Li, Zhou; Pan, Chongle; Hettich, Robert L

    2015-10-01

    The human gastrointestinal tract is a complex, dynamic ecosystem that consists of a carefully tuned balance of human host and microbiota membership. The microbiome is not merely a collection of opportunistic parasites, but rather provides important functions to the host that are absolutely critical to many aspects of health, including nutrient transformation and absorption, drug metabolism, pathogen defense, and immune system development. Microbial metaproteomics provides the ability to characterize the human gut microbiota functions and metabolic activities at a remarkably deep level, revealing information about microbiome development and stability as well as their interactions with their human host. Generally, microbial and human proteins can be extracted and then measured by high performance MS-based proteomics technology. Here, we review the field of human gut microbiome metaproteomics, with a focus on the experimental and informatics considerations involved in characterizing systems ranging from low-complexity model gut microbiota in gnotobiotic mice, to the emerging gut microbiome in the GI tract of newborn human infants, and finally to an established gut microbiota in human adults. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Exploring the under-investigated ?microbial dark matter? of drinking water treatment plants

    OpenAIRE

    Bruno, Antonia; Sandionigi, Anna; Rizzi, Ermanno; Bernasconi, Marzia; Vicario, Saverio; Galimberti, Andrea; Cocuzza, Clementina; Labra, Massimo; Casiraghi, Maurizio

    2017-01-01

    Scientists recently reported the unexpected detection of unknown or poorly studied bacterial diversity in groundwater. The ability to uncover this neglected biodiversity mainly derives from technical improvements, and the term ?microbial dark matter? was used to group taxa poorly investigated and not necessarily monophyletic. We focused on such under-investigated microbial dark matter of drinking water treatment plant from groundwater, across carbon filters, to post-chlorination. We tackled t...

  12. Investigation of Biological Soil Crusts Metabolic Webs Using Exometabolomic Analysis

    Science.gov (United States)

    Northen, T.; Karaoz, U.; Jenkins, S.; Lau, R.; Bowen, B.; Cadillo-Quiroz, H.; Garcia-Pichel, F.; Brodie, E.; Richard, B.

    2014-12-01

    Desert biological soil crusts are simple cyanobacteria-dominated surface soil microbial communities found in areas with infrequent wetting, often extreme temperatures, low coverage of vascular plants and constitute the world's largest biofilm. They exist for extended periods in a desiccated dormant state, yet rapidly re-boot metabolism within minutes of wetting. These soil microbial communities are highly dependent on filamentous cyanobacteria such as Microcoleus vaginatusto stabilize the soil and to act as primary producers for the community through the release carbon sources to feed a diversity of heterotrophs. Exometabolomic analysis was performed using liquid chromatography coupled to tandem mass spectrometry on biological soil crust pore water and spent media of key soil bacterial isolates. Comparison of spent vs. fresh media was used to determine uptake or release of metabolites by specific microbes. To link pore water experiments with isolate studies, metabolite extracts of authentic soil were used as supplements for isolate exometabolomic profiling. Our soil metabolomics methods detected hundreds of metabolites from soils including may novel compounds. Only a small set of which being targeted by all isolates. Beyond these few metabolites, the individual bacteria examined showed specialization towards specific metabolites. Surprisingly, many of the most abundant oligosaccharides and other metabolites were ignored by these isolates. The observed specialization of biological soil crust bacteria may play a significant role in determining community structure.

  13. Effects of Pheretima Guillelmi Cultivation Time on Microbial Community Diversity and Characteristics of Carbon Metabolism in Vegetable Soil

    Directory of Open Access Journals (Sweden)

    ZHENG Xian-qing

    2015-12-01

    Full Text Available In order to study the effect of different biological tillage time (Pheretima guillelmi on soil microbial community metabolic functions in different soil depths, we set a location test in vegetable field at Chongming Island in Shanghai to analyze the changes of soil microbial community and carbon utilization abilities (Average well- color development, AWCD by using biolog eco-plate method. The three-year results showed that: Bio-tillage significantly improved microbial community activity, and with the increase of tillage years, biological tillage could make the average AWCD 3 to 7 times higher. The Simpson index and Shannon index of the biological tillage treatments were significantly higher than that of the control. The cumulative increase of 0~5 cm soil layer was 49 and 6.28 respectively, and the cumulative increase of 5~20 cm soil layer was 31 and 2.55 respectively. Earthworm bio-tillage significantly increased the soil microbial metabolic ability of 6 kinds of carbon sources, and increased the carbohydrate metabolism activity. In this study, earthworm bio-tillage is an effective way to increase the microbial activity of microbial soil.

  14. Using isotopic tracers to assess the impact of tillage and straw management on the microbial metabolic network in soil

    Science.gov (United States)

    Van Groenigen, K.; Forristal, D.; Jones, M. B.; Schwartz, E.; Hungate, B. A.; Dijkstra, P.

    2013-12-01

    By decomposing soil organic matter, microbes gain energy and building blocks for biosynthesis and release CO2 to the atmosphere. Therefore, insight into the effect of management practices on microbial metabolic pathways and C use efficiency (CUE; microbial C produced per substrate C utilized) may help to predict long term changes in soil C stocks. We studied the effects of reduced (RT) and conventional tillage (CT) on the microbial central C metabolic network, using soil samples from a 12-year-old field experiment in an Irish winter wheat cropping system. Each year after harvest, straw was removed from half of the RT and CT plots or incorporated into the soil in the other half, resulting in four treatment combinations. We added 1-13C and 2,3-13C pyruvate and 1-13C and U-13C glucose as metabolic tracer isotopomers to composite soil samples taken at two depths (0-15 cm and 15-30 cm) from each treatment and used the rate of position-specific respired 13CO2 to parameterize a metabolic model. Model outcomes were then used to calculate CUE of the microbial community. We found that the composite samples differed in CUE, but the changes were small, with values ranging between 0.757-0.783 across treatments and soil depth. Increases in CUE were associated with a decrease in tricarboxylic acid cycle and reductive pentose phosphate pathway activity and increased consumption of metabolic intermediates for biosynthesis. Our results indicate that RT and straw incorporation promote soil C storage without substantially changing CUE or any of the microbial metabolic pathways. This suggests that at our site, RT and straw incorporation promote soil C storage mostly through direct effects such as increased soil C input and physical protection from decomposition, rather than by feedback responses of the microbial community.

  15. Biogeography and Metabolic Potential of Soil Microbial Communities Across Local Environmental Gradients Illuminated Through Metagenomics

    Science.gov (United States)

    Sharrar, A.; Diamond, S.; Butterfield, C.; Starr, E.; Thomas, B. C.; Banfield, J. F.

    2016-12-01

    Soils are extremely heterogeneous and diverse microbial habitats. The distribution of microbes and their metabolic functions in soil is important for carbon and nitrogen cycling and overall ecosystem functioning. Little is known about biogeographical patterns of microbes in soil and how they relate to different environmental gradients. To address this topic, we have obtained metagenomes from 86 soil samples taken at the Eel River Critical Zone Observatory and a nearby meadow in the northern California Angelo Coast Range Reserve over a period of two years. These samples span a variety of environmental parameters, including depth, relief, time since last rainfall, and proximity to root carbon inputs. Phylogenetic diversity and community overlap between these samples was analyzed using ribosomal protein sequence identity and scaffold coverage. Independent of genomic bins, de-replicated ribosomal protein sequences were used to identify thousands of unique organisms between datasets. Despite environmental differences, a subset of these organisms were found in every sample. The dominant phyla in this cosmopolitan subset were Proteobacteria, Actinobacteria, Gemmatimonadetes, Verrucomicrobia, Acidobacteria, and Rokubacteria. Archaea and Nitrospirae were particularly prevalent at depths below 30cm. Patterns of ribosomal protein scaffold coverage across samples was used to compare the similarity of the microbial communities. We found that location was the greatest predictor of community similarity, followed by depth. In a subset of 60 samples taken in the same meadow, sampling plot was a greater predictor of community similarity than time since last rainfall in the same year. In addition, genome-independent analyses revealed differences in the metabolic potential for functions involved in nitrogen and carbon metabolism across environmental gradients. This study will further our understanding of soil biogeography and its relationship to overall biogeochemical cycling.

  16. Exploring eukaryotic formate metabolisms to enhance microbial growth and lipid accumulation.

    Science.gov (United States)

    Liu, Zhiguo; Oyetunde, Tolutola; Hollinshead, Whitney D; Hermanns, Anna; Tang, Yinjie J; Liao, Wei; Liu, Yan

    2017-01-01

    C1 substrates (such as formate and methanol) are promising feedstock for biochemical/biofuel production. Numerous studies have been focusing on engineering heterologous pathways to incorporate C1 substrates into biomass, while the engineered microbial hosts often demonstrate inferior fermentation performance due to substrate toxicity, metabolic burdens from engineered pathways, and poor enzyme activities. Alternatively, exploring native C1 pathways in non-model microbes could be a better solution to address these challenges. An oleaginous fungus, Umbelopsis isabellina , demonstrates an excellent capability of metabolizing formate to promote growth and lipid accumulation. By co-feeding formate with glucose at a mole ratio of 3.9:1, biomass and lipid productivities of the culture in 7.5 L bioreactors were improved by 20 and 70%, respectively. 13 C-metabolite analysis, genome annotations, and enzyme assay further discovered that formate not only provides an auxiliary energy source [promoting NAD(P)H and ATP] for cell anabolism, but also contributes carbon backbones via folate-mediated C1 pathways. More interestingly, formate addition can tune fatty acid profile and increase the portion of medium-chain fatty acids, which would benefit conversion of fungal lipids for high-quality biofuel production. Flux balance analysis further indicates that formate co-utilization can power microbial metabolism to improve biosynthesis, particularly on glucose-limited cultures. This study demonstrates Umbelopsis isabellina's strong capability for co-utilizing formate to produce biomass and enhance fatty acid production. It is a promising non-model platform that can be potentially integrated with photochemical/electrochemical processes to efficiently convert carbon dioxide into biofuels and value-added chemicals.

  17. Investigating Microbial Habitats in Hydrothermal Chimneys using Ti-Thermocouple Arrays: Microbial Diversity

    Science.gov (United States)

    Pagé, A.; Tivey, M. K.; Stakes, D. S.; Bradley, A. M.; Seewald, J. S.; Wheat, C. G.; Reysenbach, A.

    2004-12-01

    In order to examine the changes that occur in the microbial community composition as a deep-sea hydrothermal vent chimney develops, we deployed Ti-thermocouple arrays over high temperature vents at two active sites of the Guaymas Basin Southern Trough. Chimney material that precipitated around the arrays was recovered after 4 and 72 days. Chimney material that precipitated prior to deployment of the arrays was also recovered at one of the sites (Busted Shroom). Culture-independent analysis based on the small subunit rRNA sequence (cloning and DGGE) was used to determine the microbial diversity associated with subsamples of each chimney. The original Busted Shroom chimney (BSO) was dominated by members of the Crenarchaeota Marine Group I, a group of cosmopolitan marine Archaea, ɛ -Proteobacteria, and γ -Proteobacteria, two divisions of Bacteria that are common to deep-sea vents. The 4 days old Busted Shroom chimney (BSD1) was dominated by members of the Methanocaldococcaceae, hyperthermophilic methanogens, and the 72 days old chimney (BSD2) by members of the Methanosarcinaceae, mesophilic and thermophilic methanogens. At the second site, Toadstool, the 72 days old chimney material that had precipitated around the array (TS) revealed the dominance of sequences from uncultured marine Archaea, the DHVE group I and II, and from the ɛ -Proteobacteria. Additionally, sequences belonging to the Methanocaldococcaceae and Desulfurococcaceae were recovered next to thermocouples that were at temperatures of 109° C (at Busted Shroom) and 116° C (at Toadstool), respectively. These temperatures are higher than the upper limit for growth of cultured representatives from each family.

  18. Metabolic investigation of patients with staghorn calculus: is it necessary?

    Directory of Open Access Journals (Sweden)

    Carmen R. P. Amaro

    2009-12-01

    Full Text Available Objective: To evaluate the prevalence of metabolic disorders in patients with staghorn calculi treated at the Regional Center of Lithiasis Metabolic Studies in central region of São Paulo State, Brazil. Materials and methods: Between February 2000 and February 2008, 630 patients with urinary calculi were evaluated in the lithiasis outpatient clinic. Thirty-seven of them had staghorn calculi (35 women and 2 men. The inclusion criteria for the metabolic investigation included the absence of urological manipulation 30 days before the examination, negative urine culture and creatinine clearance > 60 mL/min. The protocol for metabolic investigation consisted of qualitative search for cystinuria. Two non-consecutive 24-hour urine samples collected to measure calcium, phosphorus, uric acid, sodium, potassium, magnesium, oxalate and citrate, and serum calcium levels , phosphorus, uric acid, sodium, potassium, magnesium, chloride, parathormone and urine pH. Results: Among patients with lithiasis, 5.9% (37/ 630 had staghorn calculus and in 48.6% (18/37 were diagnosed with urinary infection. The females were predominant for 94.5% of cases. The calculi were unilateral in 31 of cases and bilateral in six. Metabolic abnormalities were found in 68.2% of patients with hypercalciuria (64.2% and hypocitraturia (53.3% being the most common disorders. Conclusions: The presence of metabolic disorders in nearly 70% of patients with staghorn calculus reinforces the necessity for evaluation of these patients. The diagnosis and treatment of identified metabolic abnormalities can contribute to the prevention of recurrent staghorn calculi.

  19. A computational tool for the simulation and optimization of microbial strains accounting integrated metabolic/regulatory information.

    Science.gov (United States)

    Vilaça, Paulo; Rocha, Isabel; Rocha, Miguel

    2011-03-01

    Recently, a number of methods and tools have been proposed to allow the use of genome-scale metabolic models for the phenotype simulation and optimization of microbial strains, within the field of Metabolic Engineering (ME). One of the limitations of most of these algorithms and tools is the fact that only metabolic information is taken into account, disregarding knowledge on regulatory events. This work proposes a novel software tool that implements methods for the phenotype simulation and optimization of microbial strains using integrated models, encompassing both metabolic and regulatory information. This tool is developed as a plug-in that runs over OptFlux, a computational platform that aims to be a reference tool for the ME community. The plug-in is made available in the OptFlux web site (www.optflux.org) together with examples and documentation. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

  20. Dietary fat content and fiber type modulate hind gut microbial community and metabolic markers in the pig.

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    Hui Yan

    Full Text Available Obesity leads to changes in the gut microbial community which contribute to the metabolic dysregulation in obesity. Dietary fat and fiber affect the caloric density of foods. The impact of dietary fat content and fiber type on the microbial community in the hind gut is unknown. Effect of dietary fat level and fiber type on hindgut microbiota and volatile fatty acid (VFA profiles was investigated. Expression of metabolic marker genes in the gut, adipose tissue and liver was determined. A 2 × 2 experiment was conducted in pigs fed at two dietary fat levels (5% or 17.5% swine grease and two fiber types (4% inulin, fermentable fructo-oligosaccharide or 4% solka floc, non-fermentable cellulose. High fat diets (HFD resulted in a higher (P<0.05 total body weight gain, feed efficiency and back fat accumulation than the low fat diet. Feeding of inulin, but not solka floc, attenuated (P<0.05 the HFD-induced higher body weight gain and fat mass accumulation. Inulin feeding tended to lead to higher total VFA production in the cecum and resulted in a higher (P<0.05 expression of acyl coA oxidase (ACO, a marker of peroxisomal β-oxidation. Inulin feeding also resulted in lower expression of sterol regulatory element binding protein 1c (SREBP-1c, a marker of lipid anabolism. Bacteria community structure characterized by DGGE analysis of PCR amplified 16S rRNA gene fragments showed that inulin feeding resulted in greater bacterial population richness than solka floc feeding. Cluster analysis of pairwise Dice similarity comparisons of the DGGE profiles showed grouping by fiber type but not the level of dietary fat. Canonical correspondence analysis (CCA of PCR- DGGE profiles showed that inulin feeding negatively correlated with back fat thickness. This study suggests a strong interplay between dietary fat level and fiber type in determining susceptibility to obesity.

  1. Effects of Conservation Tillage on Topsoil Microbial Metabolic Characteristics and Organic Carbon within Aggregates under a Rice (Oryza sativa L.-Wheat (Triticum aestivum L. Cropping System in Central China.

    Directory of Open Access Journals (Sweden)

    Li-Jin Guo

    Full Text Available Investigating microbial metabolic characteristics and soil organic carbon (SOC within aggregates and their relationships under conservation tillage may be useful in revealing the mechanism of SOC sequestration in conservation tillage systems. However, limited studies have been conducted to investigate the relationship between SOC and microbial metabolic characteristics within aggregate fractions under conservation tillage. We hypothesized that close relationships can exist between SOC and microbial metabolic characteristics within aggregates under conservation tillage. In this study, a field experiment was conducted from June 2011 to June 2013 following a split-plot design of a randomized complete block with tillage practices [conventional intensive tillage (CT and no tillage (NT] as main plots and straw returning methods [preceding crop residue returning (S, 2100-2500 kg C ha-1 and removal (NS, 0 kg C ha(-1] as subplots with three replications. The objective of this study was to reveal the effects of tillage practices and residue-returning methods on topsoil microbial metabolic characteristics and organic carbon (SOC fractions within aggregates and their relationships under a rice-wheat cropping system in central China. Microbial metabolic characteristics investigated using the Biolog system was examined within two aggregate fractions (>0.25 and 0.25 aggregate, and 0.25 mm aggregate (11.3%, and 0.25 mm aggregate, and 0.25 mm aggregate, and 0.25 and 0.25 mm aggregate in the upper (0-5 cm soil layer under conservation tillage systems, as well as directly and indirectly by promoting DOC and MBC in <0.25 mm aggregate. Our results suggested that conservation tillage increased SOC in aggregates in the topsoil by improving microbial metabolic activities.

  2. Patterns of extracellular enzyme activities and microbial metabolism in an Arctic fjord of Svalbard and in the northern Gulf of Mexico: contrasts in carbon processing by pelagic microbial communities

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    Carol eArnosti

    2013-10-01

    Full Text Available The microbial community composition of polar and temperate ocean waters differs substantially, but the potential functional consequences of these differences are largely unexplored. We measured bacterial production, glucose metabolism, and the abilities of microbial communities to hydrolyze a range of polysaccharides in an Arctic fjord of Svalbard (Smeerenburgfjord, and thus to initiate remineralization of high-molecular weight organic matter. We compared these data with similar measurements previously carried out in the northern Gulf of Mexico in order to investigate whether differences in the spectrum of enzyme activities measurable in Arctic and temperate environments are reflected in ‘downstream’ aspects of microbial metabolism (metabolism of monomers and biomass production. Only 4 of 6 polysaccharide substrates were hydrolyzed in Smeerenburgfjord; all were hydrolyzed in the upper water column of the Gulf. These patterns are consistent on an interannual basis. Bacterial protein production was comparable at both locations, but the pathways of glucose utilization differed. Glucose incorporation rate constants were comparatively higher in Svalbard, but glucose respiration rate constants were higher in surface waters of the Gulf. As a result, at the time of sampling ca. 75% of the glucose was incorporated into biomass in Svalbard, but in the northern Gulf of Mexico most of the glucose was respired to CO2. A limited range of enzyme activities is therefore not a sign of a dormant community or one unable to further process substrates resulting from extracellular enzymatic hydrolysis. The ultimate fate of carbohydrates in marine waters, however, is strongly dependent upon the specific capabilities of heterotrophic microbial communities in these disparate environments.

  3. Oral Microbiota: Microbial Biomarkers of Metabolic Syndrome Independent of Host Genetic Factors

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    Jiyeon Si

    2017-12-01

    Full Text Available The oral microbiota plays a critical role in both local and systemic inflammation. Metabolic syndrome (MetS is characterized by low-grade inflammation, and many studies have been conducted on the gut microbiota from stool specimens. However, the etiological role of the oral microbiota in the development of MetS is unclear. In this study, we analyzed the oral and gut microbiome from 228 subgingival plaque and fecal samples from a Korean twin-family cohort with and without MetS. Significant differences in microbial diversity and composition were observed in both anatomical niches. However, a host genetic effect on the oral microbiota was not observed. A co-occurrence network analysis showed distinct microbiota clusters that were dependent on the MetS status. A comprehensive analysis of the oral microbiome identified Granulicatella and Neisseria as bacteria enriched in subjects with MetS and Peptococcus as bacteria abundant in healthy controls. Validation of the identified oral bacteria by quantitative PCR (qPCR showed that healthy controls possessed significantly lower levels of G. adiacens (p = 0.023 and a higher ratio of Peptococcus to Granulicatella (p < 0.05 than MetS subjects. Our results support that local oral microbiota can be associated with systemic disorders. The microbial biomarkers identified in this study would aid in determination of which individuals develop chronic diseases from their MetS and contribute to strategic disease management.

  4. One-year calorie restriction impacts gut microbial composition but not its metabolic performance in obese adolescents.

    Science.gov (United States)

    Ruiz, Alicia; Cerdó, Tomás; Jáuregui, Ruy; Pieper, Dietmar H; Marcos, Ascensión; Clemente, Alfonso; García, Federico; Margolles, Abelardo; Ferrer, Manuel; Campoy, Cristina; Suárez, Antonio

    2017-04-01

    Recent evidence has disclosed a connection between gut microbial glycosidase activity and adiposity in obese. Here, we measured microbial α-glucosidase and β-galactosidase activities and sorted fluorescently labeled β-galactosidase containing (βGAL) microorganisms in faecal samples of eight lean and thirteen obese adolescents that followed a controlled calorie restriction program during one year. β-galactosidase is a highly distributed functional trait, mainly expressed by members of Blautia, Bacteroides, Alcaligenes, Acinetobacter and Propionibacterium. Only long-term calorie restriction induced clear changes in the microbiota of obese adolescents. Long-term calorie restriction induced significant shifts in total and βGAL gut microbiota, reducing the Firmicutes:Bacteroidetes ratio and enhancing the growth of beneficial microorganisms such as Bacteroides, Roseburia, Faecalibacterium and Clostridium XIVa. Moreover, the structure and composition of βGAL community in obese after long-term calorie restriction was highly similar to that of lean adolescents. However, despite this high compositional similarity, microbial metabolic performance was different, split in two metabolic states at a body mass index value of 25. Our study shows that calorie restriction is a strong environmental force reshaping gut microbiota though its metabolic performance is linked to host's adiposity, suggesting that functional redundancy and metabolic plasticity are fundamental properties of gut microbial ecosystem. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

  5. IMGMD: A platform for the integration and standardisation of In silico Microbial Genome-scale Metabolic Models.

    Science.gov (United States)

    Ye, Chao; Xu, Nan; Dong, Chuan; Ye, Yuannong; Zou, Xuan; Chen, Xiulai; Guo, Fengbiao; Liu, Liming

    2017-04-07

    Genome-scale metabolic models (GSMMs) constitute a platform that combines genome sequences and detailed biochemical information to quantify microbial physiology at the system level. To improve the unity, integrity, correctness, and format of data in published GSMMs, a consensus IMGMD database was built in the LAMP (Linux + Apache + MySQL + PHP) system by integrating and standardizing 328 GSMMs constructed for 139 microorganisms. The IMGMD database can help microbial researchers download manually curated GSMMs, rapidly reconstruct standard GSMMs, design pathways, and identify metabolic targets for strategies on strain improvement. Moreover, the IMGMD database facilitates the integration of wet-lab and in silico data to gain an additional insight into microbial physiology. The IMGMD database is freely available, without any registration requirements, at http://imgmd.jiangnan.edu.cn/database.

  6. In situ metabolism in halite endolithic microbial communities of the hyperarid Atacama Desert

    Directory of Open Access Journals (Sweden)

    Alfonso F Davila

    2015-10-01

    Full Text Available The Atacama Desert of northern Chile is one of the driest regions on Earth, with areas that exclude plants and where soils have extremely low microbial biomass. However, in the driest parts of the desert there are microorganisms that colonize the interior of halite nodules in fossil continental evaporites, where they are sustained by condensation of atmospheric water triggered by the salt substrate. Using a combination of in situ observations of variable chlorophyll fluorescence and controlled laboratory experiments, we show that this endolithic community is capable of carbon fixation both through oxygenic photosynthesis and potentially ammonia oxidation. We also present evidence that photosynthetic activity is finely tuned to moisture availability and solar insolation and can be sustained for days, and perhaps longer, after a wetting event. This is the first demonstration of in situ active metabolism in the hyperarid core of the Atacama Desert, and it provides the basis for proposing a self-contained, endolithic community that relies exclusively on non-rainfall sources of water. Our results contribute to an increasing body of evidence that even in hyperarid environments active metabolism, adaptation and growth can occur in highly specialized microhabitats.

  7. Metabolic engineering of ammonium release for nitrogen-fixing multispecies microbial cell-factories.

    Science.gov (United States)

    Ortiz-Marquez, Juan Cesar Federico; Do Nascimento, Mauro; Curatti, Leonardo

    2014-05-01

    The biological nitrogen fixation carried out by some Bacteria and Archaea is one of the most attractive alternatives to synthetic nitrogen fertilizers. In this study we compared the effect of controlling the maximum activation state of the Azotobacter vinelandii glutamine synthase by a point mutation at the active site (D49S mutation) and impairing the ammonium-dependent homeostatic control of nitrogen-fixation genes expression by the ΔnifL mutation on ammonium release by the cells. Strains bearing the single D49S mutation were more efficient ammonium producers under carbon/energy limiting conditions and sustained microalgae growth at the expense of atmospheric N2 in synthetic microalgae-bacteria consortia. Ammonium delivery by the different strains had implications for the microalga׳s cell-size distribution. It was uncovered an extensive cross regulation between nitrogen fixation and assimilation that extends current knowledge on this key metabolic pathway and might represent valuable hints for further improvements of versatile N2-fixing microbial-cell factories. Copyright © 2014 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

  8. Underlying mechanisms for syntrophic metabolism of essential enzyme cofactors in microbial communities.

    Science.gov (United States)

    Romine, Margaret F; Rodionov, Dmitry A; Maezato, Yukari; Osterman, Andrei L; Nelson, William C

    2017-06-01

    Many microorganisms are unable to synthesize essential B vitamin-related enzyme cofactors de novo. The underlying mechanisms by which such microbes survive in multi-species communities are largely unknown. We previously reported the near-complete genome sequence of two ~18-member unicyanobacterial microbial consortia that maintain stable membership on defined medium lacking vitamins. Here we have used genome analysis and growth studies on isolates derived from the consortia to reconstruct pathways for biogenesis of eight essential cofactors and predict cofactor usage and precursor exchange in these communities. Our analyses revealed that all but the two Halomonas and cyanobacterial community members were auxotrophic for at least one cofactor. We also observed a mosaic distribution of salvage routes for a variety of cofactor precursors, including those produced by photolysis. Potentially bidirectional transporters were observed to be preferentially in prototrophs, suggesting a mechanism for controlled precursor release. Furthermore, we found that Halomonas sp. do not require cobalamin nor control its synthesis, supporting the hypothesis that they overproduce and export vitamins. Collectively, these observations suggest that the consortia rely on syntrophic metabolism of cofactors as a survival strategy for optimization of metabolic exchange within a shared pool of micronutrients.

  9. The effect of gluten on the host-microbial metabolism assessed by urinary metabolomics

    DEFF Research Database (Denmark)

    Roager, Henrik Munch; Frandsen, Henrik Lauritz; Gøbel, Rikke Juul

    A gluten-free diet clearly improves the life of patients with celiac disease, but the scientific evidence supporting possible health benefits of a gluten-free diet for non-celiac adults is limited. Therefore, as urine reflects the host and gut microbial metabolism, the study aimed to assess...... a gluten-rich (21.6±5.7g/day) or a gluten-poor (~1g/day) diet for 8 weeks, crossing over to the other diet after 6 weeks washout. Urine samples were standardised collected at the beginning and end of each diet intervention period and were analysed by gas chromatography mass spectrometry (GC-MS) and liquid...... the long-term metabolic effect of gluten on the urine metabolome of non-celiac individuals by a cross-over intervention study (gluten-poor and gluten rich, respectively) using a non-targeted metabolomics approach. Fifty-one non-celiac adult participants (30 female, 21 male) were randomized to either...

  10. Effect of Bioprocessing on the In Vitro Colonic Microbial Metabolism of Phenolic Acids from Rye Bran Fortified Breads

    DEFF Research Database (Denmark)

    Koistinen, Ville M; Nordlund, Emilia; Katina, Kati

    2017-01-01

    minor differences in the appearance of microbial metabolites, including the diminished levels of certain phenylacetic acids in the bioprocessed bran. This may be due to rye matrix properties, saturation of ferulic acid metabolism, or a rapid formation of intermediary metabolites left undetected......Cereal bran is an important source of dietary fiber and bioactive compounds, such as phenolic acids. We aimed to study the phenolic acid metabolism of native and bioprocessed rye bran fortified refined wheat bread and to elucidate the microbial metabolic route of phenolic acids. After incubation...... in an in vitro colon model, the metabolites were analyzed using two different methods applying mass spectrometry. While phenolic acids were released more extensively from the bioprocessed bran bread and ferulic acid had consistently higher concentrations in the bread type during fermentation, there were only...

  11. Microbial food webs and metabolic state across oligotrophic waters of the Mediterranean Sea during summer

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    U. Christaki

    2011-07-01

    Full Text Available The abundance and activity of the major members of the heterotrophic microbial community – from viruses to ciliates – were studied along a longitudinal transect across the Mediterranean Sea in the summer of 2008. The Mediterranean Sea is characterized by a west to-east gradient of deepening of DCM (deep chlorophyll maximum and increasing oligotrophy reflected in gradients of biomass and production. However, within this well documented longitudinal trend, hydrological mesoscale features exist and likely influence microbial dynamics. Here we present data from a W-E transect of 17 stations during the period of summer stratification. Along the transect the production and fate of organic matter was investigated at three selected sites each one located in the centre of an anticyclonic eddy: in the Algero-Provencal Basin (St. A, the Ionian Basin (St. B, and the Levantine Basin (St. C. The 3 geographically distant eddies showed low values of the different heterotrophic compartments of the microbial food web, and except for viruses in site C, all integrated (0–150 m stocks were higher in reference stations located in the same basin outside the eddies. During our study the 3 eddies showed equilibrium between GPP (Gross Primary Production and DCR (Dark Community Respiration. Integrated PPp (Particulate Primary Production values at A, B and C varied from ~140 to ~190 mg C m−2.

  12. Investigation Of The Microbial-Induced Corrosion Potential Of Soils ...

    African Journals Online (AJOL)

    Investigation of sulphate-reducing bacteria induced corrosion potential of soils along 18-inch 45km Tebidaba/Brass underground oil pipeline in Southern Ijaw LGA of Bayelsa State, Nigeria, is carried out experimentally. The analysis involves determination of some physico-chemical parameters of soils in the pipeline route, ...

  13. Metabolic Potential and Activity in Fluids of the Coast Range Ophiolite Microbial Observatory, California, USA

    Science.gov (United States)

    Hoehler, T.; Som, S.; Schrenk, M.; McCollom, T.; Cardace, D.

    2016-01-01

    Metabolic potential and activity associated with hydrogen and carbon monoxide were characterized in fluids sampled from the the Coast Range Ophiolite Microbial Observatory (CROMO). CROMO consists of two clusters of science-dedicated wells drilled to varying depths up to 35m in the actively serpentinizing, Jurassic-age Coast Range Ophiolite of Northern California, along with a suite of pre-existing monitoring wells at the same site. Consistent with the fluid chemistry observed in other serpentinizing systems, CROMO fluids are highly alkaline, with pH up to 12.5, high in methane, with concentrations up 1600 micromolar, and low in dissolved inorganic carbon (DIC), with concentrations of 10's to 100's of micromolar. CROMO is conspicuous for fluid H2 concentrations that are consistently sub-micromolar, orders of magnitude lower than is typical of other systems. However, higher H2 concentrations (10's -100's of micromolar) at an earlier stage of fluid chemical evolution are predicted by, or consistent with: thermodynamic models for fluid chemistry based on parent rock composition equivalent to local peridotite and with water:rock ratio constrained by observed pH; the presence of magnetite at several wt% in CROMO drill cores; and concentrations of formate and carbon monoxide that would require elevated H2 if formed in equilibrium with H2 and DIC. Calculated Gibbs energy changes for reaction of H2 and CO in each of several metabolisms, across the range of fluid composition encompassed by the CROMO wells, range from bioenergetically feasible (capable of driving ATP synthesis) to thermodynamically unfavorable. Active consumption relative to killed controls was observed for both CO and H2 during incubation of fluids from the pre-existing monitoring wells; in incubations of freshly cored solids, consumption was only observed in one sample set (corresponding to the lowest pH) out of three. The specific metabolisms by which H2 and CO are consumed remain to be determined.

  14. Exploring the under-investigatedmicrobial dark matter” of drinking water treatment plants

    Science.gov (United States)

    Bruno, Antonia; Sandionigi, Anna; Rizzi, Ermanno; Bernasconi, Marzia; Vicario, Saverio; Galimberti, Andrea; Cocuzza, Clementina; Labra, Massimo; Casiraghi, Maurizio

    2017-01-01

    Scientists recently reported the unexpected detection of unknown or poorly studied bacterial diversity in groundwater. The ability to uncover this neglected biodiversity mainly derives from technical improvements, and the term “microbial dark matter” was used to group taxa poorly investigated and not necessarily monophyletic. We focused on such under-investigated microbial dark matter of drinking water treatment plant from groundwater, across carbon filters, to post-chlorination. We tackled this topic using an integrated approach where the efficacy of stringent water filtration (10000 MWCO) in recovering even the smallest environmental microorganisms was coupled with high-throughput DNA sequencing to depict an informative spectrum of the neglected microbial diversity. Our results revealed that the composition of bacterial communities varies across the plant system: Parcubacteria (OD1) superphylum is found mainly in treated water, while groundwater has the highest heterogeneity, encompassing non-OD1 candidate phyla (Microgenomates, Saccharibacteria, Dependentiae, OP3, OP1, BRC1, WS3). Carbon filters probably act as substrate for microorganism growth and contribute to seeding water downstream, since chlorination does not modify the incoming bacterial community. New questions arise about the role of microbial dark matter in drinking water. Indeed, our results suggest that these bacteria might play a central role in the microbial dynamics of drinking water. PMID:28290543

  15. Exploring the under-investigated "microbial dark matter" of drinking water treatment plants.

    Science.gov (United States)

    Bruno, Antonia; Sandionigi, Anna; Rizzi, Ermanno; Bernasconi, Marzia; Vicario, Saverio; Galimberti, Andrea; Cocuzza, Clementina; Labra, Massimo; Casiraghi, Maurizio

    2017-03-14

    Scientists recently reported the unexpected detection of unknown or poorly studied bacterial diversity in groundwater. The ability to uncover this neglected biodiversity mainly derives from technical improvements, and the term "microbial dark matter" was used to group taxa poorly investigated and not necessarily monophyletic. We focused on such under-investigated microbial dark matter of drinking water treatment plant from groundwater, across carbon filters, to post-chlorination. We tackled this topic using an integrated approach where the efficacy of stringent water filtration (10000 MWCO) in recovering even the smallest environmental microorganisms was coupled with high-throughput DNA sequencing to depict an informative spectrum of the neglected microbial diversity. Our results revealed that the composition of bacterial communities varies across the plant system: Parcubacteria (OD1) superphylum is found mainly in treated water, while groundwater has the highest heterogeneity, encompassing non-OD1 candidate phyla (Microgenomates, Saccharibacteria, Dependentiae, OP3, OP1, BRC1, WS3). Carbon filters probably act as substrate for microorganism growth and contribute to seeding water downstream, since chlorination does not modify the incoming bacterial community. New questions arise about the role of microbial dark matter in drinking water. Indeed, our results suggest that these bacteria might play a central role in the microbial dynamics of drinking water.

  16. Dihydroxylated phenolic acids derived from microbial metabolism reduce lipopolysaccharide-stimulated cytokine secretion by human peripheral blood mononuclear cells.

    Science.gov (United States)

    Monagas, María; Khan, Nasiruddin; Andrés-Lacueva, Cristina; Urpí-Sardá, Mireia; Vázquez-Agell, Mónica; Lamuela-Raventós, Rosa María; Estruch, Ramón

    2009-07-01

    Oligomers and polymers of flavan-3-ols (proanthocyanidins) are very abundant in the Mediterranean diet, but are poorly absorbed. However, when these polyphenols reach the colon, they are metabolised by the intestinal microbiota into various phenolic acids, including phenylpropionic, phenylacetic and benzoic acid derivatives. Since the biological properties of these metabolites are not completely known, in the present study, we investigated the effect of the following microbial phenolic metabolites: 3,4-dihydroxyphenylpropionic acid (3,4-DHPPA), 3-hydroxyphenylpropionic acid, 3,4-dihydroxyphenylacetic acid (3,4-DHPAA), 3-hydroxyphenylacetic acid, 4-hydroxybenzoic acid and 4-hydroxyhippuric acid (4-HHA), on modulation of the production of the main pro-inflammatory cytokines (TNF-alpha, IL-1beta and IL-6). The production of these cytokines by lipopolysaccharide (LPS)-stimulated peripheral blood mononuclear cells (PBMC) pre-treated with the phenolic metabolites was studied in six healthy volunteers. With the exception of 4-HHA for TNF-alpha secretion, only the dihydroxylated compounds, 3,4-DHPPA and 3,4-DHPAA, significantly inhibited the secretion of these pro-inflammatory cytokines in LPS-stimulated PBMC. Mean inhibition of the secretion of TNF-alpha by 3,4-DHPPA and 3,4-DHPAA was 84.9 and 86.4 %, respectively. The concentrations of IL-6 in the culture supernatant were reduced by 88.8 and 92.3 % with 3,4-DHPPA and 3,4-DHPAA pre-treatment, respectively. Finally, inhibition was slightly higher for IL-1beta, 93.1 % by 3,4-DHPPA and 97.9 % by 3,4-DHPAA. These results indicate that dihydroxylated phenolic acids derived from microbial metabolism present marked anti-inflammatory properties, providing additional information about the health benefits of dietary polyphenols and their potential value as therapeutic agents.

  17. Imaging microbial metal metabolism in situ under conditions of the deep-sea hydrothermal vents

    Science.gov (United States)

    Oger, P. M.; Daniel, I.; Simionovici, A.; Picard, A.

    2006-12-01

    High-pressure biotopes are the most widely spread biotopes on Earth. They represent one possible location for the origin of life. They also share striking similarities with extraterrestrial biotopes such as those postulated for Europe or Mars. In absence of light, dissimilatory reduction of metals (DMR) is fueling the ecosystem. Monitoring the metabolism of the deep-sea hydrothermal vent microbial fauna under P, T and chemical conditions relevant to their isolation environment can be difficult because of the confinement and because most spectroscopic probes do not sense metallic ions in solution. We demonstrated the possibility to use Xray spectroscopy to monitor the speciation of metallic species in solution. Experiments were performed at The ESRF using Selenium (Se) detoxification by Agrobacterium tumefaciens as an analog of DMR. The reduction of Se from selenite to the metal was monitored by a combiantion of two Xray spectroscopic techniques (XANES and μXRF). Cells were incubated in the low pressure DAC in growth medium supplemented with 5mM Selenite and incubated under pressures up to 60 Mpa at 30°C for 24h. The evolution of the speciation can be easily monitored and the concentration of each Se species determined from the Xray spectra by linear combinations of standard spectra. Selenite is transformed by the bacterium into a mixture of metal Se and methylated Se after 24 hours. Se detoxification is observed in situ up to at least 25 MPa. The technique, developped for Se can be adapted to monitor other elements more relevant to DMR such as As, Fe or S, which should allow to monitor in situ under controlled pressure and temperature the metabolism of vent organisms. It is also amenable to the monitoring of toxic metals. Xray spectroscopy and the lpDAC are compatible with other spectroscopic techniques, such as Raman, UV or IR spectroscopies, allowing to probe other metabolic activities. Hence, enlarging the range of metabolic information that can be obtained in

  18. Emergence of microbial diversity due to cross-feeding interactions in a spatial model of gut microbial metabolism

    NARCIS (Netherlands)

    M.J.A. van Hoek (Milan); R.M.H. Merks (Roeland)

    2017-01-01

    textabstractBackground: The human gut contains approximately 1014 bacteria, belonging to hundreds of different species. Together, these microbial species form a complex food web that can break down nutrient sources that our own digestive enzymes cannot handle, including complex polysaccharides,

  19. Emergence of microbial diversity due to cross-feeding interactions in a spatial model of gut microbial metabolism

    NARCIS (Netherlands)

    Hoek, van M.J.A.; Merks, R.M.H.

    2017-01-01

    BACKGROUND:The human gut contains approximately 10(14) bacteria, belonging to hundreds of different species. Together, these microbial species form a complex food web that can break down nutrient sources that our own digestive enzymes cannot handle, including complex polysaccharides, producing short

  20. Emergence of microbial diversity due to cross-feeding interactions in a spatial model of gut microbial metabolism

    NARCIS (Netherlands)

    M.J.A. van Hoek (Milan); R.M.H. Merks (Roeland)

    2016-01-01

    textabstractBackground: The human gut contains approximately 10e+14 bacteria, belonging to hundreds of different species. Together, these microbial species form a complex food web that can break down food sources that our own digestive enzymes cannot handle, including complex polysaccharides,

  1. Microbial regulation of glucose metabolism and cell-cycle progression in mammalian colonocytes.

    Directory of Open Access Journals (Sweden)

    Dallas R Donohoe

    Full Text Available A prodigious number of microbes inhabit the human body, especially in the lumen of the gastrointestinal (GI tract, yet our knowledge of how they regulate metabolic pathways within our cells is rather limited. To investigate the role of microbiota in host energy metabolism, we analyzed ATP levels and AMPK phosphorylation in tissues isolated from germfree and conventionally-raised C57BL/6 mice. These experiments demonstrated that microbiota are required for energy homeostasis in the proximal colon to a greater extent than other segments of the GI tract that also harbor high densities of bacteria. This tissue-specific effect is consistent with colonocytes utilizing bacterially-produced butyrate as their primary energy source, whereas most other cell types utilize glucose. However, it was surprising that glucose did not compensate for butyrate deficiency. We measured a 3.5-fold increase in glucose uptake in germfree colonocytes. However, (13C-glucose metabolic-flux experiments and biochemical assays demonstrated that they shifted their glucose metabolism away from mitochondrial oxidation/CO(2 production and toward increased glycolysis/lactate production, which does not yield enough ATPs to compensate. The mechanism responsible for this metabolic shift is diminished pyruvate dehydrogenase (PDH levels and activity. Consistent with perturbed PDH function, the addition of butyrate, but not glucose, to germfree colonocytes ex vivo stimulated oxidative metabolism. As a result of this energetic defect, germfree colonocytes exhibited a partial block in the G(1-to-S-phase transition that was rescued by a butyrate-fortified diet. These data reveal a mechanism by which microbiota regulate glucose utilization to influence energy homeostasis and cell-cycle progression of mammalian host cells.

  2. Microbial population analysis improves the evidential value of faecal traces in forensic investigations.

    Science.gov (United States)

    Quaak, Frederike C A; de Graaf, Mei-Lan M; Weterings, Rob; Kuiper, Irene

    2017-01-01

    The forensic science community has a growing interest in microbial population analysis, especially the microbial populations found inside and on the human body. Both their high abundance, microbes outnumber human cells by a factor 10, and their diversity, different sites of the human body harbour different microbial communities, make them an interesting tool for forensics. Faecal material is a type of trace evidence which can be found in a variety of criminal cases, but is often being ignored in forensic investigations. Deriving a human short tandem repeat (STR) profile from a faecal sample can be challenging. However, the microbial communities within faecal material can be of additional criminalistic value in linking a faecal trace to the possible donor. We present a microarray technique in which the faecal microbial community is used to differentiate between faecal samples and developed a decision model to predict the possible common origin of questioned samples. The results show that this technique may be a useful additional tool when no or only partial human STR profiles can be generated.

  3. Measuring and modeling C flux rates through the central metabolic pathways in microbial communities using position-specific 13C-labeled tracers

    Science.gov (United States)

    Dijkstra, P.; van Groenigen, K.; Hagerty, S.; Salpas, E.; Fairbanks, D. E.; Hungate, B. A.; KOCH, G. W.; Schwartz, E.

    2012-12-01

    The production of energy and metabolic precursors occurs in well-known processes such as glycolysis and Krebs cycle. We use position-specific 13C-labeled metabolic tracers, combined with models of microbial metabolic organization, to analyze the response of microbial community energy production, biosynthesis, and C use efficiency (CUE) in soils, decomposing litter, and aquatic communities. The method consists of adding position-specific 13C -labeled metabolic tracers to parallel soil incubations, in this case 1-13C and 2,3-13C pyruvate and 1-13C and U-13C glucose. The measurement of CO2 released from the labeled tracers is used to calculate the C flux rates through the various metabolic pathways. A simplified metabolic model consisting of 23 reactions is solved using results of the metabolic tracer experiments and assumptions of microbial precursor demand. This new method enables direct estimation of fundamental aspects of microbial energy production, CUE, and soil organic matter formation in relatively undisturbed microbial communities. We will present results showing the range of metabolic patterns observed in these communities and discuss results from testing metabolic models.

  4. The BioCyc collection of microbial genomes and metabolic pathways.

    Science.gov (United States)

    Karp, Peter D; Billington, Richard; Caspi, Ron; Fulcher, Carol A; Latendresse, Mario; Kothari, Anamika; Keseler, Ingrid M; Krummenacker, Markus; Midford, Peter E; Ong, Quang; Ong, Wai Kit; Paley, Suzanne M; Subhraveti, Pallavi

    2017-08-17

    BioCyc.org is a microbial genome Web portal that combines thousands of genomes with additional information inferred by computer programs, imported from other databases and curated from the biomedical literature by biologist curators. BioCyc also provides an extensive range of query tools, visualization services and analysis software. Recent advances in BioCyc include an expansion in the content of BioCyc in terms of both the number of genomes and the types of information available for each genome; an expansion in the amount of curated content within BioCyc; and new developments in the BioCyc software tools including redesigned gene/protein pages and metabolite pages; new search tools; a new sequence-alignment tool; a new tool for visualizing groups of related metabolic pathways; and a facility called SmartTables, which enables biologists to perform analyses that previously would have required a programmer's assistance. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  5. γ–Butyrobetaine is a pro-atherogenic intermediate in gut microbial metabolism of L-carnitine to TMAO

    Science.gov (United States)

    Koeth, Robert A.; Levison, Bruce S.; Culley, Miranda K.; Buffa, Jennifer A.; Wang, Zeneng; Gregory, Jill C.; Org, Elin; Wu, Yuping; Li, Lin; Smith, Jonathan D.; Wilson Tang, W. H.; DiDonato, Joseph A.; Lusis, Aldons J.; Hazen, Stanley L.

    2014-01-01

    Summary L- Carnitine, a nutrient in red meat, was recently reported to accelerate atherosclerosis via a metaorganismal pathway involving gut microbial trimethylamine (TMA) formation and host hepatic conversion into trimethylamine-N-oxide (TMAO). Herein we show that following L-carnitine ingestion, γ-butyrobetaine (γBB) is produced as an intermediary metabolite by gut microbes at a site anatomically proximal to and at a rate ~1000-fold higher than the formation of TMA. Moreover, we show γBB is the major gut microbial metabolite formed from dietary L-carnitine in mice, and like dietary L-carnitine, in a gut microbiota-dependent manner is converted into TMA and TMAO, and accelerates atherosclerosis. Gut microbial composition and functional metabolic studies reveal distinct taxa are associated with the production of γBB versus TMA/TMAO from dietary L-carnitine. Moreover, despite their close structural similarity, chronic dietary exposure to L-carnitine versus γBB promotes development of functionally distinct microbial communities optimized for the metabolism of L-carnitine versus γBB, respectively. PMID:25440057

  6. γ-Butyrobetaine is a proatherogenic intermediate in gut microbial metabolism of L-carnitine to TMAO.

    Science.gov (United States)

    Koeth, Robert A; Levison, Bruce S; Culley, Miranda K; Buffa, Jennifer A; Wang, Zeneng; Gregory, Jill C; Org, Elin; Wu, Yuping; Li, Lin; Smith, Jonathan D; Tang, W H Wilson; DiDonato, Joseph A; Lusis, Aldons J; Hazen, Stanley L

    2014-11-04

    L-carnitine, a nutrient in red meat, was recently reported to accelerate atherosclerosis via a metaorganismal pathway involving gut microbial trimethylamine (TMA) formation and host hepatic conversion into trimethylamine-N-oxide (TMAO). Herein, we show that following L-carnitine ingestion, γ-butyrobetaine (γBB) is produced as an intermediary metabolite by gut microbes at a site anatomically proximal to and at a rate ∼1,000-fold higher than the formation of TMA. Moreover, we show that γBB is the major gut microbial metabolite formed from dietary L-carnitine in mice, is converted into TMA and TMAO in a gut microbiota-dependent manner (like dietary L-carnitine), and accelerates atherosclerosis. Gut microbial composition and functional metabolic studies reveal that distinct taxa are associated with the production of γBB or TMA/TMAO from dietary L-carnitine. Moreover, despite their close structural similarity, chronic dietary exposure to L-carnitine or γBB promotes development of functionally distinct microbial communities optimized for the metabolism of L-carnitine or γBB, respectively. Copyright © 2014 Elsevier Inc. All rights reserved.

  7. Microbial metagenomes from three aquifers in the Fennoscandian shield terrestrial deep biosphere reveal metabolic partitioning among populations.

    Science.gov (United States)

    Wu, Xiaofen; Holmfeldt, Karin; Hubalek, Valerie; Lundin, Daniel; Åström, Mats; Bertilsson, Stefan; Dopson, Mark

    2016-05-01

    Microorganisms in the terrestrial deep biosphere host up to 20% of the earth's biomass and are suggested to be sustained by the gases hydrogen and carbon dioxide. A metagenome analysis of three deep subsurface water types of contrasting age (from 86% coverage. The populations were dominated by Proteobacteria, Candidate divisions, unclassified archaea and unclassified bacteria. The estimated genome sizes of the biosphere. The data were finally used to create a combined metabolic model of the deep terrestrial biosphere microbial community.

  8. Metabolic Strategies in Energy-Limited Microbial Communities in the Anoxic Subsurface (Frasassi Cave System, Italy)

    Science.gov (United States)

    McCauley, R. L.; Jones, D. S.; Schaperdoth, I.; Steinberg, L.; Macalady, J. L.

    2010-12-01

    Two major sources of energy, light and chemical potential, are available to microorganisms. However, energy is not always abundant and is often a limiting factor in microbial survival and replication. The anoxic, terrestrial subsurface offers a unique opportunity to study microorganisms and their potentially novel metabolic strategies that are relevant for understanding biogeochemistry and biosignatures as related to the non-photosynthetic, energy-limited environments on the modern and ancient Earth and elsewhere in the solar system. Geochemical data collected in a remote stratified lake 600 m below ground surface in the sulfidic Frasassi cave system (Italy) suggest that little redox energy is available for life, consistent with low signal from domain-specific FISH probes. The carbon isotope signatures of biofilms (-33‰) and DIC (-9‰) in the anoxic water suggest in situ production by lithoautotrophs using RuBisCO. 16S rDNA libraries constructed from the biofilm are dominated by diverse sulfate reducing bacteria. The remaining bacterial and archaeal clones affiliate with more than 11 major uncultivated or novel prokaryotic lineages. Diverse dsrAB gene sequences are consistent with high sulfate concentrations and undetectable or extremely low oxygen, nitrate, and iron concentrations. However, the electron donor for sulfate reduction is unclear. Methane is detectable in the anoxic water although no 16S rDNA sequences associated with known methanogens or anaerobic methane oxidizers were retrieved. mcrA gene sequences retrieved from the biofilm by cloning are not related to cultivated methanogens or to known anaerobic methane oxidizers. Non-purgable organic carbon (NPOC) is below detection limits (i.e. <42 μM acetate) suggesting that alternative electron donors or novel metabolisms may be important. A sample collected by cave divers in October 2009 was pyrosequenced at the Pennsylvania State University Genomics Core Facility using Titanium chemistry (454 Life

  9. [Advances in metabolic engineering for the microbial production of naturally occurring terpenes-limonene and bisabolene: a mini review].

    Science.gov (United States)

    Pang, Yaru; Hu, Zhihui; Xiao, Dongguang; Yu, Aiqun

    2018-01-25

    Limonene (C₁₀H₁₆) and bisabolene (C₁₅H₂₄) are both naturally occurring terpenes in plants. Depending on the number of C₅ units, limonene and bisabolene are recognized as representative monoterpenes and sesquiterpenes, respectively. Limonene and bisabolene are important pharmaceutical and nutraceutical products used in the prevention and treatment of cancer and many other diseases. In addition, they can be used as starting materials to produce a range of commercially valuable products, such as pharmaceuticals, nutraceuticals, cosmetics, and biofuels. The low abundance or yield of limonene and bisabolene in plants renders their isolation from plant sources non-economically viable. Isolation of limonene and bisabolene from plants also suffers from low efficiency and often requires harsh reaction conditions, prolonged reaction times, and expensive equipment cost. Recently, the rapid developments in metabolic engineering of microbes provide a promising alternative route for producing these plant natural products. Therefore, producing limonene and bisabolene by engineering microbial cells into microbial factories is becoming an attractive alternative approach that can overcome the bottlenecks, making it more sustainable, environmentally friendly and economically competitive. Here, we reviewed the status of metabolic engineering of microbes that produce limonene and bisabolene including microbial hosts, key enzymes, metabolic pathways and engineering of limonene/bisabolene biosynthesis. Furthermore, key challenges and future perspectives were discussed.

  10. Gut Microbial Metabolism of Polyphenols from Black Tea and Red Wine/Grape Juice Is Source-Specific and Colon-Region Dependent

    NARCIS (Netherlands)

    Dorsten, van F.A.; Peters, S.; Gross, G.; Gomez-Roldan, V.; Klinkenberg, M.; Vos, de Ric; Vaughan, E.E.; Duynhoven, van J.P.M.; Possemiers, S.; Wiele, van der T.; Jacobs, D.M.

    2012-01-01

    The colonic microbial degradation of a polyphenol-rich black tea extract (BTE) and red wine/grape juice extract (RWGE) was compared in a five-stage in vitro gastrointestinal model (TWINSHIME). Microbial metabolism of BTE and RWGE polyphenols in the TWINSHIME was studied subsequently in single- and

  11. Metabolic differences underlying two distinct rat urinary phenotypes, a suggested role for gut microbial metabolism of phenylalanine and a possible connection to autism.

    Science.gov (United States)

    Clayton, T Andrew

    2012-04-05

    A novel explanation is proposed for the metabolic differences underlying two distinct rat urinary compositional phenotypes i.e. that these may arise from differences in the gut microbially-mediated metabolism of phenylalanine. As part of this hypothesis, it is further suggested that elements of the mammalian gut microbiota may convert phenylalanine to cinnamic acid, either by means of an ammonia lyase-type reaction or by means of a three step route via phenylpyruvate and phenyllactate. The wider significance of such conversions is discussed with similar metabolism of tryptophan and subsequent glycine conjugation potentially explaining the origin of trans-indolylacryloylglycine, a postulated marker for autism. Copyright © 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

  12. Dynamics of Panax ginseng Rhizospheric Soil Microbial Community and Their Metabolic Function

    Directory of Open Access Journals (Sweden)

    Yong Li

    2014-01-01

    Full Text Available The bacterial communities of 1- to 6-year ginseng rhizosphere soils were characterized by culture-independent approaches, random amplified polymorphic DNA (RAPD, and amplified ribosomal DNA restriction analysis (ARDRA. Culture-dependent method (Biolog was used to investigate the metabolic function variance of microbe living in rhizosphere soil. Results showed that significant genetic and metabolic function variance were detected among soils, and, with the increasing of cultivating years, genetic diversity of bacterial communities in ginseng rhizosphere soil tended to be decreased. Also we found that Verrucomicrobia, Acidobacteria, and Proteobacteria were the dominants in rhizosphere soils, but, with the increasing of cultivating years, plant disease prevention or plant growth promoting bacteria, such as Pseudomonas, Burkholderia, and Bacillus, tended to be rare.

  13. Colonization Habitat Controls Biomass, Composition, and Metabolic Activity of Attached Microbial Communities in the Columbia River Hyporheic Corridor

    Energy Technology Data Exchange (ETDEWEB)

    Stern, Noah; Ginder-Vogel, Matthew; Stegen, James C.; Arntzen, Evan; Kennedy, David W.; Larget, Bret R.; Roden, Eric E.; Kostka, Joel E.

