Drug sensitivity patterns of bacterial isolates from septic post ...

African Journals Online (AJOL)

Background: Wound infections have been a problem in the field of surgery for a long time.Advances in control of infections have not completely eradicated this ... of bacterial isolates from septic postoperative wounds in Jinja hospital, Uganda.

Bacterial community affects toxin production by Gymnodinium catenatum.

Directory of Open Access Journals (Sweden)

Maria E Albinsson

Full Text Available The paralytic shellfish toxin (PST-producing dinoflagellate Gymnodinium catenatum grows in association with a complex marine bacterial community that is both essential for growth and can alter culture growth dynamics. Using a bacterial community replacement approach, we examined the intracellular PST content, production rate, and profile of G. catenatum cultures grown with bacterial communities of differing complexity and composition. Clonal offspring were established from surface-sterilized resting cysts (produced by sexual crosses of strain GCDE06 and strain GCLV01 and grown with: 1 complex bacterial communities derived from each of the two parent cultures; 2 simplified bacterial communities composed of the G. catenatum-associated bacteria Marinobacter sp. strain DG879 or Alcanivorax sp. strain DG881; 3 a complex bacterial community associated with an untreated, unsterilized sexual cross of the parents. Toxin content (STX-equivalent per cell of clonal offspring (134-197 fmol STX cell(-1 was similar to the parent cultures (169-206 fmol STX cell(-1, however cultures grown with single bacterial types contained less toxin (134-146 fmol STX cell(-1 than offspring or parent cultures grown with more complex mixed bacterial communities (152-176 fmol STX cell(-1. Specific toxin production rate (fmol STX day(-1 was strongly correlated with culture growth rate. Net toxin production rate (fmol STX cell(-1 day(-1 did not differ among treatments, however, mean net toxin production rate of offspring was 8-fold lower than the parent cultures, suggesting that completion of the sexual lifecycle in laboratory cultures leads to reduced toxin production. The PST profiles of offspring cultures were most similar to parent GCDE06 with the exception of cultures grown with Marinobacter sp. DG879 which produced higher proportions of dcGTX2+3 and GC1+2, and lower proportions of C1+2 and C3+4. Our data demonstrate that the bacterial community can alter intracellular STX

Bacterial community affects toxin production by Gymnodinium catenatum.

Science.gov (United States)

Albinsson, Maria E; Negri, Andrew P; Blackburn, Susan I; Bolch, Christopher J S

2014-01-01

The paralytic shellfish toxin (PST)-producing dinoflagellate Gymnodinium catenatum grows in association with a complex marine bacterial community that is both essential for growth and can alter culture growth dynamics. Using a bacterial community replacement approach, we examined the intracellular PST content, production rate, and profile of G. catenatum cultures grown with bacterial communities of differing complexity and composition. Clonal offspring were established from surface-sterilized resting cysts (produced by sexual crosses of strain GCDE06 and strain GCLV01) and grown with: 1) complex bacterial communities derived from each of the two parent cultures; 2) simplified bacterial communities composed of the G. catenatum-associated bacteria Marinobacter sp. strain DG879 or Alcanivorax sp. strain DG881; 3) a complex bacterial community associated with an untreated, unsterilized sexual cross of the parents. Toxin content (STX-equivalent per cell) of clonal offspring (134-197 fmol STX cell(-1)) was similar to the parent cultures (169-206 fmol STX cell(-1)), however cultures grown with single bacterial types contained less toxin (134-146 fmol STX cell(-1)) than offspring or parent cultures grown with more complex mixed bacterial communities (152-176 fmol STX cell(-1)). Specific toxin production rate (fmol STX day(-1)) was strongly correlated with culture growth rate. Net toxin production rate (fmol STX cell(-1) day(-1)) did not differ among treatments, however, mean net toxin production rate of offspring was 8-fold lower than the parent cultures, suggesting that completion of the sexual lifecycle in laboratory cultures leads to reduced toxin production. The PST profiles of offspring cultures were most similar to parent GCDE06 with the exception of cultures grown with Marinobacter sp. DG879 which produced higher proportions of dcGTX2+3 and GC1+2, and lower proportions of C1+2 and C3+4. Our data demonstrate that the bacterial community can alter intracellular STX

Gene calling and bacterial genome annotation with BG7.

Science.gov (United States)

Tobes, Raquel; Pareja-Tobes, Pablo; Manrique, Marina; Pareja-Tobes, Eduardo; Kovach, Evdokim; Alekhin, Alexey; Pareja, Eduardo

2015-01-01

New massive sequencing technologies are providing many bacterial genome sequences from diverse taxa but a refined annotation of these genomes is crucial for obtaining scientific findings and new knowledge. Thus, bacterial genome annotation has emerged as a key point to investigate in bacteria. Any efficient tool designed specifically to annotate bacterial genomes sequenced with massively parallel technologies has to consider the specific features of bacterial genomes (absence of introns and scarcity of nonprotein-coding sequence) and of next-generation sequencing (NGS) technologies (presence of errors and not perfectly assembled genomes). These features make it convenient to focus on coding regions and, hence, on protein sequences that are the elements directly related with biological functions. In this chapter we describe how to annotate bacterial genomes with BG7, an open-source tool based on a protein-centered gene calling/annotation paradigm. BG7 is specifically designed for the annotation of bacterial genomes sequenced with NGS. This tool is sequence error tolerant maintaining their capabilities for the annotation of highly fragmented genomes or for annotating mixed sequences coming from several genomes (as those obtained through metagenomics samples). BG7 has been designed with scalability as a requirement, with a computing infrastructure completely based on cloud computing (Amazon Web Services).

Complete genome sequence of Haliangium ochraceum type strain (SMP-2T)

Energy Technology Data Exchange (ETDEWEB)

Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Daum, Chris [U.S. Department of Energy, Joint Genome Institute; Lang, Elke [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Abt, Birte [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Kopitz, marcus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Saunders, Elizabeth H [Los Alamos National Laboratory (LANL); Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Glavina Del Rio, Tijana [U.S. Department of Energy, Joint Genome Institute; Nolan, Matt [U.S. Department of Energy, Joint Genome Institute; Tice, Hope [U.S. Department of Energy, Joint Genome Institute; Copeland, A [U.S. Department of Energy, Joint Genome Institute; Cheng, Jan-Fang [U.S. Department of Energy, Joint Genome Institute; Chen, Feng [U.S. Department of Energy, Joint Genome Institute; Bruce, David [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Chen, Amy [U.S. Department of Energy, Joint Genome Institute; Palaniappan, Krishna [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Chang, Yun-Juan [ORNL; Jeffries, Cynthia [Oak Ridge National Laboratory (ORNL); Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Brettin, Thomas S [ORNL; Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Bristow, James [U.S. Department of Energy, Joint Genome Institute; Markowitz, Victor [U.S. Department of Energy, Joint Genome Institute; Eisen, Jonathan [U.S. Department of Energy, Joint Genome Institute; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany

2010-01-01

Haliangium ochraceum Fudou et al. 2002 is the type species of the genus Haliangium in the myxococcal family Haliangiaceae . Members of the genus Haliangium are the first halophilic myxobacterial taxa described. The cells of the species follow a multicellular lifestyle in highly organized biofilms, called swarms, they decompose bacterial and yeast cells as most myxobacteria do. The fruiting bodies contain particularly small coccoid myxospores. H. ochraceum encodes the first actin homologue identified in a bacterial genome. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a member of the myxococcal suborder Nannocystineae, and the 9,446,314 bp long single replicon genome with its 6,898 protein-coding and 53 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

Resistance against bacterial leakage of four luting agents used for cementation of complete cast crowns.

Science.gov (United States)

Zmener, Osvaldo; Pameijer, Cornelis H; Hernández, Sandra

2014-02-01

To assess the sealing properties of four luting materials used for cementation of full cast crowns. 40 human premolars were prepared with a chamfer finish line. Stone dies were fabricated and copings were waxed, invested and cast in gold. Ten samples (n = 10) were randomly assigned to four groups. In two groups, resin modified glass-ionomer cements were used, ACTIVA BioACTIVE-CEMENT/BASE/LINER and FujiCem2; the third group received the self-adhesive resin cement Embrace WetBond, while the fourth group served as control with a zinc phosphate cement. After cementation, excess cement was removed followed by bench-set for 10 minutes. All samples were stored in water at 37 degrees C and subjected to thermal cycling (x2000 between 5 and 55 degrees C). Subsequently the occlusal surface was reduced exposing the dentin. After sterilization the specimens were subjected to bacterial microleakage with E. faecalis in a dual chamber apparatus for a period of 60 days. Bacterial leakage was checked daily. Data were analyzed using the Kaplan-Meyer survival test. Significant pairwise differences were analyzed using the Log Rank test and the Fishers' exact test at P < 0.05. ACTIVA BioACTIVE-CEMENT/BASE/LINER, FujiCem2 and Embrace WetBond showed the lowest microleakage scores and differed statistically significantly (P < 0.05) from zinc phosphate cement.

Bacterial prostatitis.

Science.gov (United States)

Gill, Bradley C; Shoskes, Daniel A

2016-02-01

The review provides the infectious disease community with a urologic perspective on bacterial prostatitis. Specifically, the article briefly reviews the categorization of prostatitis by type and provides a distillation of new findings published on bacterial prostatitis over the past year. It also highlights key points from the established literature. Cross-sectional prostate imaging is becoming more common and may lead to more incidental diagnoses of acute bacterial prostatitis. As drug resistance remains problematic in this condition, the reemergence of older antibiotics such as fosfomycin, has proven beneficial. With regard to chronic bacterial prostatitis, no clear clinical risk factors emerged in a large epidemiological study. However, bacterial biofilm formation has been associated with more severe cases. Surgery has a limited role in bacterial prostatitis and should be reserved for draining of a prostatic abscess or the removal of infected prostatic stones. Prostatitis remains a common and bothersome clinical condition. Antibiotic therapy remains the basis of treatment for both acute and chronic bacterial prostatitis. Further research into improving prostatitis treatment is indicated.

Anaerobic bacterial quantitation of Yucca Mountain, Nevada DOE site samples

International Nuclear Information System (INIS)

Clarkson, W.W.; Krumholz, L.R.; Suflita, J.M.

1996-01-01

Anaerobic bacteria were studied from samples of excavated rock material as one phase of the overall Yucca Mountain site characterization effort. An indication of the abundance of important groups of anaerobic bacteria would enable inferences to be made regarding the natural history of the site and allow for more complete risk evaluation of the site as a nuclear repository. Six bacterial groups were investigated including anaerobic heterotrophs, acetogens, methanogens, sulfate-, nitrate-, and iron-reducing bacteria. The purpose of this portion of the study was to detect and quantify the aforementioned bacterial groups

The influence of bacterial vaginosis on gestational week of the completion of delivery and biochemical markers of inflammation in the serum

Directory of Open Access Journals (Sweden)

Jakovljević Ana

2014-01-01

Full Text Available Bacground/Aim. Preterm delivery is one of the most common complications in pregnancy, and it is the major cause (75- 80% of all neonatal deaths. Bacterial vaginosis predisposes to an increased risk of preterm delivery, premature rupture of membrane and miscarriage. In this syndrome normal vaginal lactobacilli, which produce protective H2O2, are reduced and replaced with anaerobic, gram-negative bacteria and others. The aim of this study was to evaluate the influence of bacterial vaginosis on the week of delivery and biochemical markers of inflammation in the serum. Methods. A total of 186 pregnant women were included into this study, between the week 16 and 19 of pregnancy. In the study group there were 76 pregnant women with diagnosed bacterial vaginosis by the criteria based on vaginal Gram-stain Nugent score and Amsel criteria. In the control group there were 110 healthy women with normal vaginal flora. Ultrasound examination was performed in both groups. Vaginal fluid and blood samples were taken to determine biochemical markers with colorimetric methods. Results. The week of delivery was statistically significantly shorter in the study group and the levels of biochemical markers of inflammation (C-reactive protein and fibrinogen in the serum were statistically significantly higher in women with bacterial vaginosis comparing to the control group. Also the levels of uric acid and white blood cells in the serum were higher in the study group compared to the control one. Conclusion. Our study indicates that the pregnancy complicated with bacterial vaginosis ends much earlier than the pregnancy without it. Also, higher levels of biochemical markers of inflammation in the serum in the study group, similarly to results of other studies, suggest that pathophysiological processes responsible for preterm delivery can begin very early in pregnancy.

Analysis of five complete genome sequences for members of the class Peribacteria in the recently recognized Peregrinibacteria bacterial phylum

Directory of Open Access Journals (Sweden)

Karthik Anantharaman

2016-01-01

Full Text Available Five closely related populations of bacteria from the Candidate Phylum (CP Peregrinibacteria, part of the bacterial Candidate Phyla Radiation (CPR, were sampled from filtered groundwater obtained from an aquifer adjacent to the Colorado River near the town of Rifle, CO, USA. Here, we present the first complete genome sequences for organisms from this phylum. These bacteria have small genomes and, unlike most organisms from other lineages in the CPR, have the capacity for nucleotide synthesis. They invest significantly in biosynthesis of cell wall and cell envelope components, including peptidoglycan, isoprenoids via the mevalonate pathway, and a variety of amino sugars including perosamine and rhamnose. The genomes encode an intriguing set of large extracellular proteins, some of which are very cysteine-rich and may function in attachment, possibly to other cells. Strain variation in these proteins is an important source of genotypic variety. Overall, the cell envelope features, combined with the lack of biosynthesis capacities for many required cofactors, fatty acids, and most amino acids point to a symbiotic lifestyle. Phylogenetic analyses indicate that these bacteria likely represent a new class within the Peregrinibacteria phylum, although they ultimately may be recognized as members of a separate phylum. We propose the provisional taxonomic assignment as ‘Candidatus Peribacter riflensis’, Genus Peribacter, Family Peribacteraceae, Order Peribacterales, Class Peribacteria in the phylum Peregrinibacteria.

Bacterial Adhesion & Blocking Bacterial Adhesion

DEFF Research Database (Denmark)

Vejborg, Rebecca Munk

2008-01-01

, which influence the transition from a planktonic lifestyle to a sessile lifestyle, have been studied. Protein conditioning film formation was found to influence bacterial adhesion and subsequent biofilm formation considerable, and an aqueous extract of fish muscle tissue was shown to significantly...... tract to the microbial flocs in waste water treatment facilities. Microbial biofilms may however also cause a wide range of industrial and medical problems, and have been implicated in a wide range of persistent infectious diseases, including implantassociated microbial infections. Bacterial adhesion...... is the first committing step in biofilm formation, and has therefore been intensely scrutinized. Much however, still remains elusive. Bacterial adhesion is a highly complex process, which is influenced by a variety of factors. In this thesis, a range of physico-chemical, molecular and environmental parameters...

Bacterial consortia for crude oil spill remediation

International Nuclear Information System (INIS)

Chhatre, S.; Purohit, H.; Shanker, R.; Khanna, P.

1996-01-01

Oil spills generate enormous public concern and highlight the need for cost effective ad environmentally acceptable mitigation technologies. Physico-chemical methods are not completely effective after a spill. Hence, there is a need for improved and alternative technologies. Bioremediation is the most environmentally sound technology for clean up. This report intends to determine the potential of a bacterial consortium for degradation of Gulf and Bombay High crude oil. A four membered consortium was designed that could degrade 70% of the crude oil. A member of consortium produced a biosurfactant, rhamnolipid, that emulsified crude oil efficiently for effective degradation by the other members of consortium. The wide range of hydrocarbonoclastic capabilities of the selected members of bacterial consortium leads to the degradation of both aromatic and aliphatic fractions of crude oil in 72 hours. (Author)

Complete genome sequence of Parvibaculum lavamentivorans type strain (DS-1(T)).

Science.gov (United States)

Schleheck, David; Weiss, Michael; Pitluck, Sam; Bruce, David; Land, Miriam L; Han, Shunsheng; Saunders, Elizabeth; Tapia, Roxanne; Detter, Chris; Brettin, Thomas; Han, James; Woyke, Tanja; Goodwin, Lynne; Pennacchio, Len; Nolan, Matt; Cook, Alasdair M; Kjelleberg, Staffan; Thomas, Torsten

2011-12-31

Parvibaculum lavamentivorans DS-1(T) is the type species of the novel genus Parvibaculum in the novel family Rhodobiaceae (formerly Phyllobacteriaceae) of the order Rhizobiales of Alphaproteobacteria. Strain DS-1(T) is a non-pigmented, aerobic, heterotrophic bacterium and represents the first tier member of environmentally important bacterial communities that catalyze the complete degradation of synthetic laundry surfactants. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,914,745 bp long genome with its predicted 3,654 protein coding genes is the first completed genome sequence of the genus Parvibaculum, and the first genome sequence of a representative of the family Rhodobiaceae.

Corruption of innate immunity by bacterial proteases.

Science.gov (United States)

Potempa, Jan; Pike, Robert N

2009-01-01

The innate immune system of the human body has developed numerous mechanisms to control endogenous and exogenous bacteria and thus prevent infections by these microorganisms. These mechanisms range from physical barriers such as the skin or mucosal epithelium to a sophisticated array of molecules and cells that function to suppress or prevent bacterial infection. Many bacteria express a variety of proteases, ranging from non-specific and powerful enzymes that degrade many proteins involved in innate immunity to proteases that are extremely precise and specific in their mode of action. Here we have assembled a comprehensive picture of how bacterial proteases affect the host's innate immune system to gain advantage and cause infection. This picture is far from being complete since the numbers of mechanisms utilized are as astonishing as they are diverse, ranging from degradation of molecules vital to innate immune mechanisms to subversion of the mechanisms to allow the bacterium to hide from the system or take advantage of it. It is vital that such mechanisms are elucidated to allow strategies to be developed to aid the innate immune system in controlling bacterial infections.

Bacmeta: simulator for genomic evolution in bacterial metapopulations.

Science.gov (United States)

Sipola, Aleksi; Marttinen, Pekka; Corander, Jukka

2018-02-20

The advent of genomic data from densely sampled bacterial populations has created a need for flexible simulators by which models and hypotheses can be efficiently investigated in the light of empirical observations. Bacmeta provides fast stochastic simulation of neutral evolution within a large collection of interconnected bacterial populations with completely adjustable connectivity network. Stochastic events of mutations, recombinations, insertions/deletions, migrations and microepidemics can be simulated in discrete non-overlapping generations with a Wright-Fisher model that operates on explicit sequence data of any desired genome length. Each model component, including locus, bacterial strain, population, and ultimately the whole metapopulation, is efficiently simulated using C ++ objects, and detailed metadata from each level can be acquired. The software can be executed in a cluster environment using simple textual input files, enabling, e.g., large-scale simulations and likelihood-free inference. Bacmeta is implemented with C ++ for Linux, Mac and Windows. It is available at https://bitbucket.org/aleksisipola/bacmeta under the BSD 3-clause license. aleksi.sipola@helsinki.fi, jukka.corander@medisin.uio.no. Supplementary data are available at Bioinformatics online.

Sealing properties of three luting agents used for complete cast crowns: a bacterial leakage study.

Science.gov (United States)

Zmener, O; Pameijer, C H; Rincon, S M H; Serrano, S A; Chaves, C

2013-01-01

To assess the sealing properties of three different luting materials used for cementation of full cast crowns on extracted human premolars. Thirty noncarious human premolars were prepared in a standardized fashion for full cast crown restorations. All margins were placed in dentin. After impressions of the preparations, stone dies were fabricated on which copings were waxed, which were cast in type III alloy using standardized laboratory methods. Teeth were randomly assigned to three groups of 10 samples each (n=10), for which the following cements were used: 1) a resin-modified glass ionomer cement, Rely X Luting Plus (3M ESPE, St Paul, MN, USA); 2) a self-adhesive resin cement, Maxcem Elite (Kerr Corporation, Orange, CA, USA); and 3) a glass ionomer cement, Ketac Cem (3M ESPE), the latter used as control. After cementation the samples were allowed to bench-set for 10 minutes, stored in water at 37°C, subjected to thermal cycling (2000×, between 5°C and 55°C, dwell time 35 seconds), and then stored in sterile phosphate buffer for seven days at 37°C. Subsequently, the occlusal surface was carefully reduced until the dentin was exposed. Finishing on wet sand paper removed the gold flash caused by grinding. After sterilization, the specimens were subjected to bacterial microleakage in a dual chamber apparatus for 60 days. Bacterial leakage was checked daily. Data were analyzed using the Kaplan-Meier survival test. Significant pairwise differences were analyzed using the log-rank test followed by Fisher exact test at a p<0.05 level of significance. Rely X Luting Plus showed the lowest microleakage scores, which statistically differed significantly from Maxcem Elite and Ketac Cem (p<0.05). Rely X Luting Plus cement displayed significantly lower microleakage scores than a self-adhesive resin-based and conventional glass ionomer cement.

Experimental Study of Bacterial Penetration into Chalk Rock: Mechanisms and Effect on Permeability

DEFF Research Database (Denmark)

Halim, Amalia Yunita; Shapiro, Alexander; Eliasson Lantz, Anna

2014-01-01

Bacterial selective plugging is one of the mechanisms through which microorganisms can be applied for enhanced oil recovery, as bacteria can plug the water-swept zones of a reservoir, thus altering the flow paths and improving sweep efficiency. However, complete understanding of the penetration...... behavior of bacteria is lacking, especially in chalk formations where characteristic pore throat sizes are comparable with the sizes of bacterial cells. In this study, two bacterial strains, Bacillus licheniformis 421 (spore-forming) and Pseudomonas putida K12 (non-spore forming) were used to investigate...... the penetration of bacteria into chalk and its effect on permeability reduction. The core plugs were produced from Stevns Klint outcrop with low permeability (2–4 mD) and with pore sizes comparable to bacterial sizes. Both types of bacteria were able to penetrate and to be transported through the cores to some...

Comparison of the cytotoxic effect of polystyrene latex nanoparticles on planktonic cells and bacterial biofilms

International Nuclear Information System (INIS)

Nomura, Toshiyuki; Fujisawa, Eri; Itoh, Shikibu; Konishi, Yasuhiro

2016-01-01

The cytotoxic effect of positively charged polystyrene latex nanoparticles (PSL NPs) was compared between planktonic bacterial cells and bacterial biofilms using confocal laser scanning microscopy, atomic force microscopy, and a colony counting method. Pseudomonas fluorescens, which is commonly used in biofilm studies, was employed as the model bacteria. We found that the negatively charged bacterial surface of the planktonic cells was almost completely covered with positively charged PSL NPs, leading to cell death, as indicated by the NP concentration being greater than that required to achieve single layer coverage. In addition, the relationship between surface coverage and cell viability of P. fluorescens cells correlated well with the findings in other bacterial cells (Escherichia coli and Lactococcuslactis). However, most of the bacterial cells that formed the biofilm were viable despite the positively charged PSL NPs being highly toxic to planktonic bacterial cells. This indicated that bacterial cells embedded in the biofilm were protected by self-produced extracellular polymeric substances (EPS) that provide resistance to antibacterial agents. In conclusion, mature biofilms covered with EPS exhibit resistance to NP toxicity as well as antibacterial agents.