    2017-06-09

    Hydrologic exchange plays a critical role in biogeochemical cycling within the hyporheic zone (the interface between river water and groundwater) of riverine ecosystems. Such exchange may set limits on the rates of microbial metabolism and impose deterministic selection on microbial communities that adapt to dynamically changing dissolved organic carbon (DOC) sources. This study examined the response of attached microbial communities (in situcolonized sand packs) from groundwater, hyporheic, and riverbed habitats within the Columbia River hyporheic corridor to “cross-feeding” with either groundwater, river water, or DOC-free artificial fluids. Our working hypothesis was that deterministic selection duringin situcolonization would dictate the response to cross-feeding, with communities displaying maximal biomass and respiration when supplied with their native fluid source. In contrast to expectations, the major observation was that the riverbed colonized sand had much higher biomass and respiratory activity, as well as a distinct community structure, compared with those of the hyporheic and groundwater colonized sands. 16S rRNA gene amplicon sequencing revealed a much higher proportion of certain heterotrophic taxa as well as significant numbers of eukaryotic algal chloroplasts in the riverbed colonized sand. Significant quantities of DOC were released from riverbed sediment and colonized sand, and separate experiments showed that the released DOC stimulated respiration in the groundwater and piezometer colonized sand. These results suggest that the accumulation and degradation of labile particulate organic carbon (POC) within the riverbed are likely to release DOC, which may enter the hyporheic corridor during hydrologic exchange, thereby stimulating microbial activity and imposing deterministic selective pressure on the microbial community composition.

    IMPORTANCEThe influence of river water

  14. Genome-Enabled Modeling of Biogeochemical Processes Predicts Metabolic Dependencies that Connect the Relative Fitness of Microbial Functional Guilds

    Science.gov (United States)

    Brodie, E.; King, E.; Molins, S.; Karaoz, U.; Steefel, C. I.; Banfield, J. F.; Beller, H. R.; Anantharaman, K.; Ligocki, T. J.; Trebotich, D.

    2015-12-01

    Pore-scale processes mediated by microorganisms underlie a range of critical ecosystem services, regulating carbon stability, nutrient flux, and the purification of water. Advances in cultivation-independent approaches now provide us with the ability to reconstruct thousands of genomes from microbial populations from which functional roles may be assigned. With this capability to reveal microbial metabolic potential, the next step is to put these microbes back where they belong to interact with their natural environment, i.e. the pore scale. At this scale, microorganisms communicate, cooperate and compete across their fitness landscapes with communities emerging that feedback on the physical and chemical properties of their environment, ultimately altering the fitness landscape and selecting for new microbial communities with new properties and so on. We have developed a trait-based model of microbial activity that simulates coupled functional guilds that are parameterized with unique combinations of traits that govern fitness under dynamic conditions. Using a reactive transport framework, we simulate the thermodynamics of coupled electron donor-acceptor reactions to predict energy available for cellular maintenance, respiration, biomass development, and enzyme production. From metagenomics, we directly estimate some trait values related to growth and identify the linkage of key traits associated with respiration and fermentation, macromolecule depolymerizing enzymes, and other key functions such as nitrogen fixation. Our simulations were carried out to explore abiotic controls on community emergence such as seasonally fluctuating water table regimes across floodplain organic matter hotspots. Simulations and metagenomic/metatranscriptomic observations highlighted the many dependencies connecting the relative fitness of functional guilds and the importance of chemolithoautotrophic lifestyles. Using an X-Ray microCT-derived soil microaggregate physical model combined

  15. Metabolic and Microbial Modulation of the Large Intestine Ecosystem by Non-Absorbed Diet Phenolic Compounds: A Review

    Directory of Open Access Journals (Sweden)

    Juana I. Mosele

    2015-09-01

    Full Text Available Phenolic compounds represent a diverse group of phytochemicals whose intake is associated with a wide spectrum of health benefits. As consequence of their low bioavailability, most of them reach the large intestine where, mediated by the action of local microbiota, a series of related microbial metabolites are accumulated. In the present review, gut microbial transformations of non-absorbed phenolic compounds are summarized. Several studies have reached a general consensus that unbalanced diets are associated with undesirable changes in gut metabolism that could be detrimental to intestinal health. In terms of explaining the possible effects of non-absorbed phenolic compounds, we have also gathered information regarded their influence on the local metabolism. For this purpose, a number of issues are discussed. Firstly, we consider the possible implications of phenolic compounds in the metabolism of colonic products, such as short chain fatty acids (SCFA, sterols (cholesterol and bile acids, and microbial products of non-absorbed proteins. Due to their being recognized as affective antioxidant and anti-inflammatory agents, the ability of phenolic compounds to counteract or suppress pro-oxidant and/or pro-inflammatory responses, triggered by bowel diseases, is also presented. The modulation of gut microbiota through dietetic maneuvers including phenolic compounds is also commented on. Although the available data seems to assume positive effects in terms of gut health protection, it is still insufficient for solid conclusions to be extracted, basically due to the lack of human trials to confirm the results obtained by the in vitro and animal studies. We consider that more emphasis should be focused on the study of phenolic compounds, particularly in their microbial metabolites, and their power to influence different aspects of gut health.

  16. [Investigation of susceptibility of materials contacting with drinking water for microbial growth].

    Science.gov (United States)

    Szczotko, Maciej; Krogulska, Bozena; Krogulski, Adam

    2009-01-01

    Main purpose of this paper was to confirm of results obtained by new method based on bioluminescence technique for determination of susceptibility of materials contacting with drinking water were repeatable. Investigation was conducted during 8 weeks in dynamic conditions using continuous flow reactor UPE. Every week swabbes from tested materials were collected and level of ATP was examined. The results obtained from the surface of tested materials were repeatable and clearly approximate to those obtained from the surface of negative control material (stainless steel, low susceptibility for microbial growth). The level of the ATP on the surface of positive control material (paraffin, large susceptibility for microbial growth) was fifty times higher than that observed on other materials. Presented investigation was the main part of validation process, which in short time will serve to initiate system of complete assessment for materials contacting with drinking water according to Council Directives 89/106/EEC and 98/83/EC requirements.

  17. Investigating microbial cycling of recalcitrant organic matter in marine sediments using natural isotope respirometry in a novel, carbon-free bioreactor

    Science.gov (United States)

    Mahmoudi, N.; Beaupre, S. R.; Pearson, A.

    2016-02-01

    Marine sediments harbor complex microbial communities that play a key role in the cycling of carbon and nutrients. Reactions initiated by microbial enzymes at the molecular scale drive the rate and extent of organic matter degradation to CO2 and CH4. Organic matter is comprised of multiple carbon pools with different intrinsic turnover times. It is hypothesized that microbes will degrade younger pools with more labile compounds, while older pools with refractory compounds will remain unutilized. However, many studies have shown that microbes are capable of respiring older, refractory pools of organic matter in a number of environments. In order to better understand microbial carbon cycling and the fate of recalcitrant organic matter, we constructed a novel bioreactor system to measure carbon isotopes during microbial degradation of complex organic matter. This system enables us to measure the natural isotopic signature (δ13C and Δ14C ) of microbially-respired CO2, thereby allowing us to determine the age of the organic matter that is being respired. We investigated microbial carbon utilization in sediments from Falmouth, MA and observed a pattern of successive microbial respiration such that several peaks appear over the course of a 7-day incubation. Δ14C signatures of CO2 fractions collected during incubation ranged from -185 to +70‰ with the majority of CO2 appearing to be modern. This indicates that the microbial community is primarily are respiring labile organic matter from fast cycling pools. Interestingly, the observation of multiple peaks with similar Δ14C signatures suggests that organic matter is degraded in a step-wise manner by a succession of microbial taxa. Illumina sequencing of 16S rRNA genes will identify these successions of bacteria (and archaea), while enzymatic analyses may help determine the metabolic pathways that correspond to each peak. Our study will provide a molecular-level framework for organic matter degradation and provide

  18. New transposon tools tailored for metabolic engineering of Gram-negative microbial cell factories

    Directory of Open Access Journals (Sweden)

    Esteban eMartínez-García

    2014-10-01

    Full Text Available Re-programming microorganisms to modify their existing functions and/or to bestow bacteria with entirely new-to-Nature tasks have largely relied so far on specialized molecular biology tools. Such endeavors are not only relevant in the burgeoning metabolic engineering arena, but also instrumental to explore the functioning of complex regulatory networks from a fundamental point of view. À la carte modification of bacterial genomes thus calls for novel tools to make genetic manipulations easier. We propose the use of a series of new broad-host-range mini-Tn5 vectors, termed pBAMDs, for the delivery of gene(s into the chromosome of Gram-negative bacteria and for generating saturated mutagenesis libraries in gene function studies. These delivery vectors endow the user with the possibility of easy cloning and subsequent insertion of functional cargoes with three different antibiotic resistance markers (kanamycin, streptomycin, and gentamicin. After validating the pBAMD vectors in the environmental bacterium Pseudomonas putida KT2440, their use was also illustrated by inserting the entire poly(3-hydroxybutyrate (PHB synthesis pathway from Cupriavidus necator in the chromosome of a phosphotransacetylase mutant of Escherichia coli. PHB is a completely biodegradable polyester with a number of industrial applications that make it attractive as a potential replacement of oil-based plastics. The non-selective nature of chromosomal insertions of the biosynthetic genes was evidenced by a large landscape of PHB synthesis levels in independent clones. One clone was selected and further characterized as a microbial cell factory for PHB accumulation, and it achieved polymer accumulation levels comparable to those of a plasmid-bearing recombinant. Taken together, our results demonstrate that the new mini-Tn5 vectors can be used to confer interesting phenotypes in Gram-negative bacteria that would be very difficult to engineer through direct manipulation of the

  19. Carbon isotopic patterns of amino acids associated with various microbial metabolic pathways and physiological conditions

    Science.gov (United States)

    Wang, P. L.; Hsiao, K. T.; Lin, L. H.

    2017-12-01

    Amino acids represent one of the most important categories of biomolecule. Their abundance and isotopic patterns have been broadly used to address issues related to biochemical processes and elemental cycling in natural environments. Previous studies have shown that various carbon assimilative pathways of microorganisms (e.g. autotrophy, heterotrophy and acetotrophy) could be distinguished by carbon isotopic patterns of amino acids. However, the taxonomic and catabolic coverage are limited in previous examination. This study aims to uncover the carbon isotopic patterns of amino acids for microorganisms remaining uncharacterized but bearing biogeochemical and ecological significance in anoxic environments. To fulfill the purpose, two anaerobic strains were isolated from riverine wetland and mud volcano in Taiwan. One strain is a sulfate reducing bacterium (related to Desulfovibrio marrakechensis), which is capable of utilizing either H2 or lactate, and the other is a methanogen (related to Methanolobus profundi), which grows solely with methyl-group compounds. Carbon isotope analyses of amino acids were performed on cells grown in exponential and stationary phase. The isotopic patterns were similar for all examined cultures, showing successive 13C depletion along synthetic pathways. No significant difference was observed for the methanogen and lactate-utilizing sulfate reducer harvested in exponential and stationary phases. In contrast, the H2-utilizing sulfate reducer harvested in stationary phase depleted and enriched 13C in aspartic acid and glycine, respectively when compared with that harvested in exponential phase. Such variations might infer the change of carbon flux during synthesis of these two amino acids in the reverse TCA cycle. In addition, the discriminant function analysis for all available data from culture studies further attests the capability of using carbon isotope patterns of amino acids in identifying microbial metabolisms.

  20. New Transposon Tools Tailored for Metabolic Engineering of Gram-Negative Microbial Cell Factories

    International Nuclear Information System (INIS)

    Martínez-García, Esteban; Aparicio, Tomás; Lorenzo, Víctor de; Nikel, Pablo I.

    2014-01-01

    Re-programming microorganisms to modify their existing functions and/or to bestow bacteria with entirely new-to-Nature tasks have largely relied so far on specialized molecular biology tools. Such endeavors are not only relevant in the burgeoning metabolic engineering arena but also instrumental to explore the functioning of complex regulatory networks from a fundamental point of view. À la carte modification of bacterial genomes thus calls for novel tools to make genetic manipulations easier. We propose the use of a series of new broad-host-range mini-Tn5-vectors, termed pBAMDs, for the delivery of gene(s) into the chromosome of Gram-negative bacteria and for generating saturated mutagenesis libraries in gene function studies. These delivery vectors endow the user with the possibility of easy cloning and subsequent insertion of functional cargoes with three different antibiotic-resistance markers (kanamycin, streptomycin, and gentamicin). After validating the pBAMD vectors in the environmental bacterium Pseudomonas putida KT2440, their use was also illustrated by inserting the entire poly(3-hydroxybutyrate) (PHB) synthesis pathway from Cupriavidus necator in the chromosome of a phosphotransacetylase mutant of Escherichia coli. PHB is a completely biodegradable polyester with a number of industrial applications that make it attractive as a potential replacement of oil-based plastics. The non-selective nature of chromosomal insertions of the biosynthetic genes was evidenced by a large landscape of PHB synthesis levels in independent clones. One clone was selected and further characterized as a microbial cell factory for PHB accumulation, and it achieved polymer accumulation levels comparable to those of a plasmid-bearing recombinant. Taken together, our results demonstrate that the new mini-Tn5-vectors can be used to confer interesting phenotypes in Gram-negative bacteria that would be very difficult to engineer through direct manipulation of the structural genes.

  1. In silico investigation of lactoferrin protein characterizations for the prediction of anti-microbial properties

    OpenAIRE

    Sohrabi, Seyyed Mohsen; Niazi, Ali; Chahardoli, Mahmood; Hortamani, Ali; Setoodeh, Payam

    2014-01-01

    Lactoferrin (Lf) is an iron-binding multi-functional glycoprotein which has numerous physiological functions such as iron transportation, anti-microbial activity and immune response. In this study, different in silico approaches were exploited to investigate Lf protein properties in a number of mammalian species. Results showed that the iron-binding site, DNA and RNA-binding sites, signal peptides and transferrin motifs in the Lf structure were highly conserved. Examined sequences showed thre...

  2. Metabolic Engineering of Saccharomyces cerevisiae Microbial Cell Factories for Succinic Acid Production

    DEFF Research Database (Denmark)

    Otero, José Manuel; Nielsen, Jens; Olsson, Lisbeth

    2007-01-01

    Saccharomyces cerevisiae is a proven, robust, industrial production platform used for expression of a wide range of therapeutic agents, high added-value chemicals, and commodities. Central carbon metabolism in S. cerevisiae has been extensively investigated using a wide variety of substrates...... for determination of how glycolytic flux is distributed across C1 (CO2,g), C2 (ethanol, acetate), and C3 (glycerol, pyruvate) products. For the S. cerevisiae CEN.PK113-7D strain cultivated under carbon-limited, aerobic, well-controlled batch fermentations, the distribution of carbon across biomass, C1, C2, and C3...

  3. In Situ Search for Extraterrestrial Life: A Microbial Fuel Cell-Based Sensor for the Detection of Photosynthetic Metabolism.

    Science.gov (United States)

    Figueredo, Federico; Cortón, Eduardo; Abrevaya, Ximena C

    2015-09-01

    Microbial fuel cells (MFCs) are bioelectrochemical systems (BES) capable of harvesting electrons from redox reactions involved in metabolism. In a previous work, we used chemoorganoheterotrophic microorganisms from the three domains of life-Bacteria, Archaea, and Eukarya-to demonstrate that these BES could be applied to the in situ detection of extraterrestrial life. Since metabolism can be considered a common signature of life "as we know it," we extended in this study the ability to use MFCs as sensors for photolithoautotrophic metabolisms. To achieve this goal, two different photosynthetic microorganisms were used: the microalgae Parachlorella kessleri and the cyanobacterium Nostoc sp. MFCs were loaded with nonsterilized samples, sterilized samples, or sterilized culture medium of both microorganisms. Electric potential measurements were recorded for each group in single experiments or in continuum during light-dark cycles, and power and current densities were calculated. Our results indicate that the highest power and current density values were achieved when metabolically active microorganisms were present in the anode of the MFC. Moreover, when continuous measurements were performed during light-dark cycles, it was possible to see a positive response to light. Therefore, these BES could be used not only to detect chemoorganoheterotrophic metabolisms but also photolithoautotrophic metabolisms, in particular those involving oxygenic photosynthesis. Additionally, the positive response to light when using these BES could be employed to distinguish photosynthetic from nonphotosynthetic microorganisms in a sample.

  4. Investigating the Differences in the Total and Active Microbial Community of Mid-Atlantic Ridge Sediments

    Science.gov (United States)

    Sobol, M. S.; Zinke, L. A.; Orcutt, B.; Mills, H. J.; Edwards, K. J.; Girguis, P. R.; Reese, B. K.

    2016-02-01

    Microbes in the marine deep subsurface are key mediators of many geochemical cycles. It is important to understand how microbial communities and the diversity of those communities impacts geochemical cycling. Sediment cores were collected from IODP (Integrated Ocean Drilling Program) Expedition 336 to the western flank of the mid-Atlantic ridge also referred to as North Pond. The dissolved oxygen concentration decreased with depth for 60-70 mbsf, followed by a sharp increase in oxygen until it terminated at the basement. The 16S rRNA genes (DNA) and transcripts (RNA) were extracted simultaneously using a method designed by Reese et al. (2013) to differentiate between the total and active microbial community structures, respectively, as well as correlate the putative metabolism with the geochemistry. We observed many differences between the active and total communities. Sequences most closely related to Cyanobacteria were found to dominate the total community at both sites, but were found in small numbers in the active community. The most abundant phyla in the active community were Alphaproteobacteria, which suggests that they may have high activity even though the abundance was not as great in the total community. This suggests that, even in small numbers, bacteria are capable of contributing greatly to their environment. Principal Component Analysis (PCA) and Singular Value Decomposition (SVD) showed that iron-reducing bacteria in the active (RNA) community correlated strongly with solid phase iron oxides. SVD also showed that the putative nitrate reducers in the active community were found in greater abundance where porewater NO3- and NO2- total concentrations were elevated. Overall, the active (RNA) community correlated significantly with the geochemistry whereas the total (DNA) community did not. Therefore, RNA analysis yields a more accurate representation of how microbial communities impact geochemical cycling.

  5. Quantitative Raman Spectroscopy to monitor microbial metabolism in situ under pressure

    Science.gov (United States)

    Picard, A.; Daniel, I.; Oger, P.

    2006-12-01

    at least 65 MPa. No ethanol was detected at 100 MPa. From these data, the pressure at which ethanol fermentation stops in yeast was calculated to be 87±7 MPa. These results indicate that the activity of one or several enzymes of the glycolytic pathway is enhanced at low pressure. At higher pressure, they become progressively repressed, and are completely inhibited above 87 MPa. Our in situ monitoring constitutes a direct demonstration of yeast metabolism in situ under pressure up to 100 MPa. Our data agree with previous ex-situ data by Abe and Horikoshi (4). However, we observed that ethanol production is not completely inhibited around 50 MPa as predicted, but could be detected at significantly higher pressures (up to 87 MPa). QSR is a powerful method to monitor microbial activities, since almost any organic molecule with a carbon chain ranging from 1 to 6 carbon can be detected and quantified. The only limitation of QSR is that the Raman spectrum of the molecule exhibits at least one peak not masked by the spectrum of the growth medium. 1 Pelletier M J Appl Spectr 57:20A-42A, 2003 2 Daniel I, Oger P, Picard A, Cardon H and Chervin J-C (submitted to Rev Sci Instr) 3 Picard A, Daniel I, Montagnac G and Oger P (submitted to Extremophiles) 4 Abe F and Horikoshi K Extremophiles 1: 89-93, 1997

  6. Changes of microbial substrate metabolic patterns through a wastewater reuse process, including WWTP and SAT concerning depth.

    Science.gov (United States)

    Takabe, Yugo; Kameda, Ippei; Suzuki, Ryosuke; Nishimura, Fumitake; Itoh, Sadahiko

    2014-09-01

    In this study, changes of microbial substrate metabolic patterns by BIOLOG assay were discussed through a sequential wastewater reuse process, which includes activated sludge and treated effluent in wastewater treatment plant and soil aquifer treatment (SAT), especially focussing on the surface sand layer in conjunction with the vadose zone, concerning sand depth. A SAT pilot-scale reactor, in which the height of packed sand was 237 cm (vadose zone: 17 cm and saturated zone 220 cm), was operated and fed continuously by discharged anaerobic-anoxic-oxic (A2O) treated water. Continuous water quality measurements over a period of 10 months indicated that the treatment performance of the reactor, such as 83.2% dissolved organic carbon removal, appeared to be stable. Core sampling was conducted for the surface sand to a 30 cm depth, and the sample was divided into six 5 cm sections. Microbial activities, as evaluated by fluorescein diacetate, sharply decreased with increasing distance from the surface of the 30 cm core sample, which included significant decreases only 5 cm from the top surface. A similar microbial metabolic pattern containing a high degree of carbohydrates was obtained among the activated sludge, A2O treated water (influent to the SAT reactor) and the 0-5 cm layer of sand. Meanwhile, the 10-30 cm sand core layers showed dramatically different metabolic patterns containing a high degree of carboxylic acid and esters, and it is possible that the metabolic pattern exhibited by the 5-10 cm layer is at a midpoint of the changing pattern. This suggests that the removal of different organic compounds by biodegradation would be expected to occur in the activated sludge and in the SAT sand layers immediately below 5 cm from the top surface. It is possible that changes in the composition of the organic matter and/or transit of the limiting factor for microbial activities from carbon to phosphorus might have contributed to the observed dramatic changes

  7. Synchrotron-based micro and nanotomographic investigations of soil aggregate microbial and pore structure

    Science.gov (United States)

    Kemner, K. M.; O'Brien, S.; Whiteside, M. D.; Sholto-Douglas, D.; Antipova, O.; Bailey, V.; Boyanov, M.; Dohnalkova, A.; Gursoy, D.; Kovarik, L.; Lai, B.; Roehrig, C.; Vogt, S.

    2017-12-01

    Soil is a highly complex network of pore spaces, minerals, and organic matter (e.g., roots, fungi, and bacteria), making it physically heterogeneous over nano- to macro-scales. Such complexity arises from feedbacks between physical processes and biological activity that generate a dynamic, self-organizing 3D complex. Since we first demonstrated the utility of synchrotron-based transmission tomography to image internal soil aggregate structure [Kemner et al., 1998], we and many other researchers have made use of and have advanced the application of this technique. However, our understanding of how microbes and microbial metabolism are distributed throughout soil aggregates is limited, because no technique is available to image the soil pore network and the life that inhabits it. X-ray transmission microtomography can provide highly detailed 3D renderings of soil structure but cannot distinguish cells from other electron-light material such as air or water. However, the use of CdSe quantum dots (QDs) as a reporter of bacterial presence enables us to overcome this constraint, instilling bacterial cells with enough contrast to detect them and their metabolic functions in their opaque soil habitat, with hard x-rays capable of penetrating 3D soil structures at high resolution. Previous transmission tomographic imaging of soil aggregates with high energy synchrotron x-rays has demonstrated 700 nm3 voxel spatial resolution. These and recent results from nanotomographic x-ray transmission imaging of soil aggregates with 30 nm3 voxel resolution will be presented. In addition, results of submicron voxel-sized x-ray fluorescence 3D imaging to determine microbial distributions within soil aggregates and the critical role to be played by the upgrade of the Advanced Photon Source for 100-1000X increases in hard x-ray brilliance will also be presented. *Kemner, et al., SPIE 3449, 45-53, 1998

  8. Experimental Investigation Of Microbially Induced Corrosion Of Test Samples And Effect Of Self-assembled Hydrophobic Monolayers. Exposure Of Test Samples To Continuous Microbial Cultures, Chemical Analysis, And Biochemical Studies

    CERN Document Server

    Laurinavichius, K S

    1998-01-01

    Experimental Investigation Of Microbially Induced Corrosion Of Test Samples And Effect Of Self-assembled Hydrophobic Monolayers. Exposure Of Test Samples To Continuous Microbial Cultures, Chemical Analysis, And Biochemical Studies

  9. Establishment and metabolic analysis of a model microbial community for understanding trophic and electron accepting interactions of subsurface anaerobic environments

    Directory of Open Access Journals (Sweden)

    Yang Zamin K

    2010-05-01

    Full Text Available Abstract Background Communities of microorganisms control the rates of key biogeochemical cycles, and are important for biotechnology, bioremediation, and industrial microbiological processes. For this reason, we constructed a model microbial community comprised of three species dependent on trophic interactions. The three species microbial community was comprised of Clostridium cellulolyticum, Desulfovibrio vulgaris Hildenborough, and Geobacter sulfurreducens and was grown under continuous culture conditions. Cellobiose served as the carbon and energy source for C. cellulolyticum, whereas D. vulgaris and G. sulfurreducens derived carbon and energy from the metabolic products of cellobiose fermentation and were provided with sulfate and fumarate respectively as electron acceptors. Results qPCR monitoring of the culture revealed C. cellulolyticum to be dominant as expected and confirmed the presence of D. vulgaris and G. sulfurreducens. Proposed metabolic modeling of carbon and electron flow of the three-species community indicated that the growth of C. cellulolyticum and D. vulgaris were electron donor limited whereas G. sulfurreducens was electron acceptor limited. Conclusions The results demonstrate that C. cellulolyticum, D. vulgaris, and G. sulfurreducens can be grown in coculture in a continuous culture system in which D. vulgaris and G. sulfurreducens are dependent upon the metabolic byproducts of C. cellulolyticum for nutrients. This represents a step towards developing a tractable model ecosystem comprised of members representing the functional groups of a trophic network.

  10. Metabolic network modeling approaches for investigating the "hungry cancer".

    Science.gov (United States)

    Sharma, Ashwini Kumar; König, Rainer

    2013-08-01

    Metabolism is the functional phenotype of a cell, at a given condition, resulting from an intricate interplay of various regulatory processes. The study of these dynamic metabolic processes and their capabilities help to identify the fundamental properties of living systems. Metabolic deregulation is an emerging hallmark of cancer cells. This deregulation results in rewiring of the metabolic circuitry conferring an exploitative metabolic advantage for the tumor cells which leads to a distinct benefit in survival and lays the basis for unbound progression. Metabolism can be considered as a thermodynamic open-system in which source substrates of high value are being processed through a well established interconnected biochemical conversion system, strictly obeying physiochemical principles, generating useful intermediates and finally resulting in the release of byproducts. Based on this basic principle of an input-output balance, various models have been developed to interrogate metabolism elucidating its underlying functional properties. However, only a few modeling approaches have proved computationally feasible in elucidating the metabolic nature of cancer at a systems level. Besides this, statistical approaches have been set up to identify biochemical pathways being more relevant for specific types of tumor cells. In this review, we are briefly introducing the basic statistical approaches followed by the major modeling concepts. We have put an emphasis on the methods and their applications that have been used to a greater extent in understanding the metabolic remodeling of cancer. Copyright © 2013 Elsevier Ltd. All rights reserved.

  11. Estimation of microbial metabolism and co-occurrence patterns in fracture groundwaters of deep crystalline bedrock at Olkiluoto, Finland

    Science.gov (United States)

    Bomberg, M.; Lamminmäki, T.; Itävaara, M.

    2015-08-01

    The microbial diversity in oligotrophic isolated crystalline Fennoscandian Shield bedrock fracture groundwaters is great but the core community has not been identified. Here we characterized the bacterial and archaeal communities in 12 water conductive fractures situated at depths between 296 and 798 m by high throughput amplicon sequencing using the Illumina HiSeq platform. The great sequencing depth revealed that up to 95 and 99 % of the bacterial and archaeal communities, respectively, were composed of only a few common species, i.e. the core microbiome. However, the remaining rare microbiome contained over 3 and 6 fold more bacterial and archaeal taxa. Several clusters of co-occurring rare taxa were identified, which correlated significantly with physicochemical parameters, such as salinity, concentration of inorganic or organic carbon, sulphur, pH and depth. The metabolic properties of the microbial communities were predicted using PICRUSt. The rough prediction showed that the metabolic pathways included commonly fermentation, fatty acid oxidation, glycolysis/gluconeogenesis, oxidative phosphorylation and methanogenesis/anaerobic methane oxidation, but carbon fixation through the Calvin cycle, reductive TCA cycle and the Wood-Ljungdahl pathway was also predicted. The rare microbiome is an unlimited source of genomic functionality in all ecosystems. It may consist of remnants of microbial communities prevailing in earlier conditions on Earth, but could also be induced again if changes in their living conditions occur. In this study only the rare taxa correlated with any physicochemical parameters. Thus these microorganisms can respond to environmental change caused by physical or biological factors that may lead to alterations in the diversity and function of the microbial communities in crystalline bedrock environments.

  12. 2012 Molecular Basis of Microbial One-Carbon Metabolism Gordon Research Conferences and Gordon Research Seminar, August 4-10,2012

    Energy Technology Data Exchange (ETDEWEB)

    Hanson, Thomas

    2012-08-10

    The 2012 Gordon Conference will present and discuss cutting-edge research in the field of microbial metabolism of C1 compounds. The conference will feature the roles and application of C1 metabolism in natural and synthetic systems at scales from molecules to ecosystems. The conference will stress molecular aspects of the unique metabolism exhibited by autotrophic bacteria, methanogens, methylotrophs, aerobic and anaerobic methanotrophs, and acetogens.

  13. Bacterial communities associated with Shinkaia crosnieri from the Iheya North, Okinawa Trough: Microbial diversity and metabolic potentials

    Science.gov (United States)

    Zhang, Jian; Zeng, Zhi-gang; Chen, Shuai; Sun, Li

    2018-04-01

    Shinkaia crosnieri is a galatheid crab endemic to the deep-sea hydrothermal systems in the Okinawa Trough. In this study, we systematically analyzed and compared the diversity and metabolic potentials of the microbial communities in different tissues (setae, gill, and intestine) of S. crosnieri by high-throughput sequencing technology and quantitative real-time polymerase chain reaction. Sequence analysis based on the V3-V4 regions of the 16S rRNA gene obtained 408,079 taxon tags, which covered 15 phyla, 22 classes, 32 orders, 42 families, and 25 genera. Overall, the microbial communities in all tissues were dominated by Epsilonproteobacteria and Gammaproteobacteria, of which Epsilonproteobacteria was the largest class and accounted for 85.24% of the taxon tags. In addition, 20 classes of bacteria were discovered for the first time to be associated with S. crosnieri and no archaea were detected. Comparative analysis showed that (i) bacteria from different tissues fell into different groups by β-diversity analysis, (ii) bacterial communities in intestine were similar to that in gill and much more diverse than that in setae, and the sulfur-oxidizing genus Sulfurovum was markedly enriched in intestine and gill. Furthermore, bacteria potentially involved in methane, nitrogen, and metal metabolisms were detected in all samples. The key genes of aprA/dsrA and pmoA involved in sulfate reducing and methane oxidization, respectively, were detected in the gill and gut communities for the first time, and pmoA was significantly more abundant in gill and setae than in intestine. These results provide the first comparative and relatively complete picture of the diversity and metabolic potentials of the bacteria in different tissues of S. crosnieri. These results also indicate that the composition of the microbial communities in hydrothermal fauna changes with time, suggesting the importance of environmental influence.

  14. Graph methods for the investigation of metabolic networks in parasitology.

    Science.gov (United States)

    Cottret, Ludovic; Jourdan, Fabien

    2010-08-01

    Recently, a way was opened with the development of many mathematical methods to model and analyze genome-scale metabolic networks. Among them, methods based on graph models enable to us quickly perform large-scale analyses on large metabolic networks. However, it could be difficult for parasitologists to select the graph model and methods adapted to their biological questions. In this review, after briefly addressing the problem of the metabolic network reconstruction, we propose an overview of the graph-based approaches used in whole metabolic network analyses. Applications highlight the usefulness of this kind of approach in the field of parasitology, especially by suggesting metabolic targets for new drugs. Their development still represents a major challenge to fight against the numerous diseases caused by parasites.

  15. Investigating microbial activities of electrode-associated microorganisms in real-time

    Directory of Open Access Journals (Sweden)

    Sanja eAracic

    2014-11-01

    Full Text Available Electrode-associated microbial biofilms are essential to the function of bioelectrochemical systems. These systems exist in a number of different configurations but all rely on electroactive microorganisms utilizing an electrode as either an electron acceptor or an electron donor to catalyze biological processes. Investigations of the structure and function of electrode-associated biofilms are critical to further the understanding of how microbial communities are able to reduce and oxidize electrodes. The community structure of electrode-reducing biofilms is diverse and often dominated by Geobacter spp. whereas electrode-oxidizing biofilms are often dominated by other microorganisms. The application of a wide range of tools, such as high-throughput sequencing and metagenomic data analyses, provide insight into the structure and possible function of microbial communities on electrode surfaces. However, the development and application of techniques that monitor gene expression profiles in real-time are required for a more definite spatial and temporal understanding of the diversity and biological activities of these dynamic communities. This mini-review summarizes the key gene expression techniques used in bioelectrochemical systems research, which have led to a better understanding of population dynamics, cell-cell communication and molecule-surface interactions in mixed and pure BES communities

  16. Effects of wastewater treatment plant effluent inputs on planktonic metabolic rates and microbial community composition in the Baltic Sea

    DEFF Research Database (Denmark)

    Vaquer-Sunyer, Raquel; Reader, Heather E.; Muthusamy, Saraladevi

    2016-01-01

    community composition, and metabolic rates: gross primary production (GPP), net community production (NCP), community respiration (CR) and bacterial production (BP). Nitrogen-rich dissolved organic matter (DOM) inputs from effluents increased bacterial production and decreased primary production....... An increase in BP and decrease in CR could be caused by high lability of the DOM that can support secondary bacterial production, without an increase in respiration. Increases in bacterial production and simultaneous decreases of primary production lead to more carbon being consumed in the microbial loop...

  17. Microbial Communities and Their Predicted Metabolic Functions in Growth Laminae of a Unique Large Conical Mat from Lake Untersee, East Antarctica

    Directory of Open Access Journals (Sweden)

    Hyunmin Koo

    2017-08-01

    Full Text Available In this study, we report the distribution of microbial taxa and their predicted metabolic functions observed in the top (U1, middle (U2, and inner (U3 decadal growth laminae of a unique large conical microbial mat from perennially ice-covered Lake Untersee of East Antarctica, using NextGen sequencing of the 16S rRNA gene and bioinformatics tools. The results showed that the U1 lamina was dominated by cyanobacteria, specifically Phormidium sp., Leptolyngbya sp., and Pseudanabaena sp. The U2 and U3 laminae had high abundances of Actinobacteria, Verrucomicrobia, Proteobacteria, and Bacteroidetes. Closely related taxa within each abundant bacterial taxon found in each lamina were further differentiated at the highest taxonomic resolution using the oligotyping method. PICRUSt analysis, which determines predicted KEGG functional categories from the gene contents and abundances among microbial communities, revealed a high number of sequences belonging to carbon fixation, energy metabolism, cyanophycin, chlorophyll, and photosynthesis proteins in the U1 lamina. The functional predictions of the microbial communities in U2 and U3 represented signal transduction, membrane transport, zinc transport and amino acid-, carbohydrate-, and arsenic- metabolisms. The Nearest Sequenced Taxon Index (NSTI values processed through PICRUSt were 0.10, 0.13, and 0.11 for U1, U2, and U3 laminae, respectively. These values indicated a close correspondence with the reference microbial genome database, implying high confidence in the predicted metabolic functions of the microbial communities in each lamina. The distribution of microbial taxa observed in each lamina and their predicted metabolic functions provides additional insight into the complex microbial ecosystem at Lake Untersee, and lays the foundation for studies that will enhance our understanding of the mechanisms responsible for the formation of these unique mat structures and their evolutionary significance.

  18. Microbial transformation of biomacromolecules in a membrane bioreactor: implications for membrane fouling investigation.

    Directory of Open Access Journals (Sweden)

    Zhongbo Zhou

    Full Text Available BACKGROUND: The complex characteristics and unclear biological fate of biomacromolecules (BMM, including colloidal and soluble microbial products (SMP, extracellular polymeric substances (EPS and membrane surface foulants (MSF, are crucial factors that limit our understanding of membrane fouling in membrane bioreactors (MBRs. FINDINGS: In this study, the microbial transformation of BMM was investigated in a lab-scale MBR by well-controlled bioassay tests. The results of experimental measurements and mathematical modeling show that SMP, EPS, and MSF had different biodegradation behaviors and kinetic models. Based on the multi-exponential G models, SMP were mainly composed of slowly biodegradable polysaccharides (PS, proteins (PN, and non-biodegradable humic substances (HS. In contrast, EPS contained a large number of readily biodegradable PN, slowly biodegradable PS and HS. MSF were dominated by slowly biodegradable PS, which had a degradation rate constant similar to that of SMP-PS, while degradation behaviors of MSF-PN and MSF-HS were much more similar to those of EPS-PN and EPS-HS, respectively. In addition, the large-molecular weight (MW compounds (>100 kDa in BMM were found to have a faster microbial transformation rate compared to the small-MW compounds (<5 kDa. The parallel factor (PARAFAC modeling of three-dimensional fluorescence excitation-emission matrix (EEM spectra showed that the tryptophan-like PN were one of the major fractions in the BMM and they were more readily biodegradable than the HS. Besides microbial mineralization, humification and hydrolysis could be viewed as two important biotransformation mechanisms of large-MW compounds during the biodegradation process. SIGNIFICANCE: The results of this work can aid in tracking the origin of membrane foulants from the perspective of the biotransformation behaviors of SMP, EPS, and MSF.

  19. Molecular Basis of Microbial One-Carbon Metabolism 2008 Gordon Research Conference (July 20-25, 2008)

    Energy Technology Data Exchange (ETDEWEB)

    Stephen W. Ragsdale

    2009-08-12

    One-carbon (C-1) compounds play a central role in microbial metabolism. C-1 compounds include methane, carbon monoxide, CO2, and methanol as well as coenzyme-bound one-carbon compounds (methyl-B12, CH3-H4folate, etc). Such compounds are of broad global importance because several C-1 compounds (e.g., CH4) are important energy sources, some (e.g., CO2 and CH4) are potent greenhouse gases, and others (e.g., CH2Cl2) are xenobiotics. They are central in pathways of energy metabolism and carbon fixation by microbes and many are of industrial interest. Research on the pathways of one-carbon metabolism has added greatly to our understanding of evolution, structural biology, enzyme mechanisms, gene regulation, ecology, and applied biology. The 2008 meeting will include recent important findings in the following areas: (a) genomics, metagenomics, and proteomic studies that have expanded our understanding of autotrophy and C-1 metabolism and the evolution of these pathways; (b) redox regulation of carbon cycles and the interrelationship between the carbon cycle and other biogeochemical cycles (sulfur, nitrogen, oxygen); (c) novel pathways for carbon assimilation; (d) biotechnology related to C-1 metabolism; (e) novel enzyme mechanisms including channeling of C-1 intermediates during metabolism; and (f) the relationship between metal homeostasis and the global carbon cycle. The conference has a diverse and gender-balanced slate of speakers and session leaders. The wide variety of disciplines brought to the study of C-1 metabolism make the field an excellent one in which to train young researchers.

  20. Environmental spread of microbes impacts the development of metabolic phenotypes in mice transplanted with microbial communities from humans

    DEFF Research Database (Denmark)

    Zhang, Li; Bahl, Martin Iain; Roager, Henrik Munch

    2017-01-01

    -derived microbiotas in mice, factors affecting this process and resulting impact on metabolic health. We thus transplanted faecal microbiotas from humans (16 obese and 16 controls) separately into 64 germ-free Swiss Webster mice caged in pairs within four isolators, with two isolators assigned to each phenotype......Microbiota transplantation to germ-free animals is a powerful method to study involvement of gut microbes in the aetiology of metabolic syndrome. Owing to large interpersonal variability in gut microbiota, studies with broad coverage of donors are needed to elucidate the establishment of human......, thereby allowing us to explore the extent of microbial spread between cages in a well-controlled environment. Despite high group-wise similarity between obese and control human microbiotas, transplanted mice in the four isolators developed distinct gut bacterial composition and activity, body mass gain...

  1. Microbial metabolisms in a 2.5-km-deep ecosystem created by hydraulic fracturing in shales

    Energy Technology Data Exchange (ETDEWEB)

    Daly, Rebecca A.; Borton, Mikayla A.; Wilkins, Michael J.; Hoyt, David W.; Kountz, Duncan J.; Wolfe, Richard A.; Welch, Susan A.; Marcus, Daniel N.; Trexler, Ryan V.; MacRae, Jean D.; Krzycki, Joseph A.; Cole, David R.; Mouser, Paula J.; Wrighton, Kelly C.

    2016-09-05

    Hydraulic fracturing is the industry standard for extracting hydrocarbons from shale formations. Attention has been paid to the economic benefits and environmental impacts of this process, yet the biogeochemical changes induced in the deep subsurface are poorly understood. Recent single-gene investigations revealed that halotolerant microbial communities were enriched after hydraulic fracturing. Here the reconstruction of 31 unique genomes coupled to metabolite data from the Marcellus and Utica shales revealed that methylamine cycling supports methanogenesis in the deep biosphere. Fermentation of injected chemical additives also sustains long-term microbial persistence, while sulfide generation from thiosulfate represents a poorly recognized corrosion mechanism in shales. Extensive links between viruses and microbial hosts demonstrate active viral predation, which may contribute to the release of labile cellular constituents into the extracellular environment. Our analyses show that hydraulic fracturing provides the organismal and chemical inputs for colonization and persistence in the deep terrestrial subsurface.

  2. Investigating Microbial Activity in Diazotrophic Methane Seep Sediment via Transcript Analysis and Single-Cell FISH-NanoSIMS

    Science.gov (United States)

    Dekas, A. E.; Connon, S. A.; Chadwick, G.; Orphan, V. J.

    2012-12-01

    Methane seep microbial ecosystems are phylogenetically diverse and physiologically complex, and require culture-independent techniques to accurately investigate metabolic activity. In the present study we combine an RNA analysis of four key microbial genes with FISH-NanoSIMS analysis of single cells to determine the diversity of nitrogen fixing microorganisms (diazotrophs) present at a deep-sea methane-seeping site, as well as investigate the methane-dependency of a variety of community members. Recently, methane-dependent nitrogen fixation was observed in Mound 12 Costa Rica sediments, and was spatially correlated with the abundance of aggregates of anaerobic methanotrophic archaea (ANME) and sulfate reducing bacterial symbionts (SRB). Combined with the detection of 15N uptake from 15N2 in these aggregates, this suggested that the ANME-SRB aggregates are the primary diazotrophs in seep sediment. However, the diversity of dinitrogenase reductase (nifH) sequences recovered from several deep-sea locales, including Mound 12, suggests a greater diversity of diazotrophs in marine sediment. To investigate the activity of these potential diazotrophs in Mound 12 sediment, we investigated a suite of RNA transcripts in 15N2 incubations in both the presence and absence of methane: nifH, bacterial 16S rRNA, methyl coenzyme M reductase A (mcrA), and adenosine-5'-phosposulfate reductase alpha subunit (aprA). No nifH transcripts were recovered in incubations without methane, consistent with previous measurements lacking 15N2 uptake in the same sediments. The activity of the bacterial community in general, assessed by variable transcription, was also greatly affected by the presence or absence of methane. Single-cell fluorescence in situ hybridization coupled to nanoscale secondary ion mass spectrometry (FISH-NanoSIMS) was employed to confirm diazotrophic activity (15N2 uptake) and protein synthesis (15NH4+ uptake) of particular species implicated as ecologically important by the

  3. Host genes related to paneth cells and xenobiotic metabolism are associated with shifts in human ileum-associated microbial composition.

    Directory of Open Access Journals (Sweden)

    Tianyi Zhang

    Full Text Available The aim of this study was to integrate human clinical, genotype, mRNA microarray and 16 S rRNA sequence data collected on 84 subjects with ileal Crohn's disease, ulcerative colitis or control patients without inflammatory bowel diseases in order to interrogate how host-microbial interactions are perturbed in inflammatory bowel diseases (IBD. Ex-vivo ileal mucosal biopsies were collected from the disease unaffected proximal margin of the ileum resected from patients who were undergoing initial intestinal surgery. Both RNA and DNA were extracted from the mucosal biopsy samples. Patients were genotyped for the three major NOD2 variants (Leufs1007, R702W, and G908R and the ATG16L1T300A variant. Whole human genome mRNA expression profiles were generated using Agilent microarrays. Microbial composition profiles were determined by 454 pyrosequencing of the V3-V5 hypervariable region of the bacterial 16 S rRNA gene. The results of permutation based multivariate analysis of variance and covariance (MANCOVA support the hypothesis that host mucosal Paneth cell and xenobiotic metabolism genes play an important role in host microbial interactions.

  4. The Influence of Tallow on Rumen Metabolism, Microbial Biomass Synthesis and Fatty Acid Composition of Bacteria and Protozoa

    DEFF Research Database (Denmark)

    Weisbjerg, Martin Riis; Børsting, Christian Friis; Hvelplund, Torben

    1992-01-01

    Rumen metabolism, microbial biomass synthesis and microbial long chain fatty acid composition were studied in lactating cows fed at two levels of dry matter intake (L, 8.6 kg DM and H, 12.6 kg DM) with 0, 4 and 6% added tallow at the low feed level (L0, L4 and L6) and 0, 2, 4 and 6% at the high...... feed level (H0, H2, H4 and H6). Fibre digestibility was not significantly affected by tallow addition. Increasing tallow level in the diet decreased the total VFA concentration, the ratio of acetic acid to propionic acid and the ammonia concentration in the rumen. Crude fat and fatty acid content...... in bacterial and protozoal dry matter increased with increased tallow level, especially due to an increase in fatty acids originating from the feeds. Microbial synthesis in the rumen and flow of amino acids to the duodenum was highest for medium fat intake at the high feed level....

  5. Sulfur isotopes of organic matter preserved in 3.45-billion-year-old stromatolites reveal microbial metabolism.

    Science.gov (United States)

    Bontognali, Tomaso R R; Sessions, Alex L; Allwood, Abigail C; Fischer, Woodward W; Grotzinger, John P; Summons, Roger E; Eiler, John M

    2012-09-18

    The 3.45-billion-year-old Strelley Pool Formation of Western Australia preserves stromatolites that are considered among the oldest evidence for life on Earth. In places of exceptional preservation, these stromatolites contain laminae rich in organic carbon, interpreted as the fossil remains of ancient microbial mats. To better understand the biogeochemistry of these rocks, we performed microscale in situ sulfur isotope measurements of the preserved organic sulfur, including both Δ(33)S and . This approach allows us to tie physiological inference from isotope ratios directly to fossil biomass, providing a means to understand sulfur metabolism that is complimentary to, and independent from, inorganic proxies (e.g., pyrite). Δ(33)S values of the kerogen reveal mass-anomalous fractionations expected of the Archean sulfur cycle, whereas values show large fractionations at very small spatial scales, including values below -15‰. We interpret these isotopic patterns as recording the process of sulfurization of organic matter by H(2)S in heterogeneous mat pore-waters influenced by respiratory S metabolism. Positive Δ(33)S anomalies suggest that disproportionation of elemental sulfur would have been a prominent microbial process in these communities.

  6. MicroScope—an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data

    Science.gov (United States)

    Vallenet, David; Belda, Eugeni; Calteau, Alexandra; Cruveiller, Stéphane; Engelen, Stefan; Lajus, Aurélie; Le Fèvre, François; Longin, Cyrille; Mornico, Damien; Roche, David; Rouy, Zoé; Salvignol, Gregory; Scarpelli, Claude; Thil Smith, Adam Alexander; Weiman, Marion; Médigue, Claudine

    2013-01-01

    MicroScope is an integrated platform dedicated to both the methodical updating of microbial genome annotation and to comparative analysis. The resource provides data from completed and ongoing genome projects (automatic and expert annotations), together with data sources from post-genomic experiments (i.e. transcriptomics, mutant collections) allowing users to perfect and improve the understanding of gene functions. MicroScope (http://www.genoscope.cns.fr/agc/microscope) combines tools and graphical interfaces to analyse genomes and to perform the manual curation of gene annotations in a comparative context. Since its first publication in January 2006, the system (previously named MaGe for Magnifying Genomes) has been continuously extended both in terms of data content and analysis tools. The last update of MicroScope was published in 2009 in the Database journal. Today, the resource contains data for >1600 microbial genomes, of which ∼300 are manually curated and maintained by biologists (1200 personal accounts today). Expert annotations are continuously gathered in the MicroScope database (∼50 000 a year), contributing to the improvement of the quality of microbial genomes annotations. Improved data browsing and searching tools have been added, original tools useful in the context of expert annotation have been developed and integrated and the website has been significantly redesigned to be more user-friendly. Furthermore, in the context of the European project Microme (Framework Program 7 Collaborative Project), MicroScope is becoming a resource providing for the curation and analysis of both genomic and metabolic data. An increasing number of projects are related to the study of environmental bacterial (meta)genomes that are able to metabolize a large variety of chemical compounds that may be of high industrial interest. PMID:23193269

  7. MicroScope--an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data.

    Science.gov (United States)

    Vallenet, David; Belda, Eugeni; Calteau, Alexandra; Cruveiller, Stéphane; Engelen, Stefan; Lajus, Aurélie; Le Fèvre, François; Longin, Cyrille; Mornico, Damien; Roche, David; Rouy, Zoé; Salvignol, Gregory; Scarpelli, Claude; Thil Smith, Adam Alexander; Weiman, Marion; Médigue, Claudine

    2013-01-01

    MicroScope is an integrated platform dedicated to both the methodical updating of microbial genome annotation and to comparative analysis. The resource provides data from completed and ongoing genome projects (automatic and expert annotations), together with data sources from post-genomic experiments (i.e. transcriptomics, mutant collections) allowing users to perfect and improve the understanding of gene functions. MicroScope (http://www.genoscope.cns.fr/agc/microscope) combines tools and graphical interfaces to analyse genomes and to perform the manual curation of gene annotations in a comparative context. Since its first publication in January 2006, the system (previously named MaGe for Magnifying Genomes) has been continuously extended both in terms of data content and analysis tools. The last update of MicroScope was published in 2009 in the Database journal. Today, the resource contains data for >1600 microbial genomes, of which ∼300 are manually curated and maintained by biologists (1200 personal accounts today). Expert annotations are continuously gathered in the MicroScope database (∼50 000 a year), contributing to the improvement of the quality of microbial genomes annotations. Improved data browsing and searching tools have been added, original tools useful in the context of expert annotation have been developed and integrated and the website has been significantly redesigned to be more user-friendly. Furthermore, in the context of the European project Microme (Framework Program 7 Collaborative Project), MicroScope is becoming a resource providing for the curation and analysis of both genomic and metabolic data. An increasing number of projects are related to the study of environmental bacterial (meta)genomes that are able to metabolize a large variety of chemical compounds that may be of high industrial interest.

  8. Investigation of Microbial Diversity in Geothermal Hot Springs in Unkeshwar, India, Based on 16S rRNA Amplicon Metagenome Sequencing

    OpenAIRE

    Mehetre, Gajanan T.; Paranjpe, Aditi; Dastager, Syed G.; Dharne, Mahesh S.

    2016-01-01

    Microbial diversity in geothermal waters of the Unkeshwar hot springs in Maharashtra, India, was studied using 16S rRNA amplicon metagenomic sequencing. Taxonomic analysis revealed the presence of Bacteroidetes, Proteobacteria, Cyanobacteria, Actinobacteria, Archeae, and OD1 phyla. Metabolic function prediction analysis indicated a battery of biological information systems indicating rich and novel microbial diversity, with potential biotechnological applications in this niche.

  9. Effect of Lineage-Specific Metabolic Traits of Lactobacillus reuteri on Sourdough Microbial Ecology

    OpenAIRE

    Lin, Xiaoxi B.; Gänzle, Michael G.

    2014-01-01

    This study determined the effects of specific metabolic traits of Lactobacillus reuteri on its competitiveness in sourdoughs. The competitiveness of lactobacilli in sourdough generally depends on their growth rate; acid resistance additionally contributes to competitiveness in sourdoughs with long fermentation times. Glycerol metabolism via glycerol dehydratase (gupCDE) accelerates growth by the regeneration of reduced cofactors; glutamate metabolism via glutamate decarboxylase (gadB) increas...

  10. Bacillus licheniformis affects the microbial community and metabolic profile in the spontaneous fermentation of Daqu starter for Chinese liquor making.

    Science.gov (United States)

    Wang, Peng; Wu, Qun; Jiang, Xuejian; Wang, Zhiqiang; Tang, Jingli; Xu, Yan

    2017-06-05

    Chinese liquor is produced from spontaneous fermentation starter (Daqu) that provides the microbes, enzymes and flavors for liquor fermentation. To improve the flavor character of Daqu, we inoculated Bacillus licheniformis and studied the effect of this strain on the community structure and metabolic profile in Daqu fermentation. The microbial relative abundance changed after the inoculation, including the increase in Bacillus, Clavispora and Aspergillus, and the decrease in Pichia, Saccharomycopsis and some other genera. This variation was also confirmed by pure culture and coculture experiments. Seventy-three metabolites were identified during Daqu fermentation process. After inoculation, the average content of aromatic compounds were significantly enriched from 0.37mg/kg to 0.90mg/kg, and the average content of pyrazines significantly increased from 0.35mg/kg to 5.71mg/kg. The increase in pyrazines was positively associated with the metabolism of the inoculated Bacillus and the native genus Clavispora, because they produced much more pyrazines in their cocultures. Whereas the increase in aromatic compounds might be related to the change of in situ metabolic activity of several native genera, in particular, Aspergillus produced more aromatic compounds in cocultures with B. licheniformis. It indicated that the inoculation of B. licheniformis altered the flavor character of Daqu by both its own metabolic activity and the variation of in situ metabolic activity. Moreover, B. licheniformis inoculation influenced the enzyme activity of Daqu, including the significant increase in amylase activity (from 1.3gstarch/g/h to 1.7gstarch/g/h), and the significant decrease in glucoamylase activity (from 627.6mgglucose/g/h to 445.6mgglucose/g/h) and esterase activity (from 28.1mgethylcaproate/g/100h to 17.2mgethylcaproate/g/100h). These effects of inoculation were important factors for regulating the metabolism of microbial communities, hence for improving the flavor profile

  11. Investigating the possibility of Microbial Production of Mannitol from Waste Bread

    Directory of Open Access Journals (Sweden)

    Vajihe Sadeqi

    2016-07-01

    Full Text Available According to the significant role of sugar alcohols (Polyols in food industries, in the present study the possibility of microbial production of mannitol from bread waste was studied. Microbial growth and amylase production were investigated by five Iranian native strains of Bacillus spp in starch agar and broth. The best strain was selected, and its growth curve was determined. Leuconostoc mesentroides PTCC 1059 was used as a control strain to convert fructose to mannitol. In order to determine the ability of selected strains in converting waste breads into mannitol sugar, a culture medium was prepared from waste of Lavash and Baguette breads. Afterward, the ability to convert starch into fructose by Chemical analysis glucose test was used, and then bio-conversion analysis of fructose to mannitol by HPLC analysis was investigated. HPLC results showed that the Bacillus subtilis and Leuconostoc mesentroides PTCC 1059 had the ability of producing mannitol at a rate of 4.8g/L from fructose 5%, 0.15 g/L from Lavash bread 5%, and 0.2g/L from Baguette bread.

  12. Metabolic flexibility of the Fe(II)-oxidizing phototropic strain Rhodopseudomonas palustris TIE1 and its potential role in microbial iron cycling

    Science.gov (United States)

    Schmidt, C.; Oswald, K.; Melton, E. D.; Kappler, A.

    2012-04-01

    The biogeochemical conversion of iron(II) and iron(III) is widespread in many aquatic and terrestrial environments. In the anoxic regime of soils and sediments the conversion and alternation of the iron redox state is predominantly run by microorganisms that are thought to gain life-sustaining energy by the oxidation and/or reduction of ferrous/ferric components. The spatial arrangement of microbial iron(II) oxidation and iron(III) reduction is largely controlled by the availability of the required electron acceptor and electron donor, as well as the essential source of energy (i.e. light or chemical energy). The physico-chemical patterns of many microbial environments undergo dynamic variations (i.e. diurnal and seasonal changes) as a function of natural external forces (i.e. seasonality, storm events, algae blooms) which strongly affects the local budget of organic carbon and nutrients, as well as the day light penetration. Such fluctuations force microorganisms either to follow the flow of substrate or to switch their metabolism to alternative electron acceptors and/or donors. Different photoferrotrophic bacteria have been shown to be able to grow either on organic (heterotrophic) or inorganic (autotrophic) substrates while exploiting light as their energy source. Within the frame of this study the preference for organic substrates (lactate and acetate) and/or ferrous iron (in simultaneous presence) for photo(ferro)trophic growth of Rhodopseudomonas palustris TIE1 has been investigated in detail. Rates of iron oxidation, acetate/lactate consumption and growth have been followed over time as a function of different lactate to acetate to iron(II) ratios. Additional experiments have been designed to evaluate the potential of Rhodopseudomonas palustris TIE1 to contribute to the redox cycling of iron. TIE1 has been grown in a batch set-up in which the iron(III)-reducing strain Shewanella oneidensis MR1 has been incubated at different ferrihydrite concentrations in

  13. Diel metabolomics analysis of a hot spring chlorophototrophic microbial mat leads to new hypotheses of community member metabolisms

    Directory of Open Access Journals (Sweden)

    Young-Mo eKim

    2015-04-01

    Full Text Available Dynamic environmental factors such as light, nutrients, salt, and temperature continuously affect chlorophototrophic microbial mats, requiring adaptive and acclimative responses to stabilize composition and function. Quantitative metabolomics analysis can provide insights into metabolite dynamics for understanding community response to such changing environmental conditions. In this study, we quantified volatile organic acids, polar metabolites (amino acids, glycolytic and citric acid cycle intermediates, nucleobases, nucleosides, and sugars, wax esters, and polyhydroxyalkanoates, resulting in the identification of 104 metabolites and related molecules in thermal chlorophototrophic microbial mat cores collected over a diel cycle in Mushroom Spring, Yellowstone National Park. A limited number of predominant taxa inhabit this community and their functional potentials have been previously identified through metagenomic and metatranscriptomic analyses and in situ metabolisms, and metabolic interactions among these taxa have been hypothesized. Our metabolomics results confirmed the diel cycling of photorespiration (e.g. glycolate and fermentation (e.g. acetate, propionate, and lactate products, the carbon storage polymers polyhydroxyalkanoates, and dissolved gases (e.g. H2 and CO2 in the waters overlying the mat, which were hypothesized to occur in major mat chlorophototrophic community members. In addition, we have formulated the following new hypotheses: 1 the morning hours are a time of biosynthesis of amino acids, DNA, and RNA; 2 photo-inhibited cells may also produce lactate via fermentation as an alternate metabolism; 3 glycolate and lactate are exchanged among Synechococcus and Roseiflexus spp.; and 4 fluctuations in many metabolite pools (e.g. wax esters at different times of day result from species found at different depths within the mat responding to temporal differences in their niches

  14. Investigation of Hyporheic Microbial Biofilms as Indicators of Heavy Metal Toxicity in the Clark Fork Basin, Montana

    Science.gov (United States)

    Barnhart, E. P.; Hwang, C.; Bouskill, N.; Hornberger, M.; Fields, M. W.

    2015-12-01

    Water-saturated sediments that underlie a stream channel contain microbial biofilms that are often responsible for the majority of the metabolic activity in river and stream ecosystems. Metal contamination from mining effluent can modify the biofilm community structure, diversity, and activity. Developing a mechanistic understanding of the biofilm response to metal contamination could provide a useful bioindicator of metal toxicity due to the ease of standard biofilm sampling, environmental ubiquity of biofilms and the rapid response of biofilms to environmental perturbation and metal toxicity. Here we present data on the structure of the biofilm community (e.g., microbial population composition and diversity) and trace metal concentrations in water, bed sediment and biota (benthic insects) across 15 sites in the Clark Fork Basin. Sample sites were selected across a historically-monitored metal pollution gradient at shallow riffles with bed sediment predominantly composed of pebbles, cobbles, and sand. Bed-sediment samples (for biofilm analysis) were obtained from the top 20 centimeters of the hyporheic zone and sieved using sterile sieves to obtain homogeneous sediment samples with particle sizes ranging from 1.70 to 2.36 millimeters. Linear discriminant analysis and effect size statistical methods were used to integrate the metals concentration data (for water and benthic-insects samples) with the microbial community analysis to identify microbial biomarkers of metal toxicity. The development of rapid microbial biomarker tools could provide reproducible and quantitative insights into the effectiveness of remediation activities on metal toxicity and advances in the field of environmental biomonitoring.

  15. Variation of preserving organic matter bound in interlayer of montmorillonite induced by microbial metabolic process.

    Science.gov (United States)

    Zhao, Yulian; Dong, Faqin; Dai, Qunwei; Li, Gang; Ma, Jie

    2017-07-25

    This paper aimed to investigate the variation of preserving organic matter bound in the interlayer space of montmorillonite (Mt) induced by a microbe metabolic process. We selected Bacillus pumilus as the common soil native bacteria. The alteration of d 001 value, functional group, and C,N organic matter contents caused by bacteria were analyzed by XRD, FTIR, and elementary analyzer, respectively. XRD results showed that the d 001 value of montmorillonite increased with the concentration decreasing and decreased with the culture time increasing after interacting with bacteria indicating the interlayer space of montmorillonite was connected with the organic matter. The findings of long-term interaction by resetting culture conditions implied that the montmorillonite buffered the organic matter when the nutrition was enough and released again when the nutrition was lacking. The results of the elementary analyzer declared the content of organic matter was according to the d 001 value of montmorillonite and N organic matter which played a major impact. FTIR results confirmed that the Si-O stretching vibrations of Mt were affected by the functional group of organic matter. Our results showed that the montmorillonite under the influence of soil bacteria has a strong buffering capacity for preserving organic matter into the interlayer space in a short-term. It might provide critical implications for understanding the evolution process and the preservation of fertilization which was in the over-fertilization or less-fertilization conditions on farmland.

  16. Investigation of the in vitro metabolism of the analgesic flupirtine

    Czech Academy of Sciences Publication Activity Database

    Methling, K.; Reszka, P.; Lalk, M.; Vrána, Oldřich; Scheuch, E.; Siegmund, W.; Terhaag, B.; Bednarski, P.J.

    2009-01-01

    Roč. 37, č. 3 (2009), s. 479-493 ISSN 0090-9556 R&D Projects: GA AV ČR(CZ) 1QS500040581 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : flupirtine * analgesic * metabolism Subject RIV: BO - Biophysics Impact factor: 3.743, year: 2009

  17. Nucleic acid-based approaches to investigate microbial-related cheese quality defects

    Directory of Open Access Journals (Sweden)

    Daniel eO Sullivan

    2013-01-01

    Full Text Available AbstractThe microbial profile of cheese is a primary determinant of cheese quality. Microorganisms can contribute to aroma and taste defects, form biogenic amines, cause gas and secondary fermentation defects, and can contribute to cheese pinking and mineral deposition issues. These defects may be as a result of seasonality and the variability in the composition of the milk supplied, variations in cheese processing parameters, as well as the nature and number of the non-starter microorganisms which come from the milk or other environmental sources. Such defects can be responsible for production and product recall costs and thus represent a significant economic burden for the dairy industry worldwide. Traditional non-molecular approaches are often considered biased and have inherently slow turnaround times. Molecular techniques can provide early and rapid detection of defects that result from the presence of specific spoilage microbes and, ultimately, assist in enhancing cheese quality and reducing costs. Here we review the DNA-based methods that are available to detect/quantify spoilage bacteria, and relevant metabolic pathways, in cheeses and, in the process, highlight how these strategies can be employed to improve cheese quality and reduce the associated economic burden on cheese processors.

  18. Modeling Late-State Serpentinization on Enceladus and Implications for Methane-Utilizing Microbial Metabolisms

    Science.gov (United States)

    Hart, R.; Cardace, D.

    2017-12-01

    Modeling investigations of Enceladus and other icy-satellites have included physicochemical properties (Sohl et al., 2010; Glein et al., 2015; Neveu et al., 2015), geophysical prospects of serpentinization (Malamud and Prialnik, 2016; Vance et al., 2016), and aqueous geochemistry across different antifreeze fluid-rock scenarios (Neveu et al., 2017). To more effectively evaluate the habitability of Enceladus, in the context of recent observations (Waite et al., 2017), we model the potential bioenergetic pathways that would be thermodynamically favorable at the interface of hydrothermal water-rock reactions resulting from late stage serpentinization (>90% serpentinized), hypothesized on Enceladus. Building on previous geochemical model outputs of Enceladus (Neveu et al., 2017), and bioenergetic modeling (as in Amend and Shock, 2001; Cardace et al., 2015), we present a model of late stage serpentinization possible at the water-rock interface of Enceladus, and report changing activities of chemical species related to methane utilization by microbes over the course of serpentinization using the Geochemist's Workbench REACT code [modified Extended Debye-Hückel (Helgeson, 1969) using the thermodynamic database of SUPCRT92 (Johnson et al., 1992)]. Using a model protolith speculated to exist at Enceladus's water-rock boundary, constrained by extraterrestrial analog analytical data for subsurface serpentinites of the Coast Range Ophiolite (Lower Lake, CA, USA) mélange rocks, we deduce evolving habitability conditions as the model protolith reacts with feasible, though hypothetical, planetary ocean chemistries (from Glien et al., 2015, and Neveu et al., 2017). Major components of modeled oceans, Na-Cl, Mg-Cl, and Ca-Cl, show shifts in the feasibility of CO2-CH4-H2 driven microbial habitability, occurring early in the reaction progress, with methanogenesis being bioenergetically favored. Methanotrophy was favored late in the reaction progress of some Na-Cl systems and in the

  19. Suppression of Microbial Metabolic Pathways Inhibits the Generation of the Human Body Odor Component Diacetyl by Staphylococcus spp

    OpenAIRE

    Hara, Takeshi; Matsui, Hiroshi; Shimizu, Hironori

    2014-01-01

    Diacetyl (2,3-butanedione) is a key contributor to unpleasant odors emanating from the axillae, feet, and head regions. To investigate the mechanism of diacetyl generation on human skin, resident skin bacteria were tested for the ability to produce diacetyl via metabolism of the main organic acids contained in human sweat. L-lactate metabolism by Staphylococcus aureus and Staphylococcus epidermidis produced the highest amounts of diacetyl, as measured by high-performance liquid chromatography...

  20. Metabolism of Chicken Feathers and Concomitant Electricity Generation by Pseudomonas aeruginosa by Employing Microbial Fuel Cell (MFC

    Directory of Open Access Journals (Sweden)

    Venkatesh Chaturvedi

    2014-01-01

    Full Text Available Keratinolytic potential of Pseudomonas aeruginosa strain SDS3 has been evaluated for the metabolism of chicken feathers. Results indicated that strain SDS3 showed complete metabolism of 0.1 and 0.5% (w/v chicken feathers in minimal medium. Feathers were metabolized up to 80% at 1% (w/v concentration. Maximum soluble protein (480.8±17.1 μg/mL and keratinase (15.4±0.25 U/mL were observed in the presence of 1% chicken feathers after five days of incubation. The effect of carbon and nitrogen sources showed that feather degradation was stimulated by complex carbon/nitrogen sources such as starch, malt extract, tryptone, and beef extract and was inhibited by simple carbon and nitrogen sources. Electricity production by employing chicken feathers as a substrate in microbial fuel cell (MFC was evaluated. It was observed that maximum voltage corresponding to 141 mV was observed after 14 days of incubation. Maximum power density of 1206.78 mW/m2 and maximum current density of 8.6 mA/m2 were observed. The results clearly indicate that chicken feathers can be successfully employed as a cheap substrate for electricity production in MFC. This is the first report showing employment of chicken feathers as substrate in MFC.

  1. Recent advances in engineering propionyl-CoA metabolism for microbial production of value-added chemicals and biofuels.

    Science.gov (United States)

    Srirangan, Kajan; Bruder, Mark; Akawi, Lamees; Miscevic, Dragan; Kilpatrick, Shane; Moo-Young, Murray; Chou, C Perry

    2017-09-01

    Diminishing fossil fuel reserves and mounting environmental concerns associated with petrochemical manufacturing practices have generated significant interests in developing whole-cell biocatalytic systems for the production of value-added chemicals and biofuels. Although acetyl-CoA is a common natural biogenic precursor for the biosynthesis of numerous metabolites, propionyl-CoA is unpopular and non-native to most organisms. Nevertheless, with its C3-acyl moiety as a discrete building block, propionyl-CoA can serve as another key biogenic precursor to several biological products of industrial importance. As a result, engineering propionyl-CoA metabolism, particularly in genetically tractable hosts with the use of inexpensive feedstocks, has paved an avenue for novel biomanufacturing. Herein, we present a systematic review on manipulation of propionyl-CoA metabolism as well as relevant genetic and metabolic engineering strategies for microbial production of value-added chemicals and biofuels, including odd-chain alcohols and organic acids, bio(co)polymers and polyketides. [Formula: see text].

  2. The Impact of Oxygen on Metabolic Evolution: A Chemoinformatic Investigation

    Science.gov (United States)

    Qin, Tao; Li, Xiao; Caetano-Anollés, Gustavo; Zhang, Hong-Yu

    2012-01-01

    The appearance of planetary oxygen likely transformed the chemical and biochemical makeup of life and probably triggered episodes of organismal diversification. Here we use chemoinformatic methods to explore the impact of the rise of oxygen on metabolic evolution. We undertake a comprehensive comparative analysis of structures, chemical properties and chemical reactions of anaerobic and aerobic metabolites. The results indicate that aerobic metabolism has expanded the structural and chemical space of metabolites considerably, including the appearance of 130 novel molecular scaffolds. The molecular functions of these metabolites are mainly associated with derived aspects of cellular life, such as signal transfer, defense against biotic factors, and protection of organisms from oxidation. Moreover, aerobic metabolites are more hydrophobic and rigid than anaerobic compounds, suggesting they are better fit to modulate membrane functions and to serve as transmembrane signaling factors. Since higher organisms depend largely on sophisticated membrane-enabled functions and intercellular signaling systems, the metabolic developments brought about by oxygen benefit the diversity of cellular makeup and the complexity of cellular organization as well. These findings enhance our understanding of the molecular link between oxygen and evolution. They also show the significance of chemoinformatics in addressing basic biological questions. PMID:22438800

  3. Investigation of the rumen microbial community responsible for degradation of a putative toxin in Acacia angustissima

    International Nuclear Information System (INIS)

    Collins, E.M.C.; Blackall, L.L.; Mcsweeney, C.S.; Krause, D.O.

    2005-01-01

    Acacia angustissima has been proposed as a protein supplement in countries where availability of high quality fodder for grazing animals is a problem due to extreme, dry climates. While A. angustissima thrives in harsh environments and provides valuable nutrients required by ruminants, it has also been found to contain anti-nutritive factors that currently preclude its widespread application. A number of non-protein amino acids have been identified in the leaves of A. angustissima and in the past these have been linked to toxicity in ruminants. The non-protein amino acid 4-n-acetyl-2,4-diaminobutyric acid (ADAB) had been determined to be the major non-protein amino acid in the leaves of A. angustissima. Thus, in this study, the aim was to identify microorganisms from the rumen environment capable of degrading ADAB. Using an ADAB-containing plant extract, a mixed enrichment culture was obtained that exhibited substantial ADAB-degrading ability. Attempts to isolate an ADAB-degrading micro-organism were carried out, but no isolates were able to degrade ADAB in pure culture. The mixed microbial community of the ADAB-degrading enrichment culture was further examined through the use of pure-culture-independent techniques. Fluorescence in situ hybridization (FISH) was employed to investigate the diversity within this sample. In addition two bacterial 16S rDNA clone libraries were constructed in an attempt to further elucidate the members of the microbial population. The clone libraries were constructed from serial dilutions of the enrichment culture, a 10 -5 dilution where complete degradation of ADAB occurred, and a 10 -7 dilution where ADAB degradation did not occur. Through the comparison of these two libraries it was hypothesized that clones belonging to the Firmicutes phylum were involved in ADAB degradation. A FISH probe, ADAB1268, was then designed to target these clones and was applied to the enrichment cultures to investigate their relative abundance within the

  4. The spatial profiles and metabolic capabilities of microbial populations impact the growth of antibiotic-resistant mutants

    Science.gov (United States)

    Kaushik, Karishma S.; Ratnayeke, Nalin; Katira, Parag; Gordon, Vernita D.

    2015-01-01

    Antibiotic resistance adversely affects clinical and public health on a global scale. Using the opportunistic human pathogen Pseudomonas aeruginosa, we show that increasing the number density of bacteria, on agar containing aminoglycoside antibiotics, can non-monotonically impact the survival of antibiotic-resistant mutants. Notably, at high cell densities, mutant survival is inhibited. A wide range of bacterial species can inhibit antibiotic-resistant mutants. Inhibition results from the metabolic breakdown of amino acids, which results in alkaline by-products. The consequent increase in pH acts in conjunction with aminoglycosides to mediate inhibition. Our work raises the possibility that the manipulation of microbial population structure and nutrient environment in conjunction with existing antibiotics could provide therapeutic approaches to combat antibiotic resistance. PMID:25972434

  5. Technical note: fatty acids and purine profile of cecum and colon bacteria as indicators of equine microbial metabolism.

    Science.gov (United States)

    Santos, A S; Jerónimo, E; Ferreira, L M; Rodrigues, M A M; Bessa, R J B

    2013-04-01

    The potential use of odd- and branched-chain fatty acids (OBCFA) and purine bases (PB) as microbial markers in the equine hindgut was studied. For this purpose, feed particles adherent bacteria [solid associated bacteria (SAB)] and planktonic bacteria [liquid associated bacteria (PAB)] were isolated from total cecum and colon contents of 8 healthy, crossbred horses (9 ± 3 yr). Horses were fasted for 12 to 15 h before slaughter, and the cecum and colon were identified and clamped in their extremities to avoid mixing of digesta contents. The total cecum or colon contents was collected into thermal containers previously filled with CO2, immediately transported to the laboratory, and subjected to separation of solid and liquid phases to obtain bacterial PAB and SAB pellets from each horse. Overall differences observed were mainly between site of bacterial collection (cecum vs. colon) rather than between type of bacterial population (PAB vs. SAB). Cecal bacteria fraction had greater (P indicated that the composition of cecal and colon bacteria is very different from that of similar ecosystems (e.g., rumen). These differences can be a reflection of different growth stages or nutrition of particular populations as well as different bacterial metabolic activities. Results presented herein provide evidence that PB and fatty acids can be used as microbial markers in equine studies.

  6. Arabinoxylo-Oligosaccharides and Inulin Impact Inter-Individual Variation on Microbial Metabolism and Composition, Which Immunomodulates Human Cells.

    Science.gov (United States)

    Van den Abbeele, Pieter; Taminiau, Bernard; Pinheiro, Iris; Duysburgh, Cindy; Jacobs, Heidi; Pijls, Loek; Marzorati, Massimo

    2018-02-07

    Fecal batch fermentations coupled to cocultures of epithelial cells and macrophages were used to compare how arabinoxylo-oligosaccharides (AXOS) and inulin modulate gut microbial activity and composition of three different human donors and subsequently the epithelial permeability and immune response. Both inulin and AXOS decreased the pH during incubation (-1.5 pH units), leading to increased productions of acetate, propionate, and butyrate. Differences in terms of metabolites production could be linked to specific microbial alterations at genus level upon inulin/AXOS supplementation (i.e., Bifidobacterium, Bacteroides, Prevotella and unclassified Erysipelotrichaceae), as shown by 16S-targeted Illumina sequencing. Both products stimulated gut barrier and immune function with increases in TEER, NF-KB, IL-10, and IL-6. Ingredients with different structures selectively modulate the microbiota of a specific donor leading to differential changes at metabolic level. The extent of this effect is donor specific and is linked to a final specific modulation of the host's immune system.

  7. Metabolic Potential of Microbial Genomes Reconstructed from a Deep-Sea Oligotrophic Sediment Metagenome

    Science.gov (United States)

    Tully, B. J.; Huber, J. A.; Heidelberg, J. F.

    2016-02-01

    The South Pacific Gyre (SPG) possesses the lowest rates of sedimentation, surface chlorophyll concentration and primary productivity in the global oceans, making it one of the most oligotrophic environments on earth. As a direct result of the low-standing biomass in surface waters, deep-sea sediments are thin and contain small amount of labile organic carbon. It was recently shown that the sediment column within the SPG is fully oxic through to the underlying basalt basement and may be representative of 9-37% of the global marine environment. In addition, it appears that approximately 50% of the total organic carbon is removed from the oligotrophic sediments within the first 20 centimeters beneath the sea floor (cmbsf). To understand the microbial processes that contribute to the removal of the labile organic matter, metagenomic sequencing and analysis was carried out on a sample of sediment collected from 0-5 cmbsf from SPG site 10 (U1369). Analysis of 9 partially reconstructed environmental genomes revealed that the members of the SPG surface sediment microbial community are phylogenetically distinct from surface/upper ocean organisms, with deep branches within the Alpha- and Gammaproteobacteria, Nitrospirae, Nitrospina, the phylum NC10, and several unique phylogenetic groups. Within these partially complete genomes there is evidence for microbially mediated metal (iron/manganese) oxidation and carbon fixation linked to the nitrification. Additionally, despite low sedimentation and hypothesized energy-limitation, members of the SPG microbial community had motility and chemotactic genes and possessed mechanisms for the utilization of high molecular weight organic matter, including exoproteases and peptide specific membrane transporters. Simultaneously, the SPG genomes showed a limited potential for the degradation of recalcitrant carbon compounds. Finally, the presence of putative genes with functions involved with denitrification and the consumption of C1

  8. The microbial pharmacists within us: a metagenomic view of xenobiotic metabolism

    Science.gov (United States)

    Spanogiannopoulos, Peter; Bess, Elizabeth N.; Carmody, Rachel N.; Turnbaugh, Peter J.

    2016-01-01

    Although the significance of human genetic polymorphisms in therapeutic outcomes is well established, the importance of our “second genome” (the microbiome) has been largely overlooked. In this Review, we highlight recent studies that shed light on the mechanisms linking the human gut microbiome to the efficacy and toxicity of xenobiotics, including drugs, dietary compounds and environmental toxins. Continued progress in this area could enable more precise tools for predicting patient responses and the development of a next generation of therapeutics based on or targeted at the gut microbiome. Indeed, the admirable goal of precision medicine may require us to first understand the microbial pharmacists within. PMID:26972811

  9. Investigating microbial diversity and UV radiation impact at the high-altitude Lake Aguas Calientes, Chile

    Science.gov (United States)

    Escudero, Lorena; Chong, Guillermo; Demergasso, Cecilia; Farías, María Eugenia; Cabrol, Nathalie A.; Grin, Edmond; Minkley, Edwin, Jr.; Yu, Yeoungeob

    2007-09-01

    The High-Lakes Project is funded by the NAI and explores the highest perennial volcanic lakes on Earth in the Bolivian and Chilean Andes, including several lakes ~6,000 m elevation. These lakes represent an opportunity to study the evolution of microbial organisms in relatively shallow waters not providing substantial protection against UV radiation. Aguas Calientes (5,870 m) was investigated (November 2006) and samples of water and sediment collected at 1, 3, 5, and 10 cm depth. An Eldonet UV dosimeter positioned on the shore records UV radiation and temperature, and is logging data year round. A UV SolarLight sensor allowed acquisition of point measurements in all channels at the time of the sampling. UVA, UVB, and PAR peaks between 11:00 am and 1:00 pm reached 7.7 mW/cm2, 48.5 μW/cm2, and 511 W/m2, respectively. The chemical composition of the water sample was analyzed. DNA was extracted and DGGE analyses with bacterial and archaeal 16S fragments were performed to describe microbial diversity. Antibiotic resistances were established previously in similar environments in Argentine Andean wetlands. In order to determine these resistances in our samples, they were inoculated onto LB and R2A media and onto R2A medium containing either chloramphenicol, ampicillin or tetracycline. Bacterial was higher than archeal cell number determined by RT-PCR in all the samples, reaching maximum total values of 5x10 5 cell mL-1. DGGE results from these samples and Licancabur summit lake (5,916 m) samples were also compared. Eight antibiotic-resistant Gram negative strains have been isolated with distinct resistance patterns.

  10. Microbial quality of reclaimed water for urban reuses: Probabilistic risk-based investigation and recommendations.

    Science.gov (United States)

    Chhipi-Shrestha, Gyan; Hewage, Kasun; Sadiq, Rehan

    2017-01-15

    Although Canada has abundant freshwater resources, many cities still experience seasonal water shortage. Supply-side and demand-side management is a core strategy to address this water shortage. Under this strategy, reclaimed water, which the Canadian public is willing to use for non-potable purposes, is an option. However, no universal guidelines exist for reclaimed water use. Despite the federal government's long-term goal to develop guidelines for many water reuse applications, guidelines have only been prescribed for reclaimed water use in toilet and urinal flushing in Canada. At the provincial level, British Columbia (BC) has promulgated guidelines for wide applications of reclaimed water but only at broad class levels. This research has investigated and proposed probabilistic risk-based recommended values for microbial quality of reclaimed water in various non-potable urban reuses. The health risk was estimated by using quantitative microbial risk assessment. Two-dimensional Monte Carlo simulations were used in the analysis to include variability and uncertainty in input data. The proposed recommended values are based on the indicator organism E. coli. The required treatment levels for reuse were also estimated. In addition, the recommended values were successfully applied to three wastewater treatment effluents in the Okanagan Valley, BC, Canada. The health risks associated with other bacterial pathogens (Campylobacter jejuni and Salmonella spp.), virus (adenovirus, norovirus, and rotavirus), and protozoa (Cryptosporidium parvum and Giardia spp.), were also estimated. The estimated risks indicate the effectiveness of the E. coli-based water quality recommended values. Sensitivity analysis shows the pathogenic E. coli ratio and morbidity are the most sensitive input parameters for all water reuses. The proposed recommended values could be further improved by using national or regional data on water exposures, disease burden per case, and the susceptibility

  11. Effects of experimental warming and clipping on metabolic change of microbial community in a US Great Plains tallgrass prairie

    Energy Technology Data Exchange (ETDEWEB)

    Xie, Jianping; Liu, Xinxing; Liu, Xueduan; Nostrand, Joy D. Van; Deng, Ye; Wu, Liyou; He, Zhili; Qiu, Guanzhou; Zhou, Jizhong

    2010-05-17

    While more and more studies are being conducted on the effects of global warming, little is known regarding the response of metabolic change of whole soil microbial communities to this phenomenon. In this study, functional gene changes at the mRNA level were analyzed by our new developed GeoChip 3.0. Soil samples were taken from a long-term climate warming experiment site, which has been conducted for ~;;8 years at the Kessler Farm Field Laboratory, a 137.6-ha farm located in the Central Redbed Plains, in McClain County, Oklahoma. The experiment uses a paired factorial design with warming as the primary factor nested with clipping as a secondary factor. An infrared heater was used to simulate global warming, and clipping was used to mimic mowing hay. Twelve 2m x 2m plots were divided into six pairs of warmed and control plots. The heater generates a constant output of ~;;100 Watts m-2 to approximately 2 oC increase in soil temperature above the ambient plots, which is at the low range of the projected climate warming by IPCC. Soil whole microbial communities? mRNA was extracted, amplified, labeled and hybridized with our GeoChip 3.0, a functional gene array covering genes involved in N, C, P, and S cycling, metal resistance and contaminant degradation, to examine expressed genes. The results showed that a greater number and higher diversity of genes were expressed under warmed plots compared to control. Detrended correspondence analysis (DCA) of all detected genes showed that the soil microbial communities were clearly altered by warming, with or without clipping. The dissimilarity of the communities based on functional genes was tested and results showed that warming and control communities were significantly different (P<0.05), with or without clipping. Most genes involved in C, N, P and S cycling were expressed at higher levels in warming samples compared to control samples. All of the results demonstrated that the whole microbial communities increase functional

  12. Investigating Connections between Metabolism, Longevity, and Behavior in Caenorhabditis elegans.

    Science.gov (United States)

    Lemieux, George A; Ashrafi, Kaveh

    2016-08-01

    An overview of Caenorhabditis elegans as an experimental organism for studying energy balance is presented. Some of the unresolved questions that complicate the interpretation of lipid measurements from C. elegans are highlighted. We review studies that show that both lipid synthesis and lipid breakdown pathways are activated and needed for the longevity of hermaphrodites that lack their germlines. These findings illustrate the heterogeneity of triglyceride-rich lipid particles in C. elegans and reveal specific lipid signals that promote longevity. Finally, we provide a brief overview of feeding behavioral responses of C. elegans to varying nutritional conditions and highlight an unanticipated metabolic pathway that allows the incorporation of experience in feeding behavior. Copyright © 2016 Elsevier Ltd. All rights reserved.

  13. Investigation of glycerol assimilation and cofactor metabolism in Lactococcus lactis

    DEFF Research Database (Denmark)

    Holm, Anders Koefoed

    : anaerobic, aerobic and respiration permissive growth in combination with either glycerol as a sole substrate or with co-metabolization of glycerol with common sugar substrates. Although no growth on glycerol was seen, both positive and detrimental effects were observed from cultures with glycerol...... itself under both anaerobic and respiration permissive conditions, but was not found to have the same profound effect on other sugar substrates such as galactose or ribose. Supplementation of nucleosides to the growth medium or increased substrate concentration were found to counteract the inhibitory...... of glycerol kinase from L. lactis, introduction of a heterologous glycerol assimilation pathway and construction of a library of NADH oxidase activity. Based on a preliminary analysis of transcription level data, an attempt was made to stimulate glycerol assimilation by overexpressing the glycerol kinase...

  14. Mining metagenomic and metatranscriptomic data for clues about microbial metabolic functions in ruminants.

    Science.gov (United States)

    Li, Fuyong; Neves, Andre L A; Ghoshal, Bibaswan; Guan, Le Luo

    2017-12-20

    Metagenomics and metatranscriptomics can capture the whole genome and transcriptome repertoire of microorganisms through sequencing total DNA/RNA from various environmental samples, providing both taxonomic and functional information with high resolution. The unique and complex rumen microbial ecosystem is receiving great research attention because the rumen microbiota coevolves with the host and equips ruminants with the ability to convert cellulosic plant materials to high-protein products for human consumption. To date, hundreds to thousands of microbial phylotypes have been identified in the rumen using culture-independent molecular-based approaches, and genomic information of rumen microorganisms is rapidly accumulating through the single genome sequencing. However, functional characteristics of the rumen microbiome have not been well described because there are numerous uncultivable microorganisms in the rumen. The advent of metagenomics and metatranscriptomics along with advanced bioinformatics methods can help us better understand mechanisms of the rumen fermentation, which is vital for improving nutrient utilization and animal productivity. Therefore, in this review, we summarize a general workflow to conduct rumen metagenomics and metatranscriptomics and discuss how the data can be interpreted to be useful information. Moreover, we review recent literatures studying associations between the rumen microbiome and host phenotypes (e.g., feed efficiency and methane emissions) using these approaches, aiming to provide a useful guide to include studying the rumen microbiome as one of the research objectives using these 2 approaches. Copyright © 2018 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

  15. Effects of wastewater treatment plant effluent inputs on planktonic metabolic rates and microbial community composition in the Baltic Sea

    Science.gov (United States)

    Vaquer-Sunyer, Raquel; Reader, Heather E.; Muthusamy, Saraladevi; Lindh, Markus V.; Pinhassi, Jarone; Conley, Daniel J.; Kritzberg, Emma S.

    2016-08-01

    The Baltic Sea is the world's largest area suffering from eutrophication-driven hypoxia. Low oxygen levels are threatening its biodiversity and ecosystem functioning. The main causes for eutrophication-driven hypoxia are high nutrient loadings and global warming. Wastewater treatment plants (WWTP) contribute to eutrophication as they are important sources of nitrogen to coastal areas. Here, we evaluated the effects of wastewater treatment plant effluent inputs on Baltic Sea planktonic communities in four experiments. We tested for effects of effluent inputs on chlorophyll a content, bacterial community composition, and metabolic rates: gross primary production (GPP), net community production (NCP), community respiration (CR) and bacterial production (BP). Nitrogen-rich dissolved organic matter (DOM) inputs from effluents increased bacterial production and decreased primary production and community respiration. Nutrient amendments and seasonally variable environmental conditions lead to lower alpha-diversity and shifts in bacterial community composition (e.g. increased abundance of a few cyanobacterial populations in the summer experiment), concomitant with changes in metabolic rates. An increase in BP and decrease in CR could be caused by high lability of the DOM that can support secondary bacterial production, without an increase in respiration. Increases in bacterial production and simultaneous decreases of primary production lead to more carbon being consumed in the microbial loop, and may shift the ecosystem towards heterotrophy.

  16. ReacKnock: identifying reaction deletion strategies for microbial strain optimization based on genome-scale metabolic network.

    Directory of Open Access Journals (Sweden)

    Zixiang Xu

    Full Text Available Gene knockout has been used as a common strategy to improve microbial strains for producing chemicals. Several algorithms are available to predict the target reactions to be deleted. Most of them apply mixed integer bi-level linear programming (MIBLP based on metabolic networks, and use duality theory to transform bi-level optimization problem of large-scale MIBLP to single-level programming. However, the validity of the transformation was not proved. Solution of MIBLP depends on the structure of inner problem. If the inner problem is continuous, Karush-Kuhn-Tucker (KKT method can be used to reformulate the MIBLP to a single-level one. We adopt KKT technique in our algorithm ReacKnock to attack the intractable problem of the solution of MIBLP, demonstrated with the genome-scale metabolic network model of E. coli for producing various chemicals such as succinate, ethanol, threonine and etc. Compared to the previous methods, our algorithm is fast, stable and reliable to find the optimal solutions for all the chemical products tested, and able to provide all the alternative deletion strategies which lead to the same industrial objective.

  17. Investigating the long-term legacy of drought and warming on the soil microbial community across five European shrubland ecosystems.

    Science.gov (United States)

    Rousk, Johannes; Smith, Andrew R; Jones, Davey L

    2013-12-01

    We investigated how the legacy of warming and summer drought affected microbial communities in five different replicated long-term (>10 years) field experiments across Europe (EU-FP7 INCREASE infrastructure). To focus explicitly on legacy effects (i.e., indirect rather than direct effects of the environmental factors), we measured microbial variables under the same moisture and temperature in a brief screening, and following a pre-incubation at stable conditions. Specifically, we investigated the size and composition of the soil microbial community (PLFA) alongside measurements of bacterial (leucine incorporation) and fungal (acetate in ergosterol incorporation) growth rates, previously shown to be highly responsive to changes in environmental factors, and microbial respiration. We found no legacy effects on the microbial community size, composition, growth rates, or basal respiration rates at the effect sizes used in our experimental setup (0.6 °C, about 30% precipitation reduction). Our findings support previous reports from single short-term ecosystem studies thereby providing a clear evidence base to allow long-term, broad-scale generalizations to be made. The implication of our study is that warming and summer drought will not result in legacy effects on the microbial community and their processes within the effect sizes here studied. While legacy effects on microbial processes during perturbation cycles, such as drying-rewetting, and on tolerance to drought and warming remain to be studied, our results suggest that any effects on overall ecosystem processes will be rather limited. Thus, the legacies of warming and drought should not be prioritized factors to consider when modeling contemporary rates of biogeochemical processes in soil. © 2013 John Wiley & Sons Ltd.

  18. LC-MS-Based Metabolomic Investigation of Chemopreventive Phytochemical-Elicited Metabolic Events.

    Science.gov (United States)

    Wang, Lei; Yao, Dan; Chen, Chi

    2016-01-01

    Phytochemicals are under intensive investigation for their potential use as chemopreventive agents in blocking or suppressing carcinogenesis. Metabolic interactions between phytochemical and biological system play an important role in determining the efficacy and toxicity of chemopreventive phytochemicals. However, complexities of phytochemical biotransformation and intermediary metabolism pose challenges for studying phytochemical-elicited metabolic events. Metabolomics has become a highly effective technical platform to detect subtle changes in a complex metabolic system. Here, using green tea polyphenols as an example, we describe a workflow of LC-MS-based metabolomics study, covering the procedures and techniques in sample collection, preparation, LC-MS analysis, data analysis, and interpretation.

  19. Profiling of Indigenous Microbial Community Dynamics and Metabolic Activity During Enrichment in Molasses-Supplemented Crude Oil-Brine Mixtures for Improved Understanding of Microbial Enhanced Oil Recovery

    DEFF Research Database (Denmark)

    Halim, Amalia Yunita; Pedersen, Dorthe Skou; Nielsen, Sidsel Marie

    2015-01-01

    Anaerobic incubations using crude oil and brine from a North Sea reservoir were conducted to gain increased understanding of indigenous microbial community development, metabolite production, and the effects on the oil–brine system after addition of a complex carbon source, molasses....... The microbial growth caused changes in the crude oil–brine system: formation of oil emulsions, and reduction of interfacial tension (IFT). Reduction in IFT was associated with microbes being present at the oil–brine interphase. These findings suggest that stimulation of indigenous microbial growth by addition...... of molasses has potential as microbial enhanced oil recovery (MEOR) strategy in North Sea oil reservoirs....

  20. Framework for network modularization and Bayesian network analysis to investigate the perturbed metabolic network.

    Science.gov (United States)

    Kim, Hyun Uk; Kim, Tae Yong; Lee, Sang Yup

    2011-01-01

    Genome-scale metabolic network models have contributed to elucidating biological phenomena, and predicting gene targets to engineer for biotechnological applications. With their increasing importance, their precise network characterization has also been crucial for better understanding of the cellular physiology. We herein introduce a framework for network modularization and Bayesian network analysis (FMB) to investigate organism's metabolism under perturbation. FMB reveals direction of influences among metabolic modules, in which reactions with similar or positively correlated flux variation patterns are clustered, in response to specific perturbation using metabolic flux data. With metabolic flux data calculated by constraints-based flux analysis under both control and perturbation conditions, FMB, in essence, reveals the effects of specific perturbations on the biological system through network modularization and Bayesian network analysis at metabolic modular level. As a demonstration, this framework was applied to the genetically perturbed Escherichia coli metabolism, which is a lpdA gene knockout mutant, using its genome-scale metabolic network model. After all, it provides alternative scenarios of metabolic flux distributions in response to the perturbation, which are complementary to the data obtained from conventionally available genome-wide high-throughput techniques or metabolic flux analysis.

  1. Selection and application of microbial source tracking tools for water-quality investigations

    Science.gov (United States)

    Stoeckel, Donald M.

    2005-01-01

    Microbial source tracking (MST) is a complex process that includes many decision-making steps. Once a contamination problem has been defined, the potential user of MST tools must thoroughly consider study objectives before deciding upon a source identifier, a detection method, and an analytical approach to apply to the problem. Regardless of which MST protocol is chosen, underlying assumptions can affect the results and interpretation. It is crucial to incorporate tests of those assumptions in the study quality-control plan to help validate results and facilitate interpretation. Detailed descriptions of MST objectives, protocols, and assumptions are provided in this report to assist in selection and application of MST tools for water-quality investigations. Several case studies illustrate real-world applications of MST protocols over a range of settings, spatial scales, and types of contamination. Technical details of many available source identifiers and detection methods are included as appendixes. By use of this information, researchers should be able to formulate realistic expectations for the information that MST tools can provide and, where possible, successfully execute investigations to characterize sources of fecal contamination to resource waters.

  2. [Engineering of the xylose metabolic pathway for microbial production of bio-based chemicals].

    Science.gov (United States)

    Liu, Weixi; Fu, Jing; Zhang, Bo; Chen, Tao

    2013-08-01

    As the rapid development of economy necessitates a large number of oil, the contradiction between energy supply and demand is further exacerbated by the dwindling reserves of petroleum resource. Therefore, the research of the renewable cellulosic biomass resources is gaining unprecedented momentum. Because xylose is the second most abundant monosaccharide after glucose in lignocellulose hydrolyzes, high-efficiency bioconversion of xylose becomes one of the vital factors that affect the industrial prospects of lignocellulose application. According to the research progresses in recent years, this review summarized the advances in bioconversion of xylose, which included identification and redesign of the xylose metabolic pathway, engineering the xylose transport pathway and bio-based chemicals production. In order to solve the energy crisis and environmental pollution issues, the development of advanced bio-fuel technology, especially engineering the microbe able to metabolize xylose and produce ethanol by synthetic biology, is environmentally benign and sustainable.

  3. Effect of lineage-specific metabolic traits of Lactobacillus reuteri on sourdough microbial ecology.

    Science.gov (United States)

    Lin, Xiaoxi B; Gänzle, Michael G

    2014-09-01

    This study determined the effects of specific metabolic traits of Lactobacillus reuteri on its competitiveness in sourdoughs. The competitiveness of lactobacilli in sourdough generally depends on their growth rate; acid resistance additionally contributes to competitiveness in sourdoughs with long fermentation times. Glycerol metabolism via glycerol dehydratase (gupCDE) accelerates growth by the regeneration of reduced cofactors; glutamate metabolism via glutamate decarboxylase (gadB) increases acid resistance by generating a proton motive force. Glycerol and glutamate metabolisms are lineage-specific traits in L. reuteri; therefore, this study employed glycerol dehydratase-positive sourdough isolates of human-adapted L. reuteri lineage I, glutamate decarboxylase-positive strains of rodent-adapted L. reuteri lineage II, as well as mutants with deletions in gadB or gupCDE. The competitivenesses of the strains were quantified by inoculation of wheat and sorghum sourdoughs with defined strains, followed by propagation of doughs with a 10% inoculum and 12-h or 72-h fermentation cycles. Lineage I L. reuteri strains dominated sourdoughs propagated with 12-h fermentation cycles; lineage II L. reuteri strains dominated sourdoughs propagated with 72-h fermentation cycles. L. reuteri 100-23ΔgadB was outcompeted by its wild-type strain in sourdoughs fermented with 72-h fermentation cycles; L. reuteri FUA3400ΔgupCDE was outcompeted by its wild-type strain in sourdoughs fermented with both 12-h and 72-h fermentation cycles. Competition experiments with isogenic pairs of strains resulted in a constant rate of strain displacement of the less competitive mutant strain. In conclusion, lineage-specific traits of L. reuteri determine the competitiveness of this species in sourdough fermentations. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

  4. The Microbial Hypothesis: Contributions of Adenovirus Infection and Metabolic Endotoxaemia to the Pathogenesis of Obesity

    OpenAIRE

    Tambo, Amos; Roshan, Mohsin H. K.; Pace, Nikolai P.

    2016-01-01

    The global obesity epidemic, dubbed “globesity” by the World Health Organisation, is a pressing public health issue. The aetiology of obesity is multifactorial incorporating both genetic and environmental factors. Recently, epidemiological studies have observed an association between microbes and obesity. Obesity-promoting microbiome and resultant gut barrier disintegration have been implicated as key factors facilitating metabolic endotoxaemia. This is an influx of bacterial endotoxins into ...

  5. Shifts in coastal sediment oxygenation cause pronounced changes in microbial community composition and associated metabolism

    DEFF Research Database (Denmark)

    Broman, Elias; Sjöstedt, Johanna; Pinhassi, Jarone

    2017-01-01

    in the sediment surface. Compared to anoxic controls, oxygenation of anoxic sediment resulted in a proliferation of bacterial populations in the facultative anaerobic genus Sulfurovum that are capable of oxidizing toxic sulfide. Furthermore, the oxygenated sediment had higher amounts of RNA transcripts annotated....... In particular, the intermediate site sediments responded differently upon oxygenation compared to the anoxic and oxic site sediments. This included a microbial community composition with more habitat generalists, lower amounts of RNA transcripts attributed to methane oxidation, and a reduced rate of organic......A key characteristic of eutrophication in coastal seas is the expansion of hypoxic bottom waters, often referred to as 'dead zones'. One proposed remediation strategy for coastal dead zones in the Baltic Sea is to mix the water column using pump stations, circulating oxygenated water to the sea...

  6. The effect of saccharin on the microbial metabolism of tryptophan in man.

    Science.gov (United States)

    Roberts, A; Renwick, A G

    1985-01-01

    The microbial catabolism of tryptophan to indole has been studied in 15 human subjects by analysis of the daily urinary excretion of indican (potassium indoxylsulphate) before, during and after chronic saccharin ingestion. The daily excretion of indican during a 3-wk control period showed marked inter- and intra-subject variability. Analysis of the urinary excretion of saccharin during chronic administration demonstrated good compliance for both saccharin ingestion and urine collection. The urinary excretion of indican was not increased significantly by the ingestion of saccharin (1 g/day as divided doses with meals) for one month. These findings are consistent with epidemiology studies which show the absence of a consistent excess risk of cancer of the urinary bladder in humans ingesting saccharin as a food additive.

  7. Marking of metabolites in the diagnostics of metabolic diseases and in the investigation of xenobiotics metabolism using NMR spectroscopy.

    Science.gov (United States)

    Krawczyk, Hanna

    2016-10-25

    There are currently no sound estimates of the number of children born with a serious congenital disorder attributable to genetic or environmental causes (World Health Organization) but there is a supposed number of babies born with birth defects per year: in the world approximately 7.9 million children (6% of births). There is conducted population-based screening by the individual countries. The specialised methods are used when it is not possible to diagnose disease in screening. In recent years in the diagnostics of these disorders the methods of Magnetic Resonance Spectroscopy of the brain (in vivo 1 H-MRS) and high resolution NMR spectroscopy gain in importance. The manuscript focused on developing the method of marking the metabolic diseases markers of various origins using NMR spectroscopy (including synthesis of markers). Considering the disorders occurring among children, according to Hoffman, Zschocke, Nyhan, there are three following groups of inherited metabolic diseases: disorders of intermediary metabolism, disorders of the biosynthesis and breakdown of complex molecules and neurotransmitter defects and related disorders. The presented investigation is focused on: a study of selected compounds that cause disorders of intermediary metabolism, a study of compounds that cause disorders of the biosynthesis and breakdown of complex molecules and a study of compounds that cause neurotransmitter defects and related disorders. In the subsequent chapter of manuscript there are presented the results of investigation concerning the metabolism of xenobiotics that could potentially be used in therapy of inherited metabolic diseases, basing on stilbene derivatives. In the last chapter there are presented the results of experiments with creatinine- the metabolite produced in muscles. Copyright © 2016 Elsevier B.V. All rights reserved.

  8. Inhibition of microbial metabolism in anaerobic lagoons by selected sulfonamides, tetracyclines, lincomycin, and tylosin tartrate

    Science.gov (United States)

    Loftin, Keith A.; Henny, Cynthia; Adams, Craig D.; Surampali, Rao; Mormile, Melanie R.

    2005-01-01

    Antibiotics are used to maintain healthy livestock and to promote weight gain in concentrated animal feed operations. Antibiotics rarely are metabolized completely by livestock and, thus, are often present in livestock waste and in waste-treatment lagoons. The introduction of antibiotics into anaerobic lagoons commonly used for swine waste treatment has the potential for negative impacts on lagoon performance, which relies on a consortium of microbes ranging from fermentative microorganisms to methanogens. To address this concern, the effects of eight common veterinary antibiotics on anaerobic activity were studied. Anaerobic microcosms, prepared from freshly collected lagoon slurries, were amended with individual antibiotics at 10 mg/L for the initial screening study and at 1, 5, and 25 mg/L for the dose-response study. Monitored metabolic indicators included hydrogen, methane, and volatile fatty acid concentrations as well as chemical oxygen demand. The selected antibiotics significantly inhibited methane production relative to unamended controls, thus indicating that antibiotics at concentrations commonly found in swine lagoons can negatively impact anaerobic metabolism. Additionally, historical antibiotic usage seems to be a potential factor in affecting methane production. Specifically, less inhibition of methane production was noted in samples taken from the lagoon with a history of multiple-antibiotic use.

  9. Distributing a metabolic pathway among a microbial consortium enhances production of natural products.

    Science.gov (United States)

    Zhou, Kang; Qiao, Kangjian; Edgar, Steven; Stephanopoulos, Gregory

    2015-04-01

    Metabolic engineering of microorganisms such as Escherichia coli and Saccharomyces cerevisiae to produce high-value natural metabolites is often done through functional reconstitution of long metabolic pathways. Problems arise when parts of pathways require specialized environments or compartments for optimal function. Here we solve this problem through co-culture of engineered organisms, each of which contains the part of the pathway that it is best suited to hosting. In one example, we divided the synthetic pathway for the acetylated diol paclitaxel precursor into two modules, expressed in either S. cerevisiae or E. coli, neither of which can produce the paclitaxel precursor on their own. Stable co-culture in the same bioreactor was achieved by designing a mutualistic relationship between the two species in which a metabolic intermediate produced by E. coli was used and functionalized by yeast. This synthetic consortium produced 33 mg/L oxygenated taxanes, including a monoacetylated dioxygenated taxane. The same method was also used to produce tanshinone precursors and functionalized sesquiterpenes.

  10. Comparative multi-goal tradeoffs in systems engineering of microbial metabolism

    Science.gov (United States)

    2012-01-01

    Background Metabolic engineering design methodology has evolved from using pathway-centric, random and empirical-based methods to using systems-wide, rational and integrated computational and experimental approaches. Persistent during these advances has been the desire to develop design strategies that address multiple simultaneous engineering goals, such as maximizing productivity, while minimizing raw material costs. Results Here, we use constraint-based modeling to systematically design multiple combinations of medium compositions and gene-deletion strains for three microorganisms (Escherichia coli, Saccharomyces cerevisiae, and Shewanella oneidensis) and six industrially important byproducts (acetate, D-lactate, hydrogen, ethanol, formate, and succinate). We evaluated over 435 million simulated conditions and 36 engineering metabolic traits, including product rates, costs, yields and purity. Conclusions The resulting metabolic phenotypes can be classified into dominant clusters (meta-phenotypes) for each organism. These meta-phenotypes illustrate global phenotypic variation and sensitivities, trade-offs associated with multiple engineering goals, and fundamental differences in organism-specific capabilities. Given the increasing number of sequenced genomes and corresponding stoichiometric models, we envisage that the proposed strategy could be extended to address a growing range of biological questions and engineering applications. PMID:23009214

  11. Comparative multi-goal tradeoffs in systems engineering of microbial metabolism

    Directory of Open Access Journals (Sweden)

    Byrne David

    2012-09-01

    Full Text Available Abstract Background Metabolic engineering design methodology has evolved from using pathway-centric, random and empirical-based methods to using systems-wide, rational and integrated computational and experimental approaches. Persistent during these advances has been the desire to develop design strategies that address multiple simultaneous engineering goals, such as maximizing productivity, while minimizing raw material costs. Results Here, we use constraint-based modeling to systematically design multiple combinations of medium compositions and gene-deletion strains for three microorganisms (Escherichia coli, Saccharomyces cerevisiae, and Shewanella oneidensis and six industrially important byproducts (acetate, D-lactate, hydrogen, ethanol, formate, and succinate. We evaluated over 435 million simulated conditions and 36 engineering metabolic traits, including product rates, costs, yields and purity. Conclusions The resulting metabolic phenotypes can be classified into dominant clusters (meta-phenotypes for each organism. These meta-phenotypes illustrate global phenotypic variation and sensitivities, trade-offs associated with multiple engineering goals, and fundamental differences in organism-specific capabilities. Given the increasing number of sequenced genomes and corresponding stoichiometric models, we envisage that the proposed strategy could be extended to address a growing range of biological questions and engineering applications.

  12. Investigation the effect of ionizing radiation on the level of microbial contamination and usefulness of selected blends and seasoning

    International Nuclear Information System (INIS)

    Migdal, W.; Owczarczyk, H.B.; Malec-Czechowska, K.

    1998-01-01

    The results of investigations the electron beam irradiation on the microbial contamination of selected blends and seasoning used in meat and milk industry are reported. The irradiation doses applied were not higher than 6.0 kGy. The level of microbial contamination were determined in irradiated and nonirradiated samples by standard methods routinely used. In addition, the usefulness of irradiated samples was examined by methods used for these products. The results obtained show that radiation can be successfully used foe decontamination of blends and seasoning, without changing the quality and applicability of the product. (author)

  13. Suppression of microbial metabolic pathways inhibits the generation of the human body odor component diacetyl by Staphylococcus spp.

    Science.gov (United States)

    Hara, Takeshi; Matsui, Hiroshi; Shimizu, Hironori

    2014-01-01

    Diacetyl (2,3-butanedione) is a key contributor to unpleasant odors emanating from the axillae, feet, and head regions. To investigate the mechanism of diacetyl generation on human skin, resident skin bacteria were tested for the ability to produce diacetyl via metabolism of the main organic acids contained in human sweat. L-lactate metabolism by Staphylococcus aureus and Staphylococcus epidermidis produced the highest amounts of diacetyl, as measured by high-performance liquid chromatography. Glycyrrhiza glabra root extract (GGR) and α-tocopheryl-L-ascorbate-2-O-phosphate diester potassium salt (EPC-K1), a phosphate diester of α-tocopherol and ascorbic acid, effectively inhibited diacetyl formation without bactericidal effects. Moreover, a metabolic flux analysis revealed that GGR and EPC-K1 suppressed diacetyl formation by inhibiting extracellular bacterial conversion of L-lactate to pyruvate or by altering intracellular metabolic flow into the citrate cycle, respectively, highlighting fundamentally distinct mechanisms by GGR and EPC-K1 to suppress diacetyl formation. These results provide new insight into diacetyl metabolism by human skin bacteria and identify a regulatory mechanism of diacetyl formation that can facilitate the development of effective deodorant agents.

  14. Suppression of microbial metabolic pathways inhibits the generation of the human body odor component diacetyl by Staphylococcus spp.

    Directory of Open Access Journals (Sweden)

    Takeshi Hara

    Full Text Available Diacetyl (2,3-butanedione is a key contributor to unpleasant odors emanating from the axillae, feet, and head regions. To investigate the mechanism of diacetyl generation on human skin, resident skin bacteria were tested for the ability to produce diacetyl via metabolism of the main organic acids contained in human sweat. L-lactate metabolism by Staphylococcus aureus and Staphylococcus epidermidis produced the highest amounts of diacetyl, as measured by high-performance liquid chromatography. Glycyrrhiza glabra root extract (GGR and α-tocopheryl-L-ascorbate-2-O-phosphate diester potassium salt (EPC-K1, a phosphate diester of α-tocopherol and ascorbic acid, effectively inhibited diacetyl formation without bactericidal effects. Moreover, a metabolic flux analysis revealed that GGR and EPC-K1 suppressed diacetyl formation by inhibiting extracellular bacterial conversion of L-lactate to pyruvate or by altering intracellular metabolic flow into the citrate cycle, respectively, highlighting fundamentally distinct mechanisms by GGR and EPC-K1 to suppress diacetyl formation. These results provide new insight into diacetyl metabolism by human skin bacteria and identify a regulatory mechanism of diacetyl formation that can facilitate the development of effective deodorant agents.

  15. Specific dietary preferences are linked to differing gut microbial metabolic activity in response to dark chocolate intake.

    Science.gov (United States)

    Martin, Francois-Pierre J; Montoliu, Ivan; Nagy, Kornél; Moco, Sofia; Collino, Sebastiano; Guy, Philippe; Redeuil, Karine; Scherer, Max; Rezzi, Serge; Kochhar, Sunil

    2012-12-07

    Systems biology approaches are providing novel insights into the role of nutrition for the management of health and disease. In the present study, we investigated if dietary preference for dark chocolate in healthy subjects may lead to different metabolic response to daily chocolate consumption. Using NMR- and MS-based metabolic profiling of blood plasma and urine, we monitored the metabolic response of 10 participants stratified as chocolate desiring and eating regularly dark chocolate (CD) and 10 participants stratified as chocolate indifferent and eating rarely dark chocolate (CI) to a daily consumption of 50 g of dark chocolate as part of a standardized diet over a one week period. We demonstrated that preference for chocolate leads to different metabolic response to chocolate consumption. Daily intake of dark chocolate significantly increased HDL cholesterol by 6% and decreased polyunsaturated acyl ether phospholipids. Dark chocolate intake could also induce an improvement in the metabolism of long chain fatty acid, as noted by a compositional change in plasma fatty acyl carnitines. Moreover, a relationship between regular long-term dietary exposure to a small amount of dark chocolate, gut microbiota, and phenolics was highlighted, providing novel insights into biological processes associated with cocoa bioactives.

  16. Investigation of Microbial Diversity in Geothermal Hot Springs in Unkeshwar, India, Based on 16S rRNA Amplicon Metagenome Sequencing.