Comparison of the cytotoxic effect of polystyrene latex nanoparticles on planktonic cells and bacterial biofilms

Energy Technology Data Exchange (ETDEWEB)

Nomura, Toshiyuki, E-mail: nomura@chemeng.osakafu-u.ac.jp; Fujisawa, Eri; Itoh, Shikibu; Konishi, Yasuhiro [Osaka Prefecture University, Department of Chemical Engineering (Japan)

2016-06-15

The cytotoxic effect of positively charged polystyrene latex nanoparticles (PSL NPs) was compared between planktonic bacterial cells and bacterial biofilms using confocal laser scanning microscopy, atomic force microscopy, and a colony counting method. Pseudomonas fluorescens, which is commonly used in biofilm studies, was employed as the model bacteria. We found that the negatively charged bacterial surface of the planktonic cells was almost completely covered with positively charged PSL NPs, leading to cell death, as indicated by the NP concentration being greater than that required to achieve single layer coverage. In addition, the relationship between surface coverage and cell viability of P. fluorescens cells correlated well with the findings in other bacterial cells (Escherichia coli and Lactococcuslactis). However, most of the bacterial cells that formed the biofilm were viable despite the positively charged PSL NPs being highly toxic to planktonic bacterial cells. This indicated that bacterial cells embedded in the biofilm were protected by self-produced extracellular polymeric substances (EPS) that provide resistance to antibacterial agents. In conclusion, mature biofilms covered with EPS exhibit resistance to NP toxicity as well as antibacterial agents.

Comparison of the cytotoxic effect of polystyrene latex nanoparticles on planktonic cells and bacterial biofilms

Science.gov (United States)

Nomura, Toshiyuki; Fujisawa, Eri; Itoh, Shikibu; Konishi, Yasuhiro

2016-06-01

The cytotoxic effect of positively charged polystyrene latex nanoparticles (PSL NPs) was compared between planktonic bacterial cells and bacterial biofilms using confocal laser scanning microscopy, atomic force microscopy, and a colony counting method. Pseudomonas fluorescens, which is commonly used in biofilm studies, was employed as the model bacteria. We found that the negatively charged bacterial surface of the planktonic cells was almost completely covered with positively charged PSL NPs, leading to cell death, as indicated by the NP concentration being greater than that required to achieve single layer coverage. In addition, the relationship between surface coverage and cell viability of P. fluorescens cells correlated well with the findings in other bacterial cells ( Escherichia coli and Lactococcus lactis). However, most of the bacterial cells that formed the biofilm were viable despite the positively charged PSL NPs being highly toxic to planktonic bacterial cells. This indicated that bacterial cells embedded in the biofilm were protected by self-produced extracellular polymeric substances (EPS) that provide resistance to antibacterial agents. In conclusion, mature biofilms covered with EPS exhibit resistance to NP toxicity as well as antibacterial agents.

Inactivation of Efflux Pumps Abolishes Bacterial Biofilm Formation

DEFF Research Database (Denmark)

Kvist, Malin; Hancock, Viktoria; Klemm, Per

2008-01-01

Bacterial biofilms cause numerous problems in health care and industry; notably, biofilms are associated with a large number of infections. Biofilm-dwelling bacteria are particularly resistant to antibiotics, making it hard to eradicate biofilm-associated infections. Bacteria rely on efflux pumps...... to get rid of toxic substances. We discovered that efflux pumps are highly active in bacterial biofilms, thus making efflux pumps attractive targets for antibiofilm measures. A number of efflux pump inhibitors (EPIs) are known. EPIs were shown to reduce biofilm formation, and in combination they could...... abolish biofilm formation completely. Also, EPIs were able to block the antibiotic tolerance of biofilms. The results of this feasibility study might pave the way for new treatments for biofilm-related infections and may be exploited for prevention of biofilms in general....

UV radiation and organic matter composition shape bacterial functional diversity in sediments

NARCIS (Netherlands)

Hunting, E.R.; White, C.M.; van Gemert, M.; Mes, D.; Stam, E.; van der Geest, H.G.; Kraak, M.H.S.; Admiraal, W.

2013-01-01

UV radiation and organic matter (OM) composition are known to influence the species composition of bacterioplankton communities. Potential effects of UV radiation on bacterial communities residing in sediments remain completely unexplored to date. However, it has been demonstrated that UV radiation

Role of ascitic fluid C3 in spontaneous bacterial peritonitis

African Journals Online (AJOL)

Amany Talaat Kamal

2012-02-29

Feb 29, 2012 ... blood glucose, complete blood count, prothrombin concentra- tion and INR were ... P-value of less than 0.05 was considered significant. 3. Results ..... References. [1] Garcia Tsao G. Bacterial infection in cirrhosis: treatment and prophylaxis. J Hepatol 2005;42:585–92. [2] Saadeh S, Davis GL. Management ...

Bacterial mycophagy: definition and diagnosis of a unique bacterial-fungal interaction

NARCIS (Netherlands)

Leveau, J.H.J.; Preston, G.M.

2008-01-01

This review analyses the phenomenon of bacterial mycophagy, which we define as a set of phenotypic behaviours that enable bacteria to obtain nutrients from living fungi and thus allow the conversion of fungal into bacterial biomass. We recognize three types of bacterial strategies to derive

Risk of bacterial cross infection associated with inspiration through flow-based spirometers.

Science.gov (United States)

Bracci, Massimo; Strafella, Elisabetta; Croce, Nicola; Staffolani, Sara; Carducci, Annalaura; Verani, Marco; Valentino, Matteo; Santarelli, Lory

2011-02-01

Bacterial contamination of spirometers has been documented in water-sealed devices, mouthpieces, and connection tubes. Little information is available about bacterial contamination of flow-based apparatuses such as turbine-type spirometers and pneumotachographs. Inspiration through contaminated equipment is a potential source of cross infection. To investigate bacteria mobilization (ie, bacteria detachment and aerosolization from the instrument) during routine spirometric testing, 2 types of flow-based spirometers were used. Bacteria mobilization during artificial inspiration through in-line filters or cardboard mouthpieces was evaluated. Nine hundred workers undergoing periodic spirometric testing were enrolled at the occupational physician office in 30 sessions of 30 subjects each. The participants were asked to perform a forced vital capacity test in a turbine-type spirometer and in an unheated pneumotachograph fitted with disposable in-line filters or cardboard mouthpieces. To evaluate bacterial mobilization, an artificial inspiration was performed and bacterial growth determined. The bacterial growth analysis was assessed after the first and the thirtieth spirometric tests of each session without disinfecting the instruments between tests. In addition, instrument bacterial contamination was evaluated. No significant bacterial mobilization and instrument contamination were found in spirometric tests executed with in-line filters. Conversely, a significant bacterial mobilization and instrument contamination were observed in tests performed with cardboard mouthpieces. Differences between the 2 spirometers were not significant. In-line filters may effectively reduce the risk of bacterial cross infection. Inspiration through flow-based spirometers fitted with disposable cardboard mouthpieces is completely safe when combined with spirometer disinfection/sterilization between subjects. Copyright © 2011 Association for Professionals in Infection Control and

Evaluation of bacterial surfactant toxicity towards petroleum degrading microorganisms.

Science.gov (United States)

Lima, Tânia M S; Procópio, Lorena C; Brandão, Felipe D; Leão, Bruna A; Tótola, Marcos R; Borges, Arnaldo C

2011-02-01

The acute toxicity of bacterial surfactants LBBMA111A, LBBMA155, LBBMA168, LBBMA191 and LBBMA201 and the synthetic surfactant sodium dodecyl sulfate (SDS) on the bioluminescent bacterium Vibrio fischeri was evaluated by measuring the reduction of light emission (EC(20)) by this microorganism when exposed to different surfactant concentrations. Moreover, the toxic effects of different concentrations of biological and synthetic surfactants on the growth of pure cultures of isolates Acinetobacter baumannii LBBMA04, Acinetobacter junni LBBMA36, Pseudomonas sp. LBBMA101B and Acinetobacter baumanni LBBMAES11 were evaluated in mineral medium supplemented with glucose. The EC(20) values obtained confirmed that the biosurfactants have a significantly lower toxicity to V. fischeri than the SDS. After 30 min of exposure, bacterial luminescence was almost completely inhibited by SDS at a concentration of 4710 mg L(-1). Growth reduction of pure bacterial cultures caused by the addition of biosurfactants to the growth medium was lower than that caused by SDS. Copyright © 2010 Elsevier Ltd. All rights reserved.

Bacterial meningitis

NARCIS (Netherlands)

Roos, Karen L.; van de Beek, Diederik

2010-01-01

Bacterial meningitis is a neurological emergency. Empiric antimicrobial and adjunctive therapy should be initiated as soon as a single set of blood cultures has been obtained. Clinical signs suggestive of bacterial meningitis include fever, headache, meningismus, vomiting, photophobia, and an

Host imprints on bacterial genomes--rapid, divergent evolution in individual patients.

Directory of Open Access Journals (Sweden)

Jaroslaw Zdziarski

Full Text Available Bacteria lose or gain genetic material and through selection, new variants become fixed in the population. Here we provide the first, genome-wide example of a single bacterial strain's evolution in different deliberately colonized patients and the surprising insight that hosts appear to personalize their microflora. By first obtaining the complete genome sequence of the prototype asymptomatic bacteriuria strain E. coli 83972 and then resequencing its descendants after therapeutic bladder colonization of different patients, we identified 34 mutations, which affected metabolic and virulence-related genes. Further transcriptome and proteome analysis proved that these genome changes altered bacterial gene expression resulting in unique adaptation patterns in each patient. Our results provide evidence that, in addition to stochastic events, adaptive bacterial evolution is driven by individual host environments. Ongoing loss of gene function supports the hypothesis that evolution towards commensalism rather than virulence is favored during asymptomatic bladder colonization.

Micro-magnet arrays for specific single bacterial cell positioning

Energy Technology Data Exchange (ETDEWEB)

Pivetal, Jérémy, E-mail: jeremy.piv@netcmail.com [Ecole Centrale de Lyon, CNRS UMR 5005, Laboratoire Ampère, F-69134 Écully (France); Royet, David [Ecole Centrale de Lyon, CNRS UMR 5005, Laboratoire Ampère, F-69134 Écully (France); Ciuta, Georgeta [Univ. Grenoble Alpes, Inst NEEL, F-38042 Grenoble (France); CNRS, Inst NEEL, F-38042 Grenoble (France); Frenea-Robin, Marie [Université de Lyon, Université Lyon 1, CNRS UMR 5005, Laboratoire Ampère, F-69622 Villeurbanne (France); Haddour, Naoufel [Ecole Centrale de Lyon, CNRS UMR 5005, Laboratoire Ampère, F-69134 Écully (France); Dempsey, Nora M. [Univ. Grenoble Alpes, Inst NEEL, F-38042 Grenoble (France); CNRS, Inst NEEL, F-38042 Grenoble (France); Dumas-Bouchiat, Frédéric [Univ Limoges, CNRS, SPCTS UMR 7513, 12 Rue Atlantis, F-87068 Limoges (France); Simonet, Pascal [Ecole Centrale de Lyon, CNRS UMR 5005, Laboratoire Ampère, F-69134 Écully (France)

2015-04-15

In various contexts such as pathogen detection or analysis of microbial diversity where cellular heterogeneity must be taken into account, there is a growing need for tools and methods that enable microbiologists to analyze bacterial cells individually. One of the main challenges in the development of new platforms for single cell studies is to perform precise cell positioning, but the ability to specifically target cells is also important in many applications. In this work, we report the development of new strategies to selectively trap single bacterial cells upon large arrays, based on the use of micro-magnets. Escherichia coli bacteria were used to demonstrate magnetically driven bacterial cell organization. In order to provide a flexible approach adaptable to several applications in the field of microbiology, cells were magnetically and specifically labeled using two different strategies, namely immunomagnetic labeling and magnetic in situ hybridization. Results show that centimeter-sized arrays of targeted, isolated bacteria can be successfully created upon the surface of a flat magnetically patterned hard magnetic film. Efforts are now being directed towards the integration of a detection tool to provide a complete micro-system device for a variety of microbiological applications. - Highlights: 1.We report a new approach to selectively micropattern bacterial cells individually upon micro-magnet arrays. 2.Permanent micro-magnets of a size approaching that of bacteria could be fabricated using a Thermo-Magnetic Patterning process. 3.Bacterial cells were labeled using two different magnetic labeling strategies providing flexible approach adaptable to several applications in the field of microbiology.

Barnett shale completions

Energy Technology Data Exchange (ETDEWEB)

Schein, G. [BJ Services, Dallas, TX (United States)

2006-07-01

Fractured shales yield oil and gas in various basins across the United States. A map indicating these fractured shale source-reservoir systems in the United States was presented along with the numerous similarities and differences that exist among these systems. Hydrocarbons in the organic rich black shale come from the bacterial decomposition of organic matter, primary thermogenic decomposition of organic matter or secondary thermogenic cracking of oil. The shale may be the reservoir or other horizons may be the primary or secondary reservoir. The reservoir has induced micro fractures or tectonic fractures. This paper described the well completions in the Barnett Shale in north Texas with reference to major players, reservoir properties, mineralogy, fluid sensitivity, previous treatments, design criteria and production examples. The Barnett Shale is an organic, black shale with thickness ranging from 100 to 1000 feet. The total organic carbon (TOC) averages 4.5 per cent. The unit has undergone high rate frac treatments. A review of the vertical wells in the Barnett Shale was presented along with the fracture treatment schedule and technology changes. A discussion of refracturing opportunities and proppant settling and transport revealed that additional proppant increases fluid recovery and enhances production. Compatible scale inhibitors and biocides can be beneficial. Horizontal completions in the Barnett Shale have shown better results than vertical wells, as demonstrated in a production comparison of 3 major horizontal wells in the basin. tabs., figs.

Bacterial communities in batch and continuous-flow wetlands treating the herbicide S-metolachlor

Energy Technology Data Exchange (ETDEWEB)

Elsayed, O.F. [Laboratory of Hydrology and Geochemistry of Strasbourg (LHyGeS), UMR 7517 University of Strasbourg/ENGEES/CNRS (France); Génétique Moléculaire, Génomique, Microbiologie (GMGM), UMR 7156 University of Strasbourg/CNRS (France); Maillard, E. [Laboratory of Hydrology and Geochemistry of Strasbourg (LHyGeS), UMR 7517 University of Strasbourg/ENGEES/CNRS (France); Vuilleumier, S. [Génétique Moléculaire, Génomique, Microbiologie (GMGM), UMR 7156 University of Strasbourg/CNRS (France); Imfeld, G., E-mail: imfeld@unistra.fr [Laboratory of Hydrology and Geochemistry of Strasbourg (LHyGeS), UMR 7517 University of Strasbourg/ENGEES/CNRS (France)

2014-11-15

Knowledge of wetland bacterial communities in the context of pesticide contamination and hydrological regime is scarce. We investigated the bacterial composition in constructed wetlands receiving Mercantor Gold{sup ®} contaminated water (960 g L{sup −1} of the herbicide S-metolachlor, > 80% of the S-enantiomer) operated under continuous-flow or batch modes to evaluate the impact of the hydraulic regime. In the continuous-flow wetland, S-metolachlor mass removal was > 40%, whereas in the batch wetland, almost complete removal of S-metolachlor (93–97%) was observed. Detection of ethanesulfonic and oxanilic acid degradation products further indicated S-metolachlor biodegradation in the two wetlands. The dominant bacterial populations were characterised by terminal restriction fragment length polymorphism (T-RFLP) and 454 pyrosequencing. The bacterial profiles evolved during the first 35 days of the experiment, starting from a composition similar to that of inlet water, with the use of nitrate and to a lesser extent sulphate and manganese as terminal electron acceptors for microbial metabolism. Proteobacteria were the most abundant phylum, with Beta-, Alpha- and Gammaproteobacteria representing 26%, 19% and 17% respectively of total bacterial abundance. Bacterial composition in wetland water changed gradually over time in continuous-flow wetland and more abruptly in the batch wetland. Differences in overall bacterial water structure in the two systems were modest but significant (p = 0.008), and S-metolachlor, nitrate, and total inorganic carbon concentrations correlated with changes in the bacterial profiles. Together, the results highlight that bacterial composition profiles and their dynamics may be used as bioindicators of herbicide exposure and hydraulic disturbances in wetland systems. - Highlights: • We evaluated the bacterial composition in wetlands treating S-metolachlor • Hydraulic regime impacted biogeochemical processes and S-metolachlor removal �

Bacterial communities in batch and continuous-flow wetlands treating the herbicide S-metolachlor

International Nuclear Information System (INIS)

Elsayed, O.F.; Maillard, E.; Vuilleumier, S.; Imfeld, G.

2014-01-01

Knowledge of wetland bacterial communities in the context of pesticide contamination and hydrological regime is scarce. We investigated the bacterial composition in constructed wetlands receiving Mercantor Gold ® contaminated water (960 g L −1 of the herbicide S-metolachlor, > 80% of the S-enantiomer) operated under continuous-flow or batch modes to evaluate the impact of the hydraulic regime. In the continuous-flow wetland, S-metolachlor mass removal was > 40%, whereas in the batch wetland, almost complete removal of S-metolachlor (93–97%) was observed. Detection of ethanesulfonic and oxanilic acid degradation products further indicated S-metolachlor biodegradation in the two wetlands. The dominant bacterial populations were characterised by terminal restriction fragment length polymorphism (T-RFLP) and 454 pyrosequencing. The bacterial profiles evolved during the first 35 days of the experiment, starting from a composition similar to that of inlet water, with the use of nitrate and to a lesser extent sulphate and manganese as terminal electron acceptors for microbial metabolism. Proteobacteria were the most abundant phylum, with Beta-, Alpha- and Gammaproteobacteria representing 26%, 19% and 17% respectively of total bacterial abundance. Bacterial composition in wetland water changed gradually over time in continuous-flow wetland and more abruptly in the batch wetland. Differences in overall bacterial water structure in the two systems were modest but significant (p = 0.008), and S-metolachlor, nitrate, and total inorganic carbon concentrations correlated with changes in the bacterial profiles. Together, the results highlight that bacterial composition profiles and their dynamics may be used as bioindicators of herbicide exposure and hydraulic disturbances in wetland systems. - Highlights: • We evaluated the bacterial composition in wetlands treating S-metolachlor • Hydraulic regime impacted biogeochemical processes and S-metolachlor removal �

Detection and quantification of intracellular bacterial colonies by automated, high-throughput microscopy.

Science.gov (United States)

Ernstsen, Christina L; Login, Frédéric H; Jensen, Helene H; Nørregaard, Rikke; Møller-Jensen, Jakob; Nejsum, Lene N

2017-08-01

To target bacterial pathogens that invade and proliferate inside host cells, it is necessary to design intervention strategies directed against bacterial attachment, cellular invasion and intracellular proliferation. We present an automated microscopy-based, fast, high-throughput method for analyzing size and number of intracellular bacterial colonies in infected tissue culture cells. Cells are seeded in 48-well plates and infected with a GFP-expressing bacterial pathogen. Following gentamicin treatment to remove extracellular pathogens, cells are fixed and cell nuclei stained. This is followed by automated microscopy and subsequent semi-automated spot detection to determine the number of intracellular bacterial colonies, their size distribution, and the average number per host cell. Multiple 48-well plates can be processed sequentially and the procedure can be completed in one working day. As a model we quantified intracellular bacterial colonies formed by uropathogenic Escherichia coli (UPEC) during infection of human kidney cells (HKC-8). Urinary tract infections caused by UPEC are among the most common bacterial infectious diseases in humans. UPEC can colonize tissues of the urinary tract and is responsible for acute, chronic, and recurrent infections. In the bladder, UPEC can form intracellular quiescent reservoirs, thought to be responsible for recurrent infections. In the kidney, UPEC can colonize renal epithelial cells and pass to the blood stream, either via epithelial cell disruption or transcellular passage, to cause sepsis. Intracellular colonies are known to be clonal, originating from single invading UPEC. In our experimental setup, we found UPEC CFT073 intracellular bacterial colonies to be heterogeneous in size and present in nearly one third of the HKC-8 cells. This high-throughput experimental format substantially reduces experimental time and enables fast screening of the intracellular bacterial load and cellular distribution of multiple

Laboratory scale bioremediation of diesel hydrocarbon in soil by indigenous bacterial consortium.

Science.gov (United States)

Sharma, Anjana; Rehman, Meenal Budholia

2009-09-01

In vitro experiment was performed by taking petrol pump soils and diesel in flasks with the micronutrients and macronutrients supplements. Cemented bioreactors having sterilized soil and diesel was used for in vivo analysis of diesel hydrocarbon degradation. There were two sets of experiments, first having three bioreactors (1) inoculated by KI. pneumoniae subsp. aerogenes with soil and diesel; (2) with addition of NH4NO3; and (3) served as control. In second set, one bioreactor was inoculated by bacterial consortium containing Moraxella saccharolytica, Alteromonas putrefaciens, KI. pneumoniae subsp. aerogenes and Pseudomonas fragi along with soil and diesel. The remaining two bioreactors (having NH4NO3 and control) were similar to the first set. The experiments were incubated for 30 days. Ability of bacterial inoculum to degrade diesel was analyzed through GC-MS. Smaller chain compounds were obtained after experimental period of 30 days. Rate of diesel degradation was better with the present bacterial consortium than individual bacteria. Present bacterial consortium can be a better choice for faster and complete remediation of contaminated hydrocarbon soils.