    Science.gov (United States)

    Mehetre, Gajanan T; Paranjpe, Aditi; Dastager, Syed G; Dharne, Mahesh S

    2016-02-25

    Microbial diversity in geothermal waters of the Unkeshwar hot springs in Maharashtra, India, was studied using 16S rRNA amplicon metagenomic sequencing. Taxonomic analysis revealed the presence of Bacteroidetes, Proteobacteria, Cyanobacteria, Actinobacteria, Archeae, and OD1 phyla. Metabolic function prediction analysis indicated a battery of biological information systems indicating rich and novel microbial diversity, with potential biotechnological applications in this niche. Copyright © 2016 Mehetre et al.

  17. Massively multiplexed microbial identification using resequencing DNA microarrays for outbreak investigation

    Science.gov (United States)

    Leski, T. A.; Ansumana, R.; Jimmy, D. H.; Bangura, U.; Malanoski, A. P.; Lin, B.; Stenger, D. A.

    2011-06-01

    Multiplexed microbial diagnostic assays are a promising method for detection and identification of pathogens causing syndromes characterized by nonspecific symptoms in which traditional differential diagnosis is difficult. Also such assays can play an important role in outbreak investigations and environmental screening for intentional or accidental release of biothreat agents, which requires simultaneous testing for hundreds of potential pathogens. The resequencing pathogen microarray (RPM) is an emerging technological platform, relying on a combination of massively multiplex PCR and high-density DNA microarrays for rapid detection and high-resolution identification of hundreds of infectious agents simultaneously. The RPM diagnostic system was deployed in Sierra Leone, West Africa in collaboration with Njala University and Mercy Hospital Research Laboratory located in Bo. We used the RPM-Flu microarray designed for broad-range detection of human respiratory pathogens, to investigate a suspected outbreak of avian influenza in a number of poultry farms in which significant mortality of chickens was observed. The microarray results were additionally confirmed by influenza specific real-time PCR. The results of the study excluded the possibility that the outbreak was caused by influenza, but implicated Klebsiella pneumoniae as a possible pathogen. The outcome of this feasibility study confirms that application of broad-spectrum detection platforms for outbreak investigation in low-resource locations is possible and allows for rapid discovery of the responsible agents, even in cases when different agents are suspected. This strategy enables quick and cost effective detection of low probability events such as outbreak of a rare disease or intentional release of a biothreat agent.

  18. An Investigation of Microbial Contamination of Animal Butter at the Market Level in Zanjan

    Directory of Open Access Journals (Sweden)

    Hassan Hassanzadazar

    2017-12-01

    Full Text Available Background: Butter is one of the oldest dairy products known in the world and plays an important role in human nutrition. The aim of this study was evaluating of the microbial quality of traditional and industrial butter marketed in Zanjan. Methods: In this descriptive cross-sectional study, a total of 29 samples of butter were investigated in 2 groups which 24 samples were of traditionally producedl butter and 5 industrially produced butter samples, randomly collected from the market in Zanjan, Iran. All samples were evaluated for total bacterial count, Staphylococci, coliform, fungi and mold. Results: Fourteen samples of traditional butter had higher coliform load than allowed in standards. Eighteen samples were contaminated with Staphylococcus, and mold was found in 8 samples. Also, fifteen samples were contaminated with Escherichia coli. Among the industrial samples, one was contaminated with Staphylococcus aureus but no contamination by coliform, Escherichia coli and mold and mold was observed. Conclusion: 58.33%, 75%, 33.33% and 62.5% of the traditional butter samples had higher coliform, Staphylococcus, mold and E. coli contamination, respectively than standard limit. One of the industrial samples was contaminated with Staphylococcus. It is recommended that higher supervision on the production and distribution of these products is applied.

  19. Detailed investigation of the microbial community in foaming activated sludge reveals novel foam formers

    Science.gov (United States)

    Guo, Feng; Wang, Zhi-Ping; Yu, Ke; Zhang, T.

    2015-01-01

    Foaming of activated sludge (AS) causes adverse impacts on wastewater treatment operation and hygiene. In this study, we investigated the microbial communities of foam, foaming AS and non-foaming AS in a sewage treatment plant via deep-sequencing of the taxonomic marker genes 16S rRNA and mycobacterial rpoB and a metagenomic approach. In addition to Actinobacteria, many genera (e.g., Clostridium XI, Arcobacter, Flavobacterium) were more abundant in the foam than in the AS. On the other hand, deep-sequencing of rpoB did not detect any obligate pathogenic mycobacteria in the foam. We found that unknown factors other than the abundance of Gordonia sp. could determine the foaming process, because abundance of the same species was stable before and after a foaming event over six months. More interestingly, although the dominant Gordonia foam former was the closest with G. amarae, it was identified as an undescribed Gordonia species by referring to the 16S rRNA gene, gyrB and, most convincingly, the reconstructed draft genome from metagenomic reads. Our results, based on metagenomics and deep sequencing, reveal that foams are derived from diverse taxa, which expands previous understanding and provides new insight into the underlying complications of the foaming phenomenon in AS. PMID:25560234

  20. A Web-Based Comparative Genomics Tutorial for Investigating Microbial Genomes

    Directory of Open Access Journals (Sweden)

    Michael Strong

    2009-12-01

    Full Text Available As the number of completely sequenced microbial genomes continues to rise at an impressive rate, it is important to prepare students with the skills necessary to investigate microorganisms at the genomic level. As a part of the core curriculum for first-year graduate students in the biological sciences, we have implemented a web-based tutorial to introduce students to the fields of comparative and functional genomics. The tutorial focuses on recent computational methods for identifying functionally linked genes and proteins on a genome-wide scale and was used to introduce students to the Rosetta Stone, Phylogenetic Profile, conserved Gene Neighbor, and Operon computational methods. Students learned to use a number of publicly available web servers and databases to identify functionally linked genes in the Escherichia coli genome, with emphasis on genome organization and operon structure. The overall effectiveness of the tutorial was assessed based on student evaluations and homework assignments. The tutorial is available to other educators at http://www.doe-mbi.ucla.edu/~strong/m253.php.

  1. Understanding electricity generation in osmotic microbial fuel cells through integrated experimental investigation and mathematical modeling.

    Science.gov (United States)

    Qin, Mohan; Ping, Qingyun; Lu, Yaobin; Abu-Reesh, Ibrahim M; He, Zhen

    2015-11-01

    Osmotic microbial fuel cells (OsMFCs) are a new type of MFCs with integrating forward osmosis (FO). However, it is not well understood why electricity generation is improved in OsMFCs compared to regular MFCs. Herein, an approach integrating experimental investigation and mathematical model was adopted to address the question. Both an OsMFC and an MFC achieved similar organic removal efficiency, but the OsMFC generated higher current than the MFC with or without water flux, resulting from the lower resistance of FO membrane. Combining NaCl and glucose as a catholyte demonstrated that the catholyte conductivity affected the electricity generation in the OsMFC. A mathematical model of OsMFCs was developed and validated with the experimental data. The model predicated the variation of internal resistance with increasing water flux, and confirmed the importance of membrane resistance. Increasing water flux with higher catholyte conductivity could decrease the membrane resistance. Copyright © 2015 Elsevier Ltd. All rights reserved.

  2. Polyphenols as enzyme inhibitors in different degraded peat soils: Implication for microbial metabolism in rewetted peatlands

    Science.gov (United States)

    Zak, Dominik; Roth, Cyril; Gelbrecht, Jörg; Fenner, Nathalie; Reuter, Hendrik

    2015-04-01

    Recently, more than 30,000 ha of drained minerotrophic peatlands (= fens) in NE Germany were rewetted to restore their ecological functions. Due to an extended drainage history, a re-establishment of their original state is not expected in the short-term. Elevated concentrations of dissolved organic carbon, ammonium and phosphate have been measured in the soil porewater of the upper degraded peat layers of rewetted fens at levels of one to three orders higher than the values in pristine systems; an indicator of increased microbial activity in the upper degraded soil layers. On the other hand there is evidence that the substrate availability within the degraded peat layer is lowered since the organic matter has formerly been subject to intense decomposition over the decades of drainage and intense agricultural use of the areas. Previously however, it was suggested that inhibition of hydrolytic enzymes by polyphenolic substances is suspended during aeration of peat soils mainly due to the decomposition of the inhibiting polyphenols by oxidising enzymes such as phenol oxidase. Accordingly we hypothesised a lack of enzyme inhibiting polyphenols in degraded peat soils of rewetted fens compared to less decomposed peat of more natural fens. We collected both peat samples at the soil surface (0-20 cm) and fresh roots of dominating vascular plants and mosses (as peat parent material) from five formerly drained rewetted sites and five more natural sites of NE Germany and NW Poland. Less decomposed peat and living roots were used to obtain an internal standard for polyphenol analysis and to run enzyme inhibition tests. For all samples we determined the total phenolic contents and in addition we distinguished between the contents of hydrolysable and condensed tannic substances. From a methodical perspective the advantage of internal standards compared to the commercially available standards cyanidin chloride and tannic acid became apparent. Quantification with cyanidin or

  3. Formate as an energy source for microbial metabolism in chemosynthetic zones of hydrothermal ecosystems.

    Science.gov (United States)

    Windman, Todd; Zolotova, Natalya; Schwandner, Florian; Shock, Everett L

    2007-12-01

    Formate, a simple organic acid known to support chemotrophic hyperthermophiles, is found in hot springs of varying temperature and pH. However, it is not yet known how metabolic strategies that use formate could contribute to primary productivity in hydrothermal ecosystems. In an effort to provide a quantitative framework for assessing the role of formate metabolism, concentration data for dissolved formate and many other solutes in samples from Yellowstone hot springs were used, together with data for coexisting gas compositions, to evaluate the overall Gibbs energy for many reactions involving formate oxidation or reduction. The result is the first rigorous thermodynamic assessment of reactions involving formate oxidation to bicarbonate and reduction to methane coupled with various forms of iron, nitrogen, sulfur, hydrogen, and oxygen for hydrothermal ecosystems. We conclude that there are a limited number of reactions that can yield energy through formate reduction, in contrast to numerous formate oxidation reactions that can yield abundant energy for chemosynthetic microorganisms. Because the energy yields are so high, these results challenge the notion that hydrogen is the primary energy source of chemosynthetic microbes in hydrothermal ecosystems.

  4. Comparative analysis of fecal microbiota and intestinal microbial metabolic activity in captive polar bears.

    Science.gov (United States)

    Schwab, Clarissa; Gänzle, Michael

    2011-03-01

    The composition of the intestinal microbiota depends on gut physiology and diet. Ursidae possess a simple gastrointestinal system composed of a stomach, small intestine, and indistinct hindgut. This study determined the composition and stability of fecal microbiota of 3 captive polar bears by group-specific quantitative PCR and PCR-DGGE (denaturing gradient gel electrophoresis) using the 16S rRNA gene as target. Intestinal metabolic activity was determined by analysis of short-chain fatty acids in feces. For comparison, other Carnivora and mammals were included in this study. Total bacterial abundance was approximately log 8.5 DNA gene copies·(g feces)-1 in all 3 polar bears. Fecal polar bear microbiota was dominated by the facultative anaerobes Enterobacteriaceae and enterococci, and the Clostridium cluster I. The detection of the Clostridium perfringens α-toxin gene verified the presence of C. perfringens. Composition of the fecal bacterial population was stable on a genus level; according to results obtained by PCR-DGGE, dominant bacterial species fluctuated. The total short-chain fatty acid content of Carnivora and other mammals analysed was comparable; lactate was detected in feces of all carnivora but present only in trace amounts in other mammals. In comparison, the fecal microbiota and metabolic activity of captive polar bears mostly resembled the closely related grizzly and black bears.

  5. Single-cell genomics reveal metabolic strategies for microbial growth and survival in an oligotrophic aquifer

    Energy Technology Data Exchange (ETDEWEB)

    Wilkins, Michael J.; Kennedy, David W.; Castelle, Cindy; Field, Erin; Stepanauskas, Ramunas; Fredrickson, Jim K.; Konopka, Allan

    2014-02-09

    Bacteria from the genus Pedobacter are a major component of microbial assemblages at Hanford Site and have been shown to significantly change in abundance in response to the subsurface intrusion of Columbia River water. Here we employed single cell genomics techniques to shed light on the physiological niche of these microorganisms. Analysis of four Pedobacter single amplified genomes (SAGs) from Hanford Site sediments revealed a chemoheterotrophic lifestyle, with the potential to exist under both aerobic and microaerophilic conditions via expression of both aa3­-type and cbb3-type cytochrome c oxidases. These SAGs encoded a wide-range of both intra-and extra­-cellular carbohydrate-active enzymes, potentially enabling the degradation of recalcitrant substrates such as xylan and chitin, and the utilization of more labile sugars such as mannose and fucose. Coupled to these enzymes, a diversity of transporters and sugar-binding molecules were involved in the uptake of carbon from the extracellular local environment. The SAGs were enriched in TonB-dependent receptors (TBDRs), which play a key role in uptake of substrates resulting from degradation of recalcitrant carbon. CRISPR-Cas mechanisms for resisting viral infections were identified in all SAGs. These data demonstrate the potential mechanisms utilized for persistence by heterotrophic microorganisms in a carbon-limited aquifer, and hint at potential linkages between observed Pedobacter abundance shifts within the 300 Area subsurface and biogeochemical shifts associated with Columbia River water intrusion.

  6. Metagenomic Investigation of the Microbial Community Structure and Diversity for Sentinel Coral Reefs and Urbanized Coastal Waters in Southeast Florida, and Molecular Microbial Source Tracking to Characterize Potential LBSP Microbial Contaminant Influences

    Science.gov (United States)

    Sinigalliano, C. D.

    2016-02-01

    Coral reefs and recreational beaches provide critical ecosystem services. However, coastal waters of the Southeast Florida region receive anthropogenic discharges from highly urbanized watersheds via runoff, canals, coastal inlets, and treated wastewater outfalls. There is concern regarding the biological contaminants that enter the coastal zone from land-based sources, especially for viable pathogens and genetic elements that could confer virulence or resistance. Targeted molecular microbial source tracking (MST) by quantitative PCR allows the measurement of specific microbial contaminants such as host-specific fecal indicators. These fecal source markers can help track specific fecal contamination of public health concern in the coastal zone and may also help track exposure of coral reefs to such contamination. A range of pathogens associated with sewage/septic contamination have shown detrimental impact to coral communities, including changes to the biodiversity of coral microbiomes. High-throughput Next-Generation-Sequencing (NGS) and community genomic analysis can provide a comprehensive, culture-independent approach to investigate microbial community diversity in complex environmental samples. The combination of host-specific microbial source tracking by qPCR and metagenomic NGS can provide substantial enhancement to traditional methods of water quality assessment to better protect both environmental biodiversity and human health. Reported here is a multifaceted water quality assessment study of three coastal inlets, two treated wastewater outfalls, and four sentinel coral reef communities in the Southeast Florida coastal zone offshore of Miami-Dade and Broward Counties. This study utilized a combination of bi-monthly sampling for nutrients, fecal indicator bacteria, and human-source molecular source tracking to measure specific contaminants of ecosystem and public health concern. In addition, 16S metagenomic analysis using Illumina Next-Generation Sequencing

  7. Investigation of the selenium metabolism in cancer cell lines

    DEFF Research Database (Denmark)

    Lunøe, Kristoffer; Gabel-Jensen, Charlotte; Stürup, Stefan

    2011-01-01

    incubated with cells for 24 h and the induction of cell death was measured using flow cytometry. The amounts of total selenium in cell medium, cell lysate and the insoluble fractions was determined by ICP-MS. Speciation analysis of cellular fractions was performed by reversed phase, anion exchange and size......The aim of this work was to compare different selenium species for their ability to induce cell death in different cancer cell lines, while investigating the underlying chemistry by speciation analysis. A prostate cancer cell line (PC-3), a colon cancer cell line (HT-29) and a leukaemia cell line...... (Jurkat E6-1) were incubated with five selenium compounds representing inorganic as well as organic Se compounds in different oxidation states. Selenomethionine (SeMet), Se-methylselenocysteine (MeSeCys), methylseleninic acid (MeSeA), selenite and selenate in the concentration range 5-100 mu M were...

  8. The Investigation of Decontamination Effects of Ozone Gas on Microbial Load and Essential Oil of Several Medicinal Plants

    Directory of Open Access Journals (Sweden)

    Razieh VALI ASILL

    2013-02-01

    Full Text Available Today, Ozone as a disinfectant method, without putting on the harmful effects on human and plant products, it is alternative common methods for disinfection of plant material. The research as a factorial experiment was conducted on the basis of randomized complete block design with three replications and the effects of Ozone gas on decreasing the microbial load of some important medicinal plants include: Peppermint (Mentha piperita, Summer savory (Satureja hortensis, Indian valerian(Valeriana wallichii, Meliss (Melissa officinalis and Iranian thyme (Zataria multiflora were investigated. Medicinal plants leaves were treated with Ozone gas concentration 0.3, 0.6 and 0.9 ml/L at times of 10 and 30 then total count, coliform and mold and yeast of the samples were studied. The result showed that Ozone gas decreases microbial load of medicinal plants samples. But Ozone gas and Ozone gas in medicinal plants interaction effect had no effect on essential oil content. The lowest and the highest of microbial load were detected in samples treated with concentration of 0.9 ml/L of Ozone gas and control respectively. The highest and the lowest of microbial load were observed in Iranian thyme and Indian valerian respectively. Also result showed that Ozone gas treatment for 30 min had the greatest of effect in reducing the microbial load and 0.9 ml/L Ozone gas concentration had the lowest of microbial load. Results of this survey reflect that the use of Ozone as a method of disinfection for medicinal plants is a decontamination.

  9. Effects of Secondary Plant Metabolites on Microbial Populations: Changes in Community Structure and Metabolic Activity in Contaminated Environments

    Directory of Open Access Journals (Sweden)

    Lucie Musilova

    2016-07-01

    Full Text Available Secondary plant metabolites (SPMEs play an important role in plant survival in the environment and serve to establish ecological relationships between plants and other organisms. Communication between plants and microorganisms via SPMEs contained in root exudates or derived from litter decomposition is an example of this phenomenon. In this review, the general aspects of rhizodeposition together with the significance of terpenes and phenolic compounds are discussed in detail. We focus specifically on the effect of SPMEs on microbial community structure and metabolic activity in environments contaminated by polychlorinated biphenyls (PCBs and polyaromatic hydrocarbons (PAHs. Furthermore, a section is devoted to a complex effect of plants and/or their metabolites contained in litter on bioremediation of contaminated sites. New insights are introduced from a study evaluating the effects of SPMEs derived during decomposition of grapefruit peel, lemon peel, and pears on bacterial communities and their ability to degrade PCBs in a long-term contaminated soil. The presented review supports the “secondary compound hypothesis” and demonstrates the potential of SPMEs for increasing the effectiveness of bioremediation processes.

  10. In vitro investigation of cytochrome P450-mediated metabolism of dietary flavonoids

    DEFF Research Database (Denmark)

    Breinholt, Vibeke; Offord, E.A.; Brouwer, C.

    2002-01-01

    Human and mouse liver microsomes And membranes isolated from Escherichia coli, which expressed cytochrome P450 (CYP) 1A2, 3A4 2C9 or 2D6, were used to investigate CYP-mediated metabolism of five selected dietary flavonoids. In human and mouse liver microsomes kaempferol, apigenin and naringenin...... were hydroxylated at the 3'-position to yield their corresponding analogs quercetin, luteolin and eriodietyol, whereas hesperetin and tamarixetin were demethylated at the 4'-position to yield eriodictyol and quercetin. respectively, Microsomal flavonoid metabolism as potently inhibited by the CYP1A2...... inhibitors. fluvoxamine and alpha-naphthoflavone. Recombinant CYP1A2 as capable of metabolizing all five investigated flavonoids. CYP3A4 recombinant protein did not catalyze hesperetin demethylation. but showed similar metabolic profiles for the remaining compounds, as did human microsomes and recombinant...

  11. Gut microbial metabolism of polyphenols from black tea and red wine/grape juice is source-specific and colon-region dependent.

    Science.gov (United States)

    van Dorsten, F A; Peters, S; Gross, G; Gomez-Roldan, V; Klinkenberg, M; de Vos, R C; Vaughan, E E; van Duynhoven, J P; Possemiers, S; van de Wiele, T; Jacobs, D M

    2012-11-14

    The colonic microbial degradation of a polyphenol-rich black tea extract (BTE) and red wine/grape juice extract (RWGE) was compared in a five-stage in vitro gastrointestinal model (TWINSHIME). Microbial metabolism of BTE and RWGE polyphenols in the TWINSHIME was studied subsequently in single- and continuous-dose experiments. A combination of liquid or gas chromatography with mass spectrometry (LC-MS or GC-MS) and NMR-based metabolic profiling was used to measure selected parent polyphenols, their microbial degradation into phenolic acids, and the production of short-chain fatty acids (SCFAs) in different colon compartments. Acetate production was increased by continuous feeding of BTE but not RWGE. During RWGE feeding, gallic acid and 4-hydroxyphenylpropionic acid remained elevated throughout the colon, while during BTE feeding, they were consumed in the distal colon, while 3-phenylpropionic acid was strongly produced. Gut microbial production of phenolics and SCFAs is dependent on colon location and polyphenol source, which may influence potential health benefits.

  12. Metabolic Effects of a 24-Week Energy-Restricted Intervention Combined with Low or High Dairy Intake in Overweight Women: An NMR-Based Metabolomics Investigation

    Directory of Open Access Journals (Sweden)

    Hong Zheng

    2016-02-01

    Full Text Available We investigated the effect of a 24-week energy-restricted intervention with low or high dairy intake (LD or HD on the metabolic profiles of urine, blood and feces in overweight/obese women by NMR spectroscopy combined with ANOVA-simultaneous component analysis (ASCA. A significant effect of dairy intake was found on the urine metabolome. HD intake increased urinary citrate, creatinine and urea excretion, and decreased urinary excretion of trimethylamine-N-oxide (TMAO and hippurate relative to the LD intake, suggesting that HD intake was associated with alterations in protein catabolism, energy metabolism and gut microbial activity. In addition, a significant time effect on the blood metabolome was attributed to a decrease in blood lipid and lipoprotein levels due to the energy restriction. For the fecal metabolome, a trend for a diet effect was found and a series of metabolites, such as acetate, butyrate, propionate, malonate, cholesterol and glycerol tended to be affected. Overall, even though these effects were not accompanied by a higher weight loss, the present metabolomics data reveal that a high dairy intake is associated with endogenous metabolic effects and effects on gut microbial activity that potentially impact body weight regulation and health. Moreover, ASCA has a great potential for exploring the effect of intervention factors and identifying altered metabolites in a multi-factorial metabolomic study.

  13. Ecological distribution and population physiology defined by proteomics in a natural microbial community

    OpenAIRE

    Mueller, Ryan S.; Denef, Vincent J.; Kalnejais, Linda H.; Suttle, K. Blake; Thomas, Brian C.; Wilmes, Paul; Smith, Richard L.; Nordstrom, D. Kirk; McCleskey, R. Blaine; Shah, Manesh B.; VerBerkmoes, Nathan C.; Hettich, Robert L.; Banfield, Jillian F.

    2010-01-01

    A fundamental question in microbial ecology addresses how organisms regulate their metabolic activities within natural communities as environmental constraints and population structures change. Recent advances in molecular biology have allowed for investigation into the physiology of organisms within natural settings, opening the door to understanding microbial metabolic responses in situ. Here, we have examined how a diverse set of organisms from microbial biofilms alters their protein compl...

  14. An Investigation on Physicochemical and Microbial Water Quality of Swimming Pools in Yazd

    Directory of Open Access Journals (Sweden)

    M Dehvari

    2012-08-01

    Full Text Available Introduction: Disrespect of health regulations and proper disinfection of water and swimming pools is effective in incidence of health problems and transfer of infectious diseases to swimmers. The aim of this research was to investigate water of swimming pools in Yazd city and compare the results with national standards. Methods: In this study, 11 active covered swimming pools of Yazd city were sampled as census. Parameters of temperature, pH, amount of free and Combined chlorine residual, turbidity, alkalinity, hardness, the population of heterotrophic bacteria, Staphylococcus aureus, Pseudomonas aeruginosa, fecal streptococci, and fecal coliforms were studied. Sampling has been conducted every two weaks for 3 months and samples were analyzed under standard procedures. Results: In this research, amount of pH in 84.73%, free residual chlorine in 44.18%, Combined residual chlorine in 72.45%, alkalinity in19.82%, turbidity in 86.36%, hardness in 57.18% and temperature in 13.73% Samples were desirable. The fecal streptococci bacteria was not shown in all the swimming pools and population of heterotrophic bacteria, Staphylococcus aureus, Pseudomonas aeruginosa and fecal coliforms in 56.73%, 93.27%, 79.36% and 91.45% cases were desirable, respectively. Statistical analysis indicated that there is a direct relationship between Water turbidity and population of heterotraphic bacteria. Conclusion: According to the results, the parameters of heterotrophic bacteria population, also the alkalinity and temperature had the least compliant with the standards that shows the necessity for continuous monitoring of physical, chemical and microbial parameters and also control of filtration and disinfection of water condition of swimming pools.

  15. Investigation and Taguchi Optimization of Microbial Fuel Cell Salt Bridge Dimensional Parameters

    Science.gov (United States)

    Sarma, Dhrupad; Barua, Parimal Bakul; Dey, Nabendu; Nath, Sumitro; Thakuria, Mrinmay; Mallick, Synthia

    2018-01-01

    One major problem of two chamber salt bridge microbial fuel cells (MFCs) is the high resistance offered by the salt bridge to anion flow. Many researchers who have studied and optimized various parameters related to salt bridge MFC, have not shed much light on the effect of salt bridge dimensional parameters on the MFC performance. Therefore, the main objective of this research is to investigate the effect of length and cross sectional area of salt bridge and the effect of solar radiation and atmospheric temperature on MFC current output. An experiment has been designed using Taguchi L9 orthogonal array, taking length and cross sectional area of salt bridge as factors having three levels. Nine MFCs were fabricated as per the nine trial conditions. Trials were conducted for 3 days and output current of each of the MFCs along with solar insolation and atmospheric temperature were recorded. Analysis of variance shows that salt bridge length has significant effect both on mean (with 53.90% contribution at 95% CL) and variance (with 56.46% contribution at 87% CL), whereas the effect of cross sectional area of the salt bridge and the interaction of these two factors is significant on mean only (with 95% CL). Optimum combination was found at 260 mm salt bridge length and 506.7 mm2 cross sectional area with 4.75 mA of mean output current. The temperature and solar insolation data when correlated with each of the MFCs average output current, revealed that both external factors have significant impact on MFC current output but the correlation coefficient varies from MFC to MFC depending on salt bridge dimensional parameters.

  16. [Effects of heavy metals pollution on soil microbial communities metabolism and soil enzyme activities in coal mining area of Tongchuan, Shaanxi Province of Northwest China].

    Science.gov (United States)

    Guo, Xing-Liang; Gu, Jie; Chen, Zhi-Xue; Gao, Hua; Qin, Qing-Jun; Sun, Wei; Zhang, Wei-Juan

    2012-03-01

    This paper studied the metabolism of soil microbes, functions of soil microbial communities, and activities of soil enzymes in a coal mining area of Tongchuan. In the coal mining area, the concentrations of soil Cu, Zn, Cd, and Pb were significantly higher than those in the non-mining area, of which, Cd contributed most to the heavy metals pollution. By adopting Biolog method combining with principal component analysis (PCA) and cluster analysis, it was found that the metabolic characteristics of different soil microbial communities varied significantly with increasing soil heavy metals pollution, and the variation was mainly manifested in the metabolic patterns of carbon sources such as saccharides and amino acids. In slightly and moderately polluted soils, the utilization of carbon sources by soil microbial communities was activated; while in heavily polluted soils, the carbon sources utilization was inhibited. The activities of soil urease, protease, alkaline phosphatase, and catalase all tended to decline with intensifying soil heavy metals pollution. The soil urease, protease, alkaline phosphatase, and catalase activities in the coal mining area were 50.5%-65.1%, 19.1%-57.1%, 87.2%-97.5%, and 77.3%-86.0% higher than those in the non-mining area, respectively. The activities of soil sucrase and cellulase were activated in slightly and moderately polluted soils, but inhibited in heavily polluted soils.

  17. Metagenomic signatures of a tropical mining-impacted stream reveal complex microbial and metabolic networks.

    Science.gov (United States)

    Reis, Mariana P; Dias, Marcela F; Costa, Patrícia S; Ávila, Marcelo P; Leite, Laura R; de Araújo, Flávio M G; Salim, Anna C M; Bucciarelli-Rodriguez, Mônica; Oliveira, Guilherme; Chartone-Souza, Edmar; Nascimento, Andréa M A

    2016-10-01

    Bacteria from aquatic ecosystems significantly contribute to biogeochemical cycles, but details of their community structure in tropical mining-impacted environments remain unexplored. In this study, we analyzed a bacterial community from circumneutral-pH tropical stream sediment by 16S rRNA and shotgun deep sequencing. Carrapatos stream sediment, which has been exposed to metal stress due to gold and iron mining (21 [g Fe]/kg), revealed a diverse community, with predominance of Proteobacteria (39.4%), Bacteroidetes (12.2%), and Parcubacteria (11.4%). Among Proteobacteria, the most abundant reads were assigned to neutrophilic iron-oxidizing taxa, such as Gallionella, Sideroxydans, and Mariprofundus, which are involved in Fe cycling and harbor several metal resistance genes. Functional analysis revealed a large number of genes participating in nitrogen and methane metabolic pathways despite the low concentrations of inorganic nitrogen in the Carrapatos stream. Our findings provide important insights into bacterial community interactions in a mining-impacted environment. Copyright © 2016 Elsevier Ltd. All rights reserved.

  18. Bioethanol a Microbial Biofuel Metabolite; New Insights of Yeasts Metabolic Engineering

    Directory of Open Access Journals (Sweden)

    Khaled A. Selim

    2018-03-01

    Full Text Available Scarcity of the non-renewable energy sources, global warming, environmental pollution, and raising the cost of petroleum are the motive for the development of renewable, eco-friendly fuels production with low costs. Bioethanol production is one of the promising materials that can subrogate the petroleum oil, and it is considered recently as a clean liquid fuel or a neutral carbon. Diverse microorganisms such as yeasts and bacteria are able to produce bioethanol on a large scale, which can satisfy our daily needs with cheap and applicable methods. Saccharomyces cerevisiae and Pichia stipitis are two of the pioneer yeasts in ethanol production due to their abilities to produce a high amount of ethanol. The recent focus is directed towards lignocellulosic biomass that contains 30–50% cellulose and 20–40% hemicellulose, and can be transformed into glucose and fundamentally xylose after enzymatic hydrolysis. For this purpose, a number of various approaches have been used to engineer different pathways for improving the bioethanol production with simultaneous fermentation of pentose and hexoses sugars in the yeasts. These approaches include metabolic and flux analysis, modeling and expression analysis, followed by targeted deletions or the overexpression of key genes. In this review, we highlight and discuss the current status of yeasts genetic engineering for enhancing bioethanol production, and the conditions that influence bioethanol production.

  19. Different biochemical mechanisms ensure network-wide balancing of reducing equivalents in microbial metabolism.

    Science.gov (United States)

    Fuhrer, Tobias; Sauer, Uwe

    2009-04-01

    To sustain growth, the catabolic formation of the redox equivalent NADPH must be balanced with the anabolic demand. The mechanisms that ensure such network-wide balancing, however, are presently not understood. Based on 13C-detected intracellular fluxes, metabolite concentrations, and cofactor specificities for all relevant central metabolic enzymes, we have quantified catabolic NADPH production in Agrobacterium tumefaciens, Bacillus subtilis, Escherichia coli, Paracoccus versutus, Pseudomonas fluorescens, Rhodobacter sphaeroides, Sinorhizobium meliloti, and Zymomonas mobilis. For six species, the estimated NADPH production from glucose catabolism exceeded the requirements for biomass synthesis. Exceptions were P. fluorescens, with balanced rates, and E. coli, with insufficient catabolic production, in which about one-third of the NADPH is supplied via the membrane-bound transhydrogenase PntAB. P. versutus and B. subtilis were the only species that appear to rely on transhydrogenases for balancing NADPH overproduction during growth on glucose. In the other four species, the main but not exclusive redox-balancing mechanism appears to be the dual cofactor specificities of several catabolic enzymes and/or the existence of isoenzymes with distinct cofactor specificities, in particular glucose 6-phosphate dehydrogenase. An unexpected key finding for all species, except E. coli and B. subtilis, was the lack of cofactor specificity in the oxidative pentose phosphate pathway, which contrasts with the textbook view of the pentose phosphate pathway dehydrogenases as being NADP+ dependent.

  20. Distance-dependent varieties of microbial community structure and metabolic functions in the rhizosphere of Sedum alfredii Hance during phytoextraction of a cadmium-contaminated soil.

    Science.gov (United States)

    Yang, Wenhao; Zhang, Taoxiang; Lin, Sen; Ni, Wuzhong

    2017-06-01

    The recovery of microbial community and activities is crucial to the remediation of contaminated soils. Distance-dependent variations of microbial community composition and metabolic characteristics in the rhizospheric soil of hyperaccumulator during phytoextraction are poorly understood. A 12-month phytoextraction experiment with Sedum alfredii in a Cd-contaminated soil was conducted. A pre-stratified rhizobox was used for separating sub-layer rhizospheric (0-2, 2-4, 4-6, 6-8, 8-10 mm from the root mat)/bulk soils. Soil microbial structure and function were analyzed by phospholipid fatty acid (PLFA) and MicroResp™ methods. The concentrations of total and specified PLFA biomarkers and the utilization rates for the 14 substrates (organic carbon) in the 0-2-mm sub-layer rhizospheric soil were significantly increased, as well as decreased with the increase in the distance from the root mat. Microbial structure measured by the ratios of different groups of PLFAs such as fungal/bacterial, monounsaturated/saturated, ratios of Gram-positive to Gram-negative (GP/GN) bacterial, and cyclopropyl/monoenoic precursors and 19:0 cyclo/18:1ω7c were significantly changed in the 0-2-mm soil. The PLFA contents and substrate utilization rates were negatively correlated with pH and total, acid-soluble, and reducible fractions of Cd, while positively correlated with labile carbon. The dynamics of microbial community were likely due to root exudates and Cd uptake by S. alfredii. This study revealed the stimulations and gradient changes of rhizosphere microbial community through phytoextraction, as reduced Cd concentration, pH, and increased labile carbons are due to the microbial community responses.

  1. Metabolic versatility of Gram-positive microbial isolates from contaminated river sediments

    International Nuclear Information System (INIS)

    Narancic, Tanja; Djokic, Lidija; Kenny, Shane T.; O’Connor, Kevin E.; Radulovic, Vanja; Nikodinovic-Runic, Jasmina; Vasiljevic, Branka

    2012-01-01

    Highlights: ► Thirty-four isolated Gram-positive bacteria could degrade wide range of aromatic pollutants. ► Nine isolates could grow in the presence of extremely high levels of heavy metals. ► Twelve isolates accumulated polyphosphate, 3 polyhydroxybutyrate, 4 exopolysaccharides. ► The incidence of multiple antibiotic resistance markers among isolates was low. - Abstract: Gram-positive bacteria from river sediments affected by the proximity of a petrochemical industrial site were isolated and characterized with respect to their ability to degrade a wide range of aromatic compounds. In this study we identified metabolically diverse Gram-positive bacteria capable of growth on wide range aromatic compounds in the presence of heavy metals and with the ability to accumulate biopolymers. Thirty-four isolates that were able to use 9 or more common aromatic pollutants, such as benzene, biphenyl, naphthalene etc. as a sole source of carbon and energy included members of Bacillus, Arthrobacter, Rhodococcus, Gordonia, Streptomyces, and Staphylococcus genus. Rhodococcus sp. TN105, Gordonia sp. TN103 and Arthrobacter sp. TN221 were identified as novel strains. Nine isolates were able to grow in the presence of one or more metals (mercury, cadmium, nickel) at high concentration (100 mM). Seven isolates could degrade 15 different aromatic compounds and could grow in the presence of one or more heavy metals. Two of these isolates were resistant to multiple antibiotics including erythromycin and nalidixic acid. One third of isolates could accumulate at least one biopolymer. Twelve isolates (mainly Bacillus sp. and Arthrobacter sp.) accumulated polyphosphate, 3 Bacillus sp. accumulated polyhydroxybutyrate, while 4 isolates could accumulate exopolysaccharides.

  2. Metabolic versatility of Gram-positive microbial isolates from contaminated river sediments

    Energy Technology Data Exchange (ETDEWEB)

    Narancic, Tanja; Djokic, Lidija [Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, P.O. Box 23, 11010 Belgrade (Serbia); Kenny, Shane T.; O' Connor, Kevin E. [School of Biomolecular and Biomedical Sciences, Centre for Synthesis and Chemical Biology, University College Dublin, Belfield, Dublin 4 (Ireland); Radulovic, Vanja [Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, P.O. Box 23, 11010 Belgrade (Serbia); Nikodinovic-Runic, Jasmina, E-mail: jasminanikodinovic@gmail.com [Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, P.O. Box 23, 11010 Belgrade (Serbia); Vasiljevic, Branka [Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, P.O. Box 23, 11010 Belgrade (Serbia)

    2012-05-15

    Highlights: Black-Right-Pointing-Pointer Thirty-four isolated Gram-positive bacteria could degrade wide range of aromatic pollutants. Black-Right-Pointing-Pointer Nine isolates could grow in the presence of extremely high levels of heavy metals. Black-Right-Pointing-Pointer Twelve isolates accumulated polyphosphate, 3 polyhydroxybutyrate, 4 exopolysaccharides. Black-Right-Pointing-Pointer The incidence of multiple antibiotic resistance markers among isolates was low. - Abstract: Gram-positive bacteria from river sediments affected by the proximity of a petrochemical industrial site were isolated and characterized with respect to their ability to degrade a wide range of aromatic compounds. In this study we identified metabolically diverse Gram-positive bacteria capable of growth on wide range aromatic compounds in the presence of heavy metals and with the ability to accumulate biopolymers. Thirty-four isolates that were able to use 9 or more common aromatic pollutants, such as benzene, biphenyl, naphthalene etc. as a sole source of carbon and energy included members of Bacillus, Arthrobacter, Rhodococcus, Gordonia, Streptomyces, and Staphylococcus genus. Rhodococcus sp. TN105, Gordonia sp. TN103 and Arthrobacter sp. TN221 were identified as novel strains. Nine isolates were able to grow in the presence of one or more metals (mercury, cadmium, nickel) at high concentration (100 mM). Seven isolates could degrade 15 different aromatic compounds and could grow in the presence of one or more heavy metals. Two of these isolates were resistant to multiple antibiotics including erythromycin and nalidixic acid. One third of isolates could accumulate at least one biopolymer. Twelve isolates (mainly Bacillus sp. and Arthrobacter sp.) accumulated polyphosphate, 3 Bacillus sp. accumulated polyhydroxybutyrate, while 4 isolates could accumulate exopolysaccharides.

  3. Life under ice: Investigating microbial-related biogeochemical cycles in the seasonally-covered Great Lake Onego, Russia

    Science.gov (United States)

    Thomas, Camille; Ariztegui, Daniel; Victor, Frossard; Emilie, Lyautey; Marie-Elodie, Perga; Life Under Ice Scientific Team

    2016-04-01

    The Great European lakes Ladoga and Onego are important resources for Russia in terms of drinking water, energy, fishing and leisure. Because their northern location (North of Saint Petersburgh), these lakes are usually ice-covered during winter. Due to logistical reasons, their study has thus been limited to the ice-free periods, and very few data are available for the winter season. As a matter of fact, comprehension of large lakes behaviour in winter is very limited as compared to the knowledge available from small subpolar lakes or perennially ice-covered polar lakes. To tackle this issue, an international consortium of scientists has gathered around the « life under ice » project to investigate physical, chemical and biogeochemical changes during winter in Lake Onego. Our team has mainly focused on the characterization and quantification of biological processes, from the water column to the sediment, with a special focus on methane cycling and trophic interactions. A first « on-ice » campaign in March 2015 allowed the sampling of a 120 cm sedimentary core and the collection of water samples at multiple depths. The data resulting from this expedition will be correlated to physical and chemical parameters collected simultaneously. A rapid biological activity test was applied immediately after coring in order to test for microbial activity in the sediments. In situ adenosine-5'-triphosphate (ATP) measurements were carried out in the core and taken as an indication of living organisms within the sediments. The presence of ATP is a marker molecule for metabolically active cells, since it is not known to form abiotically. Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) were extracted from these samples, and quantified. Quantitative polymerase chain reactions (PCR) were performed on archaeal and bacterial 16S rRNA genes used to reconstruct phylogenies, as well as on their transcripts. Moreover, functional genes involved in the methane and nitrogen cycles

  4. Investigation of protein and lipid metabolism in thyroid pathology using whole-body radiometry

    International Nuclear Information System (INIS)

    Gorobets, V.F.; Matveenko, E.G.

    1987-01-01

    Radiometry of the whole body and its organs was employed to study certain aspects of protein-aminoacid and lipid metabolism in patients with thyroid diseases. Metabolism of human serum 131 I-albumin was studied in 12 patients with neurocirculatory dystonia, in 13 patients with diffuse toxic goiter (in 10 before and after drug therapy) and in 9 controls. 75 Se-methionine aminoacid metabolism was investigated in 9 patients with toxic thyroid adenoma and in 13 controls. The body cell mass was determined in 82 patients with thyrotoxicosis by a measurable amount of 40 K. These data were compared with those of 249 healthy persons. An increase in catabolism of labeled albumin, intensification of labeled methionine metabolism at the tissue level, signs of a decrease in the total amount of metabolic albumin in the body were revealed. Intensification of protein metabolism resulted in a decrease in the body cell mass of these patients. After adequate therapy the above indices of protein metabolism in patients with thyrotoxicosis returned to normal. The assimilation of fatty acids and neutral fat was disturbed both in thyrotoxicosis and hypothyroidism

  5. Investigation of triclosan contamination on microbial biomass and other soil health indicators.

    Science.gov (United States)

    Zaayman, Morkel; Siggins, Alma; Horne, Dave; Lowe, Hamish; Horswell, Jacqui

    2017-09-01

    Triclosan (TCS) is an antimicrobial compound found in personal care products, and consequently in greywater. After its release to the environment, it continues its antimicrobial action on indigenous microbial communities. Little is known about the environmental impacts of high levels of TCS, which may occur due to accumulation following long-term greywater application to soil. Soil microcosms were established using a silty clay loam and augmented with a range of TCS concentrations ranging from 500 to 7500 mg kg-1. Samples were analysed for substrate-induced respiration, microbial biomass and sulphatase activity. The soil augmented with the lowest concentration of TCS (500 mg kg-1) significantly decreased microbial biomass, with a calculated EC20 of 195 mg kg-1. Substrate-induced respiration indicated that the soil microbial community was impacted for all TCS concentrations; however, the community showed potential to recover over time. Sulphatase activity was less sensitive to TCS and was significantly impacted at high concentrations of TCS (>2500 mg kg-1). It is likely that TCS has selective toxicity for more susceptible microbes when introduced into the soil environment. At high levels, TCS could overwhelm TCS-degrading soil microbes. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  6. Investigation on Microbial Dissolution of Uranium (VI) from Autunite Mineral - 13421

    Energy Technology Data Exchange (ETDEWEB)

    Sepulveda, Paola; Katsenovich, Yelena; Lagos, Leonel [Applied Research Center, Florida International University. 10555 West Flagler St. Suite 2100, Miami Fl 33175 (United States)

    2013-07-01

    Precipitating autunite minerals by polyphosphate injection was identified as a feasible remediation strategy for sequestering uranium in contaminated groundwater and soil in situ at the Hanford Site. Autunite stability under vadose and saturated zone environmental conditions can help to determine the long-term effectiveness of this remediation strategy. The Arthrobacter bacteria are one of the most common groups in soils and are found in large numbers in Hanford soil as well as other subsurface environments contaminated with radionuclides. Ubiquitous in subsurface microbial communities, these bacteria can play a significant role in the dissolution of minerals and the formation of secondary minerals. The main objective of this investigation was to study the bacterial interactions under oxidizing conditions with uranium (VI); study the potential role of bicarbonate, which is an integral complexing ligand for U(VI) and a major ion in groundwater compositions; and present data from autunite dissolution experiments using Arthrobacter strain G968, a less U(VI)-tolerant strain. Sterile 100 mL glass mixed reactors served as the major bioreactor for initial experimentation. These autunite-containing bioreactors were injected with bacterial cells after the autunite equilibrated with the media solution amended with 0 mM, 3 mM 5 mM and 10 mM concentrations of bicarbonate. G968 Arthrobacter cells in the amount of 10{sup 6} cells/mL were injected into the reactors after 27 days, giving time for the autunite to reach steady state. Abiotic non-carbonate controls were kept without bacterial inoculation to provide a control for the biotic samples. Samples of the solution were analyzed for dissolved U(VI) by means of kinetic phosphorescence analyzer KPA-11 (Chemcheck Instruments, Richland, WA). Analysis showed that as [HCO{sub 3}{sup -}] increases, a diminishing trend on the effect of bacteria on autunite leaching is observed. Viability of cells was conducted after 24 hours of cell

  7. Investigation on Microbial Dissolution of Uranium (VI) from Autunite Mineral - 13421

    International Nuclear Information System (INIS)

    Sepulveda, Paola; Katsenovich, Yelena; Lagos, Leonel

    2013-01-01

    Precipitating autunite minerals by polyphosphate injection was identified as a feasible remediation strategy for sequestering uranium in contaminated groundwater and soil in situ at the Hanford Site. Autunite stability under vadose and saturated zone environmental conditions can help to determine the long-term effectiveness of this remediation strategy. The Arthrobacter bacteria are one of the most common groups in soils and are found in large numbers in Hanford soil as well as other subsurface environments contaminated with radionuclides. Ubiquitous in subsurface microbial communities, these bacteria can play a significant role in the dissolution of minerals and the formation of secondary minerals. The main objective of this investigation was to study the bacterial interactions under oxidizing conditions with uranium (VI); study the potential role of bicarbonate, which is an integral complexing ligand for U(VI) and a major ion in groundwater compositions; and present data from autunite dissolution experiments using Arthrobacter strain G968, a less U(VI)-tolerant strain. Sterile 100 mL glass mixed reactors served as the major bioreactor for initial experimentation. These autunite-containing bioreactors were injected with bacterial cells after the autunite equilibrated with the media solution amended with 0 mM, 3 mM 5 mM and 10 mM concentrations of bicarbonate. G968 Arthrobacter cells in the amount of 10 6 cells/mL were injected into the reactors after 27 days, giving time for the autunite to reach steady state. Abiotic non-carbonate controls were kept without bacterial inoculation to provide a control for the biotic samples. Samples of the solution were analyzed for dissolved U(VI) by means of kinetic phosphorescence analyzer KPA-11 (Chemcheck Instruments, Richland, WA). Analysis showed that as [HCO 3 - ] increases, a diminishing trend on the effect of bacteria on autunite leaching is observed. Viability of cells was conducted after 24 hours of cell incubation with

  8. Investigating the legacy effect of drought on microbial responses to drying and rewetting along a Texan precipitation gradient

    Science.gov (United States)

    Hicks, Lettice; Leizeaga, Ainara; Hawkes, Christine; Rousk, Johannes

    2017-04-01

    Hydrological regimes will intensify due to climate change, thus increasing the duration and intensity of drought and rainfall events. Rewetting of dry soil is known to stimulate dramatic CO2 releases. A clear understanding of the mechanisms that determine the dynamics of CO2 loss upon rewetting is therefore required to characterise ecosystem C-budgets and predict responses to climate change. Laboratory studies have identified two distinct responses upon rewetting; bacterial growth either increases linearly immediately, with maximal respiration also occurring immediately and decreasing exponentially with time ("Type 1"), or bacterial growth increases exponentially after a period of near-zero growth, with a sustained period of elevated respiration, sometimes followed by a secondary increase in respiration coinciding with the onset of bacterial growth ("Type 2"). A shift from a Type 1 to a Type 2 response has been observed with increasing duration and intensity of drying prior to rewetting. The size of the surviving microbial community after drying, relative to resources available after rewetting, is suggested to dictate whether a Type 1 or 2 response occurs, with more 'harsh' (i.e. longer or more severe) drying reducing microbial biomass such that carbon available upon rewetting is sufficient to support exponential growth (leading to Type 2 response). However, this is yet to be tested in intact ecosystems. We investigated the legacy of drought on microbial responses to drying and rewetting using grassland soils from a natural precipitation gradient in Texas. Mean annual precipitation spanned a 500 mm range (400-900 mm year-1) across the 400 km gradient, while mean annual temperature was constant. Soil properties (pH, SOM) did not vary systematically across the gradient, with differences reflecting land-use history rather than rainfall. Air dried soils from 18 sites were rewetted to 50 % water holding capacity with bacterial growth, fungal growth and respiration

  9. Carbon monoxide as a metabolic energy source for extremely halophilic microbes: implications for microbial activity in Mars regolith.

    Science.gov (United States)

    King, Gary M

    2015-04-07

    Carbon monoxide occurs at relatively high concentrations (≥800 parts per million) in Mars' atmosphere, where it represents a potentially significant energy source that could fuel metabolism by a localized putative surface or near-surface microbiota. However, the plausibility of CO oxidation under conditions relevant for Mars in its past or at present has not been evaluated. Results from diverse terrestrial brines and saline soils provide the first documentation, to our knowledge, of active CO uptake at water potentials (-41 MPa to -117 MPa) that might occur in putative brines at recurrent slope lineae (RSL) on Mars. Results from two extremely halophilic isolates complement the field observations. Halorubrum str. BV1, isolated from the Bonneville Salt Flats, Utah (to our knowledge, the first documented extremely halophilic CO-oxidizing member of the Euryarchaeota), consumed CO in a salt-saturated medium with a water potential of -39.6 MPa; activity was reduced by only 28% relative to activity at its optimum water potential of -11 MPa. A proteobacterial isolate from hypersaline Mono Lake, California, Alkalilimnicola ehrlichii MLHE-1, also oxidized CO at low water potentials (-19 MPa), at temperatures within ranges reported for RSL, and under oxic, suboxic (0.2% oxygen), and anoxic conditions (oxygen-free with nitrate). MLHE-1 was unaffected by magnesium perchlorate or low atmospheric pressure (10 mbar). These results collectively establish the potential for microbial CO oxidation under conditions that might obtain at local scales (e.g., RSL) on contemporary Mars and at larger spatial scales earlier in Mars' history.

  10. Microbial investigations in Opalinus clay from Mont Terri and in Callovo-Oxfordian argillite from Meuse/Haute-Marne

    International Nuclear Information System (INIS)

    Poulain, S.

    2006-12-01

    The subject of this Ph.D. thesis deals with research achieved in the context of the Axis 2 of the law Bataille voted on December 30, 1991 about the possibility of building a deep geological repository for medium or high activity and long living nuclear waste. Nearby such a site, some microorganisms may influence the mobility of radionuclides coming from the waste canisters. This work consisted in looking for autochthonous microorganisms in the Opalinus clay formation from Mont Terri (Switzerland) and in the Callovo-Oxfordian argillite from Meuse/Haute-Marne (France). Microbial Investigations in these unknown unperturbed environments suggested very low microbial densities in the clayey sediments. However, new bacterial species could be isolated from those samples. In addition, a part of the allochthonous population, which has been introduced by air and human activity, could be identified in the Meuse/Haute-Marne underground research laboratory. (author)

  11. Tracing biofouling to the structure of the microbial community and its metabolic products: a study of the three-stage MBR process.

    Science.gov (United States)

    Gao, Dawen; Fu, Yuan; Ren, Nanqi

    2013-11-01

    The biofouling characteristics of a sequential anoxic/aerobic-membrane bioreactor (A/O MBR) were analyzed during the three-stage process (fast-slow-fast transmembrane pressure (TMP) increasing). The results indicated: during the stage 1 (before day 1), the microbial communities in the activated sludge (AS), cake sludge (CS) and biofilm (BF) were similar to each other, and the adsorption of microbes and the metabolic products was the main factor that led to TMP increase; during the stage 2 (between day 1 and day 7), the cake layer begun to form and the TMP continued to rise gradually at a reduced rate compared to stage 1, at this point a characteristic microbial community colonized the CS with microorganisms such as Saprospiraceae and Comamonadaceae thriving on the membrane surface (BF) probably due to greater nutrient availability, and the predominance of these species in the microbial population led to the accumulation of biofouling metabolic products in the CS, which resulted in membrane fouling and the associated rise in TMP; during the final stage (after day 7), the biofilm had matured, and the activity of anaerobes stimulated cake compaction. The statistical analysis showed a correlation between the TMP changing rate and the carbonhydrates of soluble microbial products (SMPc) content in the CS. When the SMPc concentration rose slowly there was a low level of biofouling. However, when the SMPc accumulating rate was greater, it resulted in the more severe biofouling associated with the TMP jump. Furthermore, the correlation coefficient for the TMP increase and protein concentrations of extracellular polymeric substances (EPSp) in the CS was highly significant. The cluster analysis suggested that the AS microbial community remained stable during the three TMP change stages, while the CS and BF community were changed accompanied with the TMP change. The interaction between the microbial communities and the metabolic products lead to the significant correlation

  12. [Investigation of microbial contamination of the air and equipment of a biological waste water purification station].

    Science.gov (United States)

    Alikbaeva, L A; Figurovskiĭ, A P; Vasil'ev, O D; Ermolaev-Makovskiĭ, M A; Merkur'eva, M A

    2010-01-01

    The paper describes the results of a study of ambient air microbiological pollution in the working premises and equipment surfaces in the main shops of the biological waste water purification station of a cardboard-polygraphic plant. The findings suggest that there is high microbial contamination of the working environment, which should be born in mind on developing measures to optimize working conditions and on studying morbidity rates among the workers.

  13. In vitro investigation of cytochrome P450-mediated metabolism of dietary flavonoids

    DEFF Research Database (Denmark)

    Breinholt, Vibeke; Offord, E.A.; Brouwer, C.

    2002-01-01

    Human and mouse liver microsomes And membranes isolated from Escherichia coli, which expressed cytochrome P450 (CYP) 1A2, 3A4 2C9 or 2D6, were used to investigate CYP-mediated metabolism of five selected dietary flavonoids. In human and mouse liver microsomes kaempferol, apigenin and naringenin...

  14. Investigations on the metabolism of metals in decapod crustaceas in relation with moulting cycles and reproduction

    International Nuclear Information System (INIS)

    Martin, J.-L.M.

    1975-07-01

    A study of the metabolism of metals was carried out in decapod crustaceas; it showed that it was subject to cyclic variations during the life of the animals, closely correlated with growth moults. The metabolism of metals was also considered in its relations with reproduction, especially oogenesis and spermatogenesis, and embryonic development. In relation with moult, various factors playing a role on metal metabolism were investigated: role of metals in the organism, fasting and nutrition cycles and biochemical reserves, physico-chemical form of the metal and ultrastructure of uptake surfaces. The histological and histochemical aspects of the uptake of a number of metals were studied as well as inter-metallic and inter-organic relationships [fr

  15. Use of radiation and radioisotopes for investigating metabolic diseases of animals in India

    International Nuclear Information System (INIS)

    Arora, S.P.

    1980-01-01

    In the last one decade, radioisotopes are being used to investigate certain metabolic diseases of animals and radiations are being utilized to produce parasitic vaccines to vaccinate animals. Some studies in which radioisotopes have been used to investigate certain metabolic disorders are reviewed. In experiments, where radioimmunoassay technique for the estimation of hormones, has been utilized, the results reveal that the animals on low plane of nutrition show greater oestrous cycle lengths or even long anoestrous periods. On the other hand, irradiation has been used as a tool to produce vaccines as well as degradation of certain dietary molecules for increased utilization. A number of studies wherein 35 S and 15 N isotopes have been used, reveal that sulphur supplementation is essential for optimum utilization of nitrogen in the ratio of 1:10. There are certain antimetabolites in feed ingredients which affect endocrine function. Evidence indicates that high nitrate forages disturb thyroid function when sup(131)I is used to elucidate its secretion rate. Similarly certain toxic substances such as tannins have been shown to affect protein metabolism and phosphorus utilization when sup(32)P isotope is used in such studies. The use of radioisotopes have also been helpful to investigate the cause of ''Degnala'' disease prevalent in village cattle in certain states of India. With the help of sup(75)Se it has been possible to trace out the metabolic disturbances which lead to the onset of this disease. Another deficiency disease, hyperkeratosis, has been shown to be caused not only because of Vitamin A deficiency, but also because of zinc deficiency. The latter helps in the mobilization of normal quantity of vitamin A from the liver into the blood vitamin A pool. There is wide scope to use radioisotopes to investigate other metabolic diseases prevalent in livestock in this country. (auth.)