Bacterial Community Dynamics in Dichloromethane-Contaminated Groundwater Undergoing Natural Attenuation

Directory of Open Access Journals (Sweden)

Justin Wright

2017-11-01

Full Text Available The uncontrolled release of the industrial solvent methylene chloride, also known as dichloromethane (DCM, has resulted in widespread groundwater contamination in the United States. Here we investigate the role of groundwater bacterial communities in the natural attenuation of DCM at an undisclosed manufacturing site in New Jersey. This study investigates the bacterial community structure of groundwater samples differentially contaminated with DCM to better understand the biodegradation potential of these autochthonous bacterial communities. Bacterial community analysis was completed using high-throughput sequencing of the 16S rRNA gene of groundwater samples (n = 26 with DCM contamination ranging from 0.89 to 9,800,000 μg/L. Significant DCM concentration-driven shifts in overall bacterial community structure were identified between samples, including an increase in the abundance of Firmicutes within the most contaminated samples. Across all samples, a total of 6,134 unique operational taxonomic units (OTUs were identified, with 16 taxa having strong correlations with increased DCM concentration. Putative DCM degraders such as Pseudomonas, Dehalobacterium and Desulfovibrio were present within groundwater across all levels of DCM contamination. Interestingly, each of these taxa dominated specific DCM contamination ranges respectively. Potential DCM degrading lineages yet to be cited specifically as a DCM degrading organisms, such as the Desulfosporosinus, thrived within the most heavily contaminated groundwater samples. Co-occurrence network analysis revealed aerobic and anaerobic bacterial taxa with DCM-degrading potential were present at the study site. Our 16S rRNA gene survey serves as the first in situ bacterial community assessment of contaminated groundwater harboring DCM concentrations ranging over seven orders of magnitude. Diversity analyses revealed known as well as potentially novel DCM degrading taxa within defined DCM concentration

Inhibition of bacterial ammonia oxidation by organohydrazines in soil microcosms

Directory of Open Access Journals (Sweden)

Yucheng eWu

2012-01-01

Full Text Available Hydroxylamine oxidation by hydroxylamine oxidoreductase (HAO is a key step for energy-yielding in support of the growth of ammonia-oxidizing bacteria (AOB. Organohydrazines have been shown to inactivate HAO from Nitrosomonas europaea, and may serve as selective inhibitors to differentiate bacterial from archaeal ammonia oxidation due to the absence of bacterial HAO gene homologue in known ammonia-oxidizing archaea (AOA. In this study, the effects of three organohydrazines on activity, abundance and composition of AOB and AOA were evaluated in soil microcosms. The results indicate that phenylhydrazine and methylhydrazine at the concentration of 100 mol per gram dry weight soil completely suppressed the activity of soil nitrification. DGGE fingerprinting and sequencing analysis of bacterial ammonia monooxygenase subunit A gene (amoA clearly demonstrated that nitrification activity change is well paralleled with the growth of Nitrosomonas europaea-like AOB in soil microcosms. No significant correlation between AOA community structure and nitrification activity was observed among all treatments during the incubation period, although incomplete inhibition of nitrification activity occurred in 2-hydroxyethylhydrazine-amended soil microcosms. These findings show that the HAO-targeted organohydrazines can effectively inhibit bacterial nitrification in soil, and the mechanism of organohydrazine affecting AOA remains unclear.

Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia

Directory of Open Access Journals (Sweden)

Stott Matthew B

2008-07-01

Full Text Available Abstract Background The phylum Verrucomicrobia is a widespread but poorly characterized bacterial clade. Although cultivation-independent approaches detect representatives of this phylum in a wide range of environments, including soils, seawater, hot springs and human gastrointestinal tract, only few have been isolated in pure culture. We have recently reported cultivation and initial characterization of an extremely acidophilic methanotrophic member of the Verrucomicrobia, strain V4, isolated from the Hell's Gate geothermal area in New Zealand. Similar organisms were independently isolated from geothermal systems in Italy and Russia. Results We report the complete genome sequence of strain V4, the first one from a representative of the Verrucomicrobia. Isolate V4, initially named "Methylokorus infernorum" (and recently renamed Methylacidiphilum infernorum is an autotrophic bacterium with a streamlined genome of ~2.3 Mbp that encodes simple signal transduction pathways and has a limited potential for regulation of gene expression. Central metabolism of M. infernorum was reconstructed almost completely and revealed highly interconnected pathways of autotrophic central metabolism and modifications of C1-utilization pathways compared to other known methylotrophs. The M. infernorum genome does not encode tubulin, which was previously discovered in bacteria of the genus Prosthecobacter, or close homologs of any other signature eukaryotic proteins. Phylogenetic analysis of ribosomal proteins and RNA polymerase subunits unequivocally supports grouping Planctomycetes, Verrucomicrobia and Chlamydiae into a single clade, the PVC superphylum, despite dramatically different gene content in members of these three groups. Comparative-genomic analysis suggests that evolution of the M. infernorum lineage involved extensive horizontal gene exchange with a variety of bacteria. The genome of M. infernorum shows apparent adaptations for existence under extremely

Evaluation of synergy and bacterial regrowth in photocatalytic ozonation disinfection of municipal wastewater.

Science.gov (United States)

Mecha, Achisa C; Onyango, Maurice S; Ochieng, Aoyi; Momba, Maggy N B

2017-12-01

The use of solar and ultraviolet titanium dioxide photocatalytic ozonation processes to inactivate waterborne pathogens (Escherichia coli, Salmonella species, Shigella species and Vibrio cholerae) in synthetic water and secondary municipal wastewater effluent is presented. The performance indicators were bacterial inactivation efficiency, post-disinfection regrowth and synergy effects (collaboration) between ozonation and photocatalysis (photocatalytic ozonation). Photocatalytic ozonation effectively inactivated the target bacteria and positive synergistic interactions were observed, leading to synergy indices (SI) of up to 1.86 indicating a performance much higher than that of ozonation and photocatalysis individually (SI≤1, no synergy; SI>1 shows synergy between the two processes). Furthermore, there was a substantial reduction in contact time required for complete bacterial inactivation by 50-75% compared to the individual unit processes of ozonation and photocatalysis. Moreover, no post-treatment bacterial regrowth after 24 and 48h in the dark was observed. Therefore, the combined processes overcame the limitations of the individual unit processes in terms of the suppression of bacterial reactivation and regrowth owing to the fact that bacterial cells were irreparably damaged. The treated wastewater satisfied the bacteriological requirements in treated wastewater for South Africa. Copyright © 2017 Elsevier B.V. All rights reserved.

POLYSACCHARIDES AND eDNA AID BACTERIAL ATTACHMENT TO POLYMER BRUSH COATINGS (PLL-g-PEG)

DEFF Research Database (Denmark)

Zeng, Guanghong; Ogaki, Ryosuke; Regina, Viduthalai R.

measured the adsorption of peptides, polysaccharides and DNA to these coatings, as they represent bacterial adhesins with very different properties. While protein adsorption was minimized, we found considerable adsorption of polysaccharides, and exposure to DNA resulted in complete desorption...... of the conventional coating. These results explain why S. epidermidis, which produces polysaccharides and extracellular DNA, could successfully colonize the conventional PLL-g-PEG coatings. The ability of high-density PLL-g-PEG to resist polysaccharides, DNA, and bacterial adhesion of all strains is thus highly......Polymer brush coatings of poly(ethylene glycol) are considered the gold standard for nonfouling surfaces, but nevertheless, a few bacteria manage to attach and initiate biofilm formation on these coatings. To achieve robust resistance against bacterial adhesion and biofilm formation, grafting...

dBBQs: dataBase of Bacterial Quality scores

OpenAIRE

Wanchai, Visanu; Patumcharoenpol, Preecha; Nookaew, Intawat; Ussery, David

2017-01-01

Background: It is well-known that genome sequencing technologies are becoming significantly cheaper and faster. As a result of this, the exponential growth in sequencing data in public databases allows us to explore ever growing large collections of genome sequences. However, it is less known that the majority of available sequenced genome sequences in public databases are not complete, drafts of varying qualities. We have calculated quality scores for around 100,000 bacterial genomes from al...

Bacterial lung abscess

International Nuclear Information System (INIS)

Groskin, S.A.; Panicek, D.M.; Ewing, D.K.; Rivera, F.; Math, K.; Teixeira, J.; Heitzman, E.R.

1987-01-01

A retrospective review of patients with bacterial lung abscess was carried out. Demographic, clinical, and radiographical features of this patient group are compared with similar data from patients with empyema and/or cavitated lung carcinoma; differential diagnostic points are stressed. The entity of radiographically occult lung abscess is discussed. Complications associated with bacterial lung abscess are discussed. Current therapeutic options and treatment philosophy for patients with bacterial lung abscess are noted

Bacterial growth on macrophyte leachate and fate of bacterial production

International Nuclear Information System (INIS)

Findlay, S.; Carlough, L.; Crocker, M.T.; Gill, H.K.; Meyer, J.L.; Smith, P.J.

1986-01-01

The role bacteria play in transferring organic carbon to other trophic levels in aquatic ecosystems depends on the efficiency with which they convert dissolved organic [ 14 C]-labelled carbon into bacterial biomass and on the ability of consumers to graze bacteria. The authors have measured the conversion efficiency for bacteria growing on macrophyte-derived dissolved organic carbon and estimated the amount of bacterial production removed by grazing. Bacteria converted this DOC into new tissue with an efficiency of 53%, substantially higher than the apparent conversion efficiency of macrophyte-derived particulate organic carbon or other types of DOC. Two estimates of grazing indicate that the decline in bacterial numbers after the bloom was probably due to grazing by flagellates. These results show the significance of the bacterial link between DOC and other trophic levels

[Bacterial diversity within different sections of summer sea-ice samples from the Prydz Bay, Antarctica].

Science.gov (United States)

Ma, Jifei; Du, Zongjun; Luo, Wei; Yu, Yong; Zeng, Yixin; Chen, Bo; Li, Huirong

2013-02-04

In order to assess bacterial abundance and diversity within three different sections of summer sea-ice samples collected from the Prydz Bay, Antarctica. Fluorescence in situ hybridization was applied to determine the proportions of Bacteria in sea-ice. Bacterial community composition within sea ice was analyzed by 16S rRNA gene clone library construction. Correlation analysis was performed between the physicochemical parameters and the bacterial diversity and abundance within sea ice. The result of fluorescence in situ hybridization shows that bacteria were abundant in the bottom section, and the concentration of total organic carbon, total organic nitrogen and phosphate may be the main factors for bacterial abundance. In bacterial 16S rRNA gene libraries of sea-ice, nearly complete 16S rRNA gene sequences were grouped into three distinct lineages of Bacteria (gamma-Proteobacteria, alpha-Proteobacteria and Bacteroidetes). Most clone sequences were related to cultured bacterial isolates from the marine environment, arctic and Antarctic sea-ice with high similarity. The member of Bacteroidetes was not detected in the bottom section of sea-ice. The bacterial communities within sea-ice were little heterogeneous at the genus-level between different sections, and the concentration of NH4+ may cause this distribution. The number of bacteria was abundant in the bottom section of sea-ice. Gamma-proteobacteria was the dominant bacterial lineage in sea-ice.

Long-term follow-up of children with bacterial meningitis with emphasis on behavioural characteristics.

Science.gov (United States)

Berg, Stefan; Trollfors, Birger; Hugosson, Svante; Fernell, Elisabeth; Svensson, Elisabeth

2002-06-01

The sequelae and behaviour in children several years after an episode of bacterial meningitis were studied. All children in Sweden aged 0-4 years with bacterial meningitis between 1987 and 1989 caused by Haemophilus influenzae, Streptococcus pneumoniae and Neisseria meningitidis were identified. After exclusion of 16 children who died, 12 with severe concomitant diseases, ten with severe neurological damage obvious already at discharge from hospital and 34 with unknown address, questionnaires were sent to the parents of the remaining 463 children The nearest-age siblings were used as a comparison group. The questionnaires included questions concerning general health, schooling, motor function, speech, hearing and behaviour (inattention, hyperactivity and impulsiveness). The children were 6-14 years old when the questionnaires were completed. Questionnaires were completed for 304 pairs of patients and siblings and for 154 patients without siblings. The majority of post-meningitic children were healthy and attended normal school but they had more hearing impairment, headaches and problems with balance than their siblings. When the distributions of answers regarding behaviour were compared, the post-meningitic children had significantly more symptoms in the fields of inattention, hyperactivity and impulsiveness than their siblings. Except for hearing impairment, severe sequelae after bacterial meningitis which are not discovered at discharge do not appear later. Children who appear well after bacterial meningitis have more non-specific symptoms like headache, and more signs and symptoms indicating inattention, hyperactivity and impulsiveness than their siblings.

Structure of the Bacterial Community in Different Stages of Early Childhood Caries.

Science.gov (United States)

Ximenes, Marcos; Armas, Rafael Dutra de; Triches, Thaisa Cezária; Cardoso, Mariane; Vieira, Ricardo de Souza

2018-01-15

To characterise in vivo the structure of bacterial communities in decayed and sound primary teeth. Samples of biofilms were collected from three groups of patients with complete and exclusively primary dentition (n = 45): G1: sound teeth (n = 15); G2: enamel lesion (n = 15); G3: dentin lesion (n = 15). DNA was extracted (CTAB 2%) from the biofilm, the partial 16S rRNA gene was amplified with Bacteria Universal Primers (BA338fGC - UN518r) and subjected to DGGE (denaturing gradient gel electrophoresis). Multidimensional scaling and ANOSIM (analysis of similarity) were employed to determine the structure of the bacterial communities. The amplicon richness was determined by averaging amplicons, with the differences between treatments determined with ANOVA, while means were compared using Tukey's test (p < 0.05). Compared to sound teeth, a greater variety of bacterial communities was found in decayed teeth. Despite the differences between the bacterial communities of sound teeth and decayed teeth, the Venn diagram showed that the samples had 38 amplicons in common. Greater amplicon richness was observed in samples of decayed teeth (enamel: 20.5 ± 2.7; dentin: 20.1 ± 2.8) compared with the sound samples (12.0 ± 4.3) (p <0.05), indicating enhanced growth for specific groups of bacteria on decayed teeth. Although there is less bacterial diversity on sound than ECC-decayed teeth, the bacterial communities are very similar.

Assessment of temporal and spatial evolution of bacterial communities in a biological sand filter mesocosm treating winery wastewater.

Science.gov (United States)

Ramond, J-B; Welz, P J; Tuffin, M I; Burton, S G; Cowan, D A

2013-07-01

To assess the impact of winery wastewater (WW) on biological sand filter (BSF) bacterial community structures, and to evaluate whether BSFs can constitute alternative and valuable treatment- processes to remediate WW. During 112 days, WW was used to contaminate a BSF mesocosm (length 173 cm/width 106 cm/depth 30 cm). The effect of WW on bacterial communities of four BSF microenvironments (surface/deep, inlet/outlet) was investigated using terminal-restriction fragment length polymorphism (T-RFLP). BSF achieved high Na (95·1%), complete Cl and almost complete chemical oxygen demand (COD) (98·0%) and phenolic (99·2%) removals. T-RFLP analysis combined with anosim revealed that WW significantly modified the surface and deep BSF bacterial communities. BSF provided high COD, phenolic and salt removals throughout the experiment. WW-selected bacterial communities were thus able to tolerate and/or degrade WW, suggesting that community composition does not alter BSF performances. However, biomass increased significantly in the WW-impacted surface sediments, which could later lead to system clogging and should thus be monitored. BSFs constitute alternatives to constructed wetlands to treat agri effluents such as WW. To our knowledge, this study is the first unravelling the responses of BSF bacterial communities to contamination and suggests that WW-selected BSF communities maintained high removal performances. Journal of Applied Microbiology © 2013 The Society for Applied Microbiology.

Bacterial surface adaptation

Science.gov (United States)

Utada, Andrew

2014-03-01

Biofilms are structured multi-cellular communities that are fundamental to the biology and ecology of bacteria. Parasitic bacterial biofilms can cause lethal infections and biofouling, but commensal bacterial biofilms, such as those found in the gut, can break down otherwise indigestible plant polysaccharides and allow us to enjoy vegetables. The first step in biofilm formation, adaptation to life on a surface, requires a working knowledge of low Reynolds number fluid physics, and the coordination of biochemical signaling, polysaccharide production, and molecular motility motors. These crucial early stages of biofilm formation are at present poorly understood. By adapting methods from soft matter physics, we dissect bacterial social behavior at the single cell level for several prototypical bacterial species, including Pseudomonas aeruginosa and Vibrio cholerae.

Canopy soil bacterial communities altered by severing host tree limbs

Directory of Open Access Journals (Sweden)

Cody R. Dangerfield

2017-09-01

Full Text Available Trees of temperate rainforests host a large biomass of epiphytic plants, which are associated with soils formed in the forest canopy. Falling of epiphytic material results in the transfer of carbon and nutrients from the canopy to the forest floor. This study provides the first characterization of bacterial communities in canopy soils enabled by high-depth environmental sequencing of 16S rRNA genes. Canopy soil included many of the same major taxonomic groups of Bacteria that are also found in ground soil, but canopy bacterial communities were lower in diversity and contained different operational taxonomic units. A field experiment was conducted with epiphytic material from six Acer macrophyllum trees in Olympic National Park, Washington, USA to document changes in the bacterial communities of soils associated with epiphytic material that falls to the forest floor. Bacterial diversity and composition of canopy soil was highly similar, but not identical, to adjacent ground soil two years after transfer to the forest floor, indicating that canopy bacteria are almost, but not completely, replaced by ground soil bacteria. Furthermore, soil associated with epiphytic material on branches that were severed from the host tree and suspended in the canopy contained altered bacterial communities that were distinct from those in canopy material moved to the forest floor. Therefore, the unique nature of canopy soil bacteria is determined in part by the host tree and not only by the physical environmental conditions associated with the canopy. Connection to the living tree appears to be a key feature of the canopy habitat. These results represent an initial survey of bacterial diversity of the canopy and provide a foundation upon which future studies can more fully investigate the ecological and evolutionary dynamics of these communities.

Recurrent Bacterial Meningitis in a Child with Mondini Dysplasia

OpenAIRE

Kepenekli-Kadayifci, Eda; Karaaslan, Ayşe; Atıcı, Serkan; Binnetoğlu, Adem; Sarı, Murat; Soysal, Ahmet; Altınkanat, Gülşen; Bakır, Mustafa

2014-01-01

Mondini dysplasia, also known as Mondini malformation, is a developmental abnormality of the inner and middle ears that can cause hearing loss, cerebrospinal fluid (CSF) leakage, and recurrent bacterial meningitis (RBM), which is defined as two or more episodes of meningitis separated by a period of convalescence and the complete resolution of all signs and symptoms. An accurate diagnosis of the underlying pathology is crucial to prevent further episodes from occurring. Herein, we present a...

Bacterial Protein-Tyrosine Kinases

DEFF Research Database (Denmark)

Shi, Lei; Kobir, Ahasanul; Jers, Carsten

2010-01-01

in exopolysaccharide production, virulence, DNA metabolism, stress response and other key functions of the bacterial cell. BY-kinases act through autophosphorylation (mainly in exopolysaccharide production) and phosphorylation of other proteins, which have in most cases been shown to be activated by tyrosine......Bacteria and Eukarya share essentially the same family of protein-serine/threonine kinases, also known as the Hanks-type kinases. However, when it comes to protein-tyrosine phosphorylation, bacteria seem to have gone their own way. Bacterial protein-tyrosine kinases (BY-kinases) are bacterial...... and highlighted their importance in bacterial physiology. Having no orthologues in Eukarya, BY-kinases are receiving a growing attention from the biomedical field, since they represent a particularly promising target for anti-bacterial drug design....

COMPARATIVE ACTIVITY OF CECROPIN A AND POLYMYXIN B AGAINST FROG BACTERIAL PATHOGENS

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Ermin Schadich

2013-03-01

Full Text Available The antimicrobial activity of two antimicrobial peptides, cecropin A and polymyxin B against different bacterial pathogens associated with bacterial dermatosepticemia, a fatal bacterial infectious disease of frogs was investigated. The peptides were tested in serial of concentrations (100-0.19 µg/ml for growth inhibition of seven pathogens: Aeromonas hydrophila, Chryseobacterium meningosepticum, Citrobacter freundii, Klebsiella pneumoniae, Pseudomonas aeruginosa, Proteus mirabilis and Serratia liquefaciens. Their antimicrobial activity was compared with that of two antimicrobial peptides from frog skin, magainin 2 and aurein 2.1. Both cecropin A and polymyxin B, completely inhibited the growth of three pathogens: C. freundii, K. pneumoniae and P. aeruginosa at a concentration some sixteen times less than two skin peptides. Furthermore, cecropin A inhibited the growth of three pathogens resistant to the two skin peptides, A. hydrophila, C. meningosepticum and P. mirabilis. Polymyxin B also inhibited the growth of three pathogens resistant to the skin peptides, A. hydrophila, C. meningosepticum and S. liquefaciens. Cecropin A and polymyxin B have marked antibacterial activity against different frog bacterial pathogens indicating potential for therapeutic measures.Keywords: frogs, antimicrobial, bacteria, cecropin, polymyxin, resistance

Bacterial Cellulose-Hydroxyapatite Nanocomposites for Bone Regeneration

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S. Saska

2011-01-01

Full Text Available The aim of this study was to develop and to evaluate the biological properties of bacterial cellulose-hydroxyapatite (BC-HA nanocomposite membranes for bone regeneration. Nanocomposites were prepared from bacterial cellulose membranes sequentially incubated in solutions of CaCl2 followed by Na2HPO4. BC-HA membranes were evaluated in noncritical bone defects in rat tibiae at 1, 4, and 16 weeks. Thermogravimetric analyses showed that the amount of the mineral phase was 40%–50% of the total weight. Spectroscopy, electronic microscopy/energy dispersive X-ray analyses, and X-ray diffraction showed formation of HA crystals on BC nanofibres. Low crystallinity HA crystals presented Ca/P a molar ratio of 1.5 (calcium-deficient HA, similar to physiological bone. Fourier transformed infrared spectroscopy analysis showed bands assigned to phosphate and carbonate ions. In vivo tests showed no inflammatory reaction after 1 week. After 4 weeks, defects were observed to be completely filled in by new bone tissue. The BC-HA membranes were effective for bone regeneration.