  16. The effect of feed rations containing high moisture crimped corn ensiled with microbial inoculant or chemical additive on milk production and metabolism of dairy cows

    Directory of Open Access Journals (Sweden)

    László Könyves

    2015-01-01

    Full Text Available The study evaluated the effects of crimped corn preserved either with organic acids or with a microbial inoculant on a range of metabolic and production indicators of dairy cows. Two hundred and sixty in-calf, second and third parity cows were selected into pairs on basis of age, parity, milk production in previous lactation, days in milk and body condition score with the greatest possible conformity within pairs. Cow pairs were assigned into a 2-period crossover experiment (2 × 45 days and kept in separate groups within the same shed. Dietary treatments were TMR with crimped corn preserved with either organic acids (treatment K or microbial inoculant (treatment B. Ten superbly matched cow-pairs were selected to form nucleus pairs for metabolic studies. The preservatives had no effect on the nutrient content of crimped corn. Crimped corn preserved with the microbial inoculant were found mouldy, predominantly with Mucor sp. at a number high enough to inhibit the growth of lactic acid bacteria, and had significantly higher pH and ammonium concentration compared to the chemical treatment. The milk yield of treatment K cows was significantly higher than that of treatment B cows with identical feed intake. Blood beta-hydroxy-butyrate concentration was lower and blood aspartate amino transferase activity higher with treatment K compared to treatment B. Results of this study suggest the superiority of total mixed rations containing chemically preserved crimped corn in terms of ammonia and microbiological indicators of crimped corn, significantly higher milk yield, and balanced energy metabolism.

  17. Vitamin B12effects on chlorinated methanes-degrading microcosms: Dual isotope and metabolically active microbial populations assessment.

    Science.gov (United States)

    Rodríguez-Fernández, Diana; Torrentó, Clara; Guivernau, Miriam; Viñas, Marc; Hunkeler, Daniel; Soler, Albert; Domènech, Cristina; Rosell, Mònica

    2018-04-15

    Field-derived anoxic microcosms were used to characterize chloroform (CF) and carbon tetrachloride (CT) natural attenuation to compare it with biostimulation scenarios in which vitamin B 12 was added (B 12 /pollutant ratio of 0.01 and 0.1) by means of by-products, carbon and chlorine compound-specific stable-isotope analysis, and the active microbial community through 16S rRNA MiSeq high-throughput sequencing. Autoclaved slurry controls discarded abiotic degradation processes. B 12 catalyzed CF and CT biodegradation without the accumulation of dichloromethane, carbon disulphide, or CF. The carbon isotopic fractionation value of CF (ƐC CF ) with B 12 was -14±4‰, and the value for chlorine (ƐCl CF ) was -2.4±0.4‰. The carbon isotopic fractionation values of CT (ƐC CT ) were -16±6 with B 12 , and -13±2‰ without B 12 ; and the chlorine isotopic fractionation values of CT (ƐCl CT ) were -6±3 and -4±2‰, respectively. Acidovorax, Ancylobacter, and Pseudomonas were the most metabolically active genera, whereas Dehalobacter and Desulfitobacterium were below 0.1% of relative abundance. The dual C-Cl element isotope slope (Λ=Δδ 13 C/Δδ 37 Cl) for CF biodegradation (only detected with B 12 , 7±1) was similar to that reported for CF reduction by Fe(0) (8±2). Several reductive pathways might be competing in the tested CT scenarios, as evidenced by the lack of CF accumulation when B 12 was added, which might be linked to a major activity of Pseudomonas stutzeri; by different chlorine apparent kinetic isotope effect values and Λ which was statistically different with and without B 12 (5±1 vs 6.1±0.5), respectively. Thus, positive B 12 effects such as CT and CF degradation catalyst were quantified for the first time in isotopic terms, and confirmed with the major activity of species potentially capable of their degradation. Moreover, the indirect benefits of B 12 on the degradation of chlorinated ethenes were proved, creating a basis for remediation

  18. Assessing the bias linked to DNA recovery from biofiltration woodchips for microbial community investigation by fingerprinting.

    Science.gov (United States)

    Cabrol, Léa; Malhautier, Luc; Poly, Franck; Lepeuple, Anne-Sophie; Fanlo, Jean-Louis

    2010-01-01

    In this study, we explored methodological aspects of nucleic acid recovery from microbial communities involved in a gas biofilter filled with pine bark woodchips. DNA was recovered indirectly in two steps, comparing different methods: cell dispersion (crushing, shaking, and sonication) and DNA extraction (three commercial kits and a laboratory protocol). The objectives were (a) to optimize cell desorption from the packing material and (b) to compare the 12 combinations of desorption and extraction methods, according to three relevant criteria: DNA yield, DNA purity, and community structure representation by denaturing gradient gel electrophoresis (DGGE). Cell dispersion was not influenced by the operational parameters tested for shaking and blending, while it increased with time for sonication. DNA extraction by the laboratory protocol provided the highest DNA yields, whereas the best DNA purity was obtained by a commercial kit designed for DNA extraction from soil. After successful PCR amplification, the 12 methods did not generate the same bias in microbial community representation. Eight combinations led to high diversity estimation, independently of the experimental procedure. Among them, six provided highly similar DGGE profiles. Two protocols generated a significantly dissimilar community profile, with less diversity. This study highlighted the crucial importance of DNA recovery bias evaluation.

  19. Investigating the role for adaptation of the microbial community to transform trace organic chemicals during managed aquifer recharge

    KAUST Repository

    Alidina, Mazahirali

    2014-06-01

    This study was undertaken to investigate whether adaptation by pre-exposure to trace organic chemicals (TOrCs) was necessary for microbial transformation during managed aquifer recharge (MAR). Two pairs of laboratory-scale soil columns, each receiving a different primary substrate, were utilized to simulate the dominant bulk organic carbon present in MAR systems receiving wastewater effluent of varying quality and having undergone different degrees of pre-treatment, as well as organic carbon prevalent at different stages of subsurface travel. Each pair of columns consisted of duplicate set-ups receiving the same feed solution with only one pre-exposed to a suite of eight TOrCs for approximately ten months. Following the pre-exposure period, a spiking experiment was conducted in which the non-exposed columns also received the same suite of TOrCs. TOrC attenuation was quantified for the pre- and non-exposed columns of each pair during the spiking experiment. The microbial community structure and function of these systems were characterized by pyrosequencing of 16S rRNA gene and metagenomics, respectively. Biotransformation rather than sorption was identified as the dominant removal mechanism for almost all the TOrCs (except triclocarban). Similar removal efficiencies were observed between pre-exposed and non-exposed columns for most TOrCs. No obvious differences in microbial community structure were revealed between pre- and non-exposed columns. Using metagenomics, biotransformation capacity potentials of the microbial community present were also similar between pre- and non-exposed columns of each pair. Overall, the pre-exposure of MAR systems to TOrCs at ng/L levels did not affect their attenuation and had no obvious influence on the resulting microbial community structure and function. Thus, other factors such as bioavailability of the primary substrate play a greater role regarding biotransformation of TOrCs. These results indicate that MAR systems adapted to a

  20. Metabolic and Microbial Modulation of the Large Intestine Ecosystem by Non-Absorbed Diet Phenolic Compounds: A Review

    OpenAIRE

    Juana I. Mosele; Alba Macià; Maria-José Motilva

    2015-01-01

    Phenolic compounds represent a diverse group of phytochemicals whose intake is associated with a wide spectrum of health benefits. As consequence of their low bioavailability, most of them reach the large intestine where, mediated by the action of local microbiota, a series of related microbial metabolites are accumulated. In the present review, gut microbial transformations of non-absorbed phenolic compounds are summarized. Several studies have reached a general consensus that unbalanced die...

  1. Investigating design criteria to build a performing microbial fuel cell running on swine liquid manure

    Energy Technology Data Exchange (ETDEWEB)

    Martin, D.Y.; Hogue, R.; Dube, P.; Jeanne, T.; Levesque, A. [Inst. de recherche et de developpement en agroenvironnement Inc, Quebec City, PQ (Canada); Theriault, R.; Kaliaguine, S. [Laval Univ., Quebec City, PQ (Canada)

    2010-07-01

    This paper reported on a study that examined the bacterial and electro-chemical phenomena that takes place in a microbial fuel cell (MFC) operating on swine liquid manure as fuel. An MFC converts the available energy in a bioconvertible substrate directly into electricity while decreasing its chemical oxygen demand (COD). In this study, a first single chamber MFC operating on swine liquid manure was constructed based on a literature review. Various support media filling the anodic chamber were tested in an effort to optimize the surface area on which bacteria may develop according to the hypothesis that large bacteria concentration will improve energy production and reduce treatment time. Bacterial communities extracted from the selected support media were analyzed using molecular technologies such as DNA extraction, PCR amplification, denaturing gradient gel electrophoresis, cloning and sequencing. The analyses showed that only a few bacteria species coming from raw liquid manure were responsible for electrical activities.

  2. Surveillance of microbial indicators and physicochemical parameters to investigate pollution status of Lahore canal

    International Nuclear Information System (INIS)

    Tahir, A.; Kanwal, F.; Mateen, B.

    2011-01-01

    The Lahore canal is an important watershed in Lahore. The present study was conducted to monitor pollution load of Lahore canal. Surface water was collected from the middle of the canal at four different sites, and analysed for physicochemical parameters (temperature, pH, EC, DO, BOD/sub 5/, turbidity, nitrates, phosphates) and microbial load (bacteria (TVC), total coliform and fungi). Water quality parameters were monitored from May to August at four sites along 17Km long patch. Surface water was collected in the middle of the canal. The results were compared with IWQ guidelines proposed by WWF, Pakistan. Pollution load of Lahore Canal revealed an alarming situation. Water can be used for the irrigation purpose, but only with advanced treatment. (author)

  3. Preliminary investigation of single chamber single electrode microbial fuel cell using sewage sludge as a substrate

    Science.gov (United States)

    Sai Chaithanya, M.; Thakur, Somil; Sonu, Kumar; Das, Bhaskar

    2017-11-01

    A microbial fuel cell (MFC) consists of a cathode and anode; micro-organisms transfer electrons acquired from the degradation of organic matter in the substrate to anode; and thereby to cathode; by using an external circuit to generate electricity. In the present study, a single chamber single electrode microbial fuel cell has been fabricated to generate electricity from the sludge of the sewage treatment plant at two different ambient temperature range of 25 ± 4°C and 32 ± 4°C under aerobic condition. No work has been done yet by using the single electrode in any MFC system; it is hypothesized that single electrode submerged partially in substrate and rest to atmosphere can function as both cathode and anode. The maximum voltage obtained was about 2890 mV after 80 (hrs) at temperature range of 25 ± 4°C, with surface power density of 1108.29 mW/m2. When the ambient temperature was 32 ± 4°C, maximum voltage obtained was 1652 mV after 40 (hrs.) surface power density reduced to 865.57 mW/m2. When amount of substrate was decreased for certain area of electrode at 25 ± 4°C range, electricity generation decreased and it also shortened the time to reach peak voltage. On the other hand, when the ambient temperature was increased to 32 ± 4°C, the maximum potential energy generated was less than that of previous experiment at 25 ± 4°C for the same substrate Also the time to reach peak voltage decreased to 40 hrs. When comparing with other single chamber single electrode MFC, the present model is generating more electricity that any MFC using sewage sludge as substrate except platinum electrode, which is much costlier that electrode used in the present study.

  4. Ischaemic memory imaging using metabolic radiopharmaceuticals: overview of clinical settings and ongoing investigations

    International Nuclear Information System (INIS)

    Yoshinaga, Keiichiro; Naya, Masanao; Shiga, Tohru; Suzuki, Eriko; Tamaki, Nagara

    2014-01-01

    ''Ischaemic memory'' is defined as a prolonged functional and/or biochemical alteration remaining after a particular episode of severe myocardial ischaemia. The biochemical alteration has been reported as metabolic stunning. Metabolic imaging has been used to detect the footprint left by previous ischaemic episodes evident due to delayed recovery of myocardial metabolism (persistent dominant glucose utilization with suppression of fatty acid oxidation). β-Methyl-p-[ 123 I]iodophenylpentadecanoic acid (BMIPP) is a single-photon emission computed tomography (SPECT) radiotracer widely used for metabolic imaging in clinical settings in Japan. In patients with suspected coronary artery disease but no previous myocardial infarction, BMIPP has shown acceptable diagnostic accuracy. In particular, BMIPP plays an important role in the identification of prior ischaemic insult in patients arriving at emergency departments with acute chest pain syndrome. Recent data also show the usefulness of 123 I-BMIPP SPECT for predicting cardiovascular events in patients undergoing haemodialysis. Similarly, SPECT or PET imaging with 18 F-FDG injected during peak exercise or after exercise under fasting conditions shows an increase in FDG uptake in postischaemic areas. This article will overview the roles of ischaemic memory imaging both under established indications and in ongoing investigations. (orig.)

  5. Ischaemic memory imaging using metabolic radiopharmaceuticals: overview of clinical settings and ongoing investigations

    Energy Technology Data Exchange (ETDEWEB)

    Yoshinaga, Keiichiro [Hokkaido University Graduate School of Medicine, Department of Molecular Imaging, Sapporo (Japan); Naya, Masanao [Hokkaido University Graduate School of Medicine, Department of Cardiology, Sapporo (Japan); Shiga, Tohru; Suzuki, Eriko; Tamaki, Nagara [Hokkaido University Graduate School of Medicine, Department of Nuclear Medicine, Sapporo (Japan)

    2014-02-15

    ''Ischaemic memory'' is defined as a prolonged functional and/or biochemical alteration remaining after a particular episode of severe myocardial ischaemia. The biochemical alteration has been reported as metabolic stunning. Metabolic imaging has been used to detect the footprint left by previous ischaemic episodes evident due to delayed recovery of myocardial metabolism (persistent dominant glucose utilization with suppression of fatty acid oxidation). β-Methyl-p-[{sup 123}I]iodophenylpentadecanoic acid (BMIPP) is a single-photon emission computed tomography (SPECT) radiotracer widely used for metabolic imaging in clinical settings in Japan. In patients with suspected coronary artery disease but no previous myocardial infarction, BMIPP has shown acceptable diagnostic accuracy. In particular, BMIPP plays an important role in the identification of prior ischaemic insult in patients arriving at emergency departments with acute chest pain syndrome. Recent data also show the usefulness of {sup 123}I-BMIPP SPECT for predicting cardiovascular events in patients undergoing haemodialysis. Similarly, SPECT or PET imaging with {sup 18}F-FDG injected during peak exercise or after exercise under fasting conditions shows an increase in FDG uptake in postischaemic areas. This article will overview the roles of ischaemic memory imaging both under established indications and in ongoing investigations. (orig.)

  6. Urolithins are the main urinary microbial-derived phenolic metabolites discriminating a moderate consumption of nuts in free-living subjects with diagnosed metabolic syndrome.

    Science.gov (United States)

    Tulipani, Sara; Urpi-Sarda, Mireia; García-Villalba, Rocío; Rabassa, Montserrat; López-Uriarte, Patricia; Bulló, Mònica; Jáuregui, Olga; Tomás-Barberán, Francisco; Salas-Salvadó, Jordi; Espín, Juan Carlos; Andrés-Lacueva, Cristina

    2012-09-12

    Walnuts ( Juglans regia L.), hazelnuts ( Corylus avellana L.), and almonds ( Prunus dulcis Mill.) are rich sources of ellagitannins and proanthocyanidins. Gut microbiota plays a crucial role in modulating the bioavailability of these high molecular weight polyphenols. However, to date there are no studies evaluating the capacity to produce nut phenolic metabolites in subjects with metabolic syndrome (MetS), a pathology associated with an altered gut bacterial diversity. This study applied a LC-MS targeted approach to analyze the urinary excretion of nut phenolic metabolites in MetS subjects following 12 weeks of nut consumption, compared to sex- and age-matched individuals given a nut-free control diet. Metabolites were targeted in both hydrolyzed and nonhydrolyzed urine by LC-PDA-QqQ-MS/MS analysis, and identification of metabolites lacking available standards was confirmed by LC-ESI-ITD-FT-MS. Ellagitannin-derived urolithins A and B significantly increased after the nut-enriched-diet, urolithins C and D were also detected, and a complex combination of urolithin-conjugated forms was observed in nonhydrolyzed urine, confirming an extensive phase II metabolism after absorption. In contrast, no significant increases in proanthocyanidin microbial metabolites were observed in urine following nut consumption. Because the intestinal microbiota of the subjects in this study could catabolize ellagitannins into a wide range of urolithins, further research is strongly warranted on the in vivo potential of these microbial metabolites in reducing cardiometabolic risk.

  7. From the Cover: Sulfur isotopes of organic matter preserved in 3.45-billion-year-old stromatolites reveal microbial metabolism

    Science.gov (United States)

    Bontognali, Tomaso R. R.; Sessions, Alex L.; Allwood, Abigail C.; Fischer, Woodward W.; Grotzinger, John P.; Summons, Roger E.; Eiler, John M.

    2012-09-01

    The 3.45-billion-year-old Strelley Pool Formation of Western Australia preserves stromatolites that are considered among the oldest evidence for life on Earth. In places of exceptional preservation, these stromatolites contain laminae rich in organic carbon, interpreted as the fossil remains of ancient microbial mats. To better understand the biogeochemistry of these rocks, we performed microscale in situ sulfur isotope measurements of the preserved organic sulfur, including both Δ33S and . This approach allows us to tie physiological inference from isotope ratios directly to fossil biomass, providing a means to understand sulfur metabolism that is complimentary to, and independent from, inorganic proxies (e.g., pyrite). Δ33S values of the kerogen reveal mass-anomalous fractionations expected of the Archean sulfur cycle, whereas values show large fractionations at very small spatial scales, including values below -15‰. We interpret these isotopic patterns as recording the process of sulfurization of organic matter by H2S in heterogeneous mat pore-waters influenced by respiratory S metabolism. Positive Δ33S anomalies suggest that disproportionation of elemental sulfur would have been a prominent microbial process in these communities.

  8. Characterizing Microbial Diversity and the Potential for Metabolic Function at −15 °C in the Basal Ice of Taylor Glacier, Antarctica

    Directory of Open Access Journals (Sweden)

    Brent C. Christner

    2013-07-01

    Full Text Available Measurement of gases entrapped in clean ice from basal portions of the Taylor Glacier, Antarctica, revealed that CO2 ranged from 229 to 328 ppmv and O2 was near 20% of the gas volume. In contrast, vertically adjacent sections of the sediment laden basal ice contained much higher concentrations of CO2 (60,000 to 325,000 ppmv, whereas O2 represented 4 to 18% of the total gas volume. The deviation in gas composition from atmospheric values occurred concurrently with increased microbial cell concentrations in the basal ice profile, suggesting that in situ microbial processes (i.e., aerobic respiration may have altered the entrapped gas composition. Molecular characterization of 16S rRNA genes amplified from samples of the basal ice indicated a low diversity of bacteria, and most of the sequences characterized (87% were affiliated with the phylum, Firmicutes. The most abundant phylotypes in libraries from ice horizons with elevated CO2 and depleted O2 concentrations were related to the genus Paenisporosarcina, and 28 isolates from this genus were obtained by enrichment culturing. Metabolic experiments with Paenisporosarcina sp. TG14 revealed its capacity to conduct macromolecular synthesis when frozen in water derived from melted basal ice samples and incubated at −15 °C. The results support the hypothesis that the basal ice of glaciers and ice sheets are cryospheric habitats harboring bacteria with the physiological capacity to remain metabolically active and biogeochemically cycle elements within the subglacial environment.

  9. Tracing the fate of organic P compounds in soil - a direct investigation of microbial organic P use

    Science.gov (United States)

    Wasner, Daniel; Zezula, David; Wanek, Wolfgang

    2017-04-01

    In soils, the wide variety of organic phosphorus (Porg) compounds constitutes a large fraction of total soil P, and therefore represents an important pool of actively cycled terrestrial P. However, to date little is known about the decomposition dynamics of this highly heterogenic group of compounds in soil systems, mainly due to the lack of traceable Porg substrates for experimental approaches. It is further currently unknown whether Porg substrates released into the soil are generally mineralized to inorganic P by extracellular enzymes before microbial uptake or whether substantial amounts of low-molecular weight Porg compounds are taken up in an intact form. This study therefore aimed at directly investigating the short-term fate (0-24hours) of five different groups of 33P-labelled Porg components (teichoic acids in bacterial cell walls, DNA, RNA, phospholipids, and small organophosphates) relative to inorganic 33P in soils. To that end, depolymerization and dephosphorylation reactions of these Porg pools were measured concomitant with the uptake of organic versus inorganic 33P into soil microbial community. The purified 33P-labelled Porg components were obtained by growing Bacillus subtilis in a 33P amended liquid medium and subsequent fractionation of the biomass into the five groups of 33Porg compounds by optimized biochemical fractionation protocols. After adding these substrates to an agricultural soil and a pasture soil, the relevant organic, inorganic and microbial P pools were determined at seven timepoints over 24hours. The data of these experiments are currently under evaluation and will be presented at the conference.

  10. Metabolism

    Science.gov (United States)

    ... functions: Anabolism (uh-NAB-uh-liz-um), or constructive metabolism, is all about building and storing. It ... in infants and young children. Hypothyroidism slows body processes and causes fatigue (tiredness), slow heart rate, excessive ...

  11. Metabolism

    Science.gov (United States)

    ... a particular food provides to the body. A chocolate bar has more calories than an apple, so ... acid phenylalanine, needed for normal growth and protein production). Inborn errors of metabolism can sometimes lead to ...

  12. Microbial Murders Crime Scene Investigation: An Active Team-Based Learning Project that Enhances Student Enthusiasm and Comprehension of Clinical Microbial Pathogens.

    Science.gov (United States)

    Steel, J Jordan

    2017-01-01

    Microbial disease knowledge is a critical component of microbiology courses and is beneficial for many students' future careers. Microbiology courses traditionally cover core concepts through lectures and labs, but specific instruction on microbial diseases varies greatly depending on the instructor and course. A common project involves students researching and presenting a disease to the class. This method alone is not very effective, and course evaluations have consistently indicated that students felt they lacked adequate disease knowledge; therefore, a more hands-on and interactive disease project was developed called Microbial Murders. For this team-based project, a group of students chooses a pathogen, researches the disease, creates a "mugshot" of the pathogen, and develops a corresponding "crime scene," where a hypothetical patient has died from the microbe. Each group gives a presentation introducing the microbial pathogen, signs/symptoms, treatments, and overall characteristics. The students then visit each other's crime scenes to match the pathogen with the correct crime scene by critically thinking through the clues. This project has shown remarkable success. Surveys indicate that 73% of students thought the project helped them understand the material and 84% said it was worth their time. Student participation, excitement, understanding, and application of microbial disease knowledge have increased and are evident through an increase in course evaluations and in student assessment scores. This project is easy to implement and can be used in a wide variety of biology, microbiology, or health classes for any level (middle school through college).

  13. Strong linkage between active microbial communities and microbial carbon usage in a deglaciated terrain of the High Arctic

    Science.gov (United States)

    Kim, M.; Gyeong, H. R.; Lee, Y. K.

    2017-12-01

    Soil microorganisms play pivotal roles in ecosystem development and carbon cycling in newly exposed glacier forelands. However, little is known about carbon utilization pattern by metabolically active microbes over the course of ecosystem succession in these nutrient-poor environments. We investigated RNA-based microbial community dynamics and its relation to microbial carbon usage along the chronosequence of a High Arctic glacier foreland. Among microbial taxa surveyed (bacteria, archaea and fungi), bacteria are among the most metabolically active taxa with a dominance of Cyanobacteria and Actinobacteria. There was a strong association between microbial carbon usage and active Actinobacterial communities, suggesting that member of Actinobacteria are actively involved in organic carbon degradation in glacier forelands. Both bacterial community and microbial carbon usage are converged towards later stage of succession, indicating that the composition of soil organic carbon plays important roles in structuring bacterial decomposer communities during ecosystem development.

  14. Investigation of microbial diversity in a desert Mars-like environment: Mars Desert Research Station (MDRS), Utah

    Science.gov (United States)

    Direito, Maria Susana; Staats, Martijn; Foing, Bernard H.; Ehrenfreund, Pascale; Roling, Wilfred

    The Utah Mars Desert Research Station (MDRS) harbours geo-morphology and geo-processes analogues to the planet Mars. Soil samples were collected during the EuroGeoMars campaign (from 24 January to 1 March 2009) from different locations and depths [1]. Samples were distributed among scientific collaborator institutes for analysis of microbial diversity, amino acid content and degradation, content of PAH or larger organic molecules, and respective soil properties. Our sample analysis had the objective of characterizing the microbial communities in this Mars analogue: DNA isolation, PCR (Polymerase Chain Reaction) using primers for DNA amplification of Bacteria, Archaea and Eukarya ribosomal RNA (rRNA) gene fragments, DGGE (Denaturing Gradient Gel Electrophoresis) and clone library construction with the final aim of sequencing. Results indicate that life is present in all the three domains of life (Archaea, Bacteria and Eukarya), while the most diversity was found in the domain Bacteria. Microorgan-isms are heterogeneously present and their identities are currently investigated. The obtained information will be later related to the other scientific analysis in order to obtain a better understanding of this Mars analogue site, which in turn will provide important information for the search for life on Mars. [1] Foing, B.H. et al . (2009). Exogeolab lander/rover instruments and EuroGeoMars MDRS campaign. LPI, 40, 2567.

  15. The Dark Side of the Mushroom Spring Microbial Mat: Life in the Shadow of Chlorophototrophs. II. Metabolic Functions of Abundant Community Members Predicted from Metagenomic Analyses

    Directory of Open Access Journals (Sweden)

    Vera Thiel

    2017-06-01

    Full Text Available Microbial mat communities in the effluent channels of Octopus and Mushroom Springs within the Lower Geyser Basin of Yellowstone National Park have been extensively characterized. Previous studies have focused on the chlorophototrophic organisms of the phyla Cyanobacteria and Chloroflexi. However, the diversity and metabolic functions of the other portion of the community in the microoxic/anoxic region of the mat are poorly understood. We recently described the diverse but extremely uneven microbial assemblage in the undermat of Mushroom Spring based on 16S rRNA amplicon sequences, which was dominated by Roseiflexus members, filamentous anoxygenic chlorophototrophs. In this study, we analyzed the orange-colored undermat portion of the community of Mushroom Spring mats in a genome-centric approach and discuss the metabolic potentials of the major members. Metagenome binning recovered partial genomes of all abundant community members, ranging in completeness from ~28 to 96%, and allowed affiliation of function with taxonomic identity even for representatives of novel and Candidate phyla. Less complete metagenomic bins correlated with high microdiversity. The undermat portion of the community was found to be a mixture of phototrophic and chemotrophic organisms, which use bicarbonate as well as organic carbon sources derived from different cell components and fermentation products. The presence of rhodopsin genes in many taxa strengthens the hypothesis that light energy is of major importance. Evidence for the usage of all four bacterial carbon fixation pathways was found in the metagenome. Nitrogen fixation appears to be limited to Synechococcus spp. in the upper mat layer and Thermodesulfovibrio sp. in the undermat, and nitrate/nitrite metabolism was limited. A closed sulfur cycle is indicated by biological sulfate reduction combined with the presence of genes for sulfide oxidation mainly in phototrophs. Finally, a variety of undermat

  16. The Dark Side of the Mushroom Spring Microbial Mat: Life in the Shadow of Chlorophototrophs. II. Metabolic Functions of Abundant Community Members Predicted from Metagenomic Analyses.

    Science.gov (United States)

    Thiel, Vera; Hügler, Michael; Ward, David M; Bryant, Donald A

    2017-01-01

    Microbial mat communities in the effluent channels of Octopus and Mushroom Springs within the Lower Geyser Basin of Yellowstone National Park have been extensively characterized. Previous studies have focused on the chlorophototrophic organisms of the phyla Cyanobacteria and Chloroflexi . However, the diversity and metabolic functions of the other portion of the community in the microoxic/anoxic region of the mat are poorly understood. We recently described the diverse but extremely uneven microbial assemblage in the undermat of Mushroom Spring based on 16S rRNA amplicon sequences, which was dominated by Roseiflexus members, filamentous anoxygenic chlorophototrophs. In this study, we analyzed the orange-colored undermat portion of the community of Mushroom Spring mats in a genome-centric approach and discuss the metabolic potentials of the major members. Metagenome binning recovered partial genomes of all abundant community members, ranging in completeness from ~28 to 96%, and allowed affiliation of function with taxonomic identity even for representatives of novel and Candidate phyla. Less complete metagenomic bins correlated with high microdiversity. The undermat portion of the community was found to be a mixture of phototrophic and chemotrophic organisms, which use bicarbonate as well as organic carbon sources derived from different cell components and fermentation products. The presence of rhodopsin genes in many taxa strengthens the hypothesis that light energy is of major importance. Evidence for the usage of all four bacterial carbon fixation pathways was found in the metagenome. Nitrogen fixation appears to be limited to Synechococcus spp. in the upper mat layer and Thermodesulfovibrio sp. in the undermat, and nitrate/nitrite metabolism was limited. A closed sulfur cycle is indicated by biological sulfate reduction combined with the presence of genes for sulfide oxidation mainly in phototrophs. Finally, a variety of undermat microorganisms have genes for

  17. The Dark Side of the Mushroom Spring Microbial Mat: Life in the Shadow of Chlorophototrophs. II. Metabolic Functions of Abundant Community Members Predicted from Metagenomic Analyses

    Science.gov (United States)

    Thiel, Vera; Hügler, Michael; Ward, David M.; Bryant, Donald A.

    2017-01-01

    Microbial mat communities in the effluent channels of Octopus and Mushroom Springs within the Lower Geyser Basin of Yellowstone National Park have been extensively characterized. Previous studies have focused on the chlorophototrophic organisms of the phyla Cyanobacteria and Chloroflexi. However, the diversity and metabolic functions of the other portion of the community in the microoxic/anoxic region of the mat are poorly understood. We recently described the diverse but extremely uneven microbial assemblage in the undermat of Mushroom Spring based on 16S rRNA amplicon sequences, which was dominated by Roseiflexus members, filamentous anoxygenic chlorophototrophs. In this study, we analyzed the orange-colored undermat portion of the community of Mushroom Spring mats in a genome-centric approach and discuss the metabolic potentials of the major members. Metagenome binning recovered partial genomes of all abundant community members, ranging in completeness from ~28 to 96%, and allowed affiliation of function with taxonomic identity even for representatives of novel and Candidate phyla. Less complete metagenomic bins correlated with high microdiversity. The undermat portion of the community was found to be a mixture of phototrophic and chemotrophic organisms, which use bicarbonate as well as organic carbon sources derived from different cell components and fermentation products. The presence of rhodopsin genes in many taxa strengthens the hypothesis that light energy is of major importance. Evidence for the usage of all four bacterial carbon fixation pathways was found in the metagenome. Nitrogen fixation appears to be limited to Synechococcus spp. in the upper mat layer and Thermodesulfovibrio sp. in the undermat, and nitrate/nitrite metabolism was limited. A closed sulfur cycle is indicated by biological sulfate reduction combined with the presence of genes for sulfide oxidation mainly in phototrophs. Finally, a variety of undermat microorganisms have genes for

  18. Zirconia Dental Implants: Investigation of Clinical Parameters, Patient Satisfaction, and Microbial Contamination.

    Science.gov (United States)

    Holländer, Jens; Lorenz, Jonas; Stübinger, Stefan; Hölscher, Werner; Heidemann, Detlef; Ghanaati, Shahram; Sader, Robert

    2016-01-01

    In recent years, dental implants made from zirconia have been further developed and are considered a reliable treatment method for replacing missing teeth. The aim of this study was to analyze dental implants made from zirconia regarding their clinical performance compared with natural teeth (control). One hundred six zirconia implants in 38 adults were analyzed in a clinical study after 1 year of loading. The plaque index (PI), bleeding on probing (BOP), probing pocket depth (PPD), probing attachment level (PAL), and creeping or recession (CR/REC) of the gingiva were detected and compared with natural control teeth (CT). Furthermore, the papilla index (PAP), Periotest values (PTV), microbial colonization of the implant/dental sulcus fluid, and patient satisfaction were assessed. The survival rate was 100%. No statistical significance was observed between implants and teeth regarding BOP, PPD, and PAL. A statistical significance was detected regarding PI and CR/REC with significantly less plaque accumulation and recession in the study group. Mean PAP was 1.76 ± 0.55, whereas the mean PTV was -1.31 ± 2.24 (range from -5 to +6). A non-statistically significant higher colonization of periodontitis/peri-implantitis bacteria was observed in the implant group. The questionnaire showed that the majority of the patients were satisfied with the overall treatment. One-piece zirconia dental implants exhibited similar clinical results (BOP, PPD, and PAL) compared with natural teeth in regard to adhesion of plaque (PI) and creeping attachment (CR/REC); zirconia implants performed even better. The favorable results for PAL and CR/REC reflect the comparable low affinity of zirconia for plaque adhesion. Patient satisfaction indicated a high level of acceptance for zirconia implants. However, a long-term follow-up is needed to support these findings.

  19. Depleted δ13C Values in Salt Dome Cap Rock Organic Matter and Implications for Microbial Metabolism and Fixation

    Science.gov (United States)

    Loyd, S. J.; Lu, L.; Caesar, K. H.; Kyle, R.

    2015-12-01

    Salt domes occur throughout the Gulf Coast Region USA and are often associated with trapped hydrocarbons. These salt domes can be capped by sulfate and carbonate minerals that result from complex digenetic interactions in the subsurface. The specific natures of these interactions are poorly understood, in particular the role of microbes in facilitating mineralization and element cycling. Carbon isotope compositions of cap rock calcites (δ13Ccarb) are highly variable and range from near neutral to less than -40‰ (VPDB) indicative of methane-sourced carbon. These low values and the common coexistence of elemental sulfur and metal sulfides have spurred hypotheses invoking microbial sulfate reduction as driving carbonate mineral authigenesis. Here, we present new organic carbon isotope (δ13Corg) data that, similar to δ13Ccarb, exhibit depletions below -30 to -25‰. These δ13Corg values are lower than local liquid hydrocarbons and "normal" marine organic matter reflecting either microbial fixation of methane-sourced carbon or microbial fractionation from liquid hydrocarbon sources. The combined carbon isotope data (δ13Ccarb and δ13Corg) indicate that methane likely plays an important role in microbial cycling in salt domes. The δ13Corg values are similar to those of anaerobic oxidation of methane (AOM) related communities from methane-sulfate controlled marine sediments. Ultimately, salt dome environments may share some important characteristics with AOM systems.

  20. Metagenomic analysis revealed highly diverse microbial arsenic metabolism genes in paddy soils with low-arsenic contents

    International Nuclear Information System (INIS)

    Xiao, Ke-Qing; Li, Li-Guan; Ma, Li-Ping; Zhang, Si-Yu; Bao, Peng; Zhang, Tong; Zhu, Yong-Guan

    2016-01-01

    Microbe-mediated arsenic (As) metabolism plays a critical role in global As cycle, and As metabolism involves different types of genes encoding proteins facilitating its biotransformation and transportation processes. Here, we used metagenomic analysis based on high-throughput sequencing and constructed As metabolism protein databases to analyze As metabolism genes in five paddy soils with low-As contents. The results showed that highly diverse As metabolism genes were present in these paddy soils, with varied abundances and distribution for different types and subtypes of these genes. Arsenate reduction genes (ars) dominated in all soil samples, and significant correlation existed between the abundance of arr (arsenate respiration), aio (arsenite oxidation), and arsM (arsenite methylation) genes, indicating the co-existence and close-relation of different As resistance systems of microbes in wetland environments similar to these paddy soils after long-term evolution. Among all soil parameters, pH was an important factor controlling the distribution of As metabolism gene in five paddy soils (p = 0.018). To the best of our knowledge, this is the first study using high-throughput sequencing and metagenomics approach in characterizing As metabolism genes in the five paddy soil, showing their great potential in As biotransformation, and therefore in mitigating arsenic risk to humans. - Highlights: • Use metagenomics to analyze As metabolism genes in paddy soils with low-As content. • These genes were ubiquitous, abundant, and associated with diverse microbes. • pH as an important factor controlling their distribution in paddy soil. • Imply combinational effect of evolution and selection on As metabolism genes. - Metagenomics was used to analyze As metabolism genes in paddy soils with low-As contents. These genes were ubiquitous, abundant, and associated with diverse microbes.

  1. [Impact on the Microbial Biomass and Metabolic Function of Carbon Source by Black Soil During Rice Cultivation].

    Science.gov (United States)

    Zhao, Zhi-rui; Cui, Bing-jian; Hou, Yan-lin; Liu, Shang-qian; Wang, Yan

    2015-08-01

    The effects of rice cultivation to the black soil microbial communities, which the experimentation area of Shuangyang District Agricultural Technology Extension Station in Changchun city, Jilin Province of northeastern China, were studied by using the method of phospholipid fatty acids and Biolog ECO-microplate culture. Results showed that the content of organic matter in space was the highest, fewer in the field, and the minimum in the rhizosphere, that change trend of total nitrogen and organic matter was similar in soil. The quantity of organic matter in summer sample was the highest. The microbial fun6tional diversity was significantly higher in summer than that in spring and autumn and showed no significant difference between spring and autumn. For summer and the lowest in winter, Shannon-Wiener index and Pielou index of the space were higher than the field and the rhizosphere. The time of microbial growth into the stable period and peak value of the average well color development were different in all samples, that the time was 216 h, 192 h, 216 h, 120 h, which varied from 0.52-0.84, 0.82-1.28, 0.40-0.84, 0.05-0.48, respectively. The result showed that the time of microbial growth into the stable period was similar in spring and autumn, the highest was in summer and the lowest was in winter. Above all, these results would provide more important characteristics of microbial features in the degradation and restoration process of the quality of the black soil habitat scientifically.

  2. Methanotrophs, methanogens, and microbial community structure in livestock slurry surface crusts

    DEFF Research Database (Denmark)

    Duan, Yun-Feng (Kevin); Abu Al-Soud, Waleed; Brejnrod, Asker Daniel

    2014-01-01

    Aims: Crusts forming at the surface of liquid manure (slurry) during storage has been shown to harbor a potential for mitigating CH4 emissions. This study investigated the microbial community in surface crusts, with a focus on microorganisms related to CH4 metabolism. Methods and Results: Microbial...

  3. [Characteristics of microbial community and operation efficiency in biofilter process for drinking water purification].

    Science.gov (United States)

    Xiang, Hong; Lü, Xi-Wu; Yang, Fei; Yin, Li-Hong; Zhu, Guang-Can

    2011-04-01

    In order to explore characteristics of microbial community and operation efficiency in biofilter (biologically-enhanced active filter and biological activated carbon filter) process for drinking water purification, Biolog and polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) techniques were applied to analyze the metabolic function and structure of microbial community developing in biofilters. Water quality parameters, such as NH; -N, NO; -N, permanganate index, UV254 and BDOC etc, were determined in inflow and outflow of biofilters for investigation of operation efficiency of the biofilters. The results show that metabolic capacity of microbial community of the raw water is reduced after the biofilters, which reflect that metabolically active microbial communities in the raw water can be intercepted by biofilters. After 6 months operation of biofilters, the metabolic profiles of microbial communities are similar between two kinds of biologically-enhanced active filters, and utilization of carbon sources of microbial communities in the two filters are 73.4% and 75.5%, respectively. The metabolic profiles of microbial communities in two biological activated carbon filters showed significant difference. The carbon source utilization rate of microbial community in granule-activated carbon filter is 79.6%, which is obviously higher than 53.8% of the rate in the columnar activated carbon filter (p water purification efficiency was not significant (p > 0.05). However, in biological activated carbon filters, granule-activated carbon is conducive to microbial growth and reproduction, and the microbial communities in the biofilter present high metabolic activities, and the removal efficiency for NH4(+)-N, permanganate index and BDOC is better than the columnar activated carbon filter(p < 0.05). The results also suggest that operation efficiency of biofilter is related to the metabolic capacity of microbial community in biofilter.

  4. Metagenomic analysis revealed highly diverse microbial arsenic metabolism genes in paddy soils with low-arsenic contents.

    Science.gov (United States)

    Xiao, Ke-Qing; Li, Li-Guan; Ma, Li-Ping; Zhang, Si-Yu; Bao, Peng; Zhang, Tong; Zhu, Yong-Guan

    2016-04-01

    Microbe-mediated arsenic (As) metabolism plays a critical role in global As cycle, and As metabolism involves different types of genes encoding proteins facilitating its biotransformation and transportation processes. Here, we used metagenomic analysis based on high-throughput sequencing and constructed As metabolism protein databases to analyze As metabolism genes in five paddy soils with low-As contents. The results showed that highly diverse As metabolism genes were present in these paddy soils, with varied abundances and distribution for different types and subtypes of these genes. Arsenate reduction genes (ars) dominated in all soil samples, and significant correlation existed between the abundance of arr (arsenate respiration), aio (arsenite oxidation), and arsM (arsenite methylation) genes, indicating the co-existence and close-relation of different As resistance systems of microbes in wetland environments similar to these paddy soils after long-term evolution. Among all soil parameters, pH was an important factor controlling the distribution of As metabolism gene in five paddy soils (p = 0.018). To the best of our knowledge, this is the first study using high-throughput sequencing and metagenomics approach in characterizing As metabolism genes in the five paddy soil, showing their great potential in As biotransformation, and therefore in mitigating arsenic risk to humans. Copyright © 2015 Elsevier Ltd. All rights reserved.

  5. Recent advances in microbial production of fuels and chemicals using tools and strategies of systems metabolic engineering

    DEFF Research Database (Denmark)

    Cho, Changhee; Choi, So Young; Luo, Zi Wei

    2015-01-01

    The advent of various systems metabolic engineering tools and strategies has enabled more sophisticated engineering of microorganisms for the production of industrially useful fuels and chemicals. Advances in systems metabolic engineering have been made in overproducing natural chemicals...... and producing novel non-natural chemicals. In this paper, we review the tools and strategies of systems metabolic engineering employed for the development of microorganisms for the production of various industrially useful chemicals belonging to fuels, building block chemicals, and specialty chemicals......, in particular focusing on those reported in the last three years. It was aimed at providing the current landscape of systems metabolic engineering and suggesting directions to address future challenges towards successfully establishing processes for the bio-based production of fuels and chemicals from renewable...

  6. Recent advances in microbial production of fuels and chemicals using tools and strategies of systems metabolic engineering.

    Science.gov (United States)

    Cho, Changhee; Choi, So Young; Luo, Zi Wei; Lee, Sang Yup

    2015-11-15

    The advent of various systems metabolic engineering tools and strategies has enabled more sophisticated engineering of microorganisms for the production of industrially useful fuels and chemicals. Advances in systems metabolic engineering have been made in overproducing natural chemicals and producing novel non-natural chemicals. In this paper, we review the tools and strategies of systems metabolic engineering employed for the development of microorganisms for the production of various industrially useful chemicals belonging to fuels, building block chemicals, and specialty chemicals, in particular focusing on those reported in the last three years. It was aimed at providing the current landscape of systems metabolic engineering and suggesting directions to address future challenges towards successfully establishing processes for the bio-based production of fuels and chemicals from renewable resources. Copyright © 2014 Elsevier Inc. All rights reserved.

  7. A Novel Synthetic Pathway Enables Microbial Production of Polyphenols Independent from the Endogenous Aromatic Amino Acid Metabolism.

    Science.gov (United States)

    Kallscheuer, Nicolai; Vogt, Michael; Marienhagen, Jan

    2017-03-17

    Numerous plant polyphenols have potential applications as pharmaceuticals or nutraceuticals. Stilbenes and flavonoids as most abundant polyphenols are synthesized from phenylpropanoids, which are exclusively derived from aromatic amino acids in nature. Several microorganisms were engineered for the synthesis of biotechnologically interesting plant polyphenols; however, low activity of heterologous ammonia lyases, linking endogenous microbial aromatic amino acid biosynthesis to phenylpropanoid synthesis, turned out to be the limiting step during microbial synthesis. We here developed an alternative strategy for polyphenol production from cheap benzoic acids by reversal of a β-oxidative phenylpropanoid degradation pathway avoiding any ammonia lyase activity. The synthetic pathway running in the non-natural direction is feasible with respect to thermodynamics and involved reaction mechanisms. Instantly, product titers of 5 mg/L resveratrol could be achieved in recombinant Corynebacterium glutamicum strains indicating that phenylpropanoid synthesis from 4-hydroxybenzoic acid can in principle be implemented independently from aromatic amino acids and ammonia lyase activity.

  8. An Investigation into the Effect of Gamma Irradiation on Microbial Load of Medicinal Plant of Peppermint, Iranian Thyme, Summer Savory and Lemon Balm

    Directory of Open Access Journals (Sweden)

    R. Valiasill

    2015-01-01

    Full Text Available Gamma irradiation can be used to increase post harvest quality of medicinal plants by decreasing microbial load and decontamination. Microbiological changes associated with food irradiation include the reduction or elimination of spoilage and pathogenic microorganisms, insect disinfestation and parasite disinfection. This factorial experiment was conducted on the basis of randomized complete block design with three replications. The effects of gamma irradiation on decreasing the microbial load of some medicinal plants including (Mentha piperita, lemon balm (Melissa officinalis, Summer savory (Satureja hortensis and (Zataria multiflora were investigated. Leaves of Lemon Balm, summer savory, pepper minit and thyme were irradiated at dosages of 3, 7, 10 and 15 KGy by a Co60 source, then total count, total Coliform and mold and yeast of the samples were studied. Gamma irradiation decreased microbial load of medicinal plant samples. The microbial load was detected in samples treated with 15 KGy radiation and control. Also, the result showed the highest and the lowest microbial load in peppermint and Iranian thyme, respectively. Results of this study show that gamma irradiation can be used as an important decontamination method to reduce the microbial load of medicinal plants.

  9. Metabolic profiles and phylogenetic diversity of microbial communities from chlorinated pesticides contaminated sites of different geographical habitats of India.

    Science.gov (United States)

    Manickam, N; Pathak, A; Saini, H S; Mayilraj, S; Shanker, R

    2010-10-01

    To study the microbial communities in three sites contaminated with chlorinated pesticides and evaluation of dehydrodechlorinase (linA) gene variants involved in gamma-hexachlorocyclohexane (γ-HCH, lindane) degradation. Using a culture-independent method, 16S rRNA genes were amplified from microbial communities occurring in contaminated soils. From 375 clone libraries analysed, 55 different restriction fragment length polymorphism phylotypes were obtained. Dehydrodechlorinase (linA) gene, which initiates the γ-HCH degradation, was directly amplified by PCR from the DNA extracted from soils. Deduced amino acid sequences of eight variant genotypes of linA showed few amino acid changes. All the variants of linA had mutations of F151L and S154T, and one of the genotype carried 12 amino acid changes when compared to a linA of Sphingomonas sp. reported from the same soil. The microbial communities displayed complex and diverse groups similar to bacteria involved in biodegradation. The presence of biodegradative genes like linA indicates the presence of communities with capacity to biodegrade the persistent pesticide HCH. This study provides insights to evaluate the presence of catabolic genes and assessing the bioremediation potential of the industrial soils contaminated by chlorinated pesticides. © 2010 The Authors. Journal compilation © 2010 The Society for Applied Microbiology.

  10. Investigation of [18F]2-fluoro-2-deoxyglucose for the measure of myocardial glucose metabolism

    International Nuclear Information System (INIS)

    Phelps, M.E.; Hoffman, E.J.; Selin, C.; Huang, S.C.; Robinson, G.; MacDonald, N.; Schelbert, H.; Kuhl, D.E.

    1978-01-01

    Fluorine-18-labeled 2-deoxyglucose (FDG) was studied as a glucose analog for the measure of myocardial glucose metabolism. Myocardial uptake and retention, blood clearance, species dependence (dog, monkey, man), and effect of diet on uptake were investigated. Normal myocardial uptake of FDG was 3 to 4% of injected dose in dog and monkey, and 1 to 4% in man, compared with brain uptakes of 1.5 to 3% in dog, 5 to 6% in monkey, and 4 to 8% in man. The myocardial metabolic rate (MR) for glucose in the nonfasting (glycolytic) state was 2.8 times that in the fasting (ketogenic) state. Human subjects showed higher myocardial uptake after a normal meal than after a meal containing mostly free fatty acids (FFA). Blood clearance was rapid with initial clearance t/sub 1/2/ of 0.2 to 0.3 min, followed by a t/sub 1/2/ of 8.4 +- 1.2 min in dog and 11.6 +- 1.1 min in man. A small third component had half-times of 59 +- 10 min and 88 +- 4 min in dog and man, respectively. With the ECAT positron tomograph, high image-contrast ratios were found between heart and blood (dog 3.5/1, man 14/1), heart and lung (dog 9/1, man 20/1), and heart and liver (dog 15/1, man 10/1). The FDG was taken up rapidly by the myocardium without any significant tissue clearance over a 4-hr period. The FDG exhibited excellent imaging properties. Average counting rates of 12K, 20K, and 40K c/min-mCi injected are obtained in human subjects with high, medium, and low resolutions of the ECAT tomograph. Determination of glucose and FFA MR in vivo with EACT provides a method for investigation and assessment of changing aerobic and anaerobic metabolic rates in ischemic heart disease in man

  11. Investigation of (/sup 18/F)2-fluoro-2-deoxyglucose for the measure of myocardial glucose metabolism

    Energy Technology Data Exchange (ETDEWEB)

    Phelps, M.E.; Hoffman, E.J.; Selin, C.; Huang, S.C.; Robinson, G.; MacDonald, N.; Schelbert, H.; Kuhl, D.E.

    1978-12-01

    Fluorine-18-labeled 2-deoxyglucose (FDG) was studied as a glucose analog for the measure of myocardial glucose metabolism. Myocardial uptake and retention, blood clearance, species dependence (dog, monkey, man), and effect of diet on uptake were investigated. Normal myocardial uptake of FDG was 3 to 4% of injected dose in dog and monkey, and 1 to 4% in man, compared with brain uptakes of 1.5 to 3% in dog, 5 to 6% in monkey, and 4 to 8% in man. The myocardial metabolic rate (MR) for glucose in the nonfasting (glycolytic) state was 2.8 times that in the fasting (ketogenic) state. Human subjects showed higher myocardial uptake after a normal meal than after a meal containing mostly free fatty acids (FFA). Blood clearance was rapid with initial clearance t/sub 1/2/ of 0.2 to 0.3 min, followed by a t/sub 1/2/ of 8.4 +- 1.2 min in dog and 11.6 +- 1.1 min in man. A small third component had half-times of 59 +- 10 min and 88 +- 4 min in dog and man, respectively. With the ECAT positron tomograph, high image-contrast ratios were found between heart and blood (dog 3.5/1, man 14/1), heart and lung (dog 9/1, man 20/1), and heart and liver (dog 15/1, man 10/1). The FDG was taken up rapidly by the myocardium without any significant tissue clearance over a 4-hr period. The FDG exhibited excellent imaging properties. Average counting rates of 12K, 20K, and 40K c/min-mCi injected are obtained in human subjects with high, medium, and low resolutions of the ECAT tomograph. Determination of glucose and FFA MR in vivo with EACT provides a method for investigation and assessment of changing aerobic and anaerobic metabolic rates in ischemic heart disease in man.

  12. Measuring maximum and standard metabolic rates using intermittent-flow respirometry: a student laboratory investigation of aerobic metabolic scope and environmental hypoxia in aquatic breathers.

    Science.gov (United States)

    Rosewarne, P J; Wilson, J M; Svendsen, J C

    2016-01-01

    Metabolic rate is one of the most widely measured physiological traits in animals and may be influenced by both endogenous (e.g. body mass) and exogenous factors (e.g. oxygen availability and temperature). Standard metabolic rate (SMR) and maximum metabolic rate (MMR) are two fundamental physiological variables providing the floor and ceiling in aerobic energy metabolism. The total amount of energy available between these two variables constitutes the aerobic metabolic scope (AMS). A laboratory exercise aimed at an undergraduate level physiology class, which details the appropriate data acquisition methods and calculations to measure oxygen consumption rates in rainbow trout Oncorhynchus mykiss, is presented here. Specifically, the teaching exercise employs intermittent flow respirometry to measure SMR and MMR, derives AMS from the measurements and demonstrates how AMS is affected by environmental oxygen. Students' results typically reveal a decline in AMS in response to environmental hypoxia. The same techniques can be applied to investigate the influence of other key factors on metabolic rate (e.g. temperature and body mass). Discussion of the results develops students' understanding of the mechanisms underlying these fundamental physiological traits and the influence of exogenous factors. More generally, the teaching exercise outlines essential laboratory concepts in addition to metabolic rate calculations, data acquisition and unit conversions that enhance competency in quantitative analysis and reasoning. Finally, the described procedures are generally applicable to other fish species or aquatic breathers such as crustaceans (e.g. crayfish) and provide an alternative to using higher (or more derived) animals to investigate questions related to metabolic physiology. © 2016 The Fisheries Society of the British Isles.

  13. Evaluation of some feedstuffs with special emphasis on the effect of nitrate and other non-protein nitrogen fractions on ruminal microbial metabolism

    International Nuclear Information System (INIS)

    Nikolic, J.A.

    1988-01-01

    Green herbage grown under widely different conditions was examined for nitrate content. The mean value was 0.14% (range 0.01-0.32%) NO 3 -N in the dry matter (DM). It was concluded that the cut green fodder would induce high levels of blood methaemoglobin when fed to ruminants in mixed diets. Nevertheless, experiments in vitro indicated that relatively small amounts of dietary nitrate induced considerable microbial nitrate reducing activity in rumen contents. Moreover, nitrate reduction to ammonia was accompanied by alterations in microbial sulphur and energy metabolism. A technique for determining organic matter digestibility (OMD) in vitro was standardized and used to evaluate the potential nutritive value of some fruit wastes. Studies on apple pomace silage indicated that added urea did not significantly increase the silage protein content but remained as a potential source of non-protein nitrogen for rumen microorganisms. Apple pomace ensiled alone or preferably with other ingredients was acceptable to sheep and cattle, particularly as a supplement to their winter rations. (author). 27 refs, 2 figs, 5 tabs

  14. MicroScope-an integrated resource for community expertise of gene functions and comparative analysis of microbial genomic and metabolic data.

    Science.gov (United States)

    Médigue, Claudine; Calteau, Alexandra; Cruveiller, Stéphane; Gachet, Mathieu; Gautreau, Guillaume; Josso, Adrien; Lajus, Aurélie; Langlois, Jordan; Pereira, Hugo; Planel, Rémi; Roche, David; Rollin, Johan; Rouy, Zoe; Vallenet, David

    2017-09-12

    The overwhelming list of new bacterial genomes becoming available on a daily basis makes accurate genome annotation an essential step that ultimately determines the relevance of thousands of genomes stored in public databanks. The MicroScope platform (http://www.genoscope.cns.fr/agc/microscope) is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis. Starting from the results of our syntactic, functional and relational annotation pipelines, MicroScope provides an integrated environment for the expert annotation and comparative analysis of prokaryotic genomes. It combines tools and graphical interfaces to analyze genomes and to perform the manual curation of gene function in a comparative genomics and metabolic context. In this article, we describe the free-of-charge MicroScope services for the annotation and analysis of microbial (meta)genomes, transcriptomic and re-sequencing data. Then, the functionalities of the platform are presented in a way providing practical guidance and help to the nonspecialists in bioinformatics. Newly integrated analysis tools (i.e. prediction of virulence and resistance genes in bacterial genomes) and original method recently developed (the pan-genome graph representation) are also described. Integrated environments such as MicroScope clearly contribute, through the user community, to help maintaining accurate resources. © The Author 2017. Published by Oxford University Press.

  15. Microbial and geochemical investigations of dissolved organic carbon and microbial ecology of native waters from the Biscayne and Upper Floridan Aquifers

    Science.gov (United States)

    Lisle, John T.; Harvey, Ron W.; Aiken, George R.; Metge, David W.

    2010-01-01

    Groundwater resources in the United States are under ever-increasing demands for potable, irrigation, and recreational uses. Additionally, aquifer systems are being used or targeted for use as storage areas for treated surface waters and (or) groundwaters via injection (for example, aquifer storage and recovery). To date, the influence that the nutrients, including carbon, in the injected water have on native microbial communities and the biogeochemistry in the subsurface zones used for storage of the injectate has not been determined. In this report, we describe a series of experiments that establishes a baseline dataset for the quantity and quality of organic and inorganic carbon and nutrients in the Biscayne Aquifer (BA) and Upper Floridan Aquifer (UFA) in south Florida. The most significant differences between the BA (26 meters below surface) and UFA (366 meters below surface) are the average specific conductance (0.552 and 6.12 microsiemens per centimeter, respectively), dissolved oxygen (1.6 and 0 milligrams per liter, respectively), and oxidation-reduction potential (40.3 and -358 millivolts, respectively). The dissolved organic carbon from the BA is characterized by carbon originating from terrestrial sources and microbial activities, while the UFA has a distinctive microbial signature. Acetate and lactate are the dominant carbon constituents in both aquifers. Additionally, components of the dissolved organic carbon from the UFA have a total trihalomethane-formation potential that is approximately threefold greater than the maximum contaminat level of 80 micrograms per liter established by the U.S. Environmental Protection Agency. The average native bacterial abundances in the aquifers are similar with 4.69x10^4 cells per milliliter in the BA and 1.33x10^4 cells per milliliter in the UFA. The average bacteriophage abundances are also similar with 1.15x10^5 virus-like particles in the BA and 1.92x10^5 virus-like particles in the UFA. Interestingly, ciliated

  16. A liquid chromatography – tandem mass spectrometry method to measure a selected panel of uremic retention solutes derived from endogenous and colonic microbial metabolism

    Energy Technology Data Exchange (ETDEWEB)

    Loor, Henriette de; Poesen, Ruben [KU Leuven – University of Leuven, Department of Microbiology and Immunology, Laboratory of Nephrology, B-3000 Leuven (Belgium); De Leger, Wout; Dehaen, Wim [KU Leuven – University of Leuven, Department of Chemistry, Division of Molecular Design and Synthesis, B-3000 Leuven (Belgium); Augustijns, Patrick [KU Leuven – University of Leuven, Department of Pharmaceutical and Pharmacological Sciences, Drug Delivery and Disposition, B-3000 Leuven (Belgium); Evenepoel, Pieter [KU Leuven – University of Leuven, Department of Microbiology and Immunology, Laboratory of Nephrology, B-3000 Leuven (Belgium); University Hospitals Leuven, Department of Nephrology and Renal Transplantation, B-3000 Leuven (Belgium); Meijers, Björn, E-mail: bjorn.meijers@uzleuven.be [KU Leuven – University of Leuven, Department of Microbiology and Immunology, Laboratory of Nephrology, B-3000 Leuven (Belgium); University Hospitals Leuven, Department of Nephrology and Renal Transplantation, B-3000 Leuven (Belgium)

    2016-09-14

    Chronic kidney disease (CKD) is associated with an increased risk of mortality and cardiovascular disease, which is, at least partly, mediated by the accumulation of so-called uremic retention solutes. Although there has been an increasing interest in the behavior of these solutes, derived from both the endogenous and colonic microbial metabolism, methods to simultaneously and accurately measure a broad panel of relevant uremic retention solutes remain scarce. We developed a highly sensitive ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) method. A high throughput sample preparation was used with extraction of analytes from 50 μl serum using Ostro plate technology. For most solutes, stable isotopes labelled metabolites were used as internal standards. Chromatography was achieved using an Acquity UPLC CSH Fluoro Phenyl column. The total run time was 8 min, the mobile phase was a gradient of 0.1% formic acid in Milli-Q water and pure methanol at a flow rate of 0.5 ml min{sup −1}. Detection was performed using a tandem mass spectrometer with alternated positive and negative electrospray ionization. Calibration curves were linear for all solutes. Precision was assessed according to the NCCLS EP5-T guideline, being below 15% for all metabolites. Mean recoveries were between 83 and 104% for all metabolites. The validated method was successfully applied in a cohort of 488 patients with CKD. We developed and validated a sensitive and robust UPLC-MS/MS method for quantification of 15 uremic retention solutes derived from endogenous and colonic microbial metabolism. This method allows for studying the behavior and relevance of these solutes in patients with CKD. - Highlights: • Simultaneous quantification of fifteen relevant uremic retention solutes. • Comprehensive validation, highly sensitive and high through-put LC-MSMS method. • Comparison of different blood tubes. • Freeze-thaw stability. • Successful implementation in a

  17. Impact of airborne zinc pollution on the antimicrobial activity of olive oil and the microbial metabolic profiles of Zn-contaminated soils in an Italian olive orchard.

    Science.gov (United States)

    Sofo, Adriano; Elshafie, Hazem S; Scopa, Antonio; Mang, Stefania M; Camele, Ippolito

    2018-02-19

    The growing of microbial resistance leads to a great interest about some natural alternatives to synthetic compounds. This study was carried out in two olive orchards (Olea europaea L., cv. Coratina) South Italy (Basilicata region), one located in a polluted area near a fertilizers factory releasing Zn and the other in a control unpolluted site, both managed with similar cultivation techniques. Olive oil samples were studied from both areas during 2014 and 2015. The soil microbiological status of the polluted and unpolluted orchards has been characterized and the antimicrobial effects of olive oils extracted from polluted plants (PP) and control plants (CP) against some phytopathogens have been explored. Results showed that the antibacterial activity of PP oil was significantly higher than CP and this could be due to the high content of some phenolic compounds elicited by air and soil Zn pollution (especially in the layer 0-20 cm). There is no detectable antifungal activity of the studied oils. The metabolic activity (both total and for each carbon substrate group), diversity and evenness of PP soil bacterial communities were significantly different from CP soil, while the effects of soil depth was negligible. The same parameters measured on soil fungal communities are lower in PP soil at 0-20 cm soil depth. The current research clarified the impact of atmospheric Zn pollution on the antimicrobial activity of olive oil and the soil microbial metabolic profiles. The bioactive substances extracted from olive oils growing in Zn-polluted area might be used as antibiotics. Copyright © 2018 Elsevier GmbH. All rights reserved.

  18. Chemical Investigations of Marine Filamentous and Zoosporic Fungi and Studies in Marine Microbial Chemical Ecology

    OpenAIRE

    Jenkins, Kelly M.

    1998-01-01

    The natural products chemistry of marine microorganisms is an emerging area of organic chemistry with the aim of discovering novel secondary metabolites exhibiting both biomedical and ecological activities. While marine bacteria have proven to be a productive source of new natural products, there are many groups of marine microorganisms which have not been fully investigated. In particular, marine fungi represent an untapped and potentially novel source of bioactive secondary metabolites. Whi...

  19. Do microbial interactions and cultivation media decrease the accuracy of Salmonella surveillance systems and outbreak investigations?

    Science.gov (United States)

    Singer, Randall S; Mayer, Anne E; Hanson, Timothy E; Isaacson, Richard E

    2009-04-01

    Cultivation methods are commonly used in Salmonella surveillance systems and outbreak investigations, and consequently, conclusions about Salmonella evolution and transmission are highly dependent on the performance characteristics of these methods. Past studies have shown that Salmonella serotypes can exhibit different growth characteristics in the same enrichment and selective media. This could lead not only to biased conclusions about the dominant strain present in a sample with mixed Salmonella populations, but also to a low sensitivity for detecting a Salmonella strain in a sample with only a single strain present. The objective of this study was to determine whether cultivation media select preferentially for specific strains of Salmonella in heterogeneous cultures. In this study, four different Salmonella strains (one Salmonella Newport, two Salmonella Typhimurium, and one Salmonella Enteritidis) were competed in a broth-based experiment and a bovine fecal experiment with varied combinations and concentrations of each strain. In all experiments, the strain of Salmonella Newport was the most competitive, regardless of the starting concentration and cultivation protocol. One strain of Salmonella Typhimurium was rarely detected in competition, even when it was the only strain present in bovine feces. Overall, the probability of detecting a specific Salmonella strain had little to do with its starting concentration in the sample. The bias introduced by culture could be dramatically biasing Salmonella surveillance systems and hindering traceback investigations during Salmonella outbreaks. Future studies should focus on the microbiological explanations for this Salmonella interstrain variability, approaches for minimizing the bias, and estimations of the public health significance of this bias.

  20. γ–Butyrobetaine is a pro-atherogenic intermediate in gut microbial metabolism of L-carnitine to TMAO

    OpenAIRE

    Koeth, Robert A.; Levison, Bruce S.; Culley, Miranda K.; Buffa, Jennifer A.; Wang, Zeneng; Gregory, Jill C.; Org, Elin; Wu, Yuping; Li, Lin; Smith, Jonathan D.; Wilson Tang, W. H.; DiDonato, Joseph A.; Lusis, Aldons J.; Hazen, Stanley L.

    2014-01-01

    L- Carnitine, a nutrient in red meat, was recently reported to accelerate atherosclerosis via a metaorganismal pathway involving gut microbial trimethylamine (TMA) formation and host hepatic conversion into trimethylamine-N-oxide (TMAO). Herein we show that following L-carnitine ingestion, γ-butyrobetaine (γBB) is produced as an intermediary metabolite by gut microbes at a site anatomically proximal to and at a rate ~1000-fold higher than the formation of TMA. Moreover, we show γBB is the maj...

  1. The suppressive effect of apricot kernel extract on 5alpha-Androst-16-en-3-one generated by microbial metabolism.

    Science.gov (United States)

    Mikoshiba, S; Takenaka, H; Okumura, T; Someya, K; Ohdera, M

    2006-02-01

    Body odours are generated from dead skin cells and secreted materials, such as sweat and sebum, through the metabolism of microorganisms living on the skin. Volatile steroids, key compounds in body odours, are also generated through the metabolism of microorganisms. These volatile steroids strengthen the intensity of the overall body malodour and are sensed differently by males and females. Females are more sensitive than males to volatile steroids, especially 5alpha-androst-16-en-3-one (androstenone). To regulate body odours that are especially unpleasant for women, we devised an androstenone-generation model using the metabolism of Corynebacterium xerosis, which is one of the bacteria living on the axillary skin. Using this model, we studied the suppressive effect of plant extracts on the generation of androstenone. We found that apricot kernel extract (AKE) had the most positive effect among the plant extracts to which we applied the model. However, although AKE did suppress androstenone generation, it did not show any bactericidal effect. Using the cell-free system, AKE also suppressed the generation of androstenone. In conclusion, we found that AKE suppressed the generation of androstenone, which is especially unpleasant for women, and the mechanism was not bactericidal but metabolic inhibition. The results of these studies provide new understanding of the regulation of androstenone, which, in turn, should lead to the development of novel deodorant systems.

  2. Belowground Response to Drought in a Tropical Forest Soil. I. Changes in Microbial Functional Potential and Metabolism

    Science.gov (United States)

    Nicholas J. Bouskill; Tana E. Wood; Richard Baran; Zaw Ye; Benjamin P. Bowen; HsiaoChien Lim; Jizhong Zhou; Joy D. Van Nostrand; Peter Nico; Trent R. Northen; Whendee L. Silver; Eoin L. Brodie

    2016-01-01

    Global climate models predict a future of increased severity of drought in many tropical forests. Soil microbes are central to the balance of these systems as sources or sinks of atmospheric carbon (C), yet how they respond metabolically to drought is not well-understood. We simulated...

  3. Laxative treatment with polyethylene glycol decreases microbial primary bile salt dehydroxylation and lipid metabolism in the intestine of rats

    NARCIS (Netherlands)

    Wulp, van der N.Y.; Derrien, M.; Stellaard, F.; Wolters, H.; Kleerebezem, M.; Dekker, J.; Rings, E.H.; Groen, A.K.; Verkade, H.J.

    2013-01-01

    Polyethylene glycol (PEG) is a frequently used osmotic laxative that accelerates gastrointestinal transit. It has remained unclear, however, whether PEG affects intestinal functions. We aimed to determine the effect of PEG treatment on intestinal sterol metabolism. Rats were treated with PEG in

  4. Investigation and visualization of internal flow through particle aggregates and microbial flocs using particle image velocimetry.

    Science.gov (United States)

    Xiao, Feng; Lam, Kit Ming; Li, Xiao-yan

    2013-05-01

    An advanced particle-tracking and flow-visualization technology, particle image velocimetry (PIV), was utilized to investigate the hydrodynamic properties of large aggregates in water. The laser-based PIV system was used together with a settling column to capture the streamlines around two types of aggregates: latex particle aggregates and activated sludge (AS) flocs. Both types of the aggregates were highly porous and fractal with fractal dimensions of 2.13±0.31 for the latex particle aggregates (1210-2144 μm) and 1.78±0.24 for the AS flocs (1265-3737 μm). The results show that PIV is a powerful flow visualization technique capable of determining flow field details at the micrometer scale around and through settling aggregates and flocs. The PIV streamlines provided direct experimental proof of internal flow through the aggregate interiors. According to the PIV images, fluid collection efficiency ranged from 0.052 to 0.174 for the latex particle aggregates and from 0.008 to 0.126 for AS flocs. AS flocs are apparently less permeable than the particle aggregates, probably due to the extracellular polymeric substances (EPSs) produced by bacteria clogging the pores within the flocs. The internal permeation of fractal aggregates and bio-flocs would enhance flocculation between particles and material transport into the aggregates. Copyright © 2013 Elsevier Inc. All rights reserved.

  5. [Investigation of metabolic parame- ters in high yielding dairy cows in pasture based production systems].

    Science.gov (United States)

    Reichert, S; Wichert, B; Wanner, M; Liesegang, A

    2015-11-01

    In the present study differences in metabolism between New Zealand Holstein-Friesian (NZHF) and Brown Swiss (CH-BV) or Swiss Holstein-Friesian (CH-HF) were investigated in a grassland based milk production system in Switzerland. Therefore 14 pairs of CH-BV/NZHF and 11 pairs of CH-HF/NZHF were available. The parameters glucose, insulin, non-esterified fatty acids (NEFA), β-hydroxybutyrate (β-HB), urea and cholesterol were analysed at the times 5-3 weeks before the calculated partus and 2, 3, 5, 7, 10 and 18-22 weeks post partum. Only β-HB showed significantly higher concentrations (P = 0.0059) for both Swiss breeds compared to the NZ-HF. Regarding all other physiological parameters during early lactation New Zealand Holstein-Friesians were not different from Swiss breeds.

  6. Investigating depression-like and metabolic parameters in a chronic low-grade inflammation model

    DEFF Research Database (Denmark)

    Fischer, C. W.; Elfving, B.; Lund, S.

    2012-01-01

    that elevated markers of inflammation predict a poor response to treatment. Furthermore, increasing evidences show that metabolic abnormalities such as obesity and diabetes mellitus type 2 are associated with a low-grade inflammation. Objectives: The aim of this study is to investigate the effects of a systemic...... levels of pro-inflammatory cytokines (TNF-alpha, IL-1, IL-6) together with the expression of enzymes involved in the tryptophan-kynurenine pathway, will be analyzed in specific brain regions using real-time qPCR. Body weight and food intake was measured once a week, while fasting glucose and insulin...... sensitivity was assessed after four weeks of LPS administration. Findings and conclusion: Our results showed that a low dose of LPS increased immobility in the FST relative to vehicle treatment, indicative of depression-like behavior. We did not find any difference in body weight, fasting glucose and insulin...

  7. Investigation of 18F-2-deoxyglucose for the measure of myocardial glucose metabolism

    International Nuclear Information System (INIS)

    Phelps, M.E.; Hoffman, E.J.; Selin, C.; Huang, S.C.; Robinson, G.; MacDonald, N.; Schelbert, H.R.; Kuhl, D.E.

    1977-01-01

    18 F labeled 2-deoxyglucose ( 18 FDG) was studied as a glucose analog. Myocardial uptake and retention, blood clearance, species (dog, monkey, man) dependence and effect of diet on uptake were investigated. Normal myocardial uptake of 18 FDG was 3 to 4% in dog and monkey and 1 to 4% of injected dose in man compared to brain uptake of 2% in dog, 5 to 6% in monkey and 4 to 8% in man. The metabolic rate (MR) for glucose in non-fasting (glycolytic state) was 2.8 times greater than in fasting (ketogenic state). Human subjects showed higher myocardial uptake after a normal meal than after meal containing mostly free fatty acids (FFA). Blood clearance was rapid with initial clearance t 1 / 2 of 0.2 to 0.3 min followed by a t 1 / 2 of 8.4 +- 1.2 min in dog and 11.6 +- 1.1 min in man. A small third component had a t 1 / 2 of 59 +- 10 min and 88 +- 4 min in dog and man, respectively. High image contrast ratios between heart and blood (dog 3.5/1; man 14/1), heart and lung (dog 9/1; man 20/1), heart and liver (dog 15/1; man 10/1) were found with the ECAT positron tomograph. 18 FDG was found to be rapidly taken up by the myocardium without any significant tissue clearance over a 4 hour period. 18 FDG is transported, phosphorylated to 18 FDG-6-PO 4 and trapped in myocardial cells in the same manner as has been found for brain and exhibits excellent imaging properties. Determination of glucose and FFA MR in vivo with ECT provides a method for investigation and assessment of changing aerobic and anaerobic metabolic rates in ischemic heart disease in man

  8. Effective survival of immobilized Lactobacillus casei during ripening and heat treatment of probiotic dry-fermented sausages and investigation of the microbial dynamics.

    Science.gov (United States)

    Sidira, Marianthi; Karapetsas, Athanasios; Galanis, Alex; Kanellaki, Maria; Kourkoutas, Yiannis

    2014-02-01

    The aim was the assessment of immobilized Lactobacillus casei ATCC 393 on wheat in the production of probiotic dry-fermented sausages and the investigation of the microbial dynamics. For comparison, sausages containing either free L. casei ATCC 393 or no starter culture were also prepared. During ripening, the numbers of lactobacilli exceeded 7 log cfu/g, while a drastic decrease was observed in enterobacteria, staphylococci and pseudomonas counts. Microbial diversity was further studied applying a PCR-DGGE protocol. Members of Lactobacillus, Leuconostoc, Lactococcus, Carnobacterium, Brochothrix, Bacillus and Debaryomyces were the main microbial populations detected. Microbiological and strain-specific multiplex PCR analysis confirmed that the levels of L. casei ATCC 393 in the samples after 66 days of ripening were above the minimum concentration for conferring a probiotic effect (≥ 6 log cfu/g). However, after heat treatment, this strain was detected at the above levels, only in sausages containing immobilized cells. © 2013.

  9. Evolution of microbial activity in a mediterranean ecosystem submitted to chronic gamma irradiation. Investigation of nitrogen transfer with isotopic tracers

    International Nuclear Information System (INIS)

    Castet, R.

    1987-07-01

    A mediterranean ecosystem located on the site of Cadarache (France) has been experimentally by irradiated over the past fifteen years. The potential effects of ionizing radiations for different doses of its ecological system has been studied. The objective of the work was to demonstrate the level of soil microbial population and its activity. Chronic exposures reduced the biomass and the dehydrogenase activity by a factor of 50% and increased the amount of nitrate in the soil. To measure the direct impact of irradiations on soil microorganisms, we have irradiated soil sample in laboratory at 0.1; 0.5; 1 kGy, and observed its evolution during a period of six weeks thereafter. We have a reduction of the dehydrogenase activity and an increase of nitrate being proportionaly to the dose delivered. Using nitrogen labelled, we state that this high rate of nitrate production is due to an inhibition of the organization of this form of nitrogen. Conversely, the ammonification and the nitrification are not affected. Also, for anaerobic conditions created by glucose, the nitrate labelled (15N) permitted us to show that in untreated soil, 45% of nitrate was reduced to nitrogen gas by denitrification and 24% of nitrate was reduced to ammonium by dissimilation in the irradiated soil. These experiments show that gamma irradiations are of great interest for studying soil microorganisms. As of now, very little is known on the effects of this kind of stress for attention and need to be pursued on such ecosystems. Further investigations call [fr

  10. Investigating the effect of aqueous extracts of basil and savory on antioxidant activity, microbial and sensory properties of probiotic yogurt.

    Science.gov (United States)

    Mosiyani, Zohreh Ghaleh; Pourahmad, Rezvan; Eshaghi, Mohammad Reza

    2017-01-01

    The low viability of probiotics causes the short shelf life of fermented products. Therefore compounds which prolong the viability of probiotic bacteria can increase or at least maintain the health- benefiting properties of these products. On the other hand, the addition of antioxidants is one of the methods to increase the shelf life of food products which has recently become more prevalent. In this respect, herbal extracts which are a good source of antioxidants can be appropriate alternative. The aim of this study was  to evaluate the effect of adding basil and savory extracts on antioxidant activity, and on the microbial and organoleptic characteristics of probiotic yogurt. The effect of adding basil extract (8% and 10%) and savory extract (6% and 8%) separately to low fat yogurt (1.5% fat) containing Lactobacillus paracasei subsp. paracasei was investigated. The samples were stored at 4°C. The viability of Lactobacillus paracasei subsp. paracasei, antioxidant activ- ity and sensory properties of probiotic yogurt were evaluated on the 1st, 7th, 14th and 21st days. Basil and savory extracts significantly increased the viability of probiotic bacteria (p 0.05). During storage, there was no significant difference between the organoleptic scores of the samples (p > 0.05), but the taste score did increase significantly (p yogurt.

  11. The adsorption behavior and mechanism investigation of Pb(II) removal by flocculation using microbial flocculant GA1.

    Science.gov (United States)

    Feng, Jing; Yang, Zhaohui; Zeng, Guangming; Huang, Jing; Xu, Haiyin; Zhang, Yuanyuan; Wei, Shumei; Wang, Like

    2013-11-01

    In this work, microbial flocculant GA1 (MBFGA1) was used to remove Pb(II) ions from aqueous solution. A series of experimental parameters including initial pH, MBFGA1 dose, temperature and initial calcium ions concentration on Pb(II) uptake was evaluated. Meanwhile, the flocculation mechanism of MBFGA1 was investigated. The removal efficiency of Pb(II) reached up to 99.85% when MBFGA1 was added in two stages, separately. The results indicated that Pb(II) adsorption could be described by the Langmuir adsorption model, and being the monolayer capacity negatively affected with an increase in temperature. The adsorption process could be described by pseudo-second-order kinetic model. Fourier transform-infrared spectra and environmental scanning electron microscope analysis indicated that MBFGA1 had a large number of functional groups, which had strong capacity for removing Pb(II). The main mechanisms of Pb(II) removal by MBFGA1 could be charge neutralization and adsorption bridging. Copyright © 2013 Elsevier Ltd. All rights reserved.

  12. Enteric short-chain fatty acids: microbial messengers of metabolism, mitochondria, and mind: implications in autism spectrum disorders

    Directory of Open Access Journals (Sweden)

    Derrick F. MacFabe

    2015-05-01

    Full Text Available Clinical observations suggest that gut and dietary factors transiently worsen and, in some cases, appear to improve behavioral symptoms in a subset of persons with autism spectrum disorders (ASDs, but the reason for this is unclear. Emerging evidence suggests ASDs are a family of systemic disorders of altered immunity, metabolism, and gene expression. Pre- or perinatal infection, hospitalization, or early antibiotic exposure, which may alter gut microbiota, have been suggested as potential risk factors for ASD. Can a common environmental agent link these disparate findings? This review outlines basic science and clinical evidence that enteric short-chain fatty acids (SCFAs, present in diet and also produced by opportunistic gut bacteria following fermentation of dietary carbohydrates, may be environmental triggers in ASD. Of note, propionic acid, a major SCFA produced by ASD-associated gastrointestinal bacteria (clostridia, bacteroides, desulfovibrio and also a common food preservative, can produce reversible behavioral, electrographic, neuroinflammatory, metabolic, and epigenetic changes closely resembling those found in ASD when administered to rodents. Major effects of these SCFAs may be through the alteration of mitochondrial function via the citric acid cycle and carnitine metabolism, or the epigenetic modulation of ASD-associated genes, which may be useful clinical biomarkers. It discusses the hypothesis that ASDs are produced by pre- or post-natal alterations in intestinal microbiota in sensitive sub-populations, which may have major implications in ASD cause, diagnosis, prevention, and treatment.

  13. Metabolic and microbial community dynamics during the hydrolytic and acidogenic fermentation in a leach-bed process

    Energy Technology Data Exchange (ETDEWEB)

    Straeuber, Heike; Kleinsteuber, Sabine [UFZ - Helmholtz Centre for Environmental Research, Leipzig (Germany). Dept. of Bioenergy; UFZ - Helmholtz Centre for Environmental Research, Leipzig (Germany). Dept. of Environmental Microbiology; Schroeder, Martina [UFZ - Helmholtz Centre for Environmental Research, Leipzig (Germany). Dept. of Bioenergy

    2012-12-15

    Biogas production from lignocellulosic feedstock not competing with food production can contribute to a sustainable bioenergy system. The hydrolysis is the rate-limiting step in the anaerobic digestion of solid substrates such as straw. Hence, a detailed understanding of the metabolic processes during the steps of hydrolysis and acidogenesis is required to improve process control strategies. The fermentation products formed during the acidogenic fermentation of maize silage as a model substrate in a leach-bed process were determined by gas and liquid chromatography. The bacterial community dynamics was monitored by terminal restriction fragment length polymorphism analysis. The community profiles were correlated with the process data using multivariate statistics. The batch process comprised three metabolic phases characterized by different fermentation products. The bacterial community dynamics correlated with the production of the respective metabolites. In phase 1, lactic and acetic acid fermentations dominated. Accordingly, bacteria of the genera Lactobacillus and Acetobacter were detected. In phase 2, the metabolic pathways shifted to butyric acid fermentation, accompanied by the production of hydrogen and carbon dioxide and a dominance of the genus Clostridium. In phase 3, phylotypes affiliated with Ruminococcaceae and Lachnospiraceae prevailed, accompanied by the formation of caproic and acetic acids, and a high gas production rate. A clostridial butyric type of fermentation was predominant in the acidogenic fermentation of maize silage, whereas propionic-type fermentation was marginal. As the metabolite composition resulting from acidogenesis affects the subsequent methanogenic performance, process control should focus on hydrolysis/acidogenesis when solid substrates are digested. (orig.)

  14. Investigation on Abnormal Iron Metabolism and Related Inflammation in Parkinson Disease Patients with Probable RBD

    Science.gov (United States)

    Hu, Yang; Yu, Shu-Yang; Zuo, Li-Jun; Piao, Ying-Shan; Cao, Chen-Jie; Wang, Fang; Chen, Ze-Jie; Du, Yang; Lian, Teng-Hong; Liu, Gai-Fen; Wang, Ya-Jie; Chan, Piu; Chen, Sheng-Di; Wang, Xiao-Min; Zhang, Wei

    2015-01-01

    Objective To investigate potential mechanisms involving abnormal iron metabolism and related inflammation in Parkinson disease (PD) patients with probable rapid eye movement sleep behavior disorder (PRBD). Methods Total 210 PD patients and 31 controls were consecutively recruited. PD patients were evaluated by RBD Screening Questionnaire (RBDSQ) and classified into PRBD and probable no RBD (NPRBD) groups. Demographics information were recorded and clinical symptoms were evaluated by series of rating scales. Levels of iron and related proteins and inflammatory factors in cerebrospinal fluid (CSF) and serum were detected. Comparisons among control, NPRBD and PRBD groups and correlation analyses between RBDSQ score and levels of above factors were performed. Results (1)The frequency of PRBD in PD patients is 31.90%. (2)PRBD group has longer disease duration, more advanced disease stage, severer motor symptoms and more non-motor symptoms than NPRBD group. (3)In CSF, levels of iron, transferrin, NO and IL–1β in PRBD group are prominently increased. RBDSQ score is positively correlated with the levels of iron, transferrin, NO and IL–1β in PD group. Iron level is positively correlated with the levels of NO and IL–1β in PD group. (4)In serum, transferrin level is prominently decreased in PRBD group. PGE2 level in PRBD group is drastically enhanced. RBDSQ score exhibits a positive correlation with PGE2 level in PD group. Conclusions PRBD is common in PD patients. PRBD group has severer motor symptoms and more non-motor symptoms. Excessive iron in brain resulted from abnormal iron metabolism in central and peripheral systems is correlated with PRBD through neuroinflammation. PMID:26431210

  15. Integrated Investigation on the Production and Fate of Organo-Cr(III) Complexes from Microbial Reduction of Chromate

    Energy Technology Data Exchange (ETDEWEB)

    Xun, Luying

    2005-06-01

    Our objective is to investigate the complexity of chromium biogeocycling. Our results clearly support more complexity. In short, the chromium cycle is not as simple as the conversion between Cr(III) and Cr(VI) in inorganic forms. We have obtained more evidence to prove the formation of soluble organo-Cr(III) complexes from microbial reduction of Cr(VI). The complexes are relatively stable due to the slow ligand exchange of Cr(III). However, some microorganisms can consume the organic ligands and release Cr(III), which then precipitates. Efforts are being made to characterize the organo-Cr(III) complexes and investigate their behavior in soil. Progress and efforts are summarized for each task. Task 1. Production of soluble organo-Cr(III) complexes by selected microorganisms A total of eight organisms were screened for production of soluble organo-Cr(III) complexes by culturing in both growth and non growth media containing 4 mg/L of Cr(VI); three were Gram positive and five were Gram negative. The Gram-positive bacteria were Cellulomonas sp. ES 6, Rhodococcus sp., and Leafsonia sp., while Shewanella oneidensis MR 1, Desulfovibrio desulfuricans G20, D. vulgaris Hildenborough, Pseudomonas putida MK 1 and Ps. aeruginosa PAO 1 were Gram negative. Purifications of the soluble organo-Cr(III) complexes produced by Cellulomonas sp. ES 6, Shewanella. oneidensis MR 1, Rhodococcus sp., and D. vulgaris Hildenborough were carried out. The culture supernatants were lyophilized and extracted first with methanol followed by water. The extracts were then analyzed for soluble Cr. The majority of the Cr(III) was present in the water-soluble fraction for all of the bacteria tested (data not shown), revealing a general phenomenon of soluble Cr(III) production. Cellulomonas sp. ES6 produced the highest amount of soluble Cr(III) (364 ppm) and D. vulgaris Hildenborough produced the least (143 ppm). Seventy eight percent of the soluble Cr(III) produced by Shewanella. oneidensis MR 1 was

  16. Biosignature Preservation Vulnerability Associated with Stress Response Metabolic Redox Mode Switching in a Mars Analogue Coupled Microbial Mat Transiting Near-Space

    Science.gov (United States)

    Archer, R.; Ralat, A.

    2016-05-01

    Examination of a coupled microbial mat recovered from Death Valley failed to detect rosickyte, both before and after exposure to near-space conditions; associated redox proxies suggest diagenesis caused by rapid adaptive microbial stress response.

  17. Methanosarcina Play an Important Role in Anaerobic Co-Digestion of the Seaweed Ulva lactuca: Taxonomy and Predicted Metabolism of Functional Microbial Communities.

    Directory of Open Access Journals (Sweden)

    Jamie A FitzGerald

    Full Text Available Macro-algae represent an ideal resource of third generation biofuels, but their use necessitates a refinement of commonly used anaerobic digestion processes. In a previous study, contrasting mixes of dairy slurry and the macro-alga Ulva lactuca were anaerobically digested in mesophilic continuously stirred tank reactors for 40 weeks. Higher proportions of U. lactuca in the feedstock led to inhibited digestion and rapid accumulation of volatile fatty acids, requiring a reduced organic loading rate. In this study, 16S pyrosequencing was employed to characterise the microbial communities of both the weakest (R1 and strongest (R6 performing reactors from the previous work as they developed over a 39 and 27-week period respectively. Comparing the reactor communities revealed clear differences in taxonomy, predicted metabolic orientation and mechanisms of inhibition, while constrained canonical analysis (CCA showed ammonia and biogas yield to be the strongest factors differentiating the two reactor communities. Significant biomarker taxa and predicted metabolic activities were identified for viable and failing anaerobic digestion of U. lactuca. Acetoclastic methanogens were inhibited early in R1 operation, followed by a gradual decline of hydrogenotrophic methanogens. Near-total loss of methanogens led to an accumulation of acetic acid that reduced performance of R1, while a slow decline in biogas yield in R6 could be attributed to inhibition of acetogenic rather than methanogenic activity. The improved performance of R6 is likely to have been as a result of the large Methanosarcina population, which enabled rapid removal of acetic acid, providing favourable conditions for substrate degradation.

  18. Methanosarcina Play an Important Role in Anaerobic Co-Digestion of the Seaweed Ulva lactuca: Taxonomy and Predicted Metabolism of Functional Microbial Communities.

    Science.gov (United States)

    FitzGerald, Jamie A; Allen, Eoin; Wall, David M; Jackson, Stephen A; Murphy, Jerry D; Dobson, Alan D W

    2015-01-01

    Macro-algae represent an ideal resource of third generation biofuels, but their use necessitates a refinement of commonly used anaerobic digestion processes. In a previous study, contrasting mixes of dairy slurry and the macro-alga Ulva lactuca were anaerobically digested in mesophilic continuously stirred tank reactors for 40 weeks. Higher proportions of U. lactuca in the feedstock led to inhibited digestion and rapid accumulation of volatile fatty acids, requiring a reduced organic loading rate. In this study, 16S pyrosequencing was employed to characterise the microbial communities of both the weakest (R1) and strongest (R6) performing reactors from the previous work as they developed over a 39 and 27-week period respectively. Comparing the reactor communities revealed clear differences in taxonomy, predicted metabolic orientation and mechanisms of inhibition, while constrained canonical analysis (CCA) showed ammonia and biogas yield to be the strongest factors differentiating the two reactor communities. Significant biomarker taxa and predicted metabolic activities were identified for viable and failing anaerobic digestion of U. lactuca. Acetoclastic methanogens were inhibited early in R1 operation, followed by a gradual decline of hydrogenotrophic methanogens. Near-total loss of methanogens led to an accumulation of acetic acid that reduced performance of R1, while a slow decline in biogas yield in R6 could be attributed to inhibition of acetogenic rather than methanogenic activity. The improved performance of R6 is likely to have been as a result of the large Methanosarcina population, which enabled rapid removal of acetic acid, providing favourable conditions for substrate degradation.

  19. Involvement of gut microbial fermentation in the metabolic alterations occurring in n-3 polyunsaturated fatty acids-depleted mice

    Directory of Open Access Journals (Sweden)

    Carpentier Yvon A

    2011-06-01

    Full Text Available Abstract Backround Western diet is characterized by an insufficient n-3 polyunsaturated fatty acid (PUFA consumption which is known to promote the pathogenesis of several diseases. We have previously observed that mice fed with a diet poor in n-3 PUFA for two generations exhibit hepatic steatosis together with a decrease in body weight. The gut microbiota contributes to the regulation of host energy metabolism, due to symbiotic relationship with fermentable nutrients provided in the diet. In this study, we have tested the hypothesis that perturbations of the gut microbiota contribute to the metabolic alterations occurring in mice fed a diet poor in n-3 PUFA for two generations (n-3/- mice. Methods C57Bl/6J mice fed with a control or an n-3 PUFA depleted diet for two generations were supplemented with prebiotic (inulin-type Fructooligosaccharides, FOS, 0.20 g/day/mice during 24 days. Results n-3/-mice exhibited a marked drop in caecum weight, a decrease in lactobacilli and an increase in bifidobacteria in the caecal content as compared to control mice (n-3/+ mice. Dietary supplementation with FOS for 24 days was sufficient to increase caecal weight and bifidobacteria count in both n-3/+ and n-3/-mice. Moreover, FOS increased lactobacilli content in n-3/-mice, whereas it decreased their level in n-3/+ mice. Interestingly, FOS treatment promoted body weight gain in n-3/-mice by increasing energy efficiency. In addition, FOS treatment decreased fasting glycemia and lowered the higher expression of key factors involved in the fatty acid catabolism observed in the liver of n-3/-mice, without lessening steatosis. Conclusions the changes in the gut microbiota composition induced by FOS are different depending on the type of diet. We show that FOS may promote lactobacilli and counteract the catabolic status induced by n-3 PUFA depletion in mice, thereby contributing to restore efficient fat storage.

  20. Novel mode of microbial energy metabolism: organic carbon oxidation coupled to dissimilatory reduction of iron or manganese.

    Science.gov (United States)

    Lovley, D R; Phillips, E J

    1988-06-01

    A dissimilatory Fe(III)- and Mn(IV)-reducing microorganism was isolated from freshwater sediments of the Potomac River, Maryland. The isolate, designated GS-15, grew in defined anaerobic medium with acetate as the sole electron donor and Fe(III), Mn(IV), or nitrate as the sole electron acceptor. GS-15 oxidized acetate to carbon dioxide with the concomitant reduction of amorphic Fe(III) oxide to magnetite (Fe(3)O(4)). When Fe(III) citrate replaced amorphic Fe(III) oxide as the electron acceptor, GS-15 grew faster and reduced all of the added Fe(III) to Fe(II). GS-15 reduced a natural amorphic Fe(III) oxide but did not significantly reduce highly crystalline Fe(III) forms. Fe(III) was reduced optimally at pH 6.7 to 7 and at 30 to 35 degrees C. Ethanol, butyrate, and propionate could also serve as electron donors for Fe(III) reduction. A variety of other organic compounds and hydrogen could not. MnO(2) was completely reduced to Mn(II), which precipitated as rhodochrosite (MnCO(3)). Nitrate was reduced to ammonia. Oxygen could not serve as an electron acceptor, and it inhibited growth with the other electron acceptors. This is the first demonstration that microorganisms can completely oxidize organic compounds with Fe(III) or Mn(IV) as the sole electron acceptor and that oxidation of organic matter coupled to dissimilatory Fe(III) or Mn(IV) reduction can yield energy for microbial growth. GS-15 provides a model for how enzymatically catalyzed reactions can be quantitatively significant mechanisms for the reduction of iron and manganese in anaerobic environments.

  1. Investigation of the microbial community structure and activity as indicators of compost stability and composting process evolution.

    Science.gov (United States)

    Chroni, Christina; Kyriacou, Adamadini; Manios, Thrassyvoulos; Lasaridi, Konstantia-Ekaterini

    2009-08-01

    In a bid to identify suitable microbial indicators of compost stability, the process evolution during windrow composting of poultry manure (PM), green waste (GW) and biowaste was studied. Treatments were monitored with regard to abiotic factors, respiration activity (determined using the SOUR test) and functional microflora. The composting process went through typical changes in temperature, moisture content and microbial properties, despite the inherent feedstock differences. Nitrobacter and pathogen indicators varied as a monotonous function of processing time. Some microbial groups have shown a potential to serve as fingerprints of the different process stages, but still they should be examined in context with respirometric tests and abiotic parameters. Respiration activity reflected well the process stage, verifying the value of respirometric tests to access compost stability. SOUR values below 1 mg O(2)/g VS/h were achieved for the PM and the GW compost.

  2. Inbreeding effects on standard metabolic rate investigated at cold, benign and hot temperatures in Drosophila melanogaster

    DEFF Research Database (Denmark)

    Jensen, Palle; Overgaard, Johannes; Loeschcke, Volker

    2014-01-01

    in replicated lines of inbred and outbred Drosophila melanogaster at stressful low, benign and stressful high temperatures. The lowest measurements of metabolic rate in our study are always associated with the low activity period of the diurnal cycle and these measurements therefore serve as good estimates...... of standard metabolic rate. Due to the potentially added costs of genetic stress in inbred lines we hypothesized that inbred individuals have increased metabolic rate compared to outbred controls and that this is more pronounced at stressful temperatures due to synergistic inbreeding by environment...... interactions. Contrary to our hypothesis we found no significant difference in metabolic rate between inbred and outbred lines and no interaction between inbreeding and temperature. Inbreeding however effected the variance; the variance in metabolic rate was higher between the inbred lines compared...

  3. Investigating the microbial community responsible for unusually high soil N2O and NOx emissions in the Colorado Desert

    Science.gov (United States)

    Eberwein, J. R.; Carey, C.; Aronson, E. L.; Jenerette, D.

    2016-12-01

    Although the importance of soil nitrogenous emissions are well accepted in terms of local and global ecological relevance, there remain considerable knowledge gaps concerning the mechanisms regulating production, particularly in arid systems. This study aimed to connect desert soil trace gas emissions of nitrous oxide (N2O) and nitrogen oxides (NOx) with compositional changes in the microbial community. We quantified real-time soil trace gas emissions at two sites in the Colorado Desert experiencing contrasting anthropogenic nitrogen (N) deposition loads (characterize the soil microbial community. N2O fluxes reached as high as 1200 ng N2O-N m-2 s-1, well above most published emissions, but returned to pre-wetting conditions within 12 hours. NOx emissions reached as high as 350 ng NOx-N m-2 s-1 and remained elevated past 24 hours post-wetting. Results from the 16S analysis indicate distinct differences in the microbial community composition between the high and low N deposition sites, with less than 50% of operational taxonomic units (OTUs) in common between sites. N addition had a significant effect on the soil microbial community at the low deposition site, but not at the high deposition site. Furthermore, significant shifts in the bacterial community occurred after wetting, with only one third of the community remaining constant between time points. These results suggest that gaseous N export, particularly N2O emission, is a greater form of nitrogen loss in this system than is currently assumed. Experimental N additions and anthropogenic N deposition show potential for shifting soil microbial community composition, with implications for soil N emissions. Furthermore, shifts in the microbial community can occur as quickly as 15 minutes post-wetting, representing a remarkable ability for soil microorganisms to recover from extreme water stress. As aridlands cover approximately one third of the Earth's land surface, understanding the mechanisms that contribute to

  4. Experimental and In-Silico Investigation of Anti-Microbial Activity of 1-Chloro-2-Isocyanatoethane Derivatives of Thiomorpholine, Piperazine and Morpholine

    OpenAIRE

    Nwuche, Charles O.; Ujam, Oguejiofo T.; Ibezim, Akachukwu; Ujam, Ifeoma B.

    2017-01-01

    The Antibiogram properties of 1-chloro-2-isocyanatoethane derivatives of thiomorpholine (CTC), piperazine (CPC) and morpholine (CMC) were evaluated by the approved agar well diffusion, the minimum inhibitory concentration (MIC) and in silico techniques. A total of fourteen microbial cultures consisting of ten bacteria and four yeast strains were used in the biological study while affinity of the compounds for DNA gyrase, a validated antibacterial drug target, was investigated by docking metho...

  5. Inbreeding effects on standard metabolic rate investigated at cold, benign and hot temperatures in Drosophila melanogaster.

    Science.gov (United States)

    Jensen, Palle; Overgaard, Johannes; Loeschcke, Volker; Schou, Mads Fristrup; Malte, Hans; Kristensen, Torsten Nygaard

    2014-03-01

    Inbreeding increases homozygosity, which is known to affect the mean and variance of fitness components such as growth, fecundity and mortality rate. Across inbred lines inbreeding depression is typically observed and the variance between lines is increased in inbred compared to outbred lines. It has been suggested that damage incurred from increased homozygosity entails energetic cost associated with cellular repair. However, little is known about the effects of inbreeding on standard metabolic rate. Using stop-flow respirometry we performed repeated measurements of metabolic rate in replicated lines of inbred and outbred Drosophila melanogaster at stressful low, benign and stressful high temperatures. The lowest measurements of metabolic rate in our study are always associated with the low activity period of the diurnal cycle and these measurements therefore serve as good estimates of standard metabolic rate. Due to the potentially added costs of genetic stress in inbred lines we hypothesized that inbred individuals have increased metabolic rate compared to outbred controls and that this is more pronounced at stressful temperatures due to synergistic inbreeding by environment interactions. Contrary to our hypothesis we found no significant difference in metabolic rate between inbred and outbred lines and no interaction between inbreeding and temperature. Inbreeding however effected the variance; the variance in metabolic rate was higher between the inbred lines compared to the outbred control lines with some inbred lines having very high or low standard metabolic rate. Thus genetic drift and not inbreeding per se seem to explain variation in metabolic rate in populations of different size. Copyright © 2014 Elsevier Ltd. All rights reserved.

  6. Application of stable isotopes to investigate the metabolism of fatty acids, glycerophospholipid and sphingolipid species.

    Science.gov (United States)

    Ecker, Josef; Liebisch, Gerhard

    2014-04-01

    Nature provides an enormous diversity of lipid molecules that originate from various pathways. To gain insight into the metabolism and dynamics of lipid species, the application of stable isotope-labeled tracers combined with mass spectrometric analysis represents a perfect tool. This review provides an overview of strategies to track fatty acid, glycerophospholipid, and sphingolipid metabolism. In particular, the selection of stable isotope-labeled precursors and their mass spectrometric analysis is discussed. Furthermore, examples of metabolic studies that were performed in cell culture, animal and clinical experiments are presented. Copyright © 2014 Elsevier Ltd. All rights reserved.

  7. Autotrophic and heterotrophic metabolism of microbial planktonic communities in an oligotrophic coastal marine ecosystem: seasonal dynamics and episodic events

    Science.gov (United States)

    Bonilla-Findji, O.; Gattuso, J.-P.; Pizay, M.-D.; Weinbauer, M. G.

    2010-11-01

    A 18 month study was performed in the Bay of Villefranche to assess the episodic and seasonal variation of autotrophic and heterotrophic ecosystem processes. A typical spring bloom was encountered, where maximum of gross primary production (GPP) was followed by maxima of bacterial respiration (BR) and production (BP). The trophic balance (heterotrophy vs. autotrophy) of the system did not exhibit any seasonal trend although a strong intra-annual variability was observed. On average, the community tended to be net heterotrophic with a GPP threshold for a balanced metabolism of 1.1 μmol O2 l-1 d-1. Extended forest fires in summer 2003 and a local episodic upwelling in July 2003 likely supplied orthophosphate and nitrate into the system. These events were associated with an enhanced bacterioplankton production (up to 2.4-fold), respiration (up to 4.5-fold) and growth efficiency (up to 2.9-fold) but had no effect on GPP. A Sahara dust wet deposition event in February 2004 stimulated bacterial abundance, production and growth efficiency but not GPP. Our study suggests that short-term disturbances such as wind-driven upwelling, forest fires and Sahara dust depositions can have a significant but previously not sufficiently considered influence on phytoplankton- and bacterioplankton-mediated ecosystem functions and can modify or even mask the seasonal dynamics. The study also indicates that atmospheric deposition of nutrients and particles not only impacts phytoplankton but also bacterioplankton and could, at times, also shift systems stronger towards net heterotrophy.

  8. Investigating tumor perfusion and metabolism using multiple hyperpolarized 13C compounds: HP001, pyruvate and urea

    DEFF Research Database (Denmark)

    von Morze, Cornelius; Larson, Peder E.Z.; Hu, Simon

    2012-01-01

    by spectroscopic imaging of hyperpolarized [1-13C]pyruvate would be of great value in exploring the relationship between perfusion and metabolism in cancer. In preclinical normal murine and cancer model studies, we performed both dynamic multislice imaging of the specialized hyperpolarized perfusion compound HP001......The metabolically inactive hyperpolarized agents HP001 (bis-1,1-(hydroxymethyl)-[1-13C]cyclopropane-d8) and urea enable a new type of perfusion magnetic resonance imaging based on a direct signal source that is background-free. The addition of perfusion information to metabolic information obtained...... of separate dynamic HP001 imaging and copolarized pyruvate/urea imaging were compared. A strong and significant correlation (R=0.73, P=.02) detected between the urea and HP001 data confirmed the value of copolarizing urea with pyruvate for simultaneous assessment of perfusion and metabolism....

  9. Autotrophic and heterotrophic metabolism of microbial planktonic communities in an oligotrophic coastal marine ecosystem: seasonal dynamics and episodic events

    Directory of Open Access Journals (Sweden)

    O. Bonilla-Findji

    2010-11-01

    Full Text Available A 18 month study was performed in the Bay of Villefranche to assess the episodic and seasonal variation of autotrophic and heterotrophic ecosystem processes. A typical spring bloom was encountered, where maximum of gross primary production (GPP was followed by maxima of bacterial respiration (BR and production (BP. The trophic balance (heterotrophy vs. autotrophy of the system did not exhibit any seasonal trend although a strong intra-annual variability was observed. On average, the community tended to be net heterotrophic with a GPP threshold for a balanced metabolism of 1.1 μmol O2 l−1 d−1. Extended forest fires in summer 2003 and a local episodic upwelling in July 2003 likely supplied orthophosphate and nitrate into the system. These events were associated with an enhanced bacterioplankton production (up to 2.4-fold, respiration (up to 4.5-fold and growth efficiency (up to 2.9-fold but had no effect on GPP. A Sahara dust wet deposition event in February 2004 stimulated bacterial abundance, production and growth efficiency but not GPP. Our study suggests that short-term disturbances such as wind-driven upwelling, forest fires and Sahara dust depositions can have a significant but previously not sufficiently considered influence on phytoplankton- and bacterioplankton-mediated ecosystem functions and can modify or even mask the seasonal dynamics. The study also indicates that atmospheric deposition of nutrients and particles not only impacts phytoplankton but also bacterioplankton and could, at times, also shift systems stronger towards net heterotrophy.

  10. Investigation of the Relationship Between Molluscum Pendulum and Impairment of Carbohydrate Metabolism

    Directory of Open Access Journals (Sweden)

    Murat Kemal

    2011-12-01

    Full Text Available Background and Design: High blood sugar level, insulin resistance and dyslipidemia are accepted to be indicators of impaired carbohydrate metabolism. The potential role of these markers as well as the serum levels of insulin growth factor (IGF-1 and insulin growth factor binding protein (IGFBP-3 in the pathogenesis of molluscum pendulum were investigated in this study. Materials and methods: Forty-five molluscum pendulum patients and 45 age-, sex- and body mass index-matched healthy individuals as controls were enrolled in the study. Evaluation included dermatological examination, measurement of insulin resistance using HOMA-IR method, lipid profile, fasting blood glucose, postprandial blood glucose, fasting insulin, postprandial insulin, serum IGF-1 and IGFBP-3 levels. Results: Postprandial blood glucose, fasting insulin, postprandial insulin and Homeostazis Model Assesment (HOMA-IR levels of molluscum pendulum patients were statistically higher than those of controls (p=0.037, p=0.027, p=0.03, p=0.021 respectively, whereas serum IGF-1 and IGFBP-3 levels were significantly lower than those of controls (p=0.008, p=0.001. There was no difference in fasting glucose and lipid profile between the two groups. Three patients (6.7% had DM and one patient (13.3% had impaired glucose tolerance. Only one participant from the control group (2,2% had impaired glucose tolerance. The number of molluscum pendulum lesions correlated with fasting glucose, postprandial glucose, fasting insulin, postprandial insulin, HOMA-IR, total cholesterol and triglyceride levels. Conclusion: Molluscum pendulum patients should have blood glucose and insulin resistance measurements done and be followed up for DM. Patients with multiple lesions need to be evaluated for lipid problems. We suggest that serum IGF-1 and IGFBP-3 levels have no role in the pathogenesis of molluscum pendulum. (Turk­derm 2011; 45: 188-92

  11. Metaproteogenomic Profiling of Microbial Communities Colonizing Actively Venting Hydrothermal Chimneys

    Directory of Open Access Journals (Sweden)

    Petra Pjevac

    2018-04-01

    Full Text Available At hydrothermal vent sites, chimneys consisting of sulfides, sulfates, and oxides are formed upon contact of reduced hydrothermal fluids with oxygenated seawater. The walls and surfaces of these chimneys are an important habitat for vent-associated microorganisms. We used community proteogenomics to investigate and compare the composition, metabolic potential and relative in situ protein abundance of microbial communities colonizing two actively venting hydrothermal chimneys from the Manus Basin back-arc spreading center (Papua New Guinea. We identified overlaps in the in situ functional profiles of both chimneys, despite differences in microbial community composition and venting regime. Carbon fixation on both chimneys seems to have been primarily mediated through the reverse tricarboxylic acid cycle and fueled by sulfur-oxidation, while the abundant metabolic potential for hydrogen oxidation and carbon fixation via the Calvin–Benson–Bassham cycle was hardly utilized. Notably, the highly diverse microbial community colonizing the analyzed black smoker chimney had a highly redundant metabolic potential. In contrast, the considerably less diverse community colonizing the diffusely venting chimney displayed a higher metabolic versatility. An increased diversity on the phylogenetic level is thus not directly linked to an increased metabolic diversity in microbial communities that colonize hydrothermal chimneys.

  12. Metabolic syndrome and risk of incident diabetes: findings from the European Prospective Investigation into Cancer and Nutrition-Potsdam Study

    Directory of Open Access Journals (Sweden)

    Joost Hans-Georg

    2008-12-01

    Full Text Available Abstract Background Several aspects concerning the relationship between the metabolic syndrome and incident diabetes are incompletely understood including the magnitude of the risk estimate, potential gender differences in the associations between the metabolic syndrome and incident diabetes, the associations between the components of the metabolic syndrome and incident diabetes, and whether the metabolic syndrome provides additional prediction beyond its components. To shed light on these issues, we examined the prospective association between the metabolic syndrome defined by the National Cholesterol Education Program (NCEP and International Diabetes Federation (IDF and diabetes. Methods We used data for 2796 men and women aged 35–65 years from the European Prospective Investigation into Cancer and Nutrition-Potsdam Study followed for an average of 6.9 years. This analysis employed a case-cohort design that included 697 participants who developed diabetes and 2099 participants who did not. Incident diabetes was identified on the basis of self-reports and verified by contacting the patient's attending physician. Results The adjusted hazard ratio for the NCEP definition was 4.62 (95% confidence interval [CI]: 3.90–5.48 and that for the IDF definition was 4.59 (95% CI: 3.84–5.50. The adjusted hazard ratios for the NCEP but not IDF definition were higher for women than men. When participants who had no cardiometabolic abnormalities were used as the reference group for the NCEP definition, the adjusted hazard ratio for having 3 or more abnormalities increased to 22.50 (95% CI: 11.21–45.19. Of the five components, abdominal obesity and hyperglycemia were most strongly associated with incident diabetes. Conclusion In this study population, both definitions of the metabolic syndrome provided similar estimates of relative risk for incident diabetes. The increase in risk for participants with the metabolic syndrome according to the NCEP

  13. Effect of nanosilver on metabolism in rainbow trout (Oncorhynchus mykiss): An investigation using different respirometric approches

    DEFF Research Database (Denmark)

    Murray, Laura; Rennie, Michael D.; Svendsen, Jon Christian

    2017-01-01

    gene expression, gill damage, and impaired gas exchange, as well as mortality at high nAg concentrations. The present study reports the effects of nAg on the metabolism of rainbow trout (Oncorhynchus mykiss). Fish were exposed to environmentally relevant concentrations (0.28 ± 0.02 μg/L) and higher (47.......60 ± 5.13 μg/L) for 28 d, after which their standard metabolic rate (SMR), forced maximum metabolic rate (MMRf), and spontaneous maximum metabolic rate (MMRs) were measured. There was no effect observed in SMR, MMRf, or MMRs, suggesting that nAg is unlikely to directly affect fish metabolism. On average......, MMRs tended to be greater than MMRf, and most MMRs occurred when room lighting increased. The timing of MMRf chase protocols was found to affect both MMRf and SMR estimates, in that chasing fish before respirometric experiments caused higher MMRf estimates and lower SMR estimates. Although compounded...

  14. In Vitro Anti-Oxidant and Anti-Microbial Potentiality Investigation of Different Fractions of Caryota urens Leaves.

    Science.gov (United States)

    Azam, Shofiul; Mahmud, Md Kayes; Naquib, Md Hamza; Hossain, Saad Mosharraf; Alam, Mohammad Nazmul; Uddin, Md Josim; Sajid, Irfan; Hossain, Muhammad Sazzad; Karim, Md Salimul; Hasan, Md Ali

    2016-07-27

    Caryota urens is a member of the Arecaceae family and a common plant in the Southeast Asian region. This plant has been reported as an anti-microbial agent in recent years. Thus, we aimed to find out the MIC (minimum inhibitory concentration) against different pathogenic microorganism. The leaves of C. urens were extracted and fractioned using different reagents (chloroform, n -hexane and carbon tetrachloride). Disc diffusion method was implemented for the assessment of in vitro anti-microbial potency (500 and 250 µg/disc). The entire fraction showed good effect (with the zone of inhibition 19-25 mm) against both gram positive ( Bacillus subtilis , Bacillus megaterium , Bacillus cereus , Sarina lutea ) and gram negative ( Vibrio mimicus , Shigella boydii , Escherichia coli , Pseudomonas aeruginosa ) bacterial pathogens and fungal strains ( Aspergillus niger , Saccharomyces cerevisiae ). The plants also possess effective free radical scavenging potency with an IC 50 of 130.32 µg/mL. This finding reflects a link between the presence of anti-oxidative material and a substantial anti-microbial activity, and substantiates all previous claims against C. urens .