Differentiation of bacterial and non-bacterial community-acquired pneumonia by thin-section computed tomography

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Ito, Isao [Department of Respiratory Medicine, Kurashiki Central Hospital, 1-1-1 Miwa, Kurashiki 710-8602 (Japan); Department of Respiratory Medicine, Kyoto University, 54 Shogoin-kawaharacho, Sakyo-ku, Kyoto 606-8507 (Japan)], E-mail: isaoito@kuhp.kyoto-u.ac.jp; Ishida, Tadashi [Department of Respiratory Medicine, Kurashiki Central Hospital, 1-1-1 Miwa, Kurashiki 710-8602 (Japan)], E-mail: ishidat@kchnet.or.jp; Togashi, Kaori [Department of Diagnostic Imaging and Nuclear Medicine, Kyoto University, 54 Shogoin-kawaharacho, Sakyo-ku, Kyoto 606-8507 (Japan)], E-mail: ktogashi@kuhp.kyoto-u.ac.jp; Niimi, Akio [Department of Respiratory Medicine, Kyoto University, 54 Shogoin-kawaharacho, Sakyo-ku, Kyoto 606-8507 (Japan)], E-mail: niimi@kuhp.kyoto-u.ac.jp; Koyama, Hiroshi [General Internal Medicine, National Hospital Organization Kyoto Medical Center, 1-1 Fukakusa-Mukohatacho, Fushimi-ku, Kyoto 612-8555 (Japan)], E-mail: hkoyama-kyt@umin.ac.jp; Ishimori, Takayoshi [Department of Radiology, Kurashiki Central Hospital, 1-1-1 Miwa, Kurashiki 710-8602 (Japan)], E-mail: ti10794@kchnet.or.jp; Kobayashi, Hisataka [Department of Diagnostic Imaging and Nuclear Medicine, Kyoto University, 54 Shogoin-kawaharacho, Sakyo-ku, Kyoto 606-8507 (Japan); Molecular Imaging Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Building 10, Room 1B40, MSC1088, 10 Center Drive, Bethesda, MD 20892-1088 (United States)], E-mail: kobayash@mail.nih.gov; Mishima, Michiaki [Department of Respiratory Medicine, Kyoto University, 54 Shogoin-kawaharacho, Sakyo-ku, Kyoto 606-8507 (Japan)], E-mail: mishima@kuhp.kyoto-u.ac.jp

2009-12-15

Background and objective: The management of community-acquired pneumonia (CAP) depends, in part, on the identification of the causative agents. The objective of this study was to determine the potential of thin-section computed tomography (CT) in differentiating bacterial and non-bacterial pneumonia. Patients and methods: Thin-section CT studies were prospectively examined in hospitalized CAP patients within 2 days of admission, followed by retrospective assessment by two pulmonary radiologists. Thin-section CT findings on the pneumonias caused by each pathogen were examined, and two types of pneumonias were compared. Using multivariate logistic regression analyses, receiver operating characteristic (ROC) curves were produced. Results: Among 183 CAP episodes (181 patients, 125 men and 56 women, mean age {+-} S.D.: 61.1 {+-} 19.7) examined by thin-section CT, the etiologies of 125 were confirmed (94 bacterial pneumonia and 31 non-bacterial pneumonia). Centrilobular nodules were specific for non-bacterial pneumonia and airspace nodules were specific for bacterial pneumonia (specificities of 89% and 94%, respectively) when located in the outer lung areas. When centrilobular nodules were the principal finding, they were specific but lacked sensitivity for non-bacterial pneumonia (specificity 98% and sensitivity 23%). To distinguish the two types of pneumonias, centrilobular nodules, airspace nodules and lobular shadows were found to be important by multivariate analyses. ROC curve analysis discriminated bacterial pneumonia from non-bacterial pneumonia among patients without underlying lung diseases, yielding an optimal point with sensitivity and specificity of 86% and 79%, respectively, but was less effective when all patients were analyzed together (70% and 84%, respectively). Conclusion: Thin-section CT examination was applied for the differentiation of bacterial and non-bacterial pneumonias. Though showing some potential, this examination at the present time would

Differentiation of bacterial and non-bacterial community-acquired pneumonia by thin-section computed tomography

International Nuclear Information System (INIS)

Ito, Isao; Ishida, Tadashi; Togashi, Kaori; Niimi, Akio; Koyama, Hiroshi; Ishimori, Takayoshi; Kobayashi, Hisataka; Mishima, Michiaki

2009-01-01

Background and objective: The management of community-acquired pneumonia (CAP) depends, in part, on the identification of the causative agents. The objective of this study was to determine the potential of thin-section computed tomography (CT) in differentiating bacterial and non-bacterial pneumonia. Patients and methods: Thin-section CT studies were prospectively examined in hospitalized CAP patients within 2 days of admission, followed by retrospective assessment by two pulmonary radiologists. Thin-section CT findings on the pneumonias caused by each pathogen were examined, and two types of pneumonias were compared. Using multivariate logistic regression analyses, receiver operating characteristic (ROC) curves were produced. Results: Among 183 CAP episodes (181 patients, 125 men and 56 women, mean age ± S.D.: 61.1 ± 19.7) examined by thin-section CT, the etiologies of 125 were confirmed (94 bacterial pneumonia and 31 non-bacterial pneumonia). Centrilobular nodules were specific for non-bacterial pneumonia and airspace nodules were specific for bacterial pneumonia (specificities of 89% and 94%, respectively) when located in the outer lung areas. When centrilobular nodules were the principal finding, they were specific but lacked sensitivity for non-bacterial pneumonia (specificity 98% and sensitivity 23%). To distinguish the two types of pneumonias, centrilobular nodules, airspace nodules and lobular shadows were found to be important by multivariate analyses. ROC curve analysis discriminated bacterial pneumonia from non-bacterial pneumonia among patients without underlying lung diseases, yielding an optimal point with sensitivity and specificity of 86% and 79%, respectively, but was less effective when all patients were analyzed together (70% and 84%, respectively). Conclusion: Thin-section CT examination was applied for the differentiation of bacterial and non-bacterial pneumonias. Though showing some potential, this examination at the present time would not

Spatially resolved characterization of biogenic manganese oxideproduction within a bacterial biofilm

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Toner, Brandy; Fakra, Sirine; Villalobos, Mario; Warwick, Tony; Sposito, Garrison

2004-10-01

Pseudomonas putida strain MnB1, a biofilm forming bacteria, was used as a model for the study of bacterial Mn oxidation in freshwater and soil environments. The oxidation of Mn{sub (aq)}{sup +2} by P. putida was characterized by spatially and temporally resolving the oxidation state of Mn in the presence of a bacterial biofilm using scanning transmission x-ray microscopy (STXM) combined with near edge x-ray absorption fine structure (NEXAFS) spectroscopy at the Mn-L{sub 2,3} absorption edges. Subsamples were collected from growth flasks containing 0.1 mM and 1 mM total Mn at 16, 24, 36 and 48 hours after inoculation. Immediately after collection, the unprocessed hydrated subsamples were imaged at 40 nm resolution. Manganese NEXAFS spectra were extracted from x-ray energy sequences of STXM images (stacks) and fit with linear combinations of well characterized reference spectra to obtain quantitative relative abundances of Mn(II), Mn(III) and Mn(IV). Careful consideration was given to uncertainty in the normalization of the reference spectra, choice of reference compounds, and chemical changes due to radiation damage. The STXM results confirm that Mn{sub (aq)}{sup +2} was removed from solution by P. putida and was concentrated as Mn(III) and Mn(IV) immediately adjacent to the bacterial cells. The Mn precipitates were completely enveloped by bacterial biofilm material. The distribution of Mn oxidation states was spatially heterogeneous within and between the clusters of bacterial cells. Scanning transmission x-ray microscopy is a promising tool to advance the study of hydrated interfaces between minerals and bacteria, particularly in cases where the structure of bacterial biofilms needs to be maintained.

Getting complete genomes from complex samples using nanopore sequencing

DEFF Research Database (Denmark)

Kirkegaard, Rasmus Hansen; Karst, Søren Michael; Albertsen, Mads

Short read sequencing and metagenomic binning workflows have made it possible to extract bacterial genome bins from environmental microbial samples containing hundreds to thousands of different species. However, these genome bins often do not represent complete genomes, as they are mostly...... fragmented, incomplete and often contaminated with foreign DNA and with no robust strategies to validate the quality. The value of these `draft genomes` have limited, lasting value to the scientific community, as gene synteny is broken and the uncertainty of what is missing. The genetic material most often...... missed is important multi-copy and/or conserved marker genes such as the 16S rRNA gene, as sequence micro-heterogeneity prevents assembly of these genes in the de novo assembly. We demonstrate that using nanopore long reads it is now possible to overcome these issues and make complete genomes from...

Systematic determination of the mosaic structure of bacterial genomes: species backbone versus strain-specific loops

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Gendrault-Jacquemard A

2005-07-01

Full Text Available Abstract Background Public databases now contain multitude of complete bacterial genomes, including several genomes of the same species. The available data offers new opportunities to address questions about bacterial genome evolution, a task that requires reliable fine comparison data of closely related genomes. Recent analyses have shown, using pairwise whole genome alignments, that it is possible to segment bacterial genomes into a common conserved backbone and strain-specific sequences called loops. Results Here, we generalize this approach and propose a strategy that allows systematic and non-biased genome segmentation based on multiple genome alignments. Segmentation analyses, as applied to 13 different bacterial species, confirmed the feasibility of our approach to discern the 'mosaic' organization of bacterial genomes. Segmentation results are available through a Web interface permitting functional analysis, extraction and visualization of the backbone/loops structure of documented genomes. To illustrate the potential of this approach, we performed a precise analysis of the mosaic organization of three E. coli strains and functional characterization of the loops. Conclusion The segmentation results including the backbone/loops structure of 13 bacterial species genomes are new and available for use by the scientific community at the URL: http://genome.jouy.inra.fr/mosaic.

Time-dependent effect of graphene on the structure, abundance, and function of the soil bacterial community.

Science.gov (United States)

Ren, Wenjie; Ren, Gaidi; Teng, Ying; Li, Zhengao; Li, Lina

2015-10-30

The increased application of graphene raises concerns about its environmental impact, but little information is available on the effect of graphene on the soil microbial community. This study evaluated the impact of graphene on the structure, abundance and function of the soil bacterial community based on quantitative real-time polymerase chain reaction (qPCR), pyrosequencing and soil enzyme activities. The results show that the enzyme activities of dehydrogenase and fluorescein diacetate (FDA) esterase and the biomass of the bacterial populations were transiently promoted by the presence of graphene after 4 days of exposure, but these parameters recovered completely after 21 days. Pyrosequencing analysis suggested a significant shift in some bacterial populations after 4 days, and the shift became weaker or disappeared as the exposure time increased to 60 days. During the entire exposure process, the majority of bacterial phylotypes remained unaffected. Some bacterial populations involved in nitrogen biogeochemical cycles and the degradation of organic compounds can be affected by the presence of graphene. Copyright © 2015 Elsevier B.V. All rights reserved.

Panamanian frog species host unique skin bacterial communities

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Lisa K. Belden

2015-10-01

Full Text Available Vertebrates, including amphibians, host diverse symbiotic microbes that contribute to host disease resistance. Globally, and especially in montane tropical systems, many amphibian species are threatened by a chytrid fungus, Batrachochytrium dendrobatidis (Bd, that causes a lethal skin disease. Bd therefore may be a strong selective agent on the diversity and function of the microbial communities inhabiting amphibian skin. In Panamá, amphibian population declines and the spread of Bd have been tracked. In 2012, we completed a field survey in Panamá to examine frog skin microbiota in the context of Bd infection. We focused on three frog species and collected two skin swabs per frog from a total of 136 frogs across four sites that varied from west to east in the time since Bd arrival. One swab was used to assess bacterial community structure using 16S rRNA amplicon sequencing and to determine Bd infection status, and one was used to assess metabolite diversity, as the bacterial production of anti-fungal metabolites is an important disease resistance function. The skin microbiota of the three Panamanian frog species differed in OTU (operational taxonomic unit, ~bacterial species community composition and metabolite profiles, although the pattern was less strong for the metabolites. Comparisons between frog skin bacterial communities from Panamá and the US suggest broad similarities at the phylum level, but key differences at lower taxonomic levels. In our field survey in Panamá, across all four sites, only 35 individuals (~26% were Bd infected. There was no clustering of OTUs or metabolite profiles based on Bd infection status and no clear pattern of west-east changes in OTUs or metabolite profiles across the four sites. Overall, our field survey data suggest that different bacterial communities might be producing broadly similar sets of metabolites across frog hosts and sites. Community structure and function may not be as tightly coupled in

Bacterial Cell Mechanics.

Science.gov (United States)

Auer, George K; Weibel, Douglas B

2017-07-25

Cellular mechanical properties play an integral role in bacterial survival and adaptation. Historically, the bacterial cell wall and, in particular, the layer of polymeric material called the peptidoglycan were the elements to which cell mechanics could be primarily attributed. Disrupting the biochemical machinery that assembles the peptidoglycan (e.g., using the β-lactam family of antibiotics) alters the structure of this material, leads to mechanical defects, and results in cell lysis. Decades after the discovery of peptidoglycan-synthesizing enzymes, the mechanisms that underlie their positioning and regulation are still not entirely understood. In addition, recent evidence suggests a diverse group of other biochemical elements influence bacterial cell mechanics, may be regulated by new cellular mechanisms, and may be triggered in different environmental contexts to enable cell adaptation and survival. This review summarizes the contributions that different biomolecular components of the cell wall (e.g., lipopolysaccharides, wall and lipoteichoic acids, lipid bilayers, peptidoglycan, and proteins) make to Gram-negative and Gram-positive bacterial cell mechanics. We discuss the contribution of individual proteins and macromolecular complexes in cell mechanics and the tools that make it possible to quantitatively decipher the biochemical machinery that contributes to bacterial cell mechanics. Advances in this area may provide insight into new biology and influence the development of antibacterial chemotherapies.

Bacterial diversity associated with the rotifer Brachionus plicatilis sp. complex determined by culture-dependent and -independent methods.

Science.gov (United States)

Ishino, Ryota; Iehata, Shunpei; Nakano, Miyo; Tanaka, Reiji; Yoshimatsu, Takao; Maeda, Hiroto

2012-03-01

The bacterial communities associated with rotifers (Brachionus plicatilis sp. complex) and their culture water were determined using culture-dependent and -independent methods (16S rRNA gene clone library). The bacterial communities determined by the culture-independent method were more diverse than those determined by the culture-dependent method. Although the culture-dependent method indicated the bacterial community of rotifers was relatively similar to that of the culture water, 16S rRNA gene clone library analyses revealed a great difference between the two microbiotas. Our results suggest that most bacteria associated with rotifers are not easily cultured using conventional methods, and that the microbiota of rotifers do not correspond with that of the culture water completely.

Bioinformatic analysis reveals high diversity of bacterial genes for laccase-like enzymes.

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Luka Ausec

Full Text Available Fungal laccases have been used in various fields ranging from processes in wood and paper industries to environmental applications. Although a few bacterial laccases have been characterized in recent years, prokaryotes have largely been neglected as a source of novel enzymes, in part due to the lack of knowledge about the diversity and distribution of laccases within Bacteria. In this work genes for laccase-like enzymes were searched for in over 2,200 complete and draft bacterial genomes and four metagenomic datasets, using the custom profile Hidden Markov Models for two- and three-domain laccases. More than 1,200 putative genes for laccase-like enzymes were retrieved from chromosomes and plasmids of diverse bacteria. In 76% of the genes, signal peptides were predicted, indicating that these bacterial laccases may be exported from the cytoplasm, which contrasts with the current belief. Moreover, several examples of putatively horizontally transferred bacterial laccase genes were described. Many metagenomic sequences encoding fragments of laccase-like enzymes could not be phylogenetically assigned, indicating considerable novelty. Laccase-like genes were also found in anaerobic bacteria, autotrophs and alkaliphiles, thus opening new hypotheses regarding their ecological functions. Bacteria identified as carrying laccase genes represent potential sources for future biotechnological applications.

Inactivation of bacterial biofilms using visible-light-activated unmodified ZnO nanorods

Science.gov (United States)

Aponiene, Kristina; Serevičius, Tomas; Luksiene, Zivile; Juršėnas, Saulius

2017-09-01

Various zinc oxide (ZnO) nanostructures are widely used for photocatalytic antibacterial applications. Since ZnO possesses a wide bandgap, it is believed that only UV light may efficiently assist bacterial inactivation, and diverse crystal lattice modifications should be applied in order to narrow the bandgap for efficient visible-light absorption. In this work we show that even unmodified ZnO nanorods grown by an aqueous chemical growth technique are found to possess intrinsic defects that can be activated by visible light (λ = 405 nm) and successfully applied for total inactivation of various highly resistant bacterial biofilms rather than more sensitive planktonic bacteria. Time-resolved fluorescence analysis has revealed that visible-light excitation creates long-lived charge carriers (τ > 1 μs), which might be crucial for destructive biochemical reactions achieving significant bacterial biofilm inactivation. ZnO nanorods covered with bacterial biofilms of Enterococcus faecalis MSCL 302 after illumination by visible light (λ = 405 nm) were inactivated by 2 log, and Listeria monocytogenes ATCL3C 7644 and Escherichia coli O157:H7 biofilms by 4 log. Heterogenic waste-water microbial biofilms, consisting of a mixed population of mesophilic bacteria after illumination with visible light were also completely destroyed.

UV radiation and organic matter composition shape bacterial functional diversity in sediments

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Ellard Roy Hunting

2013-10-01

Full Text Available AbstractUV radiation and organic matter (OM composition are known to influence the speciescomposition of bacterioplankton communities. Potential effects of UV radiation onbacterial communities residing in sediments remain completely unexplored to date.However, it has been demonstrated that UV radiation can reach the bottom of shallowwaters and wetlands and alter the OM composition of the sediment, suggesting thatUV radiation may be more important for sediment bacteria than previously anticipated.It is hypothesized here that exposure of shallow OMcontaining sediments to UVradiation induces OMsource dependant shifts in the functional composition ofsediment bacterial communities. This study therefore investigated the combinedinfluence of both UV radiation and OM composition on bacterial functional diversity inlaboratory sediments. Two different organic matter sources, labile and recalcitrantorganic matter (OM, were used and metabolic diversity was measured with BiologGN. Radiation exerted strong negative effects on the metabolic diversity in thetreatments containing recalcitrant OM, more than in treatments containing labile OM.The functional composition of the bacterial community also differed significantlybetween the treatments. Our findings demonstrate that a combined effect of UVradiation and OM composition shapes the functional composition of microbialcommunities developing in sediments, hinting that UV radiation may act as animportant sorting mechanism for bacterial communities and driver for bacterialfunctioning in shallow lakes and wetlands.

Reduced Set of Virulence Genes Allows High Accuracy Prediction of Bacterial Pathogenicity in Humans

Science.gov (United States)

Iraola, Gregorio; Vazquez, Gustavo; Spangenberg, Lucía; Naya, Hugo

2012-01-01

Although there have been great advances in understanding bacterial pathogenesis, there is still a lack of integrative information about what makes a bacterium a human pathogen. The advent of high-throughput sequencing technologies has dramatically increased the amount of completed bacterial genomes, for both known human pathogenic and non-pathogenic strains; this information is now available to investigate genetic features that determine pathogenic phenotypes in bacteria. In this work we determined presence/absence patterns of different virulence-related genes among more than finished bacterial genomes from both human pathogenic and non-pathogenic strains, belonging to different taxonomic groups (i.e: Actinobacteria, Gammaproteobacteria, Firmicutes, etc.). An accuracy of 95% using a cross-fold validation scheme with in-fold feature selection is obtained when classifying human pathogens and non-pathogens. A reduced subset of highly informative genes () is presented and applied to an external validation set. The statistical model was implemented in the BacFier v1.0 software (freely available at ), that displays not only the prediction (pathogen/non-pathogen) and an associated probability for pathogenicity, but also the presence/absence vector for the analyzed genes, so it is possible to decipher the subset of virulence genes responsible for the classification on the analyzed genome. Furthermore, we discuss the biological relevance for bacterial pathogenesis of the core set of genes, corresponding to eight functional categories, all with evident and documented association with the phenotypes of interest. Also, we analyze which functional categories of virulence genes were more distinctive for pathogenicity in each taxonomic group, which seems to be a completely new kind of information and could lead to important evolutionary conclusions. PMID:22916122

Does Intraoperative Systematic Bacterial Sampling During Complete Cytoreductive Surgery (CRS) with Hyperthermic Intraoperative Peritoneal Chemotherapy (HIPEC) Influence Postoperative Treatment? A New Predictive Factor for Postoperative Abdominal Infectious Complications.

Science.gov (United States)

Dazza, Marie; Schwarz, Lilian; Coget, Julien; Frebourg, Noelle; Wood, Gregory; Huet, Emmanuel; Bridoux, Valérie; Veber, Benoit; Tuech, Jean-Jacques

2016-12-01

Cytoreductive surgery (CRS) with hyperthermic intraperitoneal chemotherapy (HIPEC) is an emerging curative treatment option for patients with peritoneal carcinomatosis. It has a long-term survival benefit but is associated with high rates of morbidity, ranging from 12 % to 65 %, mainly due to infectious complications. We sought to evaluate the clinical relevance of routine intraoperative bacteriological sampling following CRS/HIPEC. Between November 2010 and December 2014, every patients receiving CRS/HIPEC were included. Three samples were routinely collected from standardized locations for intraperitoneal rinsing liquid bacteriological analysis (RLBA) after completion of HIPEC. The clinical and surgical features, bacteriological results, and short-term outcomes were retrospectively reviewed. The overall mortality and morbidity rates were 5 and 45 %, respectively. Among the 75 included patients, 40 % (n = 30) had at least one positive bacterial culture. Risk factors for a positive culture were colorectal resection (adjusted hazard ratio [HR] = 3.072, 95 % CI 1.843-8.004; p = 0.009) and blood loss >1000 mL (HR = 4.272, 95 % CI 1.080-18.141; p = 0.031). Among 26 (35 %) patients with abdominal infectious complications, 13 (17 %) experienced isolated complications. A positive RLBA result was independently associated with abdominal infectious complications (HR = 5.108, 95 % CI 1.220-16.336; p = 0.024) and isolated abdominal infectious complications (HR = 4.199, 95 % CI 1.064-15.961; p = 0.04). Forty percent of the RLBA samples obtained following CRS/HIPEC tested positive for bacteria. Bacterial sampling of rinsing liquid should be systematically performed. An aggressive and immediate antibiotic strategy needs to be evaluated.

Depletion of dendritic cells enhances innate anti-bacterial host defense through modulation of phagocyte homeostasis.

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Stella E Autenrieth

2012-02-01

Full Text Available Dendritic cells (DCs as professional antigen-presenting cells play an important role in the initiation and modulation of the adaptive immune response. However, their role in the innate immune response against bacterial infections is not completely defined. Here we have analyzed the role of DCs and their impact on the innate anti-bacterial host defense in an experimental infection model of Yersinia enterocolitica (Ye. We used CD11c-diphtheria toxin (DT mice to deplete DCs prior to severe infection with Ye. DC depletion significantly increased animal survival after Ye infection. The bacterial load in the spleen of DC-depleted mice was significantly lower than that of control mice throughout the infection. DC depletion was accompanied by an increase in the serum levels of CXCL1, G-CSF, IL-1α, and CCL2 and an increase in the numbers of splenic phagocytes. Functionally, splenocytes from DC-depleted mice exhibited an increased bacterial killing capacity compared to splenocytes from control mice. Cellular studies further showed that this was due to an increased production of reactive oxygen species (ROS by neutrophils. Adoptive transfer of neutrophils from DC-depleted mice into control mice prior to Ye infection reduced the bacterial load to the level of Ye-infected DC-depleted mice, suggesting that the increased number of phagocytes with additional ROS production account for the decreased bacterial load. Furthermore, after incubation with serum from DC-depleted mice splenocytes from control mice increased their bacterial killing capacity, most likely due to enhanced ROS production by neutrophils, indicating that serum factors from DC-depleted mice account for this effect. In summary, we could show that DC depletion triggers phagocyte accumulation in the spleen and enhances their anti-bacterial killing capacity upon bacterial infection.

Substrate Type and Free Ammonia Determine Bacterial Community Structure in Full-Scale Mesophilic Anaerobic Digesters Treating Cattle or Swine Manure

OpenAIRE

Li, Jiabao; Rui, Junpeng; Yao, Minjie; Zhang, Shiheng; Yan, Xuefeng; Wang, Yuanpeng; Yan, Zhiying; Li, Xiangzhen

2015-01-01

The microbial-mediated anaerobic digestion (AD) process represents an efficient biological process for the treatment of organic waste along with biogas harvest. Currently, the key factors structuring bacterial communities and the potential core and unique bacterial populations in manure anaerobic digesters are not completely elucidated yet. In this study, we collected sludge samples from 20 full-scale anaerobic digesters treating cattle or swine manure, and investigated the variations of bact...

Functional Potential of Bacterial Communities using Gene Context Information

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Anwesha Mohapatra

2017-12-01

Full Text Available Estimation of the functional potential of a bacterial genome can be determined by accurate annotation of its metabolic pathways. Existing homology based methods for pathway annotation fail to account for homologous genes that participate in multiple pathways, causing overestimation of gene copy number. Mere presence of constituent genes of a candidate pathway which are dispersed on a genome often results in incorrect annotation, thereby leading to erroneous gene abundance and pathway estimation. Clusters of evolutionarily conserved coregulated genes are characteristic features in bacterial genomes and their spatial arrangement in the genome is constrained by the pathway encoded by them. Thus, in order to improve the accuracy of pathway prediction, it is important to augment homology based annotation with gene organization information. In this communication, we present a methodology considering prioritization of gene context for improved pathway annotation. Extensive literature mining was performed to confirm conserved juxtaposed arrangement of gene components of various pathways. Our method was utilized to identify and analyse the functional potential of all available completely sequenced bacterial genomes. The accuracy of the predicted gene clusters and their importance in metabolic pathways will be demonstrated using a few case studies. One of such case study corresponds to butyrate production pathways in gut bacteria where it was observed that gut pathogens and commensals possess a distinct set of pathway components. In another example, we will demonstrate how our methodology improves the prediction accuracy of carbohydrate metabolic potential in human microbial communities. Applicability of our method for estimation of functional potential in bacterial communities present in diverse environments will also be illustrated.

Efficacy of zinc as an antibacterial agent against enteric bacterial pathogens

International Nuclear Information System (INIS)

Faiz, U.; Butt, T.; Hussain, W.; Hanif, F.

2011-01-01

Background: Diarrhoea is a serious threat all over the world with great economic implications especially evident in the developing world. This study was aimed at determining in vitro efficacy of Zinc (Zn) against common enteric bacterial pathogens. Method: A total of 100 bacterial enteric pathogens: Salmonellae (n=16), enteropathogenic Escherichia coli (EPEC) (n=26), Shigellae (n=28) and Vibrio cholerae (n=30) were isolated from diarrhoeal stool specimens at Department of Microbiology, Armed Forces Institute of Pathology Rawalpindi during April 2009 to Jan 2010. These isolates were tested against various concentrations of Zn supplemented in Mueller Hinton (MH) agar using a multipoint inoculator. A minimum inhibitory concentration of active Zn in ZnSO/sub 4/.7H/sub 2/O ranging from 0.03 mg/ml to 1 mg/ml was used. Results: Zn completely inhibited the growth of all the tested pathogens and most of them were inhibited at a concentration of 0.06 mg/ml to 0.5 mg/ml of Zn. Conclusions: Zinc has an excellent antibacterial activity against enteric bacterial pathogens common in our setup which may provide basis for treatment of diarrhoea. Clinical study based on these findings is recommended. (author)

Bacterial vaginosis in pregnant adolescents: proinflammatory cytokine and bacterial sialidase profile. Cross-sectional study

Directory of Open Access Journals (Sweden)

Carolina Sanitá Tafner Ferreira

Full Text Available ABSTRACT CONTEXT AND OBJECTIVE: Bacterial vaginosis occurs frequently in pregnancy and increases susceptibility to sexually transmitted infections (STI. Considering that adolescents are disproportionally affected by STI, the aim of this study was to evaluate the cervicovaginal levels of interleukin (IL-1 beta, IL-6, IL-8 and bacterial sialidase in pregnant adolescents with bacterial vaginosis. DESIGN AND SETTING: Cross-sectional study at mother and child referral units in Belém, Pará, Brazil. METHODS: Vaginal samples from 168 pregnant adolescents enrolled were tested for trichomoniasis and candidiasis. Their vaginal microbiota was classified according to the Nugent criteria (1991 as normal, intermediate or bacterial vaginosis. Cervical infection due to Chlamydia trachomatisand Neisseria gonorrhoeae was also assessed. Cytokine and sialidase levels were measured, respectively, using enzyme-linked immunosorbent assays and MUAN conversion in cervicovaginal lavages. Forty-eight adolescents (28.6% were excluded because they tested positive for some of the infections investigated. The remaining 120 adolescents were grouped according to vaginal flora type: normal (n = 68 or bacterial vaginosis (n = 52. Their cytokine and sialidase levels were compared between the groups using the Mann-Whitney test (P < 0.05. RESULTS: The pregnant adolescents with bacterial vaginosis had higher levels of IL-1 beta, IL-6 and IL-8 (P < 0.05. Sialidase was solely detected in 35 adolescents (67.2% with bacterial vaginosis. CONCLUSIONS: Not only IL-1 beta and sialidase levels, but also IL-6 and IL-8 levels are higher in pregnant adolescents with bacterial vaginosis, thus indicating that this condition elicits a more pronounced inflammatory response in this population, which potentially increases vulnerability to STI acquisition.

Prostatitis-bacterial - self-care

Science.gov (United States)

... this page: //medlineplus.gov/ency/patientinstructions/000395.htm Prostatitis - bacterial - self-care To use the sharing features ... enable JavaScript. You have been diagnosed with bacterial prostatitis . This is an infection of the prostate gland. ...

Evolution of bacterial community during bioremediation of PAHs in a coal tar contaminated soil

Energy Technology Data Exchange (ETDEWEB)

Lors, C.; Ryngaert, A.; Perie, F.; Diels, L.; Damidot, D. [University of Lille, Lille (France)

2010-11-15

The monitoring of a windrow treatment applied to soil contaminated by mostly 2, 3- and 4-ring PAHs produced by coal tar distillation was performed by following the evolution of both PAH concentration and the bacterial community. Total and PAH-degrading bacterial community structures were followed by 165 rRNA PCR-DGGE in parallel with quantification by bacterial counts and 16 PAH measurements. Six months of biological treatment led to a strong decrease in 2-, 3- and 4-ring PAH concentrations (98, 97 and 82%, respectively). This result was associated with the activity of bacterial PAH-degraders belonging mainly to the Gamma proteobacteria, in particular the Enterobacteria and Pseudomonas genera which were detected over the course of the treatment. This group was considered to be a good bioindicator to determine the potential PAH biodegradation of contaminated soil. Conversely other species like the Beta proteobacteria were detected after 3 months when 2-, 3- and 4-ring PAHs were almost completely degraded. Thus presence of the Beta proteobacteria group could be considered a good candidate indicator to estimate the endpoint of biotreatment of this type of PAH contaminated soil.

Uji Biologis Konsumsi Pakan, Populasi Bakteri Rumen dan pH Pellet Complete Calf Starter pada Pedet Friesian Holstein Pra Sapih

Directory of Open Access Journals (Sweden)

Nadia Maharani

2015-04-01

Full Text Available (Biological test feed intake, population rumen bacteria and ph pellet complete calf starter friesian holstein on pre weaning calf  ABSTRACT. The study aims to assess the quality of the formula Complete Calf Starter (CCS with 5% molasses instead of milk to the development of rumen microbial calf Holstein Friesian (HF pre-weaning. The material used is 20 head calf FH pre weaning age of 2 weeks. Feed intake data taken from 20 respondents consisted of 16 females and 4 calf tail male calf. Data rumen bacterial populations and pH were taken from 5 head of cattle slaughtered at the age of 2 weeks (one tail, 4 weeks (2-tailed and 6 weeks (2-tailed. The study was designed as a descriptive non-parametric. Parameters measured were rumen bacterial populations, pH and feed intake. The results showed the average consumption of dry matter (DM and CCS calf milk FH ages 2, 4, 6 weeks respectively at 506, 517, 528 grams. Rumen bacterial populations in calves aged 2, 4, and 6 weeks of 80x106, 45x106 and 19x106 kol/m. ruminal pH in calves aged 2, 4 and 6 weeks was 5.71, 5.36 and 5.55. Biological test showed that the use of complete calf starter (CCS in the form of pellets FH calves at the age of 2 weeks to stimulate the development of the rumen (feed intake, the population of bacteria and pH but not in calves aged 4 and 6 weeks. This is because the number of bacterial populations declined due to impaired absorption is impaired absorption of VFA marked low rumen pH.

Monitoring of oil pollution at Gemsa Bay and bioremediation capacity of bacterial isolates with biosurfactants and nanoparticles.

Science.gov (United States)

El-Sheshtawy, H S; Khalil, N M; Ahmed, W; Abdallah, R I

2014-10-15

Fifteen crude oil-degrading bacterial isolates were isolated from an oil-polluted area in Gemsa Bay, Red Sea, Egypt. Two bacterial species showed the highest growth rate on crude oil hydrocarbons. From an analysis of 16S rRNA sequences, these isolates were identified as Pseudomonas xanthomarina KMM 1447 and Pseudomonas stutzeri ATCC 17588. Gas Chromatographic (GC) analysis of the crude oil remaining in the culture medium after one week at 30°C showed that the optimum biodegradation of crude petroleum oil was demonstrated at 50% in medium containing biosurfactant with two types of nanoparticles separately and two bacterial species. The complete degradation of some different members of polyaromatics and the percentage biodegradation of other polyaromatics increased in microcosm containing two different types of nanoparticles with biosurfactant after 7 days. In conclusion, these bacterial strains may be useful for the bioremediation process in the Gemsa Bay, Red Sea decreasing oil pollution in this marine ecosystem. Copyright © 2014 Elsevier Ltd. All rights reserved.

Towards large-scale FAME-based bacterial species identification using machine learning techniques.

Science.gov (United States)

Slabbinck, Bram; De Baets, Bernard; Dawyndt, Peter; De Vos, Paul

2009-05-01

In the last decade, bacterial taxonomy witnessed a huge expansion. The swift pace of bacterial species (re-)definitions has a serious impact on the accuracy and completeness of first-line identification methods. Consequently, back-end identification libraries need to be synchronized with the List of Prokaryotic names with Standing in Nomenclature. In this study, we focus on bacterial fatty acid methyl ester (FAME) profiling as a broadly used first-line identification method. From the BAME@LMG database, we have selected FAME profiles of individual strains belonging to the genera Bacillus, Paenibacillus and Pseudomonas. Only those profiles resulting from standard growth conditions have been retained. The corresponding data set covers 74, 44 and 95 validly published bacterial species, respectively, represented by 961, 378 and 1673 standard FAME profiles. Through the application of machine learning techniques in a supervised strategy, different computational models have been built for genus and species identification. Three techniques have been considered: artificial neural networks, random forests and support vector machines. Nearly perfect identification has been achieved at genus level. Notwithstanding the known limited discriminative power of FAME analysis for species identification, the computational models have resulted in good species identification results for the three genera. For Bacillus, Paenibacillus and Pseudomonas, random forests have resulted in sensitivity values, respectively, 0.847, 0.901 and 0.708. The random forests models outperform those of the other machine learning techniques. Moreover, our machine learning approach also outperformed the Sherlock MIS (MIDI Inc., Newark, DE, USA). These results show that machine learning proves very useful for FAME-based bacterial species identification. Besides good bacterial identification at species level, speed and ease of taxonomic synchronization are major advantages of this computational species

Effect of alginate chemical disinfection on bacterial count over gypsum cast.

Science.gov (United States)

Haralur, Satheesh B; Al-Dowah, Omir S; Gana, Naif S; Al-Hytham, Abdullah

2012-05-01

To evaluate the efficacy of sodium hypochlorite (1 : 10) and iodophor disinfectants on alginate impressions along with their effect on the survived bacterium count on the gypsum cast. Four alginate impression on each dentate patients were made, of which Group I were not washed or disinfected, Group II impressions were merely washed with water, Group III were disinfected by spraying with sodium hypochlorite (1 : 10), Group IV were disinfected with iodophor (1 : 213). Gypsum cast (type III) were made from all the impression. Impressions and gypsum cast were swabbed in mid palatal region for bacterial culture. Bacterial colony counting done after 3 days of incubation at 37℃ in blood agar media. The data obtained was analyzed by one way ANOVA test at a significant difference level of 0.05. Group I and Group II showed significantly more bacteria compared to Group III and Group IV. Bacterial colonies on the alginate impression and gypsum cast in group disinfected with Sodium hypochlorite (1 : 10) were 0.18, 0.82 respectively compared to group treated with iodophor (1 : 213). There was an increase in bacterial count on dental cast compared to source alginate impressions. Sodium hypochlorite (1 : 10) was found to be better disinfectant for alginate impression. There was an indication of increase in number of bacteria from alginate impression to making of dental cast. Additional gypsum cast disinfectant procedures need to be encouraged to completely eliminate cross infection to dental laboratory.

[Spontaneous bacterial peritonitis].

Science.gov (United States)

Velkey, Bálint; Vitális, Eszter; Vitális, Zsuzsanna

2017-01-01

Spontaneous bacterial peritonitis occurs most commonly in cirrhotic patients with ascites. Pathogens get into the circulation by intestinal translocation and colonize in peritoneal fluid. Diagnosis of spontaneous bacterial peritonitis is based on elevated polymorphonuclear leukocyte count in the ascites (>0,25 G/L). Ascites culture is often negative but aids to get information about antibiotic sensitivity in positive cases. Treatment in stable patient can be intravenous then orally administrated ciprofloxacin or amoxicillin/clavulanic acid, while in severe cases intravenous III. generation cephalosporin. Nosocomial spontaneous bacterial peritonitis often caused by Gram-positive bacteria and multi-resistant pathogens can also be expected thus carbapenem should be the choice of the empiric treatment. Antibiotic prophylaxis should be considered. Norfloxacin is used most commonly, but changes are expected due to increase in quinolone resistance. As a primary prophylaxis, a short-term antibiotic treatment is recommended after gastrointestinal bleeding for 5 days, while long-term prophylaxis is for patients with low ascites protein, and advanced disease (400 mg/day). Secondary prophylaxis is recommended for all patients recovered from spontaneous bacterial peritonitis. Due to increasing antibiotic use of antibiotics prophylaxis is debated to some degree. Orv. Hetil., 2017, 158(2), 50-57.

Effect of short-term hyperventilation on cerebral blood flow autoregulation in patients with acute bacterial meningitis

DEFF Research Database (Denmark)

Møller, Kirsten

2000-01-01

BACKGROUND AND PURPOSE: Cerebral blood flow (CBF) autoregulation is impaired in patients with acute bacterial meningitis: this may be caused by cerebral arteriolar dilatation. We tested the hypothesis that CBF autoregulation is recovered by acute mechanical hyperventilation in 9 adult patients...... with acute bacterial meningitis. METHODS: Norepinephrine was infused to increase mean arterial pressure (MAP) 30 mm Hg from baseline. Relative changes in CBF were concomitantly recorded by transcranial Doppler ultrasonography of the middle cerebral artery, measuring mean flow velocity (V...... completely during hyperventilation. The slope of the autoregulation curve decreased during hyperventilation compared with normoventilation (Pmeningitis, indicating...

Rifaximin has minor effects on bacterial composition, inflammation and bacterial translocation in cirrhosis

DEFF Research Database (Denmark)

Kimer, Nina; Pedersen, Julie S.; Tavenier, Juliette

2018-01-01

.4), and MELD score 12 (±3.9). Patients received rifaximin 550 mg BD (n=36) or placebo BD (n=18). Blood and faecal (n=15) sampling were conducted at baseline and after four weeks. Bacterial DNA in blood was determined by real-time qPCR 16S rRNA gene quantification. Bacterial composition in faeces was analysed......BACKGROUND & AIMS: Decompensated cirrhosis is characterized by disturbed haemodynamics, immune dysfunction, and high risk of infections. Translocation of viable bacteria and bacterial products from the gut to the blood is considered a key driver in this process. Intestinal decontamination...... with rifaximin may reduce bacterial translocation (BT) and decrease inflammation. In a randomized, placebo-controlled trial investigated the effects of rifaximin on inflammation and BT in decompensated cirrhosis. METHODS: Fifty-four out-patients with cirrhosis and ascites were randomized, mean age 56 years (±8...

Prevention of bacterial adhesion

DEFF Research Database (Denmark)

Klemm, Per; Vejborg, Rebecca Munk; Hancock, Viktoria

2010-01-01

. As such, adhesion represents the Achilles heel of crucial pathogenic functions. It follows that interference with adhesion can reduce bacterial virulence. Here, we illustrate this important topic with examples of techniques being developed that can inhibit bacterial adhesion. Some of these will become...

Bacterial vaginosis among African American women who have sex with women.

Science.gov (United States)

Muzny, Christina A; Sunesara, Imran R; Austin, Erika L; Mena, Leandro A; Schwebke, Jane R

2013-09-01

Bacterial vaginosis (BV) is a frequent cause of vaginal discharge that may be more common among women reporting sex with women (WSW). The objective of this study was to determine the prevalence of BV and predictors of infection among a sample of African American WSW. African American WSW aged 18 years or older presenting to the Mississippi State Department of Health STD Clinic between 2009 and 2010 and reporting a history of sexual activity with a female partner during the preceding year were invited to participate. A survey on sexual history and sexual behavior characteristics was completed. Bacterial vaginosis was defined by Amsel criteria. Associations with participant characteristics were determined using logistic regression analysis. Bacterial vaginosis was diagnosed in 93 (47.4%) of 196 women. Bisexual identity (odds ratio [OR], 1.94; 95% confidence interval [CI], 1.03-3.66; P = 0.04), douching within the past 30 days (OR, 1.93; 95% CI, 1.09-3.43; P = 0.02), age 18 years or less at first sexual encounter with a female partner (OR, 3.18; 95% CI, 1.16-8.71; P = 0.02), and report of more than 1 lifetime male sexual partners (OR, 1.94; 95% CI, 1.01-3.74; P = 0.04) were significant predictors of BV in bivariate analysis. Bacterial vaginosis was less common among women who reported more than 1 lifetime female sexual partner (OR, 0.26; 95% CI, 0.09-0.76; P = 0.01). In multivariable analysis, age 18 years or less at first sex with a female partner approached significance, while report of 1 lifetime female sexual partner remained strongly associated with BV. Bacterial vaginosis was common in this sample of African American WSW and significantly associated with report of 1 lifetime female sexual partner.

Corticosteroids for bacterial keratitis: the Steroids for Corneal Ulcers Trial (SCUT).

Science.gov (United States)

Srinivasan, Muthiah; Mascarenhas, Jeena; Rajaraman, Revathi; Ravindran, Meenakshi; Lalitha, Prajna; Glidden, David V; Ray, Kathryn J; Hong, Kevin C; Oldenburg, Catherine E; Lee, Salena M; Zegans, Michael E; McLeod, Stephen D; Lietman, Thomas M; Acharya, Nisha R

2012-02-01

To determine whether there is a benefit in clinical outcomes with the use of topical corticosteroids as adjunctive therapy in the treatment of bacterial corneal ulcers. Randomized, placebo-controlled, double-masked, multicenter clinical trial comparing prednisolone sodium phosphate, 1.0%, to placebo as adjunctive therapy for the treatment of bacterial corneal ulcers. Eligible patients had a culture-positive bacterial corneal ulcer and received topical moxifloxacin for at least 48 hours before randomization. The primary outcome was best spectacle-corrected visual acuity (BSCVA) at 3 months from enrollment. Secondary outcomes included infiltrate/scar size, reepithelialization, and corneal perforation. Between September 1, 2006, and February 22, 2010, 1769 patients were screened for the trial and 500 patients were enrolled. No significant difference was observed in the 3-month BSCVA (-0.009 logarithm of the minimum angle of resolution [logMAR]; 95% CI, -0.085 to 0.068; P = .82), infiltrate/scar size (P = .40), time to reepithelialization (P = .44), or corneal perforation (P > .99). A significant effect of corticosteroids was observed in subgroups of baseline BSCVA (P = .03) and ulcer location (P = .04). At 3 months, patients with vision of counting fingers or worse at baseline had 0.17 logMAR better visual acuity with corticosteroids (95% CI, -0.31 to -0.02; P = .03) compared with placebo, and patients with ulcers that were completely central at baseline had 0.20 logMAR better visual acuity with corticosteroids (-0.37 to -0.04; P = .02). We found no overall difference in 3-month BSCVA and no safety concerns with adjunctive corticosteroid therapy for bacterial corneal ulcers. Adjunctive topical corticosteroid use does not improve 3-month vision in patients with bacterial corneal ulcers. clinicaltrials.gov Identifier: NCT00324168.

Bacteriële meningitis

NARCIS (Netherlands)

Brouwer, M. C.; van de Beek, D.

2012-01-01

Bacterial meningitis is a severe disease which affects 35.000 Europeans each year and has a mortality rate of about 20%. During the past 25 years the epidemiology of bacterial meningitis has changed significantly due to the implementation of vaccination against Haemophilus influenzae, Neisseria

Postviral Complications: Bacterial Pneumonia.

Science.gov (United States)

Prasso, Jason E; Deng, Jane C

2017-03-01

Secondary bacterial pneumonia after viral respiratory infection remains a significant source of morbidity and mortality. Susceptibility is mediated by a variety of viral and bacterial factors, and complex interactions with the host immune system. Prevention and treatment strategies are limited to influenza vaccination and antibiotics/antivirals respectively. Novel approaches to identifying the individuals with influenza who are at increased risk for secondary bacterial pneumonias are urgently needed. Given the threat of further pandemics and the heightened prevalence of these viruses, more research into the immunologic mechanisms of this disease is warranted with the hope of discovering new potential therapies. Published by Elsevier Inc.

Biodegradability of bacterial surfactants.