  15. MICROBIAL MATS - A JOINT VENTURE

    NARCIS (Netherlands)

    VANGEMERDEN, H

    Microbial mats characteristically are dominated by a few functional groups of microbes: cyanobacteria, colorless sulfur bacteria, purple sulfur bacteria, and sulfate-reducing bacteria. Their combined metabolic activities result in steep environmental microgradients, particularly of oxygen and

  16. Investigation of cerebral metabolism by positron CT in Japanese following musical stimulation

    International Nuclear Information System (INIS)

    Wakasugi, Naotoshi

    1994-01-01

    Cerebral metabolic responses to Japanese and Western instrumental music were examined using 11 C-glucose and positron CT. Eight right-handed subjects were studied in both Japanese and Western music-stimulated states. Biaural musical stimulation with a Japanese instrument, the 'shakuhachi', produced diffuse metabolic changes in the left temporal lobe in all subjects. Biaural musical stimulation with a Western instrument, the 'violin', produced metabolic changes in the right temporal lobe in 3 subjects, changes in the left in 4, and changes on both sides in one. It was considered previously that all musical stimulation led to hypermetabolism in the right hemisphere of human beings. However, the present results indicated that Japanese music produced activation of the left hemisphere in Japanese. On the other hand, Western music produced right hemispheric hypermetabolism in Japanese with no emotion. The laterality of the hemisphere stimulated by Western music was apparently incidentally changed according to the state of mind the Japanese subjects. (author)

  17. Single-cell level based approach to investigate bacterial metabolism during batch industrial fermentation

    DEFF Research Database (Denmark)

    Nierychlo, Marta; Larsen, Poul; Eriksen, Niels T.

    , and performance of Escherichia coli. An insight into glucose and acetate fate on the level of individual cell can provide the type of information which are valuable for the understanding of bacterial metabolism in fermentation process and can shed more light on the differentiation of isogenic fermenting...... can exhibit different phenotypes under specific environmental conditions that show significant differences in physiological parameters from the population average. However, studies concerning segregation of populations into metabolically diversified subpopulations are scarce. Acetate is a product...... of Escherichia coli overflow metabolism when the bacteria are grown under aerobic conditions and glucose is present in excessive concentrations. Acetate accumulation is of the utmost importance in batch fermentation processes as it is an undesirable byproduct that negatively affects growth, physiology...

  18. Pilot investigation on formation of 2,4,6-trichloroanisole via microbial O-methylation of 2,4,6-trichlorophenol in drinking water distribution system: An insight into microbial mechanism.

    Science.gov (United States)

    Zhang, Kejia; Cao, Cong; Zhou, Xinyan; Zheng, Feifei; Sun, Youmin; Cai, Zhengqing; Fu, Jie

    2017-12-11

    Taste & odor (T&O) problems in drinking water are always complained by customers. Recent studies have indicated biofilms in drinking water distribution system (DWDS) are always ignored as potential sources of T&O compounds. In this paper, the formation of 2,4,6-trichloroanisole (2,4,6-TCA), one of the dominant T&O compounds, was investigated in a pilot-scale DWDS. The addition of precursor 2,4,6-trichlorophenol (2,4,6-TCP) of 0.2 mg/L induced the formation of 2,4,6-TCA with a maximum yield of ∼400 ng/L, and the formation kinetics can be described by a pseudo-first-order kinetic model. Effects of water distribution factors such as pipe material, temperature, flow velocity, and residual chlorine on the formation of 2,4,6-TCA were evaluated, and the pipe material was found to have the most remarkable effect. Ductile iron and stainless steel pipes produced much more 2,4,6-TCA than polyethylene (PE) pipe. The biofilm microbial communities on the three types of pipe walls were then comprehensively analyzed by heterotrophic plate count and 16S rRNA/ITS1 genes high throughput sequencing. The links between the 2,4,6-TCA formation potential and the microbial activity in genus and enzymatic levels in DWDS have been revealed for the first time. According to the characteristics of microbial assemblages of producing 2,4,6-TCA, quorum-sensing (QS) bacterial signaling system and extracellular DNA (eDNA) may be two promising targets for biofilm treatment and 2,4,6-TCA control in DWDS. Copyright © 2017 Elsevier Ltd. All rights reserved.

  19. Investigating predictors of eating: is resting metabolic rate really the strongest proxy of energy intake?

    Science.gov (United States)

    McNeil, Jessica; Lamothe, Gilles; Cameron, Jameason D; Riou, Marie-Ève; Cadieux, Sébastien; Lafrenière, Jacynthe; Goldfield, Gary; Willbond, Stephanie; Prud'homme, Denis; Doucet, Éric

    2017-11-01

    Background: Evidence suggests that fat-free mass and resting metabolic rate (RMR), but not fat mass, are strong predictors of energy intake (EI). However, body composition and RMR do not explain the entire variance in EI, suggesting that other factors may contribute to this variance. Objective: We aimed to investigate the associations between body mass index (in kg/m 2 ), fat mass, fat-free mass, and RMR with acute (1 meal) and daily (24-h) EI and between fasting appetite ratings and certain eating behavior traits with daily EI. We also evaluated whether RMR is a predictor of the error variance in acute and daily EI. Design: Data collected during the control condition of 7 studies conducted in Ottawa, Ontario, Canada, were included in these analyses ( n = 191 and 55 for acute and daily EI, respectively). These data include RMR (indirect calorimetry), body composition (dual-energy X-ray absorptiometry), fasting appetite ratings (visual analog scales), eating behavior traits (Three-Factor Eating Questionnaire), and EI (food buffet or menu). Results: Fat-free mass was the best predictor of acute EI ( R 2 = 0.46; P fasting prospective food consumption ratings and RMR was the best predictor of daily EI ( R 2 = 0.44; P < 0.0001). RMR was a statistically significant positive predictor of the error variance for acute ( R 2 = 0.20; P < 0.0001) and daily ( R 2 = 0.23; P < 0.0001) EI. RMR did, however, remain a statistically significant predictor of acute ( R 2 = 0.32; P < 0.0001) and daily ( R 2 = 0.30; P < 0.0001) EI after controlling for this error variance. Conclusions: Our findings suggest that combined measurements of appetite ratings and RMR could be used to estimate EI in weight-stable individuals. However, greater error variance in acute and daily EI with increasing RMR values was observed. Future studies are needed to identify whether greater fluctuations in daily EI over time occur with increasing RMR values. This trial was registered at clinicaltrials.gov as NCT

  20. Effects of dietary resistant starch content on metabolic status, milk composition, and microbial profiling in lactating sows and on offspring performance.

    Science.gov (United States)

    Yan, H; Lu, H; Almeida, V V; Ward, M G; Adeola, O; Nakatsu, C H; Ajuwon, K M

    2017-02-01

    In the present study, the effects of dietary resistant starch (RS) content on serum metabolite and hormone concentrations, milk composition, and faecal microbial profiling in lactating sows, as well as on offspring performance was investigated. Sixteen sows were randomly allotted at breeding to two treatments containing low- and high-RS contents from normal and high-amylose corn varieties, respectively, and each treatment had eight replicates (sows). Individual piglet body weight (BW) and litter size were recorded at birth and weaning. Milk samples were obtained on day 10 after farrowing for composition analysis. On day 2 before weaning, blood and faecal samples were collected to determine serum metabolite and hormone concentrations and faecal microbial populations, respectively. Litter size at birth and weaning were not influenced (p > 0.05) by the sow dietary treatments. Although feeding the RS-rich diet to sows reduced (p = 0.004) offspring birth BW, there was no difference in piglet BW at weaning (p > 0.05). High-RS diet increased (p content, and tended (p = 0.09) to increase milk fat content in lactating sows. Feeding the RS-rich diet to sows increased (p bacterial population diversity. These results indicate that high-RS diets induce fatty acid mobilization and a greater intestinal bacterial richness in lactating sows, as well as a greater nutrient density in maternal milk, without affecting offspring performance at weaning. Journal of Animal Physiology and Animal Nutrition © 2016 Blackwell Verlag GmbH.

  1. An Integrated Metagenomics/Metaproteomics Investigation of the Microbial Communities and Enzymes in Solid-state Fermentation of Pu-erh tea

    Science.gov (United States)

    Zhao, Ming; Zhang, Dong-lian; Su, Xiao-qin; Duan, Shuang-mei; Wan, Jin-qiong; Yuan, Wen-xia; Liu, Ben-ying; Ma, Yan; Pan, Ying-hong

    2015-01-01

    Microbial enzymes during solid-state fermentation (SSF), which play important roles in the food, chemical, pharmaceutical and environmental fields, remain relatively unknown. In this work, the microbial communities and enzymes in SSF of Pu-erh tea, a well-known traditional Chinese tea, were investigated by integrated metagenomics/metaproteomics approach. The dominant bacteria and fungi were identified as Proteobacteria (48.42%) and Aspergillus (94.98%), through pyrosequencing-based analyses of the bacterial 16S and fungal 18S rRNA genes, respectively. In total, 335 proteins with at least two unique peptides were identified and classified into 28 Biological Processes and 35 Molecular Function categories using a metaproteomics analysis. The integration of metagenomics and metaproteomics data demonstrated that Aspergillus was dominant fungus and major host of identified proteins (50.45%). Enzymes involved in the degradation of the plant cell wall were identified and associated with the soft-rotting of tea leaves. Peroxiredoxins, catalase and peroxidases were associated with the oxidation of catechins. In conclusion, this work greatly advances our understanding of the SSF of Pu-erh tea and provides a powerful tool for studying SSF mechanisms, especially in relation to the microbial communities present. PMID:25974221

  2. Longitudinal Investigation into Genetics in the Conservation of Metabolic Phenotypes in Danish and Chinese Twins

    DEFF Research Database (Denmark)

    Li, Shuxia; Kyvik, Kirsten Ohm; Duan, Haiping

    2016-01-01

    twin study on long-term stability of metabolic phenotypes in Danish and Chinese twins identified a common pattern of high genetic control over phenotype conservation, and at the same time revealed population-specific patterns of genetic and common environmental regulation on the variance as well...

  3. Shifts in the metabolic function of a benthic estuarine microbial community following a single pulse exposure to silver nanoparticles

    International Nuclear Information System (INIS)

    Echavarri-Bravo, Virginia; Paterson, Lynn; Aspray, Thomas J.; Porter, Joanne S.; Winson, Michael K.; Thornton, Barry; Hartl, Mark G.J.

    2015-01-01

    The increasing use of silver nanoparticles (AgNPs) as a biocidal agent and their potential accumulation in sediments may threaten non-target natural environmental bacterial communities. In this study a microcosm approach was established to investigate the effects of well characterized OECD AgNPs (NM-300) on the function of the bacterial community inhabiting marine estuarine sediments (salinity 31‰). The results showed that a single pulse of NM-300 AgNPs (1 mg L −1 ) that led to sediment concentrations below 6 mg Ag kg −1 dry weight inhibited the bacterial utilization of environmentally relevant carbon substrates. As a result, the functional diversity changed, but recovered after 120 h under the experimental conditions. This microcosm study suggests that AgNPs under environmentally relevant experimental conditions can negatively affect bacterial function and provides an insight into the understanding of the bacterial community response and resilience to AgNPs exposure, important for informing relevant regulatory measures. - Highlights: • AgNPs affected the bacterial community function in estuarine marine sediments. • AgNPs inhibited the bacterial utilization of environmentally relevant substrates. • Heterotrophic bacterial groups showed resilience to AgNPs after 120 h exposure. • AgNPs did not affect the bacterial community structure in sediments. - AgNPs inhibited the bacterial utilization of environmentally relevant substrates and caused temporary shifts in the bacterial functional diversity in marine estuarine sediments

  4. Investigations on the role of hemoglobin in sulfide metabolism by intact human red blood cells.

    Science.gov (United States)

    Bianco, Christopher L; Savitsky, Anton; Feelisch, Martin; Cortese-Krott, Miriam M

    2018-03-01

    In addition to their role as oxygen transporters, red blood cells (RBCs) contribute to cardiovascular homeostasis by regulating nitric oxide (NO) metabolism via interaction of hemoglobin (Hb) with nitrite and NO itself. RBCs were proposed to also participate in sulfide metabolism. Although Hb is known to react with sulfide, sulfide metabolism by intact RBCs has not been characterized so far. Therefore we explored the role of Hb in sulfide metabolism in intact human RBCs. We find that upon exposure of washed RBCs to sulfide, no changes in oxy/deoxyhemoglobin (oxy/deoxyHb) are observed by UV-vis and EPR spectroscopy. However, sulfide reacts with methemoglobin (metHb), forming a methemoglobin-sulfide (metHb-SH) complex. Moreover, while metHb-SH is stable in cell-free systems even in the presence of biologically relevant thiols, it gradually decomposes to produce oxyHb, inorganic polysulfides and thiosulfate in intact cells, as detected by EPR and mass spectrometry. Taken together, our results demonstrate that under physiological conditions RBCs are able to metabolize sulfide via intermediate formation of a metHb-SH complex, which subsequently decomposes to oxyHb. We speculate that decomposition of metHb-SH is preceded by an inner-sphere electron transfer, forming reduced Hb (which binds oxygen to form oxyHb) and thiyl radical (a process we here define as "reductive sulfhydration"), which upon release, gives rise to the oxidized products, thiosulfate and polysulfides. Thus, not only is metHb an efficient scavenger and regulator of sulfide in blood, intracellular sulfide itself may play a role in keeping Hb in the reduced oxygen-binding form and, therefore, be involved in RBC physiology and function. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

  5. Investigations on the effect of forage source, grinding, and urea supplementation on ruminal fermentation and microbial protein flow in a semi-continuous rumen simulation system.

    Science.gov (United States)

    Hildebrand, Bastian; Boguhn, Jeannette; Rodehutscord, Markus

    2011-10-01

    The objective of the present study was to compare the effect of maize silage and grass silage on microbial fermentation and protein flow in a semi-continuous rumen simulation system (Rusitec) when milling screen size (MSS) during grinding was varied. Oven-dried silages were milled through screens of 1, 4 or 9 mm pore size and incubated for 48 h in a Rusitec system. Furthermore, the effect of N supplementation to maize silage (MSS: 4 mm) was investigated and single dose vs. continuous infusion of urea-N were compared. Degradation of organic matter (OM), crude protein (CP), fibre fractions and non-structural carbohydrates (NSC) as well as short-chain fatty acid production differed significantly between forage sources. Urea-N supplementation improved the degradation of NSC, but not that of fibre fractions in maize silage. The way of urea supply had only marginal effects on fermentation characteristics. An increase in MSS, and consequently in mean feed particle size, led to an improvement in the degradation of OM, CP and NSC, but efficiency of microbial net protein synthesis (EMPS; mg microbial N flow/g degraded OM) and the microbial amino acid profile were less affected. EMPS was higher in grass silage than in maize silage and was improved by urea-N supplementation in maize silage. This study indicates that fermentation of NSC as well as EMPS during incubation of maize silage was limited by availability of NH3-N. Furthermore, an increase in MSS above 1 mm seems to improve fermentation of silages in the Rusitec system.

  6. The Fate of Terrestrial Dissolved Organic Matter in Ocean Margins Investigated through Coupled Microbial-Photochemical Incubations of Vascular Plant Leachates

    Science.gov (United States)

    Creeley, D. R.; Kaiser, K.; Hernes, P.; Spencer, R. G.

    2016-02-01

    Biological productivity, air-sea CO2 exchange and nutrient cycling in ocean margins is strongly affected by mineralization of terrigenous dissolved organic carbon (tDOC) delivered by rivers. The decomposition of tDOC was investigated with coupled photochemical-microbial incubations to assess the combined effects of microbial and photochemical processes on the structure and extent on removal of tDOM. For these incubations, vascular plant material leachates were prepared with five different materials from the Sacramento River Valley and estuarine wetlands: foothill pine, blue oak, mixed annual grasses, mixed Tule, and cattails. Incubations were done with controlled light exposure and known spectral irradiation. Samples collected along a continuum of degradation stages were analyzed for dissolved organic carbon (DOC), total hydrolysable enantiomeric amino acids (DLAA), total hydrolysable neutral sugars (THNS), total hydrolysable amino sugars (THAS), lignin phenols, and optical properties. The loss of vascular plant material was calculated at different stages of decomposition by comparison of measured C-normalized concentrations to C-normalized values in fresh leachates. This was matched with calculation of microbial contributions based on D-amino acids. As a result, calibrated biomarkers describing vascular plant decomposition and input of microbial DOC were developed for different stages of tDOC decomposition. Application of these calibrated biomarkers will be used to study riverine DOM in river plumes using transect samples from the San Francisco Bay Estuary during summer of 2014, and as well as a transect from the Brazos River mouth into the Gulf of Mexico collected during the 2015 summer flood events.

  7. Histopathologic investigation of the effects of prostaglandin E2 administered by different methods on tooth movement and bone metabolism

    OpenAIRE

    Cağlaroğlu, Murat; Erdem, Abdulvahit

    2012-01-01

    Objective The aim of this study was to investigate and compare the in vivo effects of prostaglandin E2 (PGE2) administered by different methods on orthodontic tooth movement and bone metabolism macroscopically, histopatologically, and biochemically. Methods Forty-five young adult New Zealand rabbits were randomly divided into 3 experimental groups (n = 10/group), 1 positive control group (n = 10), and 1 negative control group (n = 5). The experimental rabbits were fitted with springs exerting...

  8. Single-cell level based approach to investigate acetate metabolism during batch industrial fermentation

    DEFF Research Database (Denmark)

    Nierychlo, Marta; Larsen, Poul; Eriksen, Niels T.

    accumulation causes the decrease of productivity as it represents a waste of carbon source that would otherwise be converted to biomass and product. As the acetate accumulation problem is of the utmost importance in batch fermentation processes, various strategies have been developed to explain, understand...... during glucose fermentation. Batch fermentations were performed in order to examine consecutive stages of acetate metabolism during the fermentation process (production, co-consumption with glucose, consumption as single substrate). Uptake of glucose and acetate at single-cell level was observed...... and control the overflow metabolism phenomenon in E. coli. Even though acetate formation by E. coli have been studied for more than three decades, the literature published presents the results based on the average measurement of the whole population. The averaged data can mask the distribution of the activity...

  9. Survey of iodine metabolism in man illustrated by an iodide load investigation

    International Nuclear Information System (INIS)

    Bassoee, C.-F.; Langaasdalen, H.

    1977-12-01

    The first part of this report deals with the human metabolism of iodine, its sources, serum iodine, uptake in the thyroid, hormonal thyroid secretion and iodine excretion. The thyroid hormones are discussed as is the regulating of the iodine metabolism. The second part consists of a study performed on six healthy persons over two days. These were given 5mg iodine in aqueous solution rally and series of blood tests taken. Two persons were also given 100mg and 200mg respectively per day for 3weeks. The results are tabulated and discussed. In the third and final section the radiation hygiene aspects are treated. The basis is the uptake of large amounts of I - 131 from radioactive fallout. Carcinogenesis and hypothyroidism following this are discussed and therapy and iodine prophylaxis are described. (JIW)

  10. Investigating the link between fermentative metabolism and hydrogen production in the unicellular green alga Chlamydomonas reinhardtii

    Energy Technology Data Exchange (ETDEWEB)

    Burgess, S.J.; Nixon, P.J. [Imperial College London (United Kingdom)

    2010-07-01

    In the model green alga Chlamydomonas reinhardtii, the electrons required for hydrogen production can come from both the biophotolysis of water and from the fermentation of carbohydrate reserves. Anoxia leads to the activation of several fermentative pathways, which produce a number of end products including formic, malic and acetic acid along with ethanol, carbon dioxide and hydrogen. It has been proposed that by switching off competing fermentative pathways hydrogen production can be increased. Therefore the aim of this study was to devise an experimental strategy to down-regulate the expression of enzymes thought to control C. reinhardtii's fermentative metabolism. We demonstrate here that it is possible to use artificial microRNA (amiRNA) technology to generate knock-down mutants with reduced expression of pyruvate formate lyase (PFL1), a key fermentative enzyme in C. reinhardtii. This work opens up new possibilities to improve hydrogen yields through metabolic engineering. (orig.)

  11. Flux-Enabled Exploration of the Role of Sip1 in galactose yeast metabolism

    DEFF Research Database (Denmark)

    Shymansky, Christopher M.; Wang, George; Baidoo, Edward E. K.

    2017-01-01

    13C metabolic flux analysis (13C MFA) is an important systems biology technique that has been used to investigate microbial metabolism for decades. The heterotrimer Snf1 kinase complex plays a key role in the preference Saccharomyces cerevisiae exhibits for glucose over galactose, a phenomenon kn...

  12. Positron emission tomographic scan investigations of Huntington's disease: cerebral metabolic correlates of cognitive function

    International Nuclear Information System (INIS)

    Berent, S.; Giordani, B.; Lehtinen, S.; Markel, D.; Penney, J.B.; Buchtel, H.A.; Starosta-Rubinstein, S.; Hichwa, R.; Young, A.B.

    1988-01-01

    Fifteen drug-free patients with early to mid-stage Huntington's disease (HD) were evaluated with positron emission tomographic (PET) scans of 18 F-2-fluoro-2-deoxy-D-glucose uptake and quantitative measures of neurological function, learning, memory, and general intelligence. In comparison with a group of normal volunteers, the HD patients showed lower metabolism in both caudate (p less than 0.001) and putamen (p less than 0.001) on PET scans. A significant and positive relationship was found between neuropsychological measures of verbal learning and memory and caudate metabolism in the patient group but not in the normal group. Visual-spatial learning did not reflect a similar pattern, but performance intelligence quotient was positively related to both caudate and putamen metabolism in the HD group. Vocabulary level was unrelated to either brain structure. Discussion focuses on these and other observed brain-behavior relationships and on the implications of these findings for general behaviors such as those involved in coping and adaptation

  13. Investigating the Cellular and Metabolic Responses of World-Class Canoeists Training: A Sportomics Approach

    Directory of Open Access Journals (Sweden)

    Wagner Santos Coelho

    2016-11-01

    Full Text Available (1 Background: We have been using the Sportomics approach to evaluate biochemical and hematological changes in response to exercise. The aim of this study was to evaluate the metabolic and hematologic responses of world-class canoeists during a training session; (2 Methods: Blood samples were taken at different points and analyzed for their hematological properties, activities of selected enzymes, hormones, and metabolites; (3 Results: Muscle stress biomarkers were elevated in response to exercise which correlated with modifications in the profile of white blood cells, where a leukocyte rise was observed after the canoe session. These results were accompanied by an increase in other exercise intensity parameters such as lactatemia and ammonemia. Adrenocorticotropic hormone and cortisol increased during the exercise sessions. The acute rise in both erythrocytes and white blood profile were probably due to muscle cell damage, rather than hepatocyte integrity impairment; (4 Conclusion: The cellular and metabolic responses found here, together with effective nutrition support, are crucial to understanding the effects of exercise in order to assist in the creation of new training and recovery planning. Also we show that Sportomics is a primal tool for training management and performance improvement, as well as to the understanding of metabolic response to exercise.

  14. Investigation of central carbon metabolism and the 2-methylcitrate cycle in Corynebacterium glutamicum by metabolic profiling using gas chromatography-mass spectrometry.

    Science.gov (United States)

    Plassmeier, Jens; Barsch, Aiko; Persicke, Marcus; Niehaus, Karsten; Kalinowski, Jörn

    2007-07-15

    The 2-methylcitrate cycle as the primary way to metabolize propionate was investigated using metabolic profiling. For this purpose, a fast harvesting procedure was applied in which cells growing in liquid minimal medium were harvested by a short centrifugation and freeze-dried. Subsequently, gas chromatography-mass spectrometry of polar extracts derivatized by MSTFA was employed for metabolite characterization. Routinely more than 300 different peaks were obtained in the chromatograms, and 74 substances were identified unequivocally by using pure standards. The procedure provided reliable data which closely relate to prior knowledge on flux distributions during growth on glucose and acetate as carbon sources. Propionate degradation via the 2-methylcitrate cycle was demonstrated on the metabolite level by the detection of the intermediates 2-methylcitrate and 2-methylisocitrate. Further characterization of the 2-methylcitrate cycle was carried out by comparing different mutant strains of this pathway. The growth deficit of a prpD2-mutant strain observed when propionate is added to a culture growing on acetate indicates that the toxic effect of propionate is based on the accumulation of 2-methylcitrate. It could also be shown that the 2-methylcitrate cycle is active in the absence of propionate and might fulfill house-keeping functions in the degradation of fatty acids or branched-chain amino acids.

  15. Investigation of relationship of visceral body fat and inflammatory markers with metabolic syndrome and its components among apparently healthy individuals.

    Science.gov (United States)

    Turker, Yasemin; Baltaci, Davut; Turker, Yasin; Ozturk, Serkan; Sonmez, Cemil Isik; Deler, Mehmet Harun; Sariguzel, Yunus Cem; Sariguzel, Feyza; Ankarali, Handan

    2015-01-01

    Metabolic syndrome is a cluster of disorders and great risk for cardiovascular diseases. We aimed to investigate association between severity of metabolic syndrome (MetS) and anthropometric measurements, and to evaluate correlation of MetS and its components with metabolic deterioration and inflammatory indexes. The cross-sectional study enrolled 1474 patients with obesity and overweight. The patients were grouped as MetS and Non-MetS, and were sub-grouped as group 1 (three criteria), 2 (four criteria) and 3 (≥ five criteria) according to NCEP ATP III. Mean age was 38.7 ± 11.9 years and BMI was 35.1 ± 6.3 kg/m(2). Lipid profile, anthropometric and blood pressure measurements, liver function tests, bioelectric impedance body fat compositions, insulin resistance and HbA1c, and spot urinary albumin-creatinine ratio were significantly different between groups of MetS and Non-MetS. Age, lipid profile, bioelectric impedance fat analyses, BMI, blood pressure values, glucose, insulin resistance, uric acid and hs-CRP levels were significantly different between groups of MetS component groups. ROC analysis revealed that hs-CRP was found to be more predictive for severity of metabolic syndrome components 3 and 4 (P=0.030); uric acid and visceral fat were more actual to predict severity of metabolic syndrome between 3 and 5 MetS components, (P=0.006) and uric acid was detected as more actual to predict severity of MetS between 4 and 5 components (P=0.023). In conclusion, uric acid, hs-CRP and visceral body fat composition were useful to predict to severity of MetS in primary care.

  16. Investigation of Microbial Communities and Their Links to Biogeochemistry at the Marine Sediment-water Interface in Deep-sea Polymetallic Nodule Province

    Science.gov (United States)

    Zhou, P.; Huo, Y. Y.; Wu, Y. H.; Wang, C. S.; Xu, X. W.

    2016-12-01

    The sedimentary environment surrounding deep-sea polymetallic nodules is critical in understanding the formation of deep-sea polymetallic nodules and the connection between the biological and geological cycles of metal elements. To elucidate key microbes involved in cycling of metal elements, we particularly addressed the spatial patterns of microorganisms across scales. We collected sediments by multi-corer at ten sampling sites around Clarion-Clipperton Fracture Zone. To study the sediment-water interface, the sediments were divided into samples according to three layers of 0-5cm, 5-10cm, and 10-15cm. The metal composition in these 30 samples was investigated, such as the richness of manganese, cobalt, copper, and nickel. We found that the metals, including manganese, iron, aluminum, copper, vanadium, nickel, cobalt, even sodium, usually decreased with the increasing depth away from the sediment-water interface, while calcium usually increased. The content of calcium varied significantly in particular samples. To find the relationship between microbes and metal cycling, the biodiversity and relative abundance of taxa in the microbial communities was investigated by using culture-independent high-throughput sequencing, followed by classification and statistical analyses. Correlations among the microbes and metals were calculated, and correlation-based network was established, which helped us obtain a comprehensive understanding of relationships between metals and microorganisms. The roles of Rhizobiales and Solirubrobacterales and other microbial taxa in elementary cycling in sediments and polymetallic nodules were discussed. Here we will present our findings linking seafloor metal cycling to the diversity of deep ocean microbial community, which helps understand the biotic formation of polymetallic nodules and benefits the sustainable use and conversation of biodiversity during deep-sea mining.

  17. Investigations with tritium-labelled glycerol of the triglyceride metabolism in patients

    International Nuclear Information System (INIS)

    Leonhardt, W.; Julius, U.; Koch, R.; Schulze, J.

    1980-01-01

    Triglycerides, being components of lipoproteins, are secreted by the liver into the blood and climinated from the blood by adipose and muscle tissue. The kinetics of this metabolic pathway were studied after injection of tritium-labelled glycerol which is incorporated into triglycerides by the liver. The serum triglyceride radioactivity-time curve was analysed with a computer. 99 examinations showed a decrease of the fractional turnover rate and an increase of the turnover rate with the triglyceride level. The test enables to decide whether an increased triglyceride concentration is caued by overproduction or by disturbed climination. (author)

  18. Biodiversity of the microbial mat of the Garga hot spring.

    Science.gov (United States)

    Rozanov, Alexey Sergeevich; Bryanskaya, Alla Victorovna; Ivanisenko, Timofey Vladimirovich; Malup, Tatyana Konstantinovna; Peltek, Sergey Evgenievich

    2017-12-28

    Microbial mats are a good model system for ecological and evolutionary analysis of microbial communities. There are more than 20 alkaline hot springs on the banks of the Barguzin river inflows. Water temperature reaches 75 °C and pH is usually 8.0-9.0. The formation of microbial mats is observed in all hot springs. Microbial communities of hot springs of the Baikal rift zone are poorly studied. Garga is the biggest hot spring in this area. In this study, we investigated bacterial and archaeal diversity of the Garga hot spring (Baikal rift zone, Russia) using 16S rRNA metagenomic sequencing. We studied two types of microbial communities: (i) small white biofilms on rocks in the points with the highest temperature (75 °C) and (ii) continuous thick phototrophic microbial mats observed at temperatures below 70 °C. Archaea (mainly Crenarchaeota; 19.8% of the total sequences) were detected only in the small biofilms. The high abundance of Archaea in the sample from hot springs of the Baikal rift zone supplemented our knowledge of the distribution of Archaea. Most archaeal sequences had low similarity to known Archaea. In the microbial mats, primary products were formed by cyanobacteria of the genus Leptolyngbya. Heterotrophic microorganisms were mostly represented by Actinobacteria and Proteobacteria in all studied samples of the microbial mats. Planctomycetes, Chloroflexi, and Chlorobi were abundant in the middle layer of the microbial mats, while heterotrophic microorganisms represented mostly by Firmicutes (Clostridia, strict anaerobes) dominated in the bottom part. Besides prokaryotes, we detect some species of Algae with help of detection their chloroplasts 16 s rRNA. High abundance of Archaea in samples from hot springs of the Baikal rift zone supplemented our knowledge of the distribution of Archaea. Most archaeal sequences had low similarity to known Archaea. Metagenomic analysis of microbial communities of the microbial mat of Garga hot spring showed that

  19. Zebrafish as a Model System for Investigating the Compensatory Regulation of Ionic Balance during Metabolic Acidosis

    Directory of Open Access Journals (Sweden)

    Lletta Lewis

    2018-04-01

    Full Text Available Zebrafish (Danio rerio have become an important model for integrative physiological research. Zebrafish inhabit a hypo-osmotic environment; to maintain ionic and acid-base homeostasis, they must actively take up ions and secrete acid to the water. The gills in the adult and the skin at larval stage are the primary sites of ionic regulation in zebrafish. The uptake of ions in zebrafish is mediated by specific ion transporting cells termed ionocytes. Similarly, in mammals, ion reabsorption and acid excretion occur in specific cell types in the terminal region of the renal tubules (distal convoluted tubule and collecting duct. Previous studies have suggested that functional regulation of several ion transporters/channels in the zebrafish ionocytes resembles that in the mammalian renal cells. Additionally, several mechanisms involved in regulating the epithelial ion transport during metabolic acidosis are found to be similar between zebrafish and mammals. In this article, we systemically review the similarities and differences in ionic regulation between zebrafish and mammals during metabolic acidosis. We summarize the available information on the regulation of epithelial ion transporters during acidosis, with a focus on epithelial Na+, Cl− and Ca2+ transporters in zebrafish ionocytes and mammalian renal cells. We also discuss the neuroendocrine responses to acid exposure, and their potential role in ionic compensation. Finally, we identify several knowledge gaps that would benefit from further study.

  20. Investigations on the transport and metabolism of high density lipoprotein cholesteryl esters in African green monkeys

    International Nuclear Information System (INIS)

    Sorci-Thomas, M.G.

    1984-01-01

    The metabolic fate of circulating high density lipoprotein cholesteryl esters was studied in African green monkeys to determine the significance of the lipid transfer reaction on the catabolism of lipoprotein cholesteryl esters. A method of doubly labeling both moieties of lipoprotein cholesteryl esters with [ 3 He]cholesteryl oleate and cholesteryl [ 14 C]oleate was developed for the purpose of studying plasma cholesteryl ester metabolism in vivo. In these studies the total plasma [ 3 He]cholesterol turnover resulted in production rates, which ranged from 10-17 mg/kg day, similar to previously reported values in African green monkeys and in normal lipoproteinemic humans. In contrast to the production rates calculated from the decay of plasma 3 He-radioactivity, the production rates calculated from lipoproteins labeled with cholesteryl [ 14 C]oleate were approximately 2-3 times greater. In addition to these studies, a plasma cholesteryl ester transacylation activity was demonstrated in vitro when HDL containing doubly labeled cholesteryl esters were incubated with fresh plasma. These results demonstrated that high density lipoprotein cholesteryl esters undergo transacylation in vitro, resulting in release and reesterification of free [ 3 H]cholesterol

  1. Microbial network of the carbonate precipitation process induced by microbial consortia and the potential application to crack healing in concrete.

    Science.gov (United States)

    Zhang, Jiaguang; Zhou, Aijuan; Liu, Yuanzhen; Zhao, Bowei; Luan, Yunbo; Wang, Sufang; Yue, Xiuping; Li, Zhu

    2017-11-06

    Current studies have employed various pure-cultures for improving concrete durability based on microbially induced carbonate precipitation (MICP). However, there have been very few reports concerned with microbial consortia, which could perform more complex tasks and be more robust in their resistance to environmental fluctuations. In this study, we constructed three microbial consortia that are capable of MICP under aerobic (AE), anaerobic (AN) and facultative anaerobic (FA) conditions. The results showed that AE consortia showed more positive effects on inorganic carbon conversion than AN and FA consortia. Pyrosequencing analysis showed that clear distinctions appeared in the community structure between different microbial consortia systems. Further investigation on microbial community networks revealed that the species in the three microbial consortia built thorough energetic and metabolic interaction networks regarding MICP, nitrate-reduction, bacterial endospores and fermentation communities. Crack-healing experiments showed that the selected cracks of the three consortia-based concrete specimens were almost completely healed in 28 days, which was consistent with the studies using pure cultures. Although the economic advantage might not be clear yet, this study highlights the potential implementation of microbial consortia on crack healing in concrete.

  2. Investigation of the metabolic consequences of impregnating spinach leaves with trehalose and applying a pulsed electric field.

    Science.gov (United States)

    Dymek, Katarzyna; Panarese, Valentina; Herremans, Els; Cantre, Dennis; Schoo, Rick; Toraño, Javier Sastre; Schluepmann, Henriette; Wadso, Lars; Verboven, Pieter; Nicolai, Bart M; Dejmek, Petr; Gómez Galindo, Federico

    2016-12-01

    The impregnation of leafy vegetables with cryoprotectants using a combination of vacuum impregnation (VI) and pulsed electric fields (PEF) has been proposed by our research group as a method of improving their freezing tolerance and consequently their general quality after thawing. In this study, we have investigated the metabolic consequences of the combination of these unit operations on spinach. The vacuum impregnated spinach leaves showed a drastic decrease in the porosity of the extracellular space. However, at maximum weight gain, randomly located air pockets remained, which may account for oxygen-consuming pathways in the cells being active after VI. The metabolic activity of the impregnated leaves showed a drastic increase that was further enhanced by the application of PEF to the impregnated tissue. Impregnating the leaves with trehalose by VI led to a significant accumulation of trehalose-6-phosphate (T6P), however, this was not further enhanced by PEF. It is suggested that the accumulation of T6P in the leaves may increase metabolic activity, and increase tissue resistance to abiotic stress. Copyright © 2016 Elsevier B.V. All rights reserved.

  3. Investigation of metabolic stability of the novel ALK inhibitor brigatinib by liquid chromatography tandem mass spectrometry.

    Science.gov (United States)

    Darwish, Hany W; Kadi, Adnan A; Attwa, Mohamed W; Almutairi, Halah S

    2018-02-16

    Brigatinib (BGB) belongs to a class of drugs called ALK inhibitor. On April 28, 2017, BGB has been approved by U.S. FDA for use in metastatic ALK-positive NSCLC. A fast, specific, sensitive and validated LC-MS/MS method was developed for the quantification of BGB in human plasma matrix. This method was applied successfully to study metabolic stability of BGB. Reversed phase (C18 column) and isocratic binary mobile phase (55% 0.1% formic acid: 45% ACN) were used for chromatographic separation of BGB and ponatinib (IS). The flow rate, total run time and injection volume were fixed at 0.2 mL/min, 4 min, 5 μL respectively. ESI source was utilized for ions formation, while multiple reaction monitoring (MRM) mode was used for ion analysis. In human plasma matrix, the Linearity range of the calibration curve was 5-500 ng/mL (r 2  ≥ 0.9982). LOQ and LOD were found to be 1.89 and 5.72 ng/mL. The precision and accuracy for the intra-day and inter-day were 0.45 to 1.85% and 97.37 to 104.85%. In vitro half-life (t 1/2 ) and intrinsic clearance (CL int ) were equal to 12.0 min and 13.1 ± 0.15 mL/min/kg respectively. The quantification of BGB in human plasma or its metabolic stability has not been studied as seen in literature review. Copyright © 2018 Elsevier B.V. All rights reserved.

  4. An investigation into the activation and deactivation of chlorinated hydrocarbons to genotoxins in metabolically competent human cells.

    Science.gov (United States)

    Doherty, A T; Ellard, S; Parry, E M; Parry, J M

    1996-05-01

    We have investigated the induction of micronuclei by 15 chlorinated hydrocarbons in the cytochalasin B-blocked micronucleus assay utilizing genetically engineered cell lines. The human lymphoblastoid cell line AHH-1, with native cytochrome CYP1A1 activity, the MCL-5 cell line, which stably expresses cDNAs encoding human CYP1A2, 2A6, 3A4, 2E1 and microsomal epoxide hydrolase, and the h2E1 cell line, containing a cDNA for CYP2E1, were used in this study. We have demonstrated the induction of kinetochore-positive micronuclei by two chlorinated solvents, 2,3-dichlorobutane and 1,1, 2-trichloroethane, in the metabolically competent cell lines MCL-5 and h2E1. The MCL-5 and h2E1 cell lines have in addition shown the capacity to produce metabolites in the presence of methylene chloride, carbon tetrachloride, 1,2,3-trichloropropane, tetrachloroethylene, toluene and n-hexane, wich yield elevated micronucleus frequencies compared with the parental cell line AHH-1. Hexachloroethane failed to induce micronuclei in any of the cell lines and 1,2-dichloroethane and 1-chlorohexane induced micronuclei without the requirement for metabolic activation in all three cell lines. The MCL-5 cell line exhibited reduced micronucleus frequencies compared with the AHH-1 and h2E1 cell lines following exposure to 1,2-dichloroethylene, 1,3-dichloropropane, 1,1, 1-trichloroethane and 1,2,3-trichloropropane. The methodology used has shown the ability of metabolically competent cell lines expressing cDNAs encoding the cytochrome P450 isoenzymes to metabolize halogenated hydrocarbons to genotoxic species, including both clastogens and aneugens. The biotransformation of chemicals to aneugenic species has not previously been demonstrated.

  5. Integrated experimental investigation and mathematical modeling of brackish water desalination and wastewater treatment in microbial desalination cells.

    Science.gov (United States)

    Ping, Qingyun; Huang, Zuyi; Dosoretz, Carlos; He, Zhen

    2015-06-15

    Desalination of brackish water can provide freshwater for potable use or non potable applications such as agricultural irrigation. Brackish water desalination is especially attractive to microbial desalination cells (MDCs) because of its low salinity, but this has not been well studied before. Herein, three brackish waters prepared according to the compositions of actual brackish water in three locations in Israel were examined with domestic wastewater as an electron source in a bench-scale MDC. All three brackish waters could be effectively desalinated with simultaneous wastewater treatment. The MDC achieved the highest salt removal rate of 1.2 g L(-1) d(-1) with an initial salinity of 5.9 g L(-1) and a hydraulic retention time (HRT) of 0.8 d. The desalinated brackish water could meet the irrigation standard of both salinity (450 mg L(-1) TDS) and the concentrations of major ionic species, given a sufficient HRT. The MDC also accomplished nearly 70% removal of organic compounds in wastewater with Coulombic efficiency varied between 5 and 10%. A previously developed MDC model was improved for brackish water desalination, and could well predict salinity variation and the concentrations of individual ions. The model also simulated a staged operation mode with improved desalination performance. This integrated experiment and mathematical modeling approach provides an effective method to understand the key factors in brackish water desalination by MDCs towards further system development. Copyright © 2015 Elsevier Ltd. All rights reserved.

  6. Microbial diversity and dynamics throughout manufacturing and ripening of surface ripened semi-hard Danish Danbo cheeses investigated by culture-independent techniques.

    Science.gov (United States)

    Ryssel, Mia; Johansen, Pernille; Al-Soud, Waleed Abu; Sørensen, Søren; Arneborg, Nils; Jespersen, Lene

    2015-12-23

    Microbial successions on the surface and in the interior of surface ripened semi-hard Danish Danbo cheeses were investigated by culture-dependent and -independent techniques. Culture-independent detection of microorganisms was obtained by denaturing gradient gel electrophoresis (DGGE) and pyrosequencing, using amplicons of 16S and 26S rRNA genes for prokaryotes and eukaryotes, respectively. With minor exceptions, the results from the culture-independent analyses correlated to the culture-dependent plating results. Even though the predominant microorganisms detected with the two culture-independent techniques correlated, a higher number of genera were detected by pyrosequencing compared to DGGE. Additionally, minor parts of the microbiota, i.e. comprising 4.0% of the OTUs), as well as Pseudoclavibacter, Alkalibacterium and Marinilactibacillus, which represented <2% of the OTUs. At smearing, yeast counts were low with Debaryomyces being the dominant genus accounting for 46.5% of the OTUs. During ripening the yeast counts increased significantly with Debaryomyces being the predominant genus, on average accounting for 96.7%±4.1% of the OTUs. The interior of the cheeses was dominated by Lactococcus spp. comprising on average 93.9%±7.8% of the OTUs throughout the cheese processing. The microbial dynamics described at genus level in this study add to a comprehensive understanding of the complex microbiota existing especially on surface ripened semi-hard cheeses. Copyright © 2015 Elsevier B.V. All rights reserved.

  7. Metabolic Imaging of Infection

    NARCIS (Netherlands)

    Lawal, Ismaheel; Zeevaart, JanRijn; Ebenhan, Thomas; Ankrah, Alfred; Vorster, Mariza; Kruger, Hendrik G.; Govender, Thavendran; Sathekge, Mike

    2017-01-01

    Metabolic imaging has come to occupy a prominent place in the diagnosis and management of microbial infection. Molecular probes available for infection imaging have undergone a rapid evolution starting with nonspecific agents that accumulate similarly in infection, sterile inflammation, and

  8. Novel Approaches to Investigate One-Carbon Metabolism and Related B-Vitamins in Blood Pressure

    Directory of Open Access Journals (Sweden)

    Amy McMahon

    2016-11-01

    Full Text Available Hypertension, a major risk factor for heart disease and stroke, is the world’s leading cause of preventable, premature death. A common polymorphism (677C→T in the gene encoding the folate metabolizing enzyme methylenetetrahydrofolate reductase (MTHFR is associated with increased blood pressure, and there is accumulating evidence demonstrating that this phenotype can be modulated, specifically in individuals with the MTHFR 677TT genotype, by the B-vitamin riboflavin, an essential co-factor for MTHFR. The underlying mechanism that links this polymorphism, and the related gene-nutrient interaction, with hypertension is currently unknown. Previous research has shown that 5-methyltetrahydrofolate, the product of the reaction catalysed by MTHFR, appears to be a positive allosteric modulator of endothelial nitric oxide synthase (eNOS and may thus increase the production of nitric oxide, a potent vasodilator. Blood pressure follows a circadian pattern, peaking shortly after wakening and falling during the night, a phenomenon known as ‘dipping’. Any deviation from this pattern, which can only be identified using ambulatory blood pressure monitoring (ABPM, has been associated with increased cardiovascular disease (CVD risk. This review will consider the evidence linking this polymorphism and novel gene-nutrient interaction with hypertension and the potential mechanisms that might be involved. The role of ABPM in B-vitamin research and in nutrition research generally will also be reviewed.

  9. Novel Approaches to Investigate One-Carbon Metabolism and Related B-Vitamins in Blood Pressure

    Science.gov (United States)

    McMahon, Amy; McNulty, Helene; Hughes, Catherine F.; Strain, J. J.; Ward, Mary

    2016-01-01

    Hypertension, a major risk factor for heart disease and stroke, is the world’s leading cause of preventable, premature death. A common polymorphism (677C→T) in the gene encoding the folate metabolizing enzyme methylenetetrahydrofolate reductase (MTHFR) is associated with increased blood pressure, and there is accumulating evidence demonstrating that this phenotype can be modulated, specifically in individuals with the MTHFR 677TT genotype, by the B-vitamin riboflavin, an essential co-factor for MTHFR. The underlying mechanism that links this polymorphism, and the related gene-nutrient interaction, with hypertension is currently unknown. Previous research has shown that 5-methyltetrahydrofolate, the product of the reaction catalysed by MTHFR, appears to be a positive allosteric modulator of endothelial nitric oxide synthase (eNOS) and may thus increase the production of nitric oxide, a potent vasodilator. Blood pressure follows a circadian pattern, peaking shortly after wakening and falling during the night, a phenomenon known as ‘dipping’. Any deviation from this pattern, which can only be identified using ambulatory blood pressure monitoring (ABPM), has been associated with increased cardiovascular disease (CVD) risk. This review will consider the evidence linking this polymorphism and novel gene-nutrient interaction with hypertension and the potential mechanisms that might be involved. The role of ABPM in B-vitamin research and in nutrition research generally will also be reviewed. PMID:27845713

  10. Inhibition of in vitro metabolism of testosterone in human, dog and horse liver microsomes to investigate species differences.

    Science.gov (United States)

    Zielinski, Jana; Mevissen, Meike

    2015-04-01

    Testosterone hydroxylation was investigated in human, canine and equine liver microsomes and in human and canine single CYPs. The contribution of the CYP families 1, 2 and 3 was studied using chemical inhibitors. Testosterone metabolites were analyzed by HPLC. The metabolites androstenedione, 6β- and 11β-hydroxytestosterone were found in microsomes of all species, but the pattern of metabolites varied within species. Androstenedione was more prominent in the animal species, and an increase over time was seen in equines. Testosterone hydroxylation was predominantly catalyzed by the CYP3A subfamily in all three species. While CYP2C9 did not metabolise testosterone, the canine ortholog CYP2C21 produced androstenedione. Quercetin significantly inhibited 6β- and 11β-hydroxytestosterone in all species investigated, suggesting that CYP2C8 is involved in testosterone metabolism, whereas sulfaphenazole significantly inhibited the formation of 6β- and 11β-hydroxytestosterone in human microsomes, at 60 min in equine microsomes, but not in canine microsomes. A contribution of CYP2B6 in testosterone metabolism was only found in human and equine microsomes. Inhibition of 17β-hydroxysteroid dehydrogenase 2 indicated its involvement in androstenedione formation in humans, increased androstenedione formation was found in equines and no involvement in canines. These findings provide improved understanding of differences in testosterone biotransformation in animal species. Copyright © 2014 Elsevier Ltd. All rights reserved.

  11. Final Scientific/Technical Report, DE-FG02-06ER64171, Integrated Nucleic Acid System for In-Field Monitoring of Microbial Community Dynamics and Metabolic Activity – Subproject to Co-PI Eric E. Roden

    Energy Technology Data Exchange (ETDEWEB)

    Eric E. Roden

    2009-07-08

    This report summarizes research conducted in conjunction with a project entitled “Integrated Nucleic Acid System for In-Field Monitoring of Microbial Community Dynamics and Metabolic Activity”, which was funded through the Integrative Studies Element of the former NABIR Program (now the Environmental Remediation Sciences Program) within the Office of Biological and Environmental Research. Dr. Darrell Chandler (originally at Argonne National Laboratory, now with Akonni Biosystems) was the overall PI/PD for the project. The overall project goals were to (1) apply a model iron-reducer and sulfate-reducer microarray and instrumentation systems to sediment and groundwater samples from the Scheibe et al. FRC Area 2 field site, UMTRA sediments, and other DOE contaminated sites; (2) continue development and expansion of a 16S rRNA/rDNA¬-targeted probe suite for microbial community dynamics as new sequences are obtained from DOE-relevant sites; and (3) address the fundamental molecular biology and analytical chemistry associated with the extraction, purification and analysis of functional genes and mRNA in environmental samples. Work on the UW subproject focused on conducting detailed batch and semicontinuous culture reactor experiments with uranium-contaminated FRC Area 2 sediment. The reactor experiments were designed to provide coherent geochemical and microbiological data in support of microarray analyses of microbial communities in Area 2 sediments undergoing biostimulation with ethanol. A total of four major experiments were conducted (one batch and three semicontinuous culture), three of which (the batch and two semicontinuous culture) provided samples for DNA microarray analysis. A variety of other molecular analyses (clone libraries, 16S PhyloChip, RT-PCR, and T-RFLP) were conducted on parallel samples from the various experiments in order to provide independent information on microbial community response to biostimulation.

  12. Investigating Stream Metabolism and Nutrient Dynamics in Contrasting Ecosystems: The Role of Hydrologic Compartments

    Science.gov (United States)

    Gonzalez-Pinzon, R.; Riveros-Iregui, D. A.; Covino, T. P.

    2015-12-01

    The interactions between mobile and less mobile hydrologic compartments affect the quality and quantity of water in streams and aquifers, and the cycling of dissolved carbon and nutrients. As new laboratory and field techniques become available, new questions and challenges emerge, including: What do we measure, where, and for how long to fully characterize a system? and, What is the ideal cost-maintenance-benefit relationship that we should strive for to maximize knowledge gained in different field settings? We recently performed a series of field experiments to measure aquatic metabolism and nutrient dynamics in two highly contrasting hydrologic systems, i.e., 1) a wetland-stream alpine, tropical system in Colombia (South America) and 2) a dryland river continuum (1st - 5th stream orders) in New Mexico. In this presentation we discuss how multiple lines of evidence can support the analysis of key aquatic processes and how co-interpretation provides a more complete picture of stream complexity. For this analysis, we deployed YSI EXO2 and 6920 sondes, Turner Designs C-sense and C6 sensors, and Onset HOBO water quality data loggers. Parameters measured by these instruments include conductivity, temperature, dissolved oxygen, pH, turbidity, pCO2, chlorophyll-a, phycocyanin, fluorescein, CDOM, brighteners and water depth. We also injected conservative tracers (i.e., NaCl and NaBr) and the bioreactive tracer resazurin in both experimental sites, and NO3 in the dryland river continuum. NO3 was measured in-situ with Satlantic Submersible Ultraviolet Nitrate Analyzers (SUNA) sensors and in the laboratory using Ion Chromatograph techniques using stream grab samples. Our results highlight the role of both residence times and chemical fluxes in regulating the effective processing of carbon and nutrients. Our results also demonstrate that stream stimuli from controlled experiments are ideal for maximizing the information content derived from short (hours to days) and mid

  13. Microbial composition and ecological features of phototrophic biofilms proliferating in the Moidons Caves (France): investigation at the single-cell level.

    Science.gov (United States)

    Borderie, Fabien; Denis, Michel; Barani, Aude; Alaoui-Sossé, Badr; Aleya, Lotfi

    2016-06-01

    The authors investigated the microbial composition of phototrophic biofilms proliferating in a show cave using flow cytometry for the first time in such a context. Results are based on several biofilms sampled in the Moidons Caves (France) and concern both heterotrophic prokaryotes and autotrophic microorganisms. Heterotrophic microorganisms with low nucleic acid content were dominant in biofilms, as can be expected from the oligotrophic conditions prevailing within the cave. Analysis of the biofilm autotrophic components revealed the presence of several taxa, particularly the unicellular green algae Chlorella minutissima, specifically well adapted to this cave. Relationships between flow cytometry results and environmental variables determined in the cave were established and discussed so as to better understand biofilm proliferation processes in caves.

  14. Does iron inhibit cryptoendolithic microbial communities?

    Science.gov (United States)

    Johnston, C. G.; Vestal, J. R.; Friedmann, E. I. (Principal Investigator)

    1988-01-01

    Photosynthetic activity of three cryptoendolithic microbial communities was studied under controlled conditions in the laboratory. In two of these communities, the dominant organisms were lichens, collected from Linnaeus Terrace and from Battleship Promontory. The third community, dominated by cyanobacteria, was collected from Battleship Promontory. Both sites are in the ice-free valleys of southern Victoria Land. Previous efforts have shown how physical conditions can influence metabolic activity in endolithic communities (Kappen and Friedmann 1983; Kappen, Friedmann, and Garty 1981; Vestal, Federle, and Friedmann 1984). Biological activity can also be strongly influenced by the chemical environment. Inorganic nutrients such as nitrate, ammonia, and phosphate are often limiting factors, so their effects on photosynthetic carbon-14 bicarbonate incorporation were investigated. Iron and manganese are two metals present in Linnaeus Terrace and Battleship Promontory sandstones, and their effects on photosynthesis were also studied. The results may add to our understanding of biogeochemical interactions within this unique microbial community.

  15. Methodical investigations on the determination of metabolic lysine requirements in broiler chickens. 1

    International Nuclear Information System (INIS)

    Bergner, H.; Nguyen Thi Nhan; Wilke, A.

    1987-01-01

    For the estimation of lysine requirement 128 male broiler chickens were used at an age of 7 to 21 days posthatching. They received a lysine-deficient diet composed of wheat and wheat gluten. To this basal diet L-lysine-HCL was supplemented successively resulting in 8 lysine levels ranging from 5.8 to 23.3 g lysine per kg dry matter (DM) (2.2 to 8.7 g lysine per 16 g N). At the end of the two-week feeding period of the experimental diets 14 C-lysine was injected intravenously 1.5 and 5.5 hours after feed withdrawal. During the following 4 hours the exretion of CO 2 and 14 CO 2 was measured. The highest daily gain of 21.5 g was observed in animals fed 13.3 g lysine-kg DM. Lysine concentrations exceeding 18.3 g/kg DM depressed body weight gain. The CO 2 excretion was not influenced by lysine intake. 14 CO 2 excretion was low with diets low in lysine content and increased 3 to 4 times with diets meeting the lysine requirement. Based on measurements 1.5 to 5.5 hours after feed withdrawal the saturation value for lysine was reached at 13.3 g/kg DM. This value was lowered (10.8 g/kg DM), however, if the estimation was carried out 5.5 to 9.5 hours after feed withdrawal. These results suggest a higher metabolic lysine requirement during the earlier period after feed intake. Both, reduced weight gain and non linearity in 14 CO 2 excretion in diets exceeding a lysine content of 18.3 g/kg DM indicate a limited capacity of the organism to degrade excessive lysine. According to the results a lysine requirement betwen 10.8 and 13.3 g/kg DM (27% CP and 660 EFU/sub hen//kg DM) was estimated for broiler chickens 3 weeks posthatching. (author)

  16. [Investigation of the properties of the soil microbial consortium as a test objects for estimation of integral toxicity].

    Science.gov (United States)

    Dudchik, N V

    2012-01-01

    The properties of a consortium of microorganisms InMI/CH7 selected from of industrial effluent samples have been investigated. The ability of strains to form biofilms was shown to be correlated with their sensitivity to toxicants.

  17. Biochar affects soil organic matter cycling and microbial functions but does not alter microbial community structure in a paddy soil.