Science.gov (United States)

Lima, Tânia M S; Procópio, Lorena C; Brandão, Felipe D; Carvalho, André M X; Tótola, Marcos R; Borges, Arnaldo C

2011-06-01

This work aimed at evaluating the biodegradability of different bacterial surfactants in liquid medium and in soil microcosms. The biodegradability of biosurfactants by pure and mixed bacterial cultures was evaluated through CO(2) evolution. Three bacterial strains, Acinetobacter baumanni LBBMA ES11, Acinetobacter haemolyticus LBBMA 53 and Pseudomonas sp. LBBMA 101B, used the biosurfactants produced by Bacillus sp. LBBMA 111A (mixed lipopeptide), Bacillus subtilis LBBMA 155 (lipopeptide), Flavobacterium sp. LBBMA 168 (mixture of flavolipids), Dietzia Maris LBBMA 191(glycolipid) and Arthrobacter oxydans LBBMA 201(lipopeptide) as carbon sources in minimal medium. The synthetic surfactant sodium dodecyl sulfate (SDS) was also mineralized by these microorganisms, but at a lower rate. CO(2) emitted by a mixed bacterial culture in soil microcosms with biosurfactants was higher than in the microcosm containing SDS. Biosurfactant mineralization in soil was confirmed by the increase in surface tension of the soil aqueous extracts after incubation with the mixed bacterial culture. It can be concluded that, in terms of biodegradability and environmental security, these compounds are more suitable for applications in remediation technologies in comparison to synthetic surfactants. However, more information is needed on structure of biosurfactants, their interaction with soil and contaminants and scale up and cost for biosurfactant production.

Complete genome sequence of the myxobacterium Sorangium cellulosum

DEFF Research Database (Denmark)

Schneiker, S; Perlova, O; Kaiser, O

2007-01-01

The genus Sorangium synthesizes approximately half of the secondary metabolites isolated from myxobacteria, including the anti-cancer metabolite epothilone. We report the complete genome sequence of the model Sorangium strain S. cellulosum Soce56, which produces several natural products and has...... morphological and physiological properties typical of the genus. The circular genome, comprising 13,033,779 base pairs, is the largest bacterial genome sequenced to date. No global synteny with the genome of Myxococcus xanthus is apparent, revealing an unanticipated level of divergence between...... these myxobacteria. A large percentage of the genome is devoted to regulation, particularly post-translational phosphorylation, which probably supports the strain's complex, social lifestyle. This regulatory network includes the highest number of eukaryotic protein kinase-like kinases discovered in any organism...

Code-assisted discovery of TAL effector targets in bacterial leaf streak of rice reveals contrast with bacterial blight and a novel susceptibility gene.

Directory of Open Access Journals (Sweden)

Raul A Cernadas

2014-02-01

Full Text Available Bacterial leaf streak of rice, caused by Xanthomonas oryzae pv. oryzicola (Xoc is an increasingly important yield constraint in this staple crop. A mesophyll colonizer, Xoc differs from X. oryzae pv. oryzae (Xoo, which invades xylem to cause bacterial blight of rice. Both produce multiple distinct TAL effectors, type III-delivered proteins that transactivate effector-specific host genes. A TAL effector finds its target(s via a partially degenerate code whereby the modular effector amino acid sequence identifies nucleotide sequences to which the protein binds. Virulence contributions of some Xoo TAL effectors have been shown, and their relevant targets, susceptibility (S genes, identified, but the role of TAL effectors in leaf streak is uncharacterized. We used host transcript profiling to compare leaf streak to blight and to probe functions of Xoc TAL effectors. We found that Xoc and Xoo induce almost completely different host transcriptional changes. Roughly one in three genes upregulated by the pathogens is preceded by a candidate TAL effector binding element. Experimental analysis of the 44 such genes predicted to be Xoc TAL effector targets verified nearly half, and identified most others as false predictions. None of the Xoc targets is a known bacterial blight S gene. Mutational analysis revealed that Tal2g, which activates two genes, contributes to lesion expansion and bacterial exudation. Use of designer TAL effectors discriminated a sulfate transporter gene as the S gene. Across all targets, basal expression tended to be higher than genome-average, and induction moderate. Finally, machine learning applied to real vs. falsely predicted targets yielded a classifier that recalled 92% of the real targets with 88% precision, providing a tool for better target prediction in the future. Our study expands the number of known TAL effector targets, identifies a new class of S gene, and improves our ability to predict functional targeting.

Bacterial community analysis of contaminant soils from Chernobyl

International Nuclear Information System (INIS)

Sergeant, C.; Vesvres, M.H.; Chapon, V.; Berthomieu, C.; Piette, L.; Le Marrec, C.; Coppin, F.; Fevrier, L.; Martin-Garin, A.

2010-01-01

Complete text of publication follows: Shortly after the Chernobyl accident in 1986, vegetation, contaminated soil and other radioactive debris were buried in situ in trenches. The aims of this work are to analyse the structure of bacterial communities evolving in this environment since 20 years, and to evaluate the potential role of microorganisms in radionuclide migration in soils. Therefore, soil samples exhibiting contrasted radionuclides content were collected in and around the trench number 22. Bacterial communities were examined using a genetic fingerprinting method that allowed a comparative profiling of the samples (DGGE), with universal and group-specific PCR primers. Our results indicate that Chernobyl soil samples host a wide diversity of Bacteria, with stable patterns for Firmicutes and Actinobacteria and more variable for Proteobacteria. A collection of 650 aerobic and anaerobic culturable isolates was also constructed. A phylogenetic analysis of 250 heterotrophic aerobic isolates revealed that 5 phyla are represented: Beta-, Gamma-proteobacteria, Actinobacteria, Bacteroidetes and spore-forming Firmicutes, which is largely dominant. These collection will be screened for the presence of radionuclide-accumulating species in order to estimate the potential influence of microorganisms in radionuclides migration in soils

Molecular approaches for bacterial azoreductases

Directory of Open Access Journals (Sweden)

Montira Leelakriangsak

2013-12-01

Full Text Available Azo dyes are the dominant types of synthetic dyes, widely used in textiles, foods, leather, printing, tattooing, cosmetics, and pharmaceutical industries. Many microorganisms are able to decolorize azo dyes, and there is increasing interest in biological waste treatment methods. Bacterial azoreductases can cleave azo linkages (-N=N- in azo dyes, forming aromatic amines. This review mainly focuses on employing molecular approaches, including gene manipulation and recombinant strains, to study bacterial azoreductases. The construction of the recombinant protein by cloning and the overexpression of azoreductase is described. The mechanisms and function of bacterial azoreductases can be studied by other molecular techniques discussed in this review, such as RT-PCR, southern blot analysis, western blot analysis, zymography, and muta-genesis in order to understand bacterial azoreductase properties, function and application. In addition, understanding the regulation of azoreductase gene expression will lead to the systematic use of gene manipulation in bacterial strains for new strategies in future waste remediation technologies.

Succession of Bacterial Communities in a Seasonally Stratified Lake with an Anoxic and Sulfidic Hypolimnion

Directory of Open Access Journals (Sweden)

Muhe Diao

2017-12-01

Full Text Available Although bacteria play key roles in aquatic food webs and biogeochemical cycles, information on the seasonal succession of bacterial communities in lakes is still far from complete. Here, we report results of an integrative study on the successional trajectories of bacterial communities in a seasonally stratified lake with an anoxic hypolimnion. The bacterial community composition of epilimnion, metalimnion, and hypolimnion diverged during summer stratification and converged when the lake was mixed. In contrast, bacterial communities in the sediment remained relatively stable over the year. Phototrophic Cyanobacteria and heterotrophic Actinobacteria, Alphaproteobacteria and Planktomycetes were abundant in the aerobic epilimnion, Gammaproteobacteria (mainly Chromatiaceae dominated in the metalimnion, and Chlorobi, Betaproteobacteria, Deltaproteobacteria, and Firmicutes were abundant in the anoxic sulfidic hypolimnion. Anoxic but nonsulfidic conditions expanded to the surface layer during fall turnover, when the epilimnion, metalimnion and upper hypolimnion mixed. During this period, phototrophic sulfur bacteria (Chromatiaceae and Chlorobi disappeared, Polynucleobacter (Betaproteobacteria and Methylobacter (Gammaproteobacteria spread out from the former meta- and hypolimnion to the surface layer, and Epsilonproteobacteria dominated in the bottom water layer. Cyanobacteria and Planktomycetes regained dominance in early spring, after the oxygen concentration was restored by winter mixing. In total, these results show large spatio-temporal changes in bacterial community composition, especially during transitions from oxic to anoxic and from sulfidic to nonsulfidic conditions.

Helicobacter pylori infection: An overview of bacterial virulence factors and pathogenesis

Directory of Open Access Journals (Sweden)

Cheng-Yen Kao

2016-02-01

Full Text Available Helicobacter pylori pathogenesis and disease outcomes are mediated by a complex interplay between bacterial virulence factors, host, and environmental factors. After H. pylori enters the host stomach, four steps are critical for bacteria to establish successful colonization, persistent infection, and disease pathogenesis: (1 Survival in the acidic stomach; (2 movement toward epithelium cells by flagella-mediated motility; (3 attachment to host cells by adhesins/receptors interaction; (4 causing tissue damage by toxin release. Over the past 20 years, the understanding of H. pylori pathogenesis has been improved by studies focusing on the host and bacterial factors through epidemiology researches and molecular mechanism investigations. These include studies identifying the roles of novel virulence factors and their association with different disease outcomes, especially the bacterial adhesins, cag pathogenicity island, and vacuolating cytotoxin. Recently, the development of large-scale screening methods, including proteomic, and transcriptomic tools, has been used to determine the complex gene regulatory networks in H. pylori. In addition, a more available complete genomic database of H. pylori strains isolated from patients with different gastrointestinal diseases worldwide is helpful to characterize this bacterium. This review highlights the key findings of H. pylori virulence factors reported over the past 20 years.

Report on assessment of the mechanism of bacterially assisted oxidation of pyritic uranium tailings

International Nuclear Information System (INIS)

Halbert, B.B.; Scharer, J.M.; Knapp, R.A.

1984-07-01

The oxidation of pyritic minerals has been shown to be catalyzed by the presence of iron- and sulphur-oxidizing bacteria. Thiobacillus ferroxidans plays the most significant role in the formation and propagation of acidic conditions. Optimum growth conditions for the T. ferroxidans occurs at a temperature of 35 degrees C and pH of 2 to 3. Bacterially assisted oxidation of pyrite involves both direct and indirect contact mechanisms. The direct contact mechanism entails enzymatic oxidation of the insoluble sulphide moiety. The indirect mechanism involves bacterial oxidation of the dissolved ferrous component to the ferric state. The ferric iron, in turn, acts as the prime oxidant of pyrite and is reduced to ferrous iron. The re-oxidation of the dissolved ferrous component which is catalyzed by bacterial activity, completes the cyclic process. The rate of bacterial oxidation is affected by: the geochemistry and reactivity of the pyritic material; the amount of pyrite present in the waste material and the exposed surface area of the pyritic component; the availability of oxygen and carbon dioxide; the pH and temperature of the leach solution; and the presence (or absence) of organic inhibitors. Of the above factors, oxygen has been frequently identified as the rate limiting reactant in tailings

A Phosphorylation Switch on Lon Protease Regulates Bacterial Type III Secretion System in Host

Directory of Open Access Journals (Sweden)

Xiaofeng Zhou

2018-01-01

Full Text Available Most pathogenic bacteria deliver virulence factors into host cytosol through type III secretion systems (T3SS to perturb host immune responses. The expression of T3SS is often repressed in rich medium but is specifically induced in the host environment. The molecular mechanisms underlying host-specific induction of T3SS expression is not completely understood. Here we demonstrate in Xanthomonas citri that host-induced phosphorylation of the ATP-dependent protease Lon stabilizes HrpG, the master regulator of T3SS, conferring bacterial virulence. Ser/Thr/Tyr phosphoproteome analysis revealed that phosphorylation of Lon at serine 654 occurs in the citrus host. In rich medium, Lon represses T3SS by degradation of HrpG via recognition of its N terminus. Genetic and biochemical data indicate that phosphorylation at serine 654 deactivates Lon proteolytic activity and attenuates HrpG proteolysis. Substitution of alanine for Lon serine 654 resulted in repression of T3SS gene expression in the citrus host through robust degradation of HrpG and reduced bacterial virulence. Our work reveals a novel mechanism for distinct regulation of bacterial T3SS in different environments. Additionally, our data provide new insight into the role of protein posttranslational modification in the regulation of bacterial virulence.

The complete structure of the large subunit of the mammalian mitochondrial ribosome.

Science.gov (United States)

Greber, Basil J; Boehringer, Daniel; Leibundgut, Marc; Bieri, Philipp; Leitner, Alexander; Schmitz, Nikolaus; Aebersold, Ruedi; Ban, Nenad

2014-11-13

Mitochondrial ribosomes (mitoribosomes) are extensively modified ribosomes of bacterial descent specialized for the synthesis and insertion of membrane proteins that are critical for energy conversion and ATP production inside mitochondria. Mammalian mitoribosomes, which comprise 39S and 28S subunits, have diverged markedly from the bacterial ribosomes from which they are derived, rendering them unique compared to bacterial, eukaryotic cytosolic and fungal mitochondrial ribosomes. We have previously determined at 4.9 Å resolution the architecture of the porcine (Sus scrofa) 39S subunit, which is highly homologous to the human mitoribosomal large subunit. Here we present the complete atomic structure of the porcine 39S large mitoribosomal subunit determined in the context of a stalled translating mitoribosome at 3.4 Å resolution by cryo-electron microscopy and chemical crosslinking/mass spectrometry. The structure reveals the locations and the detailed folds of 50 mitoribosomal proteins, shows the highly conserved mitoribosomal peptidyl transferase active site in complex with its substrate transfer RNAs, and defines the path of the nascent chain in mammalian mitoribosomes along their idiosyncratic exit tunnel. Furthermore, we present evidence that a mitochondrial tRNA has become an integral component of the central protuberance of the 39S subunit where it architecturally substitutes for the absence of the 5S ribosomal RNA, a ubiquitous component of all cytoplasmic ribosomes.

Discovering Complete Quasispecies In Bacterial Genomes

OpenAIRE

Bertels, Frederic; Gokhale, Chaitanya; Traulsen, Arne

2017-01-01

Mobile genetic elements can be found in almost all genomes. Possibly the most common nonautonomous mobile genetic elements in bacteria are repetitive extragenic palindromic doublets forming hairpins (REPINs) that can occur hundreds of times within a genome. The sum of all REPINs in a genome can be viewed as an evolving population because REPINs replicate and mutate. In contrast to most other biological populations, we know the exact composition of the REPIN population and the sequence of each...

Complete genome sequence of Coraliomargarita akajimensis type strain (04OKA010-24T)

Energy Technology Data Exchange (ETDEWEB)

Mavromatis, Konstantinos; Abt, Birte; Brambilla, Evelyne; Lapidus, Alla; Copeland, Alex; Desphande, Shweta; Nolan, Matt; Lucas, Susan; Tice, Hope; Cheng, Jan-Fang; Han, Cliff; Detter, John C.; Woyke, Tanja; Goodwin, Lynne; Pitluck, Sam; Held, Brittany; Brettin, Thomas; Tapia, Roxanne; Ivanova, Natalia; Mikhailova, Natalia; Pati, Amrita; Liolios, Konstantinos; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Rohde, Manfred; G& #246; ker, Markus; Bristow, James; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Klenk, Hans-Peter; Kyrpides, Nikos C.

2010-06-25

Coraliomargarita akajimensis Yoon et al. 2007 the type species of the genus Coraliomargarita. C. akajimensis is an obligately aerobic, Gram-negative, non-spore-forming, non-motile, spherical bacterium which was isolated from seawater surrounding the hard coral Galaxea fascicularis. C. akajimensis organism is of special interest because of its phylogenetic position in a genomically purely studied area in the bacterial diversity. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a member of the family Puniceicoccaceae. The 3,750,771 bp long genome with its 3,137 protein-coding and 55 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

BPhyOG: An interactive server for genome-wide inference of bacterial phylogenies based on overlapping genes

Directory of Open Access Journals (Sweden)

Lin Kui

2007-07-01

Full Text Available Abstract Background Overlapping genes (OGs in bacterial genomes are pairs of adjacent genes of which the coding sequences overlap partly or entirely. With the rapid accumulation of sequence data, many OGs in bacterial genomes have now been identified. Indeed, these might prove a consistent feature across all microbial genomes. Our previous work suggests that OGs can be considered as robust markers at the whole genome level for the construction of phylogenies. An online, interactive web server for inferring phylogenies is needed for biologists to analyze phylogenetic relationships among a set of bacterial genomes of interest. Description BPhyOG is an online interactive server for reconstructing the phylogenies of completely sequenced bacterial genomes on the basis of their shared overlapping genes. It provides two tree-reconstruction methods: Neighbor Joining (NJ and Unweighted Pair-Group Method using Arithmetic averages (UPGMA. Users can apply the desired method to generate phylogenetic trees, which are based on an evolutionary distance matrix for the selected genomes. The distance between two genomes is defined by the normalized number of their shared OG pairs. BPhyOG also allows users to browse the OGs that were used to infer the phylogenetic relationships. It provides detailed annotation for each OG pair and the features of the component genes through hyperlinks. Users can also retrieve each of the homologous OG pairs that have been determined among 177 genomes. It is a useful tool for analyzing the tree of life and overlapping genes from a genomic standpoint. Conclusion BPhyOG is a useful interactive web server for genome-wide inference of any potential evolutionary relationship among the genomes selected by users. It currently includes 177 completely sequenced bacterial genomes containing 79,855 OG pairs, the annotation and homologous OG pairs of which are integrated comprehensively. The reliability of phylogenies complemented by

Bacterial adaptation to the gut environment favors successful colonization: microbial and metabonomic characterization of a simplified microbiota mouse model.

Science.gov (United States)

Rezzonico, Enea; Mestdagh, Renaud; Delley, Michèle; Combremont, Séverine; Dumas, Marc-Emmanuel; Holmes, Elaine; Nicholson, Jeremy; Bibiloni, Rodrigo

2011-01-01

Rodent models harboring a simple yet functional human intestinal microbiota provide a valuable tool to study the relationships between mammals and their bacterial inhabitants. In this study, we aimed to develop a simplified gnotobiotic mouse model containing 10 easy-to-grow bacteria, readily available from culture repositories, and of known genome sequence, that overall reflect the dominant commensal bacterial makeup found in adult human feces. We observed that merely inoculating a mix of fresh bacterial cultures into ex-germ free mice did not guarantee a successful intestinal colonization of the entire bacterial set, as mice inoculated simultaneously with all strains only harbored 3 after 21 d. Therefore, several inoculation procedures were tested and levels of individual strains were quantified using molecular tools. Best results were obtained by inoculating single bacterial strains into individual animals followed by an interval of two weeks before allowing the animals to socialize to exchange their commensal microbes. Through this procedure, animals were colonized with almost the complete bacterial set (9/10). Differences in the intestinal composition were also reflected in the urine and plasma metabolic profiles, where changes in lipids, SCFA, and amino acids were observed. We conclude that adaptation of bacterial strains to the host's gut environment (mono-colonization) may predict a successful establishment of a more complex microbiota in rodents.

Molecular diagnosis of bacterial vaginosis: Does adjustment for total bacterial load or human cellular content improve diagnostic performance?

Science.gov (United States)

Plummer, E L; Garland, S M; Bradshaw, C S; Law, M G; Vodstrcil, L A; Hocking, J S; Fairley, C K; Tabrizi, S N

2017-02-01

We investigated the utility of quantitative PCR assays for diagnosis of bacterial vaginosis and found that while the best model utilized bacterial copy number adjusted for total bacterial load (sensitivity=98%, specificity=93%, AUC=0.95[95%CI=0.93,0.97]), adjusting for total bacterial or human cell load did not consistently increase the diagnostic performance of the assays. Copyright © 2017 Elsevier B.V. All rights reserved.

Arsenic uptake in bacterial calcite

Science.gov (United States)

Catelani, Tiziano; Perito, Brunella; Bellucci, Francesco; Lee, Sang Soo; Fenter, Paul; Newville, Matthew; Rimondi, Valentina; Pratesi, Giovanni; Costagliola, Pilario

2018-02-01

Bio-mediated processes for arsenic (As) uptake in calcite were investigated by means of X-ray Diffraction (XRD) and X-ray Absorption Spectroscopy (XAS) coupled with X-ray Fluorescence measurements. The environmental bacterial strain Bacillus licheniformis BD5, sampled at the Bullicame Hot Springs (Viterbo, Central Italy), was used to synthesize calcite from As-enriched growth media. Both liquid and solid cultures were applied to simulate planktonic and biofilm community environments, respectively. Bacterial calcite samples cultured in liquid media had an As enrichment factor (Kd) 50 times higher than that from solid media. The XRD analysis revealed an elongation of the crystal lattice along the c axis (by 0.03 Å) for biogenic calcite, which likely resulted from the substitution of larger arsenate for carbonate in the crystal. The XAS data also showed a clear difference in the oxidation state of sorbed As between bacterial and abiotic calcite. Abiotic chemical processes yielded predominantly As(V) uptake whereas bacterial precipitation processes led to the uptake of both As(III) and As(V). The presence of As(III) in bacterial calcite is proposed to result from subsequent reduction of arsenate to arsenite by bacterial activities. To the best of our knowledge, this is the first experimental observation of the incorporation of As(III) in the calcite crystal lattice, revealing a critical role of biochemical processes for the As cycling in nature.

Arsenic uptake in bacterial calcite

Energy Technology Data Exchange (ETDEWEB)

Catelani, Tiziano; Perito, Brunella; Bellucci, Francesco; Lee, Sang Soo; Fenter, Paul; Newville, Matthew G.; Rimondi, Valentina; Pratesi, Giovanni; Costagliola, Pilario

2018-02-01

Bio-mediated processes for arsenic (As) uptake in calcite were investigated by means of X-ray Diffraction (XRD) and Xray Absorption Spectroscopy (XAS) coupled with X-ray Fluorescence measurements. The environmental bacterial strain Bacillus licheniformis BD5, sampled at the Bullicame Hot Springs (Viterbo, Central Italy), was used to synthesize calcite from As-enriched growth media. Both liquid and solid cultures were applied to simulate planktonic and biofilm community environments, respectively. Bacterial calcite samples cultured in liquid media had an As enrichment factor (Kd) 50 times higher than that from solid media. The XRD analysis revealed an elongation of the crystal lattice along the c axis (by 0.03Å) for biogenic calcite, which likely resulted from the substitution of larger arsenate for carbonate in the crystal. The XAS data also showed a clear difference in the oxidation state of sorbed As between bacterial and abiotic calcite. Abiotic chemical processes yielded predominantly As(V) uptake whereas bacterial precipitation processes led to the uptake of both As(III) and As(V). The presence of As(III) in bacterial calcite is proposed to result from subsequent reduction of arsenate to arsenite by bacterial activities. To the best of our knowledge, this is the first experimental observation of the incorporation of As(III) in the calcite crystal lattice, revealing a critical role of biochemical processes for the As cycling in nature.

Bacterial communities of two ubiquitous Great Barrier Reef corals reveals both site- and species-specificity of common bacterial associates.

Directory of Open Access Journals (Sweden)

E Charlotte E Kvennefors

Full Text Available BACKGROUND: Coral-associated bacteria are increasingly considered to be important in coral health, and altered bacterial community structures have been linked to both coral disease and bleaching. Despite this, assessments of bacterial communities on corals rarely apply sufficient replication to adequately describe the natural variability. Replicated data such as these are crucial in determining potential roles of bacteria on coral. METHODOLOGY/PRINCIPAL FINDINGS: Denaturing Gradient Gel Electrophoresis (DGGE of the V3 region of the 16S ribosomal DNA was used in a highly replicated approach to analyse bacterial communities on both healthy and diseased corals. Although site-specific variations in the bacterial communities of healthy corals were present, host species-specific bacterial associates within a distinct cluster of gamma-proteobacteria could be identified, which are potentially linked to coral health. Corals affected by "White Syndrome" (WS underwent pronounced changes in their bacterial communities in comparison to healthy colonies. However, the community structure and bacterial ribotypes identified in diseased corals did not support the previously suggested theory of a bacterial pathogen as the causative agent of the syndrome. CONCLUSIONS/SIGNIFICANCE: This is the first study to employ large numbers of replicated samples to assess the bacterial communities of healthy and diseased corals, and the first culture-independent assessment of bacterial communities on WS affected Acroporid corals on the GBR. Results indicate that a minimum of 6 replicate samples are required in order to draw inferences on species, spatial or health-related changes in community composition, as a set of clearly distinct bacterial community profiles exist in healthy corals. Coral bacterial communities may be both site and species specific. Furthermore, a cluster of gamma-proteobacterial ribotypes may represent a group of specific common coral and marine

Bacterial meningitis in children

International Nuclear Information System (INIS)

Marji, S.

2007-01-01

To demonstrate the epidemiology, clinical manifestations and bacteriological profile of bacterial meningitis in children beyond the neonatal period in our hospital. This was a retrospective descriptive study conducted at Prince Rashid Hospital in Irbid, Jordan. The medical records of 50 children with the diagnosis of bacterial meningitis during 4 years period, were reviewed. The main cause of infection was streptococcus pneumoniae, followed by Haemophilus influenza and Niesseria meningitides. Mortality was higher in infants and meningococcal infection, while complications were more encountered in cases of streptococcus pneumoniae. Cerebrospinal fluid culture was positive in 11 cases and Latex agglutination test in 39. There is a significant reduction of the numbers of bacterial meningitis caused by Haemophilus influenza type B species. (author)

Bacterial growth kinetics

International Nuclear Information System (INIS)

Boonkitticharoen, V.; Ehrhardt, J.C.; Kirchner, P.T.

1989-01-01

Quantitative measurement of bacterial growth may be made using a radioassay technique. This method measures, by scintillation counting, the 14 CO 2 derived from the bacterial metabolism of a 14 C-labeled substrate. Mathematical growth models may serve as reliable tools for estimation of the generation rate constant (or slope of the growth curve) and provide a basis for evaluating assay performance. Two models, i.e., exponential and logistic, are proposed. Both models yielded an accurate fit to the data from radioactive measurement of bacterial growth. The exponential model yielded high precision values of the generation rate constant, with an average relative standard deviation of 1.2%. Under most conditions the assay demonstrated no changes in the slopes of growth curves when the number of bacteria per inoculation was changed. However, the radiometric assay by scintillation method had a growth-inhibiting effect on a few strains of bacteria. The source of this problem was thought to be hypersensitivity to trace amounts of toluene remaining on the detector

Bacterial infec tions in travellers

African Journals Online (AJOL)

namely bacterial causes of travellers' diarrhoea and skin infections, as well as .... Vaccination: protective efficacy against typhoid may be overcome by ingesting a high bacterial load. Vaccine ..... preparation such as cream sauce. Only after ...

Bacterial carbon cycling in a subarctic fjord

DEFF Research Database (Denmark)

Middelboe, Mathias; Glud, Ronnie Nøhr; Sejr, M.K.

2012-01-01

of viruses on bacterial mortality (4–36% of cell production) and carbon cycling. Heterotrophic bacterial consumption was closely coupled with autochthonous BDOC production, and the majority of the primary production was consumed by pelagic bacteria at all seasons. The relatively low measured BGE emphasized......In this seasonal study, we examined the environmental controls and quantitative importance of bacterial carbon consumption in the water column and the sediment in the subarctic Kobbefjord, Greenland. Depth-integrated bacterial production in the photic zone varied from 5.0 ± 2.7 mg C m−2 d−1...... in February to 42 ± 28 mg C m−2 d−1 in May and 34 ± 7 mg C m−2 d−1 in September, corresponding to a bacterial production to primary production ratio of 0.34 ± 0.14, 0.07 ± 0.04, and 0.08 ± 0.06, respectively. Based on measured bacterial growth efficiencies (BGEs) of 0.09–0.10, pelagic bacterial carbon...

Real-time monitoring of bacterial infection in vivo: development of bioluminescent staphylococcal foreign-body and deep-thigh-wound mouse infection models.

Science.gov (United States)

Kuklin, Nelly A; Pancari, Gregory D; Tobery, Timothy W; Cope, Leslie; Jackson, Jesse; Gill, Charles; Overbye, Karen; Francis, Kevin P; Yu, Jun; Montgomery, Donna; Anderson, Annaliesa S; McClements, William; Jansen, Kathrin U

2003-09-01

Staphylococcal infections associated with catheter and prosthetic implants are difficult to eradicate and often lead to chronic infections. Development of novel antibacterial therapies requires simple, reliable, and relevant models for infection. Using bioluminescent Staphylococcus aureus, we have adapted the existing foreign-body and deep-wound mouse models of staphylococcal infection to allow real-time monitoring of the bacterial colonization of catheters or tissues. This approach also enables kinetic measurements of bacterial growth and clearance in each infected animal. Persistence of infection was observed throughout the course of the study until termination of the experiment at day 16 in a deep-wound model and day 21 in the foreign-body model, providing sufficient time to test the effects of antibacterial compounds. The usefulness of both animal models was assessed by using linezolid as a test compound and comparing bioluminescent measurements to bacterial counts. In the foreign-body model, a three-dose antibiotic regimen (2, 5, and 24 h after infection) resulted in a decrease in both luminescence and bacterial counts recovered from the implant compared to those of the mock-treated infected mice. In addition, linezolid treatment prevented the formation of subcutaneous abscesses, although it did not completely resolve the infection. In the thigh model, the same treatment regimen resulted in complete resolution of the luminescent signal, which correlated with clearance of the bacteria from the thighs.

Bacterial cells with improved tolerance to polyamines

DEFF Research Database (Denmark)

2017-01-01

Provided are bacterial cells genetically modified to improve their tolerance to certain commodity chemicals, such as polyamines, and methods of preparing and using such bacterial cells for production of polyamines and other compounds.......Provided are bacterial cells genetically modified to improve their tolerance to certain commodity chemicals, such as polyamines, and methods of preparing and using such bacterial cells for production of polyamines and other compounds....

Viral-bacterial associations in acute apical abscesses.

Science.gov (United States)

Ferreira, Dennis C; Rôças, Isabela N; Paiva, Simone S M; Carmo, Flávia L; Cavalcante, Fernanda S; Rosado, Alexandre S; Santos, Kátia R N; Siqueira, José F

2011-08-01

Viral-bacterial and bacterial synergism have been suggested to contribute to the pathogenesis of several human diseases. This study sought to investigate the possible associations between 9 candidate endodontic bacterial pathogens and 9 human viruses in samples from acute apical abscesses. DNA extracts from purulent exudate aspirates of 33 cases of acute apical abscess were surveyed for the presence of 9 selected bacterial species using a 16S ribosomal RNA gene-based nested polymerase chain reaction (PCR) approach. Single or nested PCR assays were used for detection of the human papillomavirus (HPV) and herpesviruses types 1 to 8. Two-thirds of the abscess samples were positive for at least one of the target viruses. Specifically, the most frequently detected viruses were HHV-8 (54.5%); HPV (9%); and varicella zoster virus (VZV), Epstein-Barr virus (EBV), and HHV-6 (6%). Bacterial DNA was present in all cases and the most prevalent bacterial species were Treponema denticola (70%), Tannerella forsythia (67%), Porphyromonas endodontalis (67%), Dialister invisus (61%), and Dialister pneumosintes (57.5%). HHV-8 was positively associated with 7 of the target bacterial species and HPV with 4, but all these associations were weak. Several bacterial pairs showed a moderate positive association. Viral coinfection was found in 6 abscess cases, but no significant viral association could be determined. Findings demonstrated that bacterial and viral DNA occurred concomitantly in two-thirds of the samples from endodontic abscesses. Although this may suggest a role for viruses in the etiology of apical abscesses, the possibility also exists that the presence of viruses in abscess samples is merely a consequence of the bacterially induced disease process. Further studies are necessary to clarify the role of these viral-bacterial interactions, if any, in the pathogenesis of acute apical abscesses. Copyright © 2011 Mosby, Inc. All rights reserved.

The DinJ/RelE Toxin-Antitoxin System Suppresses Bacterial Proliferation and Virulence of Xylella fastidiosa in Grapevine.

Science.gov (United States)

Burbank, Lindsey P; Stenger, Drake C

2017-04-01

Xylella fastidiosa, the causal agent of Pierce's disease of grapes, is a slow-growing, xylem-limited, bacterial pathogen. Disease progression is characterized by systemic spread of the bacterium through xylem vessel networks, causing leaf-scorching symptoms, senescence, and vine decline. It appears to be advantageous to this pathogen to avoid excessive blockage of xylem vessels, because living bacterial cells are generally found in plant tissue with low bacterial cell density and minimal scorching symptoms. The DinJ/RelE toxin-antitoxin system is characterized here for a role in controlling bacterial proliferation and population size during plant colonization. The DinJ/RelE locus is transcribed from two separate promoters, allowing for coexpression of antitoxin DinJ with endoribonuclease toxin RelE, in addition to independent expression of RelE. The ratio of antitoxin/toxin expressed is dependent on bacterial growth conditions, with lower amounts of antitoxin present under conditions designed to mimic grapevine xylem sap. A knockout mutant of DinJ/RelE exhibits a hypervirulent phenotype, with higher bacterial populations and increased symptom development and plant decline. It is likely that DinJ/RelE acts to prevent excessive population growth, contributing to the ability of the pathogen to spread systemically without completely blocking the xylem vessels and increasing probability of acquisition by the insect vector.

Adult bacterial meningitis

DEFF Research Database (Denmark)

Meyer, C N; Samuelsson, I S; Galle, M

2004-01-01

Episodes of adult bacterial meningitis (ABM) at a Danish hospital in 1991-2000 were identified from the databases of the Department of Clinical Microbiology, and compared with data from the Danish National Patient Register and the Danish National Notification System. Reduced penicillin susceptibi......Episodes of adult bacterial meningitis (ABM) at a Danish hospital in 1991-2000 were identified from the databases of the Department of Clinical Microbiology, and compared with data from the Danish National Patient Register and the Danish National Notification System. Reduced penicillin...

Bacterial Communities: Interactions to Scale

Directory of Open Access Journals (Sweden)

Reed M. Stubbendieck

2016-08-01

Full Text Available In the environment, bacteria live in complex multispecies communities. These communities span in scale from small, multicellular aggregates to billions or trillions of cells within the gastrointestinal tract of animals. The dynamics of bacterial communities are determined by pairwise interactions that occur between different species in the community. Though interactions occur between a few cells at a time, the outcomes of these interchanges have ramifications that ripple through many orders of magnitude, and ultimately affect the macroscopic world including the health of host organisms. In this review we cover how bacterial competition influences the structures of bacterial communities. We also emphasize methods and insights garnered from culture-dependent pairwise interaction studies, metagenomic analyses, and modeling experiments. Finally, we argue that the integration of multiple approaches will be instrumental to future understanding of the underlying dynamics of bacterial communities.

Substrate Type and Free Ammonia Determine Bacterial Community Structure in Full-Scale Mesophilic Anaerobic Digesters Treating Cattle or Swine Manure.

Science.gov (United States)

Li, Jiabao; Rui, Junpeng; Yao, Minjie; Zhang, Shiheng; Yan, Xuefeng; Wang, Yuanpeng; Yan, Zhiying; Li, Xiangzhen

2015-01-01

The microbial-mediated anaerobic digestion (AD) process represents an efficient biological process for the treatment of organic waste along with biogas harvest. Currently, the key factors structuring bacterial communities and the potential core and unique bacterial populations in manure anaerobic digesters are not completely elucidated yet. In this study, we collected sludge samples from 20 full-scale anaerobic digesters treating cattle or swine manure, and investigated the variations of bacterial community compositions using high-throughput 16S rRNA amplicon sequencing. Clustering and correlation analysis suggested that substrate type and free ammonia (FA) play key roles in determining the bacterial community structure. The COD: [Formula: see text] (C:N) ratio of substrate and FA were the most important available operational parameters correlating to the bacterial communities in cattle and swine manure digesters, respectively. The bacterial populations in all of the digesters were dominated by phylum Firmicutes, followed by Bacteroidetes, Proteobacteria and Chloroflexi. Increased FA content selected Firmicutes, suggesting that they probably play more important roles under high FA content. Syntrophic metabolism by Proteobacteria, Chloroflexi, Synergistetes and Planctomycetes are likely inhibited when FA content is high. Despite the different manure substrates, operational conditions and geographical locations of digesters, core bacterial communities were identified. The core communities were best characterized by phylum Firmicutes, wherein Clostridium predominated overwhelmingly. Substrate-unique and abundant communities may reflect the properties of manure substrate and operational conditions. These findings extend our current understanding of the bacterial assembly in full-scale manure anaerobic digesters.

USE OF SCORE AND CEREBROSPINAL FLUID LACTATE DOSAGE IN DIFFERENTIAL DIAGNOSIS OF BACTERIAL AND ASEPTIC MENINGITIS.

Science.gov (United States)

Pires, Frederico Ribeiro; Franco, Andréia Christine Bonotto Farias; Gilio, Alfredo Elias; Troster, Eduardo Juan

2017-01-01

To evaluate Bacterial Meningitis Score (BMS) on its own and in association with Cerebrospinal Fluid (CSF) lactate dosage in order to distinguish bacterial from aseptic meningitis. Children diagnosed with meningitis at a tertiary hospital between January/2011 and December/2014 were selected. All data were obtained upon admission. BMS was applied and included: CSF Gram staining (2 points); CSF neutrophil count ≥1,000 cells/mm3 (1 point); CSF protein ≥80 mg/dL (1 point); peripheral blood neutrophil count ≥10,000 cells/mm3 (1 point) and seizures upon/before arrival (1 point). Cutoff value for CSF lactate was ≥30 mg/dL. Sensitivity, specificity and negative predictive value of several BMS cutoffs and BMS associated with high CSF lactate were evaluated for prediction of bacterial meningitis. Among 439 eligible patients, 94 did not have all data available to complete the score, and 345 patients were included: 7 in bacterial meningitis group and 338 in aseptic meningitis group. As predictive factors of bacterial meningitis, BMS ≥1 had 100% sensitivity (95%CI 47.3-100), 64.2% specificity (58.8-100) and 100% negative predictive value (97.5-100); BMS ≥2 or BMS ≥1 associated with high CSF lactate also showed 100% sensitivity (47.3-100); but 98.5% specificity (96.6-99.5) and 100% negative predictive value (98.3-100). 2 point BMS in association with CSF lactate dosage had the same sensitivity and negative predictive value, with increased specificity for diagnosis of bacterial meningitis when compared with 1-point BMS.

Use of dextran nanoparticle: A paradigm shift in bacterial exopolysaccharide based biomedical applications.

Science.gov (United States)

Banerjee, Aparna; Bandopadhyay, Rajib

2016-06-01

This review is a concise compilation of all the major researches on dextran nanoparticle based biomedical applications. Dextran is a highly biocompatible and biodegradable neutral bacterial exopolysaccharide with simple repeating glucose subunits. It's simple yet unique biopolymeric nature made it highly suitable as nanomedicine, nanodrug carrier, and cell imaging system or nanobiosensor. Most importantly, it is extremely water soluble and shows no post drug delivery cellular toxicity. Complete metabolism of dextran is possible inside body thus possibility of renal failure is minimum. Dextran based nanoparticles have superior aqueous solubility, high cargo capacity and intrinsic viscosity, and short storage period. The main focus area of this review is- past and present of major biomedical applications of dextran based nanomaterials thus showing a paradigm shift in bacterial exopolysaccharide based nanobiotechnology. Copyright © 2016 Elsevier B.V. All rights reserved.

Oral bacterial DNA findings in pericardial fluid

Directory of Open Access Journals (Sweden)

Anne-Mari Louhelainen

2014-11-01

Full Text Available Background: We recently reported that large amounts of oral bacterial DNA can be found in thrombus aspirates of myocardial infarction patients. Some case reports describe bacterial findings in pericardial fluid, mostly done with conventional culturing and a few with PCR; in purulent pericarditis, nevertheless, bacterial PCR has not been used as a diagnostic method before. Objective: To find out whether bacterial DNA can be measured in the pericardial fluid and if it correlates with pathologic–anatomic findings linked to cardiovascular diseases. Methods: Twenty-two pericardial aspirates were collected aseptically prior to forensic autopsy at Tampere University Hospital during 2009–2010. Of the autopsies, 10 (45.5% were free of coronary artery disease (CAD, 7 (31.8% had mild and 5 (22.7% had severe CAD. Bacterial DNA amounts were determined using real-time quantitative PCR with specific primers and probes for all bacterial strains associated with endodontic disease (Streptococcus mitis group, Streptococcus anginosus group, Staphylococcus aureus/Staphylococcus epidermidis, Prevotella intermedia, Parvimonas micra and periodontal disease (Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, Treponema denticola, Fusobacterium nucleatus, and Dialister pneumosintes. Results: Of 22 cases, 14 (63.6% were positive for endodontic and 8 (36.4% for periodontal-disease-associated bacteria. Only one case was positive for bacterial culturing. There was a statistically significant association between the relative amount of bacterial DNA in the pericardial fluid and the severity of CAD (p=0.035. Conclusions: Oral bacterial DNA was detectable in pericardial fluid and an association between the severity of CAD and the total amount of bacterial DNA in pericardial fluid was found, suggesting that this kind of measurement might be useful for clinical purposes.

Endocarditis in adults with bacterial meningitis.

Science.gov (United States)

Lucas, Marjolein J; Brouwer, Matthijs C; van der Ende, Arie; van de Beek, Diederik

2013-05-21

Endocarditis may precede or complicate bacterial meningitis, but the incidence and impact of endocarditis in bacterial meningitis are unknown. We assessed the incidence and clinical characteristics of patients with meningitis and endocarditis from a nationwide cohort study of adults with community-acquired bacterial meningitis in the Netherlands from 2006 to 2012. Endocarditis was identified in 24 of 1025 episodes (2%) of bacterial meningitis. Cultures yielded Streptococcus pneumoniae in 13 patients, Staphylococcus aureus in 8 patients, and Streptococcus agalactiae, Streptococcus pyogenes, and Streptococcus salivarius in 1 patient each. Clues leading to the diagnosis of endocarditis were cardiac murmurs, persistent or recurrent fever, a history of heart valve disease, and S aureus as the causative pathogen of bacterial meningitis. Treatment consisted of prolonged antibiotic therapy in all patients and surgical valve replacement in 10 patients (42%). Two patients were treated with oral anticoagulants, and both developed life-threatening intracerebral hemorrhage. Systemic (70%) and neurological (54%) complications occurred frequently, leading to a high proportion of patients with unfavorable outcome (63%). Seven of 24 patients (29%) with meningitis and endocarditis died. Endocarditis is an uncommon coexisting condition in bacterial meningitis but is associated with a high rate of unfavorable outcome.

[The composition of the gastrointestinal bacterial flora of mouse embryos and the placenta tissue bacterial flora].

Science.gov (United States)

Lei, D; Lin, Y; Jiang, X; Lan, L; Zhang, W; Wang, B X

2017-03-02

Objective: To explore the composition of the gastrointestinal bacterial flora of mouse embryos and the placenta tissue bacterial flora. Method: Twenty-four specimens were collected from pregnant Kunming mouse including 8 mice of early embryonic (12-13 days) gastrointestinal tissues, 8 cases of late embryonic (19-20 days)gastrointestinal tissues, 8 of late pregnancy placental tissues.The 24 samples were extracted by DNeasy Blood & Tissue kit for high-throughput DNA sequencing. Result: The level of Proteobacteria, Bacteroidetes, Actino-bacteria and Firmicutes were predominantin all specimens.The relative content of predominant bacterial phyla in each group: Proteobacteria (95.00%, 88.14%, 87.26%), Bacteroidetes(1.71%, 2.15%, 2.63%), Actino-Bacteria(1.16%, 4.10%, 3.38%), Firmicutes(0.75%, 2.62%, 2.01%). At the level of family, there were nine predominant bacterial families in which Enterobacteriaeae , Shewanel laceae and Moraxellaceae were dominant.The relative content of dominant bacterial family in eachgroup: Enterobacteriaeae (46.99%, 44.34%, 41.08%), Shewanellaceae (21.99%, 21.10%, 19.05%), Moraxellaceae (9.18%, 7.09%, 5.64%). From the species of flora, the flora from fetal gastrointestinal in early pregnancy and late pregnancy (65.44% and 62.73%) were the same as that from placenta tissue in the late pregnancy.From the abundance of bacteria, at the level of family, the same content of bacteria in three groups accounted for 78.16%, 72.53% and 65.78% respectively. Conclusion: It was proved that the gastrointestinal bacterial flora of mouse embryos and the placenta tissue bacterial flora were colonized. At the same time the bacteria are classified.

C-reactive protein and bacterial meningitis

DEFF Research Database (Denmark)

Gerdes, Lars Ulrik; Jørgensen, P E; Nexø, E

1998-01-01

The aim of the study was to review published articles on the diagnostic accuracy of C-reactive protein (CRP) tests with cerebrospinal fluid and serum in diagnosing bacterial meningitis. The literature from 1980 and onwards was searched using the electronic databases of MEDLINE, and we used summary...... measured in serum, and 4 in which it had been measured in both cerebrospinal fluid and serum. The odds ratio for bacterial meningitis versus aseptic meningitis for a positive CRP test with cerebrospinal fluid was estimated at 241 (95% confidence interval [CI]: 59-980), and the central tendencies.......06-0.08, respectively, the post-test probability of not having bacterial meningitis given a negative test is very high (> or = 97%), in the range of a pre-test probability (prevalence of bacterial meningitis) from 10 to 30%, whereas the post-test probability of bacterial meningitis given a positive test is considerably...