    Science.gov (United States)

    Tian, Jing; Wang, Jingyuan; Dippold, Michaela; Gao, Yang; Blagodatskaya, Evgenia; Kuzyakov, Yakov

    2016-06-15

    The application of biochar (BC) in conjunction with mineral fertilizers is one of the most promising management practices recommended to improve soil quality. However, the interactive mechanisms of BC and mineral fertilizer addition affecting microbial communities and functions associated with soil organic matter (SOM) cycling are poorly understood. We investigated the SOM in physical and chemical fractions, microbial community structure (using phospholipid fatty acid analysis, PLFA) and functions (by analyzing enzymes involved in C and N cycling and Biolog) in a 6-year field experiment with BC and NPK amendment. BC application increased total soil C and particulate organic C for 47.4-50.4% and 63.7-74.6%, respectively. The effects of BC on the microbial community and C-cycling enzymes were dependent on fertilization. Addition of BC alone did not change the microbial community compared with the control, but altered the microbial community structure in conjunction with NPK fertilization. SOM fractions accounted for 55% of the variance in the PLFA-related microbial community structure. The particulate organic N explained the largest variation in the microbial community structure. Microbial metabolic activity strongly increased after BC addition, particularly the utilization of amino acids and amines due to an increase in the activity of proteolytic (l-leucine aminopeptidase) enzymes. These results indicate that microorganisms start to mine N from the SOM to compensate for high C:N ratios after BC application, which consequently accelerate cycling of stable N. Concluding, BC in combination with NPK fertilizer application strongly affected microbial community composition and functions, which consequently influenced SOM cycling. Copyright © 2016 Elsevier B.V. All rights reserved.

  18. Microbial Community Profiles in Wastewaters from Onsite Wastewater Treatment Systems Technology

    Science.gov (United States)

    Jałowiecki, Łukasz; Chojniak, Joanna Małgorzata; Dorgeloh, Elmar; Hegedusova, Berta; Ejhed, Helene; Magnér, Jörgen; Płaza, Grażyna Anna

    2016-01-01

    The aim of the study was to determine the potential of community-level physiological profiles (CLPPs) methodology as an assay for characterization of the metabolic diversity of wastewater samples and to link the metabolic diversity patterns to efficiency of select onsite biological wastewater facilities. Metabolic fingerprints obtained from the selected samples were used to understand functional diversity implied by the carbon substrate shifts. Three different biological facilities of onsite wastewater treatment were evaluated: fixed bed reactor (technology A), trickling filter/biofilter system (technology B), and aerated filter system (the fluidized bed reactor, technology C). High similarities of the microbial community functional structures were found among the samples from the three onsite wastewater treatment plants (WWTPs), as shown by the diversity indices. Principal components analysis (PCA) showed that the diversity and CLPPs of microbial communities depended on the working efficiency of the wastewater treatment technologies. This study provided an overall picture of microbial community functional structures of investigated samples in WWTPs and discerned the linkages between microbial communities and technologies of onsite WWTPs used. The results obtained confirmed that metabolic profiles could be used to monitor treatment processes as valuable biological indicators of onsite wastewater treatment technologies efficiency. This is the first step toward understanding relations of technology types with microbial community patterns in raw and treated wastewaters. PMID:26807728

  19. Investigation on the Metabolic Regulation of pgi gene knockout Escherichia coli by Enzyme Activities and Intracellular Metabolite Concentrations

    Directory of Open Access Journals (Sweden)

    Nor ‘Aini, A. R.

    2006-01-01

    Full Text Available An integrated analysis of the cell growth characteristics, enzyme activities, intracellular metabolite concentrations was made to investigate the metabolic regulation of pgi gene knockout Escherichia coli based on batch culture and continuous culture which was performed at the dilution rate of 0.2h-1. The enzymatic study identified that pathways of pentose phosphate, ED pathway and glyoxylate shunt were all active in pgi mutant. The glycolysis enzymes i.e glyceraldehyde-3-phosphate dehydrogenase, fructose diphosphatase, pyruvate kinase, triose phosphate isomerase were down regulated implying that the inactivation of pgi gene reduced the carbon flux through glycolytic pathway. Meanwhile, the pentose phosphate pathway was active as a major route for intermediary carbohydrate metabolism instead of glycolysis. The pentose phosphate pathway generates most of the major reducing co-factor NADPH as shown by the increased of NADPH/NADP+ ratio in the mutant when compared with the parent strain. The fermentative enzymes such as acetate kinase and lactate dehydrogenase were down regulated in the mutant. Knockout of pgi gene results in the significant increase in the intracellular concentration of glucose-6-phosphate and decrease in the concentration of oxaloacetate. The slow growth rate of the mutant was assumed to be affected by the accumulation of glucose-6-phosphate and imbalance of NADPH reoxidation.

  20. Metabolic Therapy for Temporal Lobe Epilepsy in a Dish: Investigating Mechanisms of Ketogenic Diet using Electrophysiological Recordings in Hippocampal Slices.

    Science.gov (United States)

    Kawamura, Masahito Jr; Ruskin, David N; Masino, Susan A

    2016-01-01

    The hippocampus is prone to epileptic seizures and is a key brain region and experimental platform for investigating mechanisms associated with the abnormal neuronal excitability that characterizes a seizure. Accordingly, the hippocampal slice is a common in vitro model to study treatments that may prevent or reduce seizure activity. The ketogenic diet is a metabolic therapy used to treat epilepsy in adults and children for nearly 100 years; it can reduce or eliminate even severe or refractory seizures. New insights into its underlying mechanisms have been revealed by diverse types of electrophysiological recordings in hippocampal slices. Here we review these reports and their relevant mechanistic findings. We acknowledge that a major difficulty in using hippocampal slices is the inability to reproduce precisely the in vivo condition of ketogenic diet feeding in any in vitro preparation, and progress has been made in this in vivo/in vitro transition. Thus far at least three different approaches are reported to reproduce relevant diet effects in the hippocampal slices: (1) direct application of ketone bodies; (2) mimicking the ketogenic diet condition during a whole-cell patch-clamp technique; and (3) reduced glucose incubation of hippocampal slices from ketogenic diet-fed animals. Significant results have been found with each of these methods and provide options for further study into short- and long-term mechanisms including Adenosine triphosphate (ATP)-sensitive potassium (K ATP ) channels, vesicular glutamate transporter (VGLUT), pannexin channels and adenosine receptors underlying ketogenic diet and other forms of metabolic therapy.

  1. Histopathologic investigation of the effects of prostaglandin E2 administered by different methods on tooth movement and bone metabolism.

    Science.gov (United States)

    Cağlaroğlu, Murat; Erdem, Abdulvahit

    2012-06-01

    The aim of this study was to investigate and compare the in vivo effects of prostaglandin E2 (PGE2) administered by different methods on orthodontic tooth movement and bone metabolism macroscopically, histopatologically, and biochemically. Forty-five young adult New Zealand rabbits were randomly divided into 3 experimental groups (n = 10/group), 1 positive control group (n = 10), and 1 negative control group (n = 5). The experimental rabbits were fitted with springs exerting 20-g reciprocal force on the maxillary incisors and PGE2 (10 µg/mL) was administered by the intravenous, submucosal, or intraligamentous route after appliance insertion and on days 1, 3, 7, and 14 thereafter. All rabbits were sacrificed on day 21 and their premaxillae were resected for histologic evaluation. Tooth movement was observed in the experimental and positive control groups, but the intraligamentous PGE2 group had the highest values of all analyzed parameters, including serum calcium and phosphorus levels and osteoclastic and osteoblastic populations (p orthodontic tooth movement and bone metabolism, but the intraligamentous route seems to be more effective.

  2. Metabolic Therapy for Temporal Lobe Epilepsy in a Dish: Investigating Mechanisms of Ketogenic Diet using Electrophysiological Recordings in Hippocampal Slices

    Science.gov (United States)

    Kawamura, Masahito Jr.; Ruskin, David N.; Masino, Susan A.

    2016-01-01

    The hippocampus is prone to epileptic seizures and is a key brain region and experimental platform for investigating mechanisms associated with the abnormal neuronal excitability that characterizes a seizure. Accordingly, the hippocampal slice is a common in vitro model to study treatments that may prevent or reduce seizure activity. The ketogenic diet is a metabolic therapy used to treat epilepsy in adults and children for nearly 100 years; it can reduce or eliminate even severe or refractory seizures. New insights into its underlying mechanisms have been revealed by diverse types of electrophysiological recordings in hippocampal slices. Here we review these reports and their relevant mechanistic findings. We acknowledge that a major difficulty in using hippocampal slices is the inability to reproduce precisely the in vivo condition of ketogenic diet feeding in any in vitro preparation, and progress has been made in this in vivo/in vitro transition. Thus far at least three different approaches are reported to reproduce relevant diet effects in the hippocampal slices: (1) direct application of ketone bodies; (2) mimicking the ketogenic diet condition during a whole-cell patch-clamp technique; and (3) reduced glucose incubation of hippocampal slices from ketogenic diet–fed animals. Significant results have been found with each of these methods and provide options for further study into short- and long-term mechanisms including Adenosine triphosphate (ATP)-sensitive potassium (KATP) channels, vesicular glutamate transporter (VGLUT), pannexin channels and adenosine receptors underlying ketogenic diet and other forms of metabolic therapy. PMID:27847463

  3. Metabolic therapy for temporal lobe epilepsy in a dish: investigating mechanisms of ketogenic diet using electrophysiological recordings in hippocampal slices

    Directory of Open Access Journals (Sweden)

    Masahito Kawamura

    2016-11-01

    Full Text Available The hippocampus is prone to epileptic seizures and is a key brain region and experimental platform for investigating mechanisms associated with the abnormal neuronal excitability that characterizes a seizure. Accordingly, the hippocampal slice is a common in vitro model to study treatments that may prevent or reduce seizure activity. The ketogenic diet is a metabolic therapy used to treat epilepsy in adults and children for nearly 100 years; it can reduce or eliminate even severe or refractory seizures. New insights into its underlying mechanisms have been revealed by diverse types of electrophysiological recordings in hippocampal slices. Here we review these reports and their relevant mechanistic findings. We acknowledge that a major difficulty in using hippocampal slices is the inability to reproduce precisely the in vivo condition of ketogenic diet feeding in any in vitro preparation, and progress has been made in this in vivo/in vitro transition. Thus far at least three different approaches are reported to reproduce relevant diet effects in the hippocampal slices: (1 direct application of ketone bodies, (2 mimicking the ketogenic diet condition during a whole-cell patch-clamp technique, and (3 reduced glucose incubation of hippocampal slices from ketogenic diet–fed animals. Significant results have been found with each of these methods and provide options for further study into short- and long-term mechanisms including ATP-sensitive potassium channels, vesicular glutamate transporter, pannexin channels and adenosine receptors underlying ketogenic diet and other forms of metabolic therapy.

  4. Initial investigation of glucose metabolism in mouse brain using enriched 17 O-glucose and dynamic 17 O-MRS.

    Science.gov (United States)

    Borowiak, Robert; Reichardt, Wilfried; Kurzhunov, Dmitry; Schuch, Christian; Leupold, Jochen; Krafft, Axel Joachim; Reisert, Marco; Lange, Thomas; Fischer, Elmar; Bock, Michael

    2017-08-01

    In this initial work, the in vivo degradation of 17 O-labeled glucose was studied during cellular glycolysis. To monitor cellular glucose metabolism, direct 17 O-magnetic resonance spectroscopy (MRS) was used in the mouse brain at 9.4 T. Non-localized spectra were acquired with a custom-built transmit/receive (Tx/Rx) two-turn surface coil and a free induction decay (FID) sequence with a short TR of 5.4 ms. The dynamics of labeled oxygen in the anomeric 1-OH and 6-CH 2 OH groups was detected using a Hankel-Lanczos singular value decomposition (HLSVD) algorithm for water suppression. Time-resolved 17 O-MRS (temporal resolution, 42/10.5 s) was performed in 10 anesthetized (1.25% isoflurane) mice after injection of a 2.2 M solution containing 2.5 mg/g body weight of differently labeled 17 O-glucose dissolved in 0.9% physiological saline. From a pharmacokinetic model fit of the H 2 17 O concentration-time course, a mean apparent cerebral metabolic rate of 17 O-labeled glucose in mouse brain of CMR Glc  = 0.07 ± 0.02 μmol/g/min was extracted, which is of the same order of magnitude as a literature value of 0.26 ± 0.06 μmol/g/min reported by 18 F-fluorodeoxyglucose ( 18 F-FDG) positron emission tomography (PET). In addition, we studied the chemical exchange kinetics of aqueous solutions of 17 O-labeled glucose at the C1 and C6 positions with dynamic 17 O-MRS. In conclusion, the results of the exchange and in vivo experiments demonstrate that the C6- 17 OH label in the 6-CH 2 OH group is transformed only glycolytically by the enzyme enolase into the metabolic end-product H 2 17 O, whereas C1- 17 OH ends up in water via direct hydrolysis as well as glycolysis. Therefore, dynamic 17 O-MRS of highly labeled 17 O-glucose could provide a valuable non-radioactive alternative to FDG PET in order to investigate glucose metabolism. Copyright © 2017 John Wiley & Sons, Ltd.

  5. A Nested Case-Control Study of Metabolically Defined Body Size Phenotypes and Risk of Colorectal Cancer in the European Prospective Investigation into Cancer and Nutrition (EPIC.

    Directory of Open Access Journals (Sweden)

    Neil Murphy

    2016-04-01

    Full Text Available Obesity is positively associated with colorectal cancer. Recently, body size subtypes categorised by the prevalence of hyperinsulinaemia have been defined, and metabolically healthy overweight/obese individuals (without hyperinsulinaemia have been suggested to be at lower risk of cardiovascular disease than their metabolically unhealthy (hyperinsulinaemic overweight/obese counterparts. Whether similarly variable relationships exist for metabolically defined body size phenotypes and colorectal cancer risk is unknown.The association of metabolically defined body size phenotypes with colorectal cancer was investigated in a case-control study nested within the European Prospective Investigation into Cancer and Nutrition (EPIC study. Metabolic health/body size phenotypes were defined according to hyperinsulinaemia status using serum concentrations of C-peptide, a marker of insulin secretion. A total of 737 incident colorectal cancer cases and 737 matched controls were divided into tertiles based on the distribution of C-peptide concentration amongst the control population, and participants were classified as metabolically healthy if below the first tertile of C-peptide and metabolically unhealthy if above the first tertile. These metabolic health definitions were then combined with body mass index (BMI measurements to create four metabolic health/body size phenotype categories: (1 metabolically healthy/normal weight (BMI < 25 kg/m2, (2 metabolically healthy/overweight (BMI ≥ 25 kg/m2, (3 metabolically unhealthy/normal weight (BMI < 25 kg/m2, and (4 metabolically unhealthy/overweight (BMI ≥ 25 kg/m2. Additionally, in separate models, waist circumference measurements (using the International Diabetes Federation cut-points [≥80 cm for women and ≥94 cm for men] were used (instead of BMI to create the four metabolic health/body size phenotype categories. Statistical tests used in the analysis were all two-sided, and a p-value of <0.05 was

  6. Metabolic syndrome and risk of incident diabetes: findings from the European Prospective Investigation into Cancer and Nutrition-Potsdam Study

    OpenAIRE

    Joost Hans-Georg; Bergmann Manuela M; Pischon Tobias; Schulze Matthias B; Ford Earl S; Boeing Heiner

    2008-01-01

    Abstract Background Several aspects concerning the relationship between the metabolic syndrome and incident diabetes are incompletely understood including the magnitude of the risk estimate, potential gender differences in the associations between the metabolic syndrome and incident diabetes, the associations between the components of the metabolic syndrome and incident diabetes, and whether the metabolic syndrome provides additional prediction beyond its components. To shed light on these is...

  7. Unexplained developmental delay/learning disability: guidelines for best practice protocol for first line assessment and genetic/metabolic/radiological investigations.

    Science.gov (United States)

    O'Byrne, J J; Lynch, S A; Treacy, E P; King, M D; Betts, D R; Mayne, P D; Sharif, F

    2016-02-01

    Investigation of patients, particularly children, with unexplained global developmental delay (GDD)/learning disability (LD) has been challenging due to a lack of clear guidance from specialised centres. Limited knowledge of rare diseases and a poor understanding of the purpose or limitations of appropriate investigations have been some of the principal reasons for this difficulty. A guideline development group was formed to recommend on appropriate, first line metabolic, genetic and radiological investigations for children and adults with unexplained GDD/ID. A comprehensive literature search was conducted, evaluated and reviewed by the guideline committee and a best practice protocol for first line assessment and genetic, metabolic and radiological investigations was decided upon after considering diagnostic yield, practicality, treatability and costs. It is hoped that these recommendations will become national guidelines for the first line metabolic, genetic and radiological investigation of patients presenting with unexplained GDD/ID.

  8. Deep subsurface microbial processes

    Science.gov (United States)

    Lovley, D.R.; Chapelle, F.H.

    1995-01-01

    Information on the microbiology of the deep subsurface is necessary in order to understand the factors controlling the rate and extent of the microbially catalyzed redox reactions that influence the geophysical properties of these environments. Furthermore, there is an increasing threat that deep aquifers, an important drinking water resource, may be contaminated by man's activities, and there is a need to predict the extent to which microbial activity may remediate such contamination. Metabolically active microorganisms can be recovered from a diversity of deep subsurface environments. The available evidence suggests that these microorganisms are responsible for catalyzing the oxidation of organic matter coupled to a variety of electron acceptors just as microorganisms do in surface sediments, but at much slower rates. The technical difficulties in aseptically sampling deep subsurface sediments and the fact that microbial processes in laboratory incubations of deep subsurface material often do not mimic in situ processes frequently necessitate that microbial activity in the deep subsurface be inferred through nonmicrobiological analyses of ground water. These approaches include measurements of dissolved H2, which can predict the predominant microbially catalyzed redox reactions in aquifers, as well as geochemical and groundwater flow modeling, which can be used to estimate the rates of microbial processes. Microorganisms recovered from the deep subsurface have the potential to affect the fate of toxic organics and inorganic contaminants in groundwater. Microbial activity also greatly influences 1 the chemistry of many pristine groundwaters and contributes to such phenomena as porosity development in carbonate aquifers, accumulation of undesirably high concentrations of dissolved iron, and production of methane and hydrogen sulfide. Although the last decade has seen a dramatic increase in interest in deep subsurface microbiology, in comparison with the study of

  9. The maturing of microbial ecology.

    Science.gov (United States)

    Schmidt, Thomas M

    2006-09-01

    A.J. Kluyver and C.B. van Niel introduced many scientists to the exceptional metabolic capacity of microbes and their remarkable ability to adapt to changing environments in The Microbe's Contribution to Biology. Beyond providing an overview of the physiology and adaptability of microbes, the book outlined many of the basic principles for the emerging discipline of microbial ecology. While the study of pure cultures was highlighted, provided a unifying framework for understanding the vast metabolic potential of microbes and their roles in the global cycling of elements, extrapolation from pure cultures to natural environments has often been overshadowed by microbiologists inability to culture many of the microbes seen in natural environments. A combination of genomic approaches is now providing a culture-independent view of the microbial world, revealing a more diverse and dynamic community of microbes than originally anticipated. As methods for determining the diversity of microbial communities become increasingly accessible, a major challenge to microbial ecologists is to link the structure of natural microbial communities with their functions. This article presents several examples from studies of aquatic and terrestrial microbial communities in which culture and culture-independent methods are providing an enhanced appreciation for the microbe's contribution to the evolution and maintenance of life on Earth, and offers some thoughts about the graduate-level educational programs needed to enhance the maturing field of microbial ecology.

  10. Investigating the Burden of Chronic Pain: An Inflammatory and Metabolic Composite

    Directory of Open Access Journals (Sweden)

    Kimberly T. Sibille

    2016-01-01

    Full Text Available Background. Chronic pain is associated with increased morbidity and mortality, predominated by cardiovascular disease and cancer. Investigating related risk factor measures may elucidate the biological burden of chronic pain. Objectives. We hypothesized that chronic pain severity would be positively associated with the risk factor composite. Methods. Data from 12,982 participants in the 6th Tromsø study were analyzed. Questionnaires included demographics, health behaviors, medical comorbidities, and chronic pain symptoms. The risk factor composite was comprised of body mass index, fibrinogen, C-reactive protein, and triglycerides. Chronic pain severity was characterized by frequency, intensity, time/duration, and total number of pain sites. Results. Individuals with chronic pain had a greater risk factor composite than individuals without chronic pain controlling for covariates and after excluding inflammation-related health conditions (p<0.001. A significant “dose-response” relationship was demonstrated with pain severity (p<0.001. In individuals with chronic pain, the risk factor composite varied by health behavior, exercise, lower levels and smoking, and higher levels. Discussion. The risk factor composite was higher in individuals with chronic pain, greater with increasing pain severity, and influenced by health behaviors. Conclusions. Identification of a biological composite sensitive to pain severity and adaptive/maladaptive behaviors would have significant clinical and research utility.

  11. Investigation into endogenous N metabolism in 15N-labelled pigs. 1

    International Nuclear Information System (INIS)

    Bergner, H.; Bergner, U.; Adam, K.

    1984-01-01

    4 male castrated pigs (55-65 kg) either received a wheat-fish meal diet (1 and 2) or a wheat-horse bean diet (3 and 4) without straw meal supplement (1 and 3) or with a supplement of 20% dry matter (2 and 4). In order to investigate whether a 15 N labelling of the pigs is also possible with a protein excess in the ration, the animals received 24.8 g (1 and 2) and 11.6 g crude protein/kg/sup 0.75/ live weight (3 and 4). During a 10-day 15 N-labelling 385 mg 15 N excess ( 15 N') per kg/sup 0.75/ were applied with 15 N labelling the following quotas of the applied 15 N amount were incorporated: 1 = 10.2%, 2 = 7.2%, 3 = 18.7%, 4 = 14.4%. 15 N excretion in both TCA fractions of feces showed a highly significant positive correlation to the increasing content of crude fibre in the 4 diets. The immediate 15 N incorporation into the TCA-precipitable fraction of feces proves that 15 N enters the large intestine endogenously and serves bacterial protein synthesis. 3 days after the last 15 application the pigs were killed. The values of atom-% 15 N' were determined in the TCA-precipitable blood plasma and in the TCA-precipitable fraction of the liver. The other examined organs and tissues showed smaller differences between the test animals. The results show that the 15 N labelling of tissues and organs of pigs is also possible at a high level of protein supply by means of an oral application of [ 15 N] ammonia salts. (author)

  12. Examinations to investigate the effects of feeding propylene glycol, glycerin and L-carnitin on metabolism and parameters of efficiency of dairy cows concerning ketosis prevention

    OpenAIRE

    Malchau, Inke

    2011-01-01

    The prevalence of subclinical ketosis and metabolic disorders caused by negative energy balance in many modern dairy farms often are a reason for insufficient milk yield, high rate of disease and impaired reproduction performance. The aim of this study was to investigate the effects of feeding propylene glycol, glycerin, and L-carnitin on metabolism and milk production. 97 Holstein Friesian cows were divided into four groups, at least five days before calving. All four groups were fed w...

  13. Effect of the combination of crude extracts of Penicillium griseofulvum and Fusarium graminearum containing patulin and zearalenone on rumen microbial fermentation and on their metabolism in continuous culture fermenters.

    Science.gov (United States)

    Riccio, María Belén; Tapia, María Ofelia; Martínez, Guadalupe; Aranguren, Sandra Mariela; Dieguez, Susana Neyi; Soraci, Alejandro Luis; Rodríguez, Edgardo

    2014-01-01

    Six single-flow continuous cultures were used to study the effects of the mycotoxins patulin (PAT) and zearalenone (ZEN) alone or in combination on rumen microbial fermentation. In each of the four 7-d periods, the fermenters were supplemented in a 2 × 3 factorial arrangement with two levels of PAT (0 and 20 mg/l) and three levels of ZEN (0, 5 and 10 mg/l). The treatments did not affect the apparent and true digestibility of organic matter. PAT alone decreased the digestibility of neutral detergent fibre (NDF) and acid detergent fibre (ADF) (p zearalenol and β-zearalenol expressed as a proportion of administered ZEN was less than 50% in effluents from fermenters receiving only ZEN and ZEN plus PAT, respectively. With exception of fibre digestion, the co-administration of PAT and ZEN did not elicit interaction effects on most measured parameters of rumen metabolism.

  14. Investigation on electrical surface modification of waste to energy ash for possible use as an electrode material in microbial fuel cells.

    Science.gov (United States)

    Webster, Megan; Lee, Hae Yang; Pepa, Kristi; Winkler, Nathan; Kretzschmar, Ilona; Castaldi, Marco J

    2018-03-01

    With the world population expected to reach 8.5 billion by 2030, demand for access to electricity and clean water will grow at unprecedented rates. Municipal solid waste combusted at waste to energy (WtE) facilities decreases waste volume and recovers energy, but yields ash as a byproduct, the beneficial uses of which are actively being investigated. Ash is intrinsically hydrophobic, highly oxidized, and exhibits high melting points and low conductivities. The research presented here explores the potential of ash to be used as an electrode material for a microbial fuel cell (MFC). This application requires increased conductivity and hydrophilicity, and a lowered melting point. Three ash samples were investigated. By applying an electric potential in the range 50-125 V across the ash in the presence of water, several key property changes were observed: lower melting point, a color change within the ash, evidence of changes in surface morphologies of ash particles, and completely wetting water-ash contact angles. We analyzed this system using a variety of analytical techniques including sector field inductively coupled plasma mass spectrometry, scanning electron microscopy, X-ray diffraction, differential scanning calorimetry, and tensiometry. Ability to make such surface modifications and significant property changes could allow ash to become useful in an application such as an electrode material for a MFC.

  15. Seasonal and spatial variations in microbial activity at various phylogenetic resolutions at a groundwater – surface water interface

    DEFF Research Database (Denmark)

    Yu, Ran; Smets, Barth F.; Gan, Ping

    2014-01-01

    We investigated the seasonal and spatial variation in activity and density of the metabolically active in situ microbial community (AIMC) at a landfill leachate-impacted groundwater – surface water interface (GSI). A series of AIMC traps were designed and implemented for AIMC sampling and microbial...... analysis. Consistently higher microbial activities with less variation in depth were measured in the AIMC traps than in the ambient sediments. Flood disturbance appeared to control AIMC activity distributions at the gradually elevated GSI. The highest AIMC activities were generally obtained from locations...

  16. Functional bacteria and process metabolism of the Denitrifying Sulfur conversion-associated Enhanced Biological Phosphorus Removal (DS-EBPR) system: An investigation by operating the system from deterioration to restoration.

    Science.gov (United States)

    Guo, Gang; Wu, Di; Hao, Tianwei; Mackey, Hamish Robert; Wei, Li; Wang, Haiguang; Chen, Guanghao

    2016-05-15

    A sulfur conversion-associated Enhanced Biological Phosphorus (P) Removal (EBPR) system is being developed to cater for the increasing needs to treat saline/brackish wastewater resulting from seawater intrusion into groundwater and sewers and frequent use of sulfate coagulants during drinking water treatment, as well as to meet the demand for eutrophication control in warm climate regions. However, the major functional bacteria and metabolism in this emerging biological nutrient removal system are still poorly understood. This study was thus designed to explore the functional microbes and metabolism in this new EBPR system by manipulating the deterioration, failure and restoration of a lab-scale system. This was achieved by changing the mixed liquor suspended solids (MLSS) concentration to monitor and evaluate the relationships among sulfur conversion (including sulfate reduction and sulfate production), P removal, variation in microbial community structures, and stoichiometric parameters. The results show that the stable Denitrifying Sulfur conversion-associated EBPR (DS-EBPR) system was enriched by sulfate-reducing bacteria (SRB) and sulfide-oxidizing bacteria (SOB). These bacteria synergistically participated in this new EBPR process, thereby inducing an appropriate level of sulfur conversion crucial for achieving a stable DS-EBPR performance, i.e. maintaining sulfur conversion intensity at 15-40 mg S/L, corresponding to an optimal sludge concentration of 6.5 g/L. This range of sulfur conversion favors microbial community competition and various energy flows from internal polymers (i.e. polysulfide or elemental sulfur (poly-S(2-)/S(0)) and poly-β-hydroxyalkanoates (PHA)) for P removal. If this range was exceeded, the system might deteriorate or even fail due to enrichment of glycogen-accumulating organisms (GAOs). Four methods of restoring the failed system were investigated: increasing the sludge concentration, lowering the salinity or doubling the COD

  17. Microbial pesticides

    Science.gov (United States)

    Michael L. McManus

    1991-01-01

    Interest in the use of microbial pesticides has intensified because of public concern about the safety of chemical pesticides and their impact in the environment. Characteristics of the five groups of entomopathogens that have potential as microbial pesticides are briefly discussed and an update is provided on research and development activities underway to enhance the...

  18. Anti-Microbial Activity and Spectro-Chemical Investigation of Ink Extracts of Sepiella inermis (Van Hasselt 1835

    Directory of Open Access Journals (Sweden)

    Dasal VASANTHARAJA

    2014-09-01

    Full Text Available The crude petroleum ether and methanol ink extracts of Sepiella inermis were tested for their antimicrobial activity against human pathogenic fungi and bacteria by disc diffusion method. Spectral analysis was carried out by UV-VIS spectrophotometer, FT-IR, Raman IR and GC-MS. Of the two solvent extracts, only methanol extract was active and no activity was detected in petroleum ether extract. The human pathogenic fungus Candida albicans and bacterium Proteus vulgaris were found to be highly sensitive, with an inhibition zone of 20 and 19 mm respectively. GC-MS of methanol ink extract revealed sixteen compounds belonging to the derivatives of dihydroxy indole-2-carboxylic acid and dihydroxyindole. These investigations proved that methanol ink extract of Sepiella inermis possess significant antimicrobial property against both fungus and gram –ve bacteria. Since ink of sepia is available abundantly as a waste material, studies focused on isolation and characterization of bioactive substances pave the way for new antimicrobial compounds.

  19. 3-Fluorophenmetrazine, a fluorinated analogue of phenmetrazine: Studies on in vivo metabolism in rat and human, in vitro metabolism in human CYP isoenzymes and microbial biotransformation in Pseudomonas Putida and wastewater using GC and LC coupled to (HR)-MS techniques.

    Science.gov (United States)

    Mardal, Marie; Miserez, Bram; Bade, Richard; Portolés, Tania; Bischoff, Markus; Hernández, Félix; Meyer, Markus R

    2016-09-05

    Wastewater-based epidemiology (WBE) as means to estimate illicit drug and new psychoactive substance (NPS) consumption with spatial and temporal resolution is gaining increasing attention. In order to evaluate a given NPS using WBE, in vivo metabolism and microbial biotransformation of excretion products and unchanged compounds need evaluation. The aims of this study were to identify in vivo phase I and II metabolites of the NPS 3-fluorophenmetrazine (3-FPM) in human and rat urine and study the in vitro contribution of Cytochrome P450 (CYP) isoenzymes in phase I metabolism. Additionally, to study microbial biotransformation products (MBPs) of 3-FPM from incubations in wastewater and in a wastewater isolated Pseudomonas Putida strain. To these aims gas chromatography and liquid chromatography coupled to mass spectrometry were applied. Metabolites and MBPs were isolated from urine and microbial incubations after solid phase extraction and precipitation with or without enzymatic conjungate cleaving. The main transformation pathways were N-oxidation, aryl hydroxylation and subsequent O-methylation, alkyl hydroxylation, oxidation, and degradation of the ethyl-bridge yielding the O/N-bis-dealkylated metabolite, combinations thereof and further glucuronidation or sulfations. The main excretion products in the human urine sample were the unchanged compound and the N-oxide, and the main MBPs were the N-oxide and hydroxylation with subsequent oxidations on the alpha-methyl position. Based on these findings, the proposed strategy for WBE analysis of 3-FPM is quantitative determination of unchanged 3-FPM together with qualitative verification of a number of selected metabolites to verify consumption and rule out discharge. Copyright © 2016 Elsevier B.V. All rights reserved.

  20. When microbial conversations get physical

    OpenAIRE

    Reguera, Gemma

    2011-01-01

    It is widely accepted that microorganisms are social beings. Whereas communication via chemical signals (e.g. quorum sensing) has been the focus of most investigations, the use of physical signals for microbial cell-cell communication has received only limited attention. Here, I argue that physical modes of microbial communication could be widespread in nature. This is based on experimental evidence on the microbial emission and response to three physical signals: sound waves, electromagnetic...

  1. Microbial quality of a marine tidal pool

    CSIR Research Space (South Africa)

    Genthe, Bettina

    1995-01-01

    Full Text Available In this study the source of microbial pollution to a tidal pool was investigated. Both adjacent seawater which could contribute to possible faecal pollution and potential direct bather pollution were studied. The microbial quality of the marine...

  2. Host–Microbiota Mutualism in Metabolic Diseases

    Directory of Open Access Journals (Sweden)

    Salvatore Fabbiano

    2017-10-01

    Full Text Available The intestinal microbiota is a plastic ecosystem that is shaped by environmental and genetic factors, interacting with virtually all tissues of the host. Many signals result from the interplay between the microbiota with its mammalian symbiont that can lead to altered metabolism. Disruptions in the microbial composition are associated with a number of comorbidities linked to the metabolic syndrome. Promoting the niche expansion of beneficial bacteria through diet and supplements can improve metabolic disorders. Reintroducing bacteria through probiotic treatment or fecal transplant is a strategy under active investigation for multiple pathological conditions. Here, we review the recent knowledge of microbiota’s contribution to host pathology, the modulation of the microbiota by dietary habits, and the potential therapeutic benefits of reshaping the gut bacterial landscape in context of metabolic disorders such as obesity.

  3. Host–Microbiota Mutualism in Metabolic Diseases

    Science.gov (United States)

    Fabbiano, Salvatore; Suárez-Zamorano, Nicolas; Trajkovski, Mirko

    2017-01-01

    The intestinal microbiota is a plastic ecosystem that is shaped by environmental and genetic factors, interacting with virtually all tissues of the host. Many signals result from the interplay between the microbiota with its mammalian symbiont that can lead to altered metabolism. Disruptions in the microbial composition are associated with a number of comorbidities linked to the metabolic syndrome. Promoting the niche expansion of beneficial bacteria through diet and supplements can improve metabolic disorders. Reintroducing bacteria through probiotic treatment or fecal transplant is a strategy under active investigation for multiple pathological conditions. Here, we review the recent knowledge of microbiota’s contribution to host pathology, the modulation of the microbiota by dietary habits, and the potential therapeutic benefits of reshaping the gut bacterial landscape in context of metabolic disorders such as obesity. PMID:29056925

  4. Investigations on the activation of recombinant microbial pro-transglutaminase: in contrast to proteinase K, dispase removes the histidine-tag.

    Science.gov (United States)

    Sommer, Christian; Hertel, Thomas C; Schmelzer, Christian E H; Pietzsch, Markus

    2012-02-01

    In order to produce recombinant microbial transglutaminase (rMTG) which is free of the activating protease, dispase was used to activate the pro-rMTG followed by immobilized metal affinity chromatography (IMAC). As shown by MALDI-MS, the dispase does not only cleave the pro-sequence, but unfortunately also cleaves within the C-terminal histidine-tag. Hence, the active rMTG cannot properly bind to the IMAC material. As an alternative, proteinase K was investigated. This protease was successfully applied for the activation of purified pro-rMTG either as free or immobilized enzyme and the free enzyme was also applicable directly in the crude cell extract of E. coli. Thus, it enables a simple two-step activation/purification procedure resulting in protease-free and almost pure transglutaminase preparations. The protocol has been successfully applied to both, wild-type transglutaminase of Streptomyces mobaraensis as well as to the highly active variant S2P. Proteinase K activates the pro-rMTG without unwanted degradation of the histidine-tag. It turned out to be very important to inhibit proteinase K activity, e.g., by PMSF, prior to protein separation by SDS-PAGE.

  5. Hand Hygiene Practices and Microbial Investigation of Hand Contact Swab among Physiotherapists in an Ebola Endemic Region: Implications for Public Health

    Directory of Open Access Journals (Sweden)

    S. Ibeneme

    2017-01-01

    Full Text Available Background. Hand hygiene practices (HHP, as a critical component of infection prevention/control, were investigated among physiotherapists in an Ebola endemic region. Method. A standardized instrument was administered to 44 randomly selected physiotherapists (23 males and 21 females, from three tertiary hospitals in Enugu, Nigeria. Fifteen participants (aged 22–59 years participated in focus group discussions (FGDs and comprised 19 participants in a subsequent laboratory study. After treatment, the palms/fingers of physiotherapists were swabbed and cultured, then incubated aerobically overnight at 37°C, and examined for microbial growths. An antibiogram of the bacterial isolates was obtained. Results. The majority (34/77.3% of physiotherapists were aware of the HHP protocol, yet only 15/44.1% rated self-compliance at 71–100%. FGDs identified forgetfulness/inadequate HHP materials/infrastructure as the major barriers to HHP. Staphylococcus aureus were the most prevalent organisms, prior to (8/53.33% and after (4/26.67% HPP, while Pseudomonas spp. were acquired thereafter. E. coli were the most antibiotic resistant microbes but were completely removed after HHP. Ciprofloxacin and streptomycin were the most effective antibiotics. Conclusion. Poor implementation of HPP was observed due to inadequate materials/infrastructure/poor behavioral orientation. Possibly, some HPP materials were contaminated; hence, new microbes were acquired. Since HPP removed the most antibiotic resistant microbes, it might be more effective in infection control than antibiotic medication.

  6. Modeling Studies on Microbial Effects on Groundwater Chemistry

    International Nuclear Information System (INIS)

    Yoshikatsu Tochigi; Hideki Yoshikawa; Mikazu Yui

    2007-01-01

    The overall goal of this project is to develop a model to predict microbial effects on the performance of a high-level radioactive waste (HLW) repository. As a first step, the effects of microbes on groundwater chemistry have been evaluated with the numerical code 'MINT', using data collected from the borehole HDB-6 in the Horonobe underground research laboratory (URL) in Japan. The MINT code models biochemistry and geochemical equilibrium, with consideration of transport of solute and microbial activity. The MINT code simulates the activities of six major groups of microbes, classified by their metabolism as 'aerobic', 'denitrifying', 'manganese reducing', 'iron reducing', 'sulfate reducing' and 'methanogenic'. The specific activity of each of these groups will depend on the redox potential (Eh) of the groundwater. Sensitivity analyses were performed to investigate the consequences of changes in groundwater composition on the effects of microbial activity. This indicates that the activities of Sulfate Reducing Bacteria (SRB) and methanogens are relatively high. The concentration of dissolved methane produced by such microbial activity is seen to be influenced by sulfate concentration. Based on the observed data from Horonobe URL, the concentration in oxygen is relatively high and the activity of denitrifying bacteria is the highest of the major six groups of microbes. This can, however, be attributable to chemical / microbial contamination of the groundwater during sampling. The modeling results indicate that the concentration of dissolved oxygen and nitrate ion should be quickly reduced by microbial metabolism, reducing the redox potential to a level low enough for active methano-genesis to commence. Such assessment can be important to evaluate the reliability of sampling and measurement techniques for sensitive geochemical parameters in general - and microbiology in particular. (authors)

  7. Biodegradation of different petroleum hydrocarbons by free and immobilized microbial consortia.

    Science.gov (United States)

    Shen, Tiantian; Pi, Yongrui; Bao, Mutai; Xu, Nana; Li, Yiming; Lu, Jinren

    2015-12-01

    The efficiencies of free and immobilized microbial consortia in the degradation of different types of petroleum hydrocarbons were investigated. In this study, the biodegradation rates of naphthalene, phenanthrene, pyrene and crude oil reached about 80%, 30%, 56% and 48% under the optimum environmental conditions of free microbial consortia after 7 d. We evaluated five unique co-metabolic substances with petroleum hydrocarbons, α-lactose was the best co-metabolic substance among glucose, α-lactose, soluble starch, yeast powder and urea. The orthogonal biodegradation analysis results showed that semi-coke was the best immobilized carrier followed by walnut shell and activated carbon. Meanwhile, the significance of various factors that contribute to the biodegradation of semi-coke immobilized microbial consortia followed the order of: α-lactose > semi-coke > sodium alginate > CaCl2. Moreover, the degradation rate of the immobilized microbial consortium (47%) was higher than that of a free microbial consortium (26%) under environmental conditions such as the crude oil concentration of 3 g L(-1), NaCl concentration of 20 g L(-1), pH at 7.2-7.4 and temperature of 25 °C after 5 d. SEM and FTIR analyses revealed that the structure of semi-coke became more porous and easily adhered to the microbial consortium; the functional groups (e.g., hydroxy and phosphate) were identified in the microbial consortium and were changed by immobilization. This study demonstrated that the ability of microbial adaptation to the environment can be improved by immobilization which expands the application fields of microbial remediation.

  8. Investigations to determine whether viable microorganisms are required during intestinal lactose hydrolysis of fermented milk products by microbial ß-galactosidase using gnotobiotic Göttingen minipigs

    OpenAIRE

    Winchenbach, Andrea

    2010-01-01

    The most common reason worldwide for the indigestibility of milk is the lack of ß-galactosidases in the small intestine, leading to the malabsorbtion of lactose. Fermented dairy products are very often much better tolerated than raw (not fermented) milk, because of the microbial ß-galactosidases they contain. The aim of this thesis was to elucidate the question as to weather lactose hydrolysis in the small intestine requires the presence of living bacteria (with their microbial ß-galac...

  9. Investigation of gut microbial communities associated with indigenous honey bee (Apis mellifera jemenitica) from two different eco-regions of Saudi Arabia

    OpenAIRE

    Khan, Khalid Ali; Ansari, Mohammad Javed; Al-Ghamdi, Ahmad; Nuru, Adgaba; Harakeh, Steve; Iqbal, Javaid

    2017-01-01

    The microbial communities associated with the alimentary tract of honey bees are very important as they help with food digestion, provide essential nutrients, protect the host from pathogens, detoxify harmful molecules, and increase host immunity. In this study, the structural diversity of the gut microbial communities of native honey bees, Apis mellifera jemenitica from two different geographical regions (Riyadh and Al-Baha) of Saudi Arabia was analyzed by culture-dependent methods and 16S r...

  10. Spatially matched in vivo and ex vivo MR metabolic profiles of prostate cancer - investigation of a correlation with Gleason score

    NARCIS (Netherlands)

    Selnaes, K.M.; Gribbestad, I.S.; Bertilsson, H.; Wright, A.; Angelsen, A.; Heerschap, A.; Tessem, M.B.

    2013-01-01

    MR metabolic profiling of the prostate is promising as an additional diagnostic approach to separate indolent from aggressive prostate cancer. The objective of this study was to assess the relationship between the Gleason score and the metabolic biomarker (choline + creatine + spermine)/citrate

  11. A pilot study to investigate effects of inulin on Caco-2 cells through in vitro metabolic fingerprinting

    NARCIS (Netherlands)

    Lamers, R.-J.A.N.; Wessels, E.C.H.H.; Sandt, J.J.M. van de; Venema, K.; Schaafsma, G.; Greef, J. van der; Nesselrooij, J.H.J. van

    2003-01-01

    Metabolic fingerprints are novel measurement tools to evaluate the biochemical status of a living organism by using 1H NMR and multivariate data analysis (MVDA). In this way, a quick evaluation of changes in health or diseased state can be made, reflected in alterations of metabolic patterns.

  12. Role of the microbiome in energy regulation and metabolism

    NARCIS (Netherlands)

    Nieuwdorp, Max; Gilijamse, Pim W.; Pai, Nikhil; Kaplan, Lee M.

    2014-01-01

    Intestinal microbes regulate metabolic function and energy balance; an altered microbial ecology is believed to contribute to the development of several metabolic diseases. Relative species abundance and metabolic characteristics of the intestinal microbiota change substantially in those who are

  13. First Investigation of Microbial Community Composition in the Bridge (Gadeok Channel) between the Jinhae-Masan Bay and the South Sea of Korea

    Science.gov (United States)

    Lee, Jiyoung; Lim, Jae-Hyun; Park, Junhyung; Youn, Seok-Hyun; Oh, Hyun-Ju; Kim, Ju-Hyoung; Kim, Myung Kyum; Cho, Hyeyoun; Yoon, Joo-Eun; Kim, Soyeon; Markkandan, Kesavan; Park, Ki-Tae; Kim, Il-Nam

    2018-02-01

    Microbial community composition varies based on seasonal dynamics (summer: strongly stratified water column; autumn: weakly stratified water column; winter: vertically homogeneous water column) and vertical distributions (surface, middle, and bottom depths) in the Gadeok Channel, which is the primary passage to exchange waters and materials between the Jinhae-Masan Bay and the South Sea waters. The microbial community composition was analyzed from June to December 2016 using 16S rRNA gene sequencing. The community was dominated by the phyla Proteobacteria (45%), Bacteroidetes (18%), Cyanobacteria (15%), Verrucomicrobia (6%), and Actinobacteria (6%). Alphaproteobacteria (29%) was the most abundant microbial class, followed by Flavobacteria (15%) and Gammaproteobacteria (15%) in all samples. The composition of the microbial communities was found to vary vertically and seasonally. The orders Flavobacteriales and Stramenopiles showed opposing seasonal patterns; Flavobacteriales was more abundant in August and December while Stramenopiles showed high abundance in June and October at all depths. The genus Synechococcus reached extremely high abundance (14%) in the June surface water column, but was much less abundant in December water columns. Clustering analysis showed that there was a difference in the microbial community composition pattern between the strongly stratified season and well-mixed season. These results indicate that the seasonal dynamics of physicochemical and hydrologic conditions throughout the water column are important parameters in shaping the microbial community composition in the Gadeok Channel.

  14. Experimental and In-Silico Investigation of Anti-Microbial Activity of 1-Chloro-2-Isocyanatoethane Derivatives of Thiomorpholine, Piperazine and Morpholine.

    Directory of Open Access Journals (Sweden)

    Charles O Nwuche

    Full Text Available The Antibiogram properties of 1-chloro-2-isocyanatoethane derivatives of thiomorpholine (CTC, piperazine (CPC and morpholine (CMC were evaluated by the approved agar well diffusion, the minimum inhibitory concentration (MIC and in silico techniques. A total of fourteen microbial cultures consisting of ten bacteria and four yeast strains were used in the biological study while affinity of the compounds for DNA gyrase, a validated antibacterial drug target, was investigated by docking method. Results indicate that both thiomorpholine and piperazine had zero activity against the Gram negative organisms tested. With morpholine, similar result was obtained except that cultures of Escherichia coli (ATCC 15442 and Salmonella typhi (ATCC 6539 presented with weak sensitivity (7-8 mm as shown by the inhibition zone diameter (IZD measurement. The Gram positive organisms were more sensitive to morpholine than the other compounds. The highest IZD values of 15-18 mm were achieved except for Streptococcus pneumoniae (ATCC 49619 in which mobility of the compound stopped after 12 mm. S. pneumoniae was resistant to both thiomorpholine and piperazine. The yeast strains were not sensitive to any of the studied compounds investigated. The MIC tests evaluated against a reference antibiotic show that while morpholine was most active at 4 μg.ml-1 against both B. cereus ATCC (14579 and B. subtilis, the least active compound was thiomorpholine which inhibited S. aureus (ATCC 25923 at 64 μg.ml-1. The three compounds demonstrated high affinity for the target protein (DNA gyrase ranging from -4.63 to -5.64 Kcal/mol and even showed better ligand efficiencies than three known antibiotics; chlorobiocin, ciprofloxacin and tetracycline. This study identified the studied compounds as potential antibiotic leads with acceptable physicochemical properties and gave the molecular basis for the observed interactions between the compounds and the target protein which can be harnessed

  15. Experimental and In-Silico Investigation of Anti-Microbial Activity of 1-Chloro-2-Isocyanatoethane Derivatives of Thiomorpholine, Piperazine and Morpholine.

    Science.gov (United States)

    Nwuche, Charles O; Ujam, Oguejiofo T; Ibezim, Akachukwu; Ujam, Ifeoma B

    2017-01-01

    The Antibiogram properties of 1-chloro-2-isocyanatoethane derivatives of thiomorpholine (CTC), piperazine (CPC) and morpholine (CMC) were evaluated by the approved agar well diffusion, the minimum inhibitory concentration (MIC) and in silico techniques. A total of fourteen microbial cultures consisting of ten bacteria and four yeast strains were used in the biological study while affinity of the compounds for DNA gyrase, a validated antibacterial drug target, was investigated by docking method. Results indicate that both thiomorpholine and piperazine had zero activity against the Gram negative organisms tested. With morpholine, similar result was obtained except that cultures of Escherichia coli (ATCC 15442) and Salmonella typhi (ATCC 6539) presented with weak sensitivity (7-8 mm) as shown by the inhibition zone diameter (IZD) measurement. The Gram positive organisms were more sensitive to morpholine than the other compounds. The highest IZD values of 15-18 mm were achieved except for Streptococcus pneumoniae (ATCC 49619) in which mobility of the compound stopped after 12 mm. S. pneumoniae was resistant to both thiomorpholine and piperazine. The yeast strains were not sensitive to any of the studied compounds investigated. The MIC tests evaluated against a reference antibiotic show that while morpholine was most active at 4 μg.ml-1 against both B. cereus ATCC (14579) and B. subtilis, the least active compound was thiomorpholine which inhibited S. aureus (ATCC 25923) at 64 μg.ml-1. The three compounds demonstrated high affinity for the target protein (DNA gyrase) ranging from -4.63 to -5.64 Kcal/mol and even showed better ligand efficiencies than three known antibiotics; chlorobiocin, ciprofloxacin and tetracycline. This study identified the studied compounds as potential antibiotic leads with acceptable physicochemical properties and gave the molecular basis for the observed interactions between the compounds and the target protein which can be harnessed in

  16. Omics-Based Strategies in Precision Medicine: Toward a Paradigm Shift in Inborn Errors of Metabolism Investigations

    Directory of Open Access Journals (Sweden)

    Abdellah Tebani

    2016-09-01

    Full Text Available The rise of technologies that simultaneously measure thousands of data points represents the heart of systems biology. These technologies have had a huge impact on the discovery of next-generation diagnostics, biomarkers, and drugs in the precision medicine era. Systems biology aims to achieve systemic exploration of complex interactions in biological systems. Driven by high-throughput omics technologies and the computational surge, it enables multi-scale and insightful overviews of cells, organisms, and populations. Precision medicine capitalizes on these conceptual and technological advancements and stands on two main pillars: data generation and data modeling. High-throughput omics technologies allow the retrieval of comprehensive and holistic biological information, whereas computational capabilities enable high-dimensional data modeling and, therefore, accessible and user-friendly visualization. Furthermore, bioinformatics has enabled comprehensive multi-omics and clinical data integration for insightful interpretation. Despite their promise, the translation of these technologies into clinically actionable tools has been slow. In this review, we present state-of-the-art multi-omics data analysis strategies in a clinical context. The challenges of omics-based biomarker translation are discussed. Perspectives regarding the use of multi-omics approaches for inborn errors of metabolism (IEM are presented by introducing a new paradigm shift in addressing IEM investigations in the post-genomic era.

  17. Omics-Based Strategies in Precision Medicine: Toward a Paradigm Shift in Inborn Errors of Metabolism Investigations.

    Science.gov (United States)

    Tebani, Abdellah; Afonso, Carlos; Marret, Stéphane; Bekri, Soumeya

    2016-09-14

    The rise of technologies that simultaneously measure thousands of data points represents the heart of systems biology. These technologies have had a huge impact on the discovery of next-generation diagnostics, biomarkers, and drugs in the precision medicine era. Systems biology aims to achieve systemic exploration of complex interactions in biological systems. Driven by high-throughput omics technologies and the computational surge, it enables multi-scale and insightful overviews of cells, organisms, and populations. Precision medicine capitalizes on these conceptual and technological advancements and stands on two main pillars: data generation and data modeling. High-throughput omics technologies allow the retrieval of comprehensive and holistic biological information, whereas computational capabilities enable high-dimensional data modeling and, therefore, accessible and user-friendly visualization. Furthermore, bioinformatics has enabled comprehensive multi-omics and clinical data integration for insightful interpretation. Despite their promise, the translation of these technologies into clinically actionable tools has been slow. In this review, we present state-of-the-art multi-omics data analysis strategies in a clinical context. The challenges of omics-based biomarker translation are discussed. Perspectives regarding the use of multi-omics approaches for inborn errors of metabolism (IEM) are presented by introducing a new paradigm shift in addressing IEM investigations in the post-genomic era.

  18. Microbial Diversity in Sediment Ecosystems (Evaporites Domes, Microbial Mats, and Crusts) of Hypersaline Laguna Tebenquiche, Salar de Atacama, Chile

    Science.gov (United States)

    Fernandez, Ana B.; Rasuk, Maria C.; Visscher, Pieter T.; Contreras, Manuel; Novoa, Fernando; Poire, Daniel G.; Patterson, Molly M.; Ventosa, Antonio; Farias, Maria E.

    2016-01-01

    We combined nucleic acid-based molecular methods, biogeochemical measurements, and physicochemical characteristics to investigate microbial sedimentary ecosystems of Laguna Tebenquiche, Atacama Desert, Chile. Molecular diversity, and biogeochemistry of hypersaline microbial mats, rhizome-associated concretions, and an endoevaporite were compared with: The V4 hypervariable region of the 16S rRNA gene was amplified by pyrosequencing to analyze the total microbial diversity (i.e., bacteria and archaea) in bulk samples, and in addition, in detail on a millimeter scale in one microbial mat and in one evaporite. Archaea were more abundant than bacteria. Euryarchaeota was one of the most abundant phyla in all samples, and particularly dominant (97% of total diversity) in the most lithified ecosystem, the evaporite. Most of the euryarchaeal OTUs could be assigned to the class Halobacteria or anaerobic and methanogenic archaea. Planctomycetes potentially also play a key role in mats and rhizome-associated concretions, notably the aerobic organoheterotroph members of the class Phycisphaerae. In addition to cyanobacteria, members of Chromatiales and possibly the candidate family Chlorotrichaceae contributed to photosynthetic carbon fixation. Other abundant uncultured taxa such as the candidate division MSBL1, the uncultured MBGB, and the phylum Acetothermia potentially play an important metabolic role in these ecosystems. Lithifying microbial mats contained calcium carbonate precipitates, whereas endoevoporites consisted of gypsum, and halite. Biogeochemical measurements revealed that based on depth profiles of O2 and sulfide, metabolic activities were much higher in the non-lithifying mat (peaking in the least lithified systems) than in lithifying mats with the lowest activity in endoevaporites. This trend in decreasing microbial activity reflects the increase in salinity, which may play an important role in the biodiversity. PMID:27597845

  19. Microbial diversity in sediment ecosystems (evaporites domes, microbial mats and crusts of hypersaline Laguna Tebenquiche, Salar de Atacama, Chile

    Directory of Open Access Journals (Sweden)

    Ana Beatriz Fernandez

    2016-08-01

    Full Text Available We combined nucleic acid-based molecular methods, biogeochemical measurements and physicochemical characteristics to investigate microbial sedimentary ecosystems of Laguna Tebenquiche, Atacama Desert, Chile. Molecular diversity and biogeochemistry of hypersaline microbial mats, rhizome-associated concretions and an endoevaporite were compared with: The V4 hypervariable region of the 16S rRNA gene was amplified by pyrosequencing to analyze the total microbial diversity (i.e., bacteria and archaea in bulk samples and, in addition, in detail on a millimeter scale in one microbial mat and in one evaporite. Archaea were more abundant than bacteria. Euryarchaeota was one of the most abundant phyla in all samples, and particularly dominant (97% of total diversity in the most lithified ecosystem, the evaporite. Most of the euryarchaeal OTUs could be assigned to the class Halobacteria or anaerobic and methanogenic archaea. Planctomycetes potentially also play a key role in mats and rhizome-associated concretions, notably the aerobic organoheterotroph members of the class Phycisphaerae. In addition to cyanobacteria, members of Chromatiales and possibly the candidate family Chlorotrichaceae contributed to photosynthetic carbon fixation. Other abundant uncultured taxa such as the candidate division MSBL1, the uncultured MBGB and the phylum Acetothermia potentially play an important metabolic role in these ecosystems. Lithifying microbial mats contained calcium carbonate precipitates, whereas endoevoporites consisted of gypsum and halite. Biogeochemical measurements revealed that based on depth profiles of O2 and sulfide, metabolic activities were much higher in the non-lithifying mat (peaking in the least lithified systems than in lithifying mats with the lowest activity in endoevaporites. This trend in decreasing microbial activity reflects the increase in salinity, which may play an important role in the biodiversity.

  20. Metabolic imaging of hyperpolarized [1-(13) C]acetate and [1-(13) C]acetylcarnitine - investigation of the influence of dobutamine induced stress.

    Science.gov (United States)

    Koellisch, Ulrich; Gringeri, Concetta V; Rancan, Giaime; Farell, Eliane V; Menzel, Marion I; Haase, Axel; Schwaiger, Markus; Schulte, Rolf F

    2015-10-01

    The metabolism of acetate in the heart resembles fatty acid metabolism, which is altered in several diseases like ischemia, diabetes mellitus, and heart failure. A signal-to-noise ratio (SNR) optimized imaging fr