Bacterial microflora of poultry feed and its control by gamma irradiation

International Nuclear Information System (INIS)

El-Zawahry, Y.A.; Youssef, Y.A.; Roushdy, H.M.; Aziz, N.H.

1986-01-01

The common bacteria isolated from the poultry feed samples were classified in the families of Pseudomonadaceae, Micrococcacae, Bacililaceae and Enterobacteriaceae. These species of bacteria were identified as 10 species of Gram-negative and 13 species of Gram-positive. We found that radiation dose required to inhibit completely the natural bacterial flora in tested samples of poultry feed was 20 KGY. The most radioresistant bacterial isolates which resisted a sublethal dose of 15 KGY were identified as bacillus cereus, Bacillus polymxa and Bacillus megaterium. The dose response curves of B, cereus and B, polymxa started by shoulder portion followed by an exponential death, whereas, B, megaterium exhibited straight line relationship directly. The D 10 -value of B. megaterium spores (3.30 KGY) was about 1.5 and 1.7 folds as the D 10 value B. polymxa and B, cereus, respectively. The present work indicated also that the exposure of poultry feed to irradiation dose 10 KGY (1 Mrad) reduced greatly number of bacteria destroyed all spoilage and pathogenic bacteria especially Salmonella, and finally increased the shelf-life during storage periods. Higher radiation dose 15 KGY, failed to show any better reduction of viable bacterial counts. Part of this work presented in (FAO/IAEA) international symposium for food irradiation processing, Washington, D.C., U.S.A. (4-8 March, 1985)

Bacterial meningitis in immunocompromised patients

NARCIS (Netherlands)

van Veen, K.E.B.

2018-01-01

Bacterial meningitis is an acute infection of the meninges, in The Netherlands most commonly caused by Streptococcus pneumoniae and Neisseria meningitides. Risk factors for acquiring bacterial meningitis include a decreased function of the immune system. The aim of this thesis was to study

Bacterial cellulose/boehmite composites

International Nuclear Information System (INIS)

Salvi, Denise T.B. de; Barud, Hernane S.; Messaddeq, Younes; Ribeiro, Sidney J.L.; Caiut, Jose Mauricio A.

2011-01-01

Composites based on bacterial cellulose membranes and boehmite were obtained. SEM results indicate that the bacterial cellulose (BC) membranes are totally covered by boehmite and obtained XRD patterns suggest structural changes due to this boehmite addition. Thermal stability is accessed through TG curves and is dependent on boehmite content. Transparency is high comparing to pure BC as can be seen through UV-vis absorption spectroscopy. (author)

Guanidino Groups Greatly Enhance the Action of Antimicrobial Peptidomimetics Against Bacterial Cytoplasmic Membranes

Science.gov (United States)

2014-05-28

permeated is not completely understood, and several models have been proposed based on studies conducted with various peptidic structures [1]. Moreover...approach has been successfully used in conjunction with liquid surface X-ray scattering to study bacterial membrane lysis by human antimicrobial peptide...diluted in MHB pH 7.4 to a final concentration of approx. 5 × 105 CFU/mL in each well. Polypropylene plates (Nunc 442587) were used to minimize peptide

Molecular detection of human bacterial pathogens

National Research Council Canada - National Science Library

Liu, Dongyou

2011-01-01

.... Molecular Detection of Human Bacterial Pathogens addresses this issue, with international scientists in respective bacterial pathogen research and diagnosis providing expert summaries on current...

Effect of irradiation upon the bacterial flora in patients with head and neck cancer

International Nuclear Information System (INIS)

Rice, D.H.; Gill, G.

1979-01-01

Twenty-two consecutive patients with cancer of the head and neck, who were to receive a full tumoricidal dose of irradiation to a field that included the oral cavity and pharynx, were studied to determine the effect of the irradiation on their local bacterial flora. Aerobic cultures were taken prior to, at the completion of, and one month after the completion of their irradiation. The percentage of patients with potentially pathogenic organisms increased dramatically as the effect of the irradiation increased. This change in the local flora has obvious implications concerning the increased incidence of postoperative wound infections in patients who have received prior irradiation

[Bacterial vaginosis].

Science.gov (United States)

Romero Herrero, Daniel; Andreu Domingo, Antonia

2016-07-01

Bacterial vaginosis (BV) is the main cause of vaginal dysbacteriosis in the women during the reproductive age. It is an entity in which many studies have focused for years and which is still open for discussion topics. This is due to the diversity of microorganisms that cause it and therefore, its difficult treatment. Bacterial vaginosis is probably the result of vaginal colonization by complex bacterial communities, many of them non-cultivable and with interdependent metabolism where anaerobic populations most likely play an important role in its pathogenesis. The main symptoms are an increase of vaginal discharge and the unpleasant smell of it. It can lead to serious consequences for women, such as an increased risk of contracting sexually transmitted infections including human immunodeficiency virus and upper genital tract and pregnancy complications. Gram stain is the gold standard for microbiological diagnosis of BV, but can also be diagnosed using the Amsel clinical criteria. It should not be considered a sexually transmitted disease but it is highly related to sex. Recurrence is the main problem of medical treatment. Apart from BV, there are other dysbacteriosis less characterized like aerobic vaginitis of which further studies are coming slowly but are achieving more attention and consensus among specialists. Copyright © 2016 Elsevier España, S.L.U. All rights reserved.

Complete genome sequence of Denitrovibrio acetiphilus type strain (N2460T)

Energy Technology Data Exchange (ETDEWEB)

Kiss, Hajnalka; Lang, Elke; Lapidus, Alla; Copeland, Alex; Nolan, Matt; Glavina Del Rio, Tijana; Chen, Feng; Lucas, Susan; Tice, Hope; Cheng, Jan-Fang; Han, Cliff; Goodwin, Lynne; Pitluck, Sam; Liolios, Konstantinos; Pati, Amrita; Ivanova, Natalia; Mavromatis, Konstantinos; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Detter, John C.; Brettin, Thomas; Spring, Stefan; Rohde, Manfred; Goker, Markus; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C.; Klenk, Hans-Peter

2010-06-25

Denitrovibrio acetiphilus Myhr and Torsvik 2000 is the type species of the genus Denitrovibrio in the bacterial family Deferribacteraceae. It is of phylogenetic interest because there are only six genera described in the family Deferribacteraceae. D. acetiphilus was isolated as a representative of a population reducing nitrate to ammonia in a laboratory column simulating the conditions in off-shore oil recovery fields. When nitrate was added to this column undesirable hydrogen sulfide production was stopped because the sulfate reducing populations were superseded by these nitrate reducing bacteria. Here we describe the features of this marine, mesophilic, obligately anaerobic organism respiring by nitrate reduction, together with the complete genome sequence, and annotation. This is the second complete genome sequence of the order Deferribacterales and the class Deferribacteres, which is the sole class in the phylum Deferribacteres. The 3,222,077 bp genome with its 3,034 protein-coding and 51 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

Radiological aspects of bacterial lung abscess

International Nuclear Information System (INIS)

Groskin, S.A.; Panicek, D.; Ewing, D.; Rivera, F.; Math, K.; Teixeira, J.; Heitzman, E.R.

1987-01-01

Clinical, radiological, and pathological data derived from an analysis of over 70 cases of bacterial lung abscess are presented. Etiologic agents and risk factors are presented. Key radiographic findings are discussed, and those that are most useful in differentiating bacterial lung abscess from cavitated carcinoma, infected cyst, and emphysema are emphasized. Radiographic aspects of the complications of bacterial lung abscess are illustrated, and radiological approaches to their therapy are discussed

Bacterial, Fungal, Parasitic, and Viral Myositis

OpenAIRE

Crum-Cianflone, Nancy F.

2008-01-01

Infectious myositis may be caused by a broad range of bacterial, fungal, parasitic, and viral agents. Infectious myositis is overall uncommon given the relative resistance of the musculature to infection. For example, inciting events, including trauma, surgery, or the presence of foreign bodies or devitalized tissue, are often present in cases of bacterial myositis. Bacterial causes are categorized by clinical presentation, anatomic location, and causative organisms into the categories of pyo...

Bacterial cells with improved tolerance to polyols

DEFF Research Database (Denmark)

2017-01-01

The present invention relates to bacterial cells genetically modified to improve their tolerance to certain commodity chemicals, such as diols and other polyols, and to methods of preparing and using such bacterial cells for production of polyols and other compounds.......The present invention relates to bacterial cells genetically modified to improve their tolerance to certain commodity chemicals, such as diols and other polyols, and to methods of preparing and using such bacterial cells for production of polyols and other compounds....

Bacterial Vaginosis

Science.gov (United States)

... Archive STDs Home Page Bacterial Vaginosis (BV) Chlamydia Gonorrhea Genital Herpes Hepatitis HIV/AIDS & STDs Human Papillomavirus ( ... of getting other STDs, such as chlamydia and gonorrhea . These bacteria can sometimes cause pelvic inflammatory disease ( ...

The intrinsic resistome of bacterial pathogens.

Science.gov (United States)

Olivares, Jorge; Bernardini, Alejandra; Garcia-Leon, Guillermo; Corona, Fernando; B Sanchez, Maria; Martinez, Jose L

2013-01-01

Intrinsically resistant bacteria have emerged as a relevant health problem in the last years. Those bacterial species, several of them with an environmental origin, present naturally low-level susceptibility to several drugs. It has been proposed that intrinsic resistance is mainly the consequence of the impermeability of cellular envelopes, the activity of multidrug efflux pumps or the lack of appropriate targets for a given family of drugs. However, recently published articles indicate that the characteristic phenotype of susceptibility to antibiotics of a given bacterial species depends on the concerted activity of several elements, what has been named as intrinsic resistome. These determinants comprise not just classical resistance genes. Other elements, several of them involved in basic bacterial metabolic processes, are of relevance for the intrinsic resistance of bacterial pathogens. In the present review we analyze recent publications on the intrinsic resistomes of Escherichia coli and Pseudomonas aeruginosa. We present as well information on the role that global regulators of bacterial metabolism, as Crc from P. aeruginosa, may have on modulating bacterial susceptibility to antibiotics. Finally, we discuss the possibility of searching inhibitors of the intrinsic resistome in the aim of improving the activity of drugs currently in use for clinical practice.

The intrinsic resistome of bacterial pathogens

Directory of Open Access Journals (Sweden)

Jorge Andrés Olivares Pacheco

2013-04-01

Full Text Available Intrinsically resistant bacteria have emerged as a relevant health problem in the last years. Those bacterial species, several of them with an environmental origin, present naturally a low-level susceptibility to several drugs. It has been proposed that intrinsic resistance is mainly the consequence of the impermeability of cellular envelopes, the activity of multidrug efflux pumps or the lack of appropriate targets for a given family of drugs. However, recently published articles indicate that the characteristic phenotype of susceptibility to antibiotics of a given bacterial species depends on the concerted activity of several elements, what has been named as intrinsic resistome. These determinants comprise not just classical resistance genes. Other elements, several of them involved in basic bacterial metabolic processes, are of relevance for the intrinsic resistance of bacterial pathogens. In the present review we analyse recent publications on the intrinsic resistomes of Escherichia coli and Pseudomonas aeruginosa. We present as well information on the role that global regulators of bacterial metabolism, as Crc from P. aeruginosa, may have on modulating bacterial susceptibility to antibiotics. Finally, we discuss the possibility of searching inhibitors of the intrinsic resistome in the aim of improving the activity of drugs currently in use for clinical practice.

Bacterial flora of sturgeon fingerling

International Nuclear Information System (INIS)

Arani, A.S.; Mosahab, R.

2008-01-01

The study on microbial populations is a suitable tool to understand and apply control methods to improve the sanitary level of production in fish breeding and rearing centers, ensure health of sturgeon fingerlings at the time of their release into the rivers and also in the conversation and restoration of these valuable stocks in the Caspian Sea, Iran. A laboratory research based on Austin methods (Austin, B., Austin, D.A. 1993) was conducted for bacterial study on 3 sturgeon species naming A. persicus, A. stellatus and A. nudiventris during different growth stages. Bacterial flora of Acinetobacter, Moraxella, Aeromonas, Vibrio, Edwardsiella, Staphylococcus, Proteus, Yersinia, Pseudomonas and Plesiomonas were determined. The factors which may induce changes in bacterial populations during different stages of fife are the followings: quality of water in rearing ponds, different conditions for growth stages, suitable time for colonization of bacterial flora in rearing pond, water temperature increase in fingerlings size and feeding condition. (author)

dBBQs: dataBase of Bacterial Quality scores.

Science.gov (United States)

Wanchai, Visanu; Patumcharoenpol, Preecha; Nookaew, Intawat; Ussery, David

2017-12-28

It is well-known that genome sequencing technologies are becoming significantly cheaper and faster. As a result of this, the exponential growth in sequencing data in public databases allows us to explore ever growing large collections of genome sequences. However, it is less known that the majority of available sequenced genome sequences in public databases are not complete, drafts of varying qualities. We have calculated quality scores for around 100,000 bacterial genomes from all major genome repositories and put them in a fast and easy-to-use database. Prokaryotic genomic data from all sources were collected and combined to make a non-redundant set of bacterial genomes. The genome quality score for each was calculated by four different measurements: assembly quality, number of rRNA and tRNA genes, and the occurrence of conserved functional domains. The dataBase of Bacterial Quality scores (dBBQs) was designed to store and retrieve quality scores. It offers fast searching and download features which the result can be used for further analysis. In addition, the search results are shown in interactive JavaScript chart framework using DC.js. The analysis of quality scores across major public genome databases find that around 68% of the genomes are of acceptable quality for many uses. dBBQs (available at http://arc-gem.uams.edu/dbbqs ) provides genome quality scores for all available prokaryotic genome sequences with a user-friendly Web-interface. These scores can be used as cut-offs to get a high-quality set of genomes for testing bioinformatics tools or improving the analysis. Moreover, all data of the four measurements that were combined to make the quality score for each genome, which can potentially be used for further analysis. dBBQs will be updated regularly and is freely use for non-commercial purpose.

Characterisation of the gill mucosal bacterial communities of four butterflyfish species: a reservoir of bacterial diversity in coral reef ecosystems.

Science.gov (United States)

Reverter, Miriam; Sasal, Pierre; Tapissier-Bontemps, N; Lecchini, D; Suzuki, M

2017-06-01

While recent studies have suggested that fish mucus microbiota play an important role in homeostasis and prevention of infections, very few studies have investigated the bacterial communities of gill mucus. We characterised the gill mucus bacterial communities of four butterflyfish species and although the bacterial diversity of gill mucus varied significantly between species, Shannon diversities were high (H = 3.7-5.7) in all species. Microbiota composition differed between butterflyfishes, with Chaetodon lunulatus and C. ornatissimus having the most similar bacterial communities, which differed significantly from C. vagabundus and C. reticulatus. The core bacterial community of all species consisted of mainly Proteobacteria followed by Actinobacteria and Firmicutes. Chaetodonlunulatus and C. ornatissimus bacterial communities were mostly dominated by Gammaproteobacteria with Vibrio as the most abundant genus. Chaetodonvagabundus and C. reticulatus presented similar abundances of Gammaproteobacteria and Alphaproteobacteria, which were well represented by Acinetobacter and Paracoccus, respectively. In conclusion, our results indicate that different fish species present specific bacterial assemblages. Finally, as mucus layers are nutrient hotspots for heterotrophic bacteria living in oligotrophic environments, such as coral reef waters, the high bacterial diversity found in butterflyfish gill mucus might indicate external fish mucus surfaces act as a reservoir of coral reef bacterial diversity. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Mechanical Homogenization Increases Bacterial Homogeneity in Sputum

Science.gov (United States)

Stokell, Joshua R.; Khan, Ammad

2014-01-01

Sputum obtained from patients with cystic fibrosis (CF) is highly viscous and often heterogeneous in bacterial distribution. Adding dithiothreitol (DTT) is the standard method for liquefaction prior to processing sputum for molecular detection assays. To determine if DTT treatment homogenizes the bacterial distribution within sputum, we measured the difference in mean total bacterial abundance and abundance of Burkholderia multivorans between aliquots of DTT-treated sputum samples with and without a mechanical homogenization (MH) step using a high-speed dispersing element. Additionally, we measured the effect of MH on bacterial abundance. We found a significant difference between the mean bacterial abundances in aliquots that were subjected to only DTT treatment and those of the aliquots which included an MH step (all bacteria, P = 0.04; B. multivorans, P = 0.05). There was no significant effect of MH on bacterial abundance in sputum. Although our results are from a single CF patient, they indicate that mechanical homogenization increases the homogeneity of bacteria in sputum. PMID:24759710

Traditional insulin-use practices and the incidence of bacterial contamination and infection.

Science.gov (United States)

Borders, L M; Bingham, P R; Riddle, M C

1984-01-01

While complex procedures are usually recommended to prevent infection at insulin injection sites, adherence to these procedures is imperfect and their value incompletely established. Among 254 adult insulin users in two clinic populations, the reported prevalence of complete performance of four traditional insulin-use practices (handwashing, vial prep, skin prep, discarding of plastic syringes after one use) was 29%, and none of the individual practices considered was performed regularly by more than two-thirds of the subjects. Even so, there was no infection at 2828 injection sites, and there was no significant bacterial contamination of insulin or syringes. These findings fail to support the view that traditional practices provide protection to insulin users against infection or bacterial growth in insulin or syringes. The authors suggest that modification of traditional teaching methods would do no harm, and that benefits could include financial savings, improved client success with self-care, and enhanced health care provider credibility.

Bacterial cooperation in the wild and in the clinic: are pathogen social behaviours relevant outside the laboratory?

Science.gov (United States)

Harrison, Freya

2013-02-01

Individual bacterial cells can communicate via quorum sensing, cooperate to harvest nutrients from their environment, form multicellular biofilms, compete over resources and even kill one another. When the environment that bacteria inhabit is an animal host, these social behaviours mediate virulence. Over the last decade, much attention has focussed on the ecology, evolution and pathology of bacterial cooperation, and the possibility that it could be exploited or destabilised to treat infections. But how far can we really extrapolate from theoretical predictions and laboratory experiments to make inferences about 'cooperative' behaviours in hosts and reservoirs? To determine the likely importance and evolution of cooperation 'in the wild', several questions must be addressed. A recent paper that reports the dynamics of bacterial cooperation and virulence in a field experiment provides an excellent nucleus for bringing together key empirical and theoretical results which help us to frame - if not completely to answer - these questions. Copyright © 2013 WILEY Periodicals, Inc.

Chirality Switching by Martensitic Transformation in Protein Cylindrical Crystals: Application to Bacterial Flagella

Science.gov (United States)

Komai, Ricardo Kiyohiro

Martensitic transformations provide unique engineering properties that, when designed properly, become important parts of new technology. Martensitic transformations have been studied for many years in traditional alloys (iron, steel, titanium, etc.), however there is still much to be learned in regards to these transformations in biological materials. Olson and Hartman showed in 1982 that these transformations are also observed in bacterial flagella and T4 bacteriophage viral sheaths, allowing for propulsion of bacteria in a fluid environment and, for the virus, is responsible for the infection mechanism. This work demonstrates, using the bacterial flagella as an example, that these transformations can be modelled using thermodynamic methods that are also used to model the transformations in alloys. This thesis work attempts to explain the transformations that occur in bacterial flagella, which are capable of small strain, highly reversible martensitic transformations. The first stress/temperature phase diagrams of these flagella were created by adding the mechanical energy of the transformation of the flagella to limited chemical thermodynamics information of the transformation. Mechanical energy is critical to the transformation process because the bacterial body applies a torque to the radius of the flagella. Finally, work has begun and will be completed in regards to understanding the kinetics of the transformation of the flagella. The motion of the transformation interface can be predicted by using a Landau-Ginzburg model. The crystallography of the transformation in bacterial flagella is also being computed to determine the invariant lines of transformation that occur within this cylindrical crystal. This work has shown that it is possible to treat proteins in a similar manner that alloys are treated when using thermodynamic modelling. Much can be learned from translating what is known regarding phase transformations in hard material systems to soft, organic

Substrate type and free ammonia determine bacterial community structure in full-scale mesophilic anaerobic digesters treating cattle or swine manure

Directory of Open Access Journals (Sweden)

Jiabao eLi

2015-11-01

Full Text Available The microbial-mediated anaerobic digestion (AD process represents an efficient biological process for the treatment of organic waste along with biogas harvest. Currently, the key factors structuring bacterial communities and the potential core and unique bacterial populations in manure anaerobic digesters are not completely elucidated yet. In this study, we collected sludge samples from 20 full-scale anaerobic digesters treating cattle or swine manure, and investigated the variations of bacterial community compositions using high-throughput 16S rRNA amplicon sequencing. Clustering and correlation analysis suggested that substrate type and free ammonia (FA play key roles in determining the bacterial community structure. The COD: NH4+-N (C:N ratio of substrate and FA were the most important available operational parameters correlating to the bacterial communities in cattle and swine manure digesters, respectively. The bacterial populations in all of the digesters were dominated by phylum Firmicutes, followed by Bacteroidetes, Proteobacteria and Chloroflexi. Increased FA content selected Firmicutes, suggesting that they probably play more important roles under high FA content. Syntrophic metabolism by Proteobacteria, Chloroflexi, Synergistetes and Planctomycetes are likely inhibited when FA content is high. Despite the different manure substrates, operational conditions and geographical locations of digesters, core bacterial communities were identified. The core communities were best characterized by phylum Firmicutes, wherein Clostridium predominated overwhelmingly. Substrate-unique and abundant communities may reflect the properties of manure substrate and operational conditions. These findings extend our current understanding of the bacterial assembly in full-scale manure anaerobic digesters.

White blood cell count, absolute neutrophil count, as predictors of hidden bacterial infections in febrile children 1-18 months of age without focus

International Nuclear Information System (INIS)

AL-Majali, R.M.

2004-01-01

Objectives: To study the relationship between White Blood Cell (WBC), Absolute Neutrophil Count (ANC) in febrile children 1-18 months of age as predictor of bacterial infection, so as to improve our predictability of bacterial infections in emergency room to decrease unnecessary admissions and antibiotic use. Methods: Retrospective review was performed on febrile patients 1-18 months of age that were admitted to hospital between August 2002 and March 2003 on the presumptive diagnosis of fever without focus, Complete septic work up was done for all patients according to local hospital protocol including Complete blood count (CBC), blood culture, urine culture, Chest X-Ray (CXR) and lumbar puncture, Patients who had history of antibiotics use within 48 hours of admission were excluded from the study, History, physical examination, laboratory and radiology data were reviewed. Data about the age, sex, temperature, presence or absence of focal bacterial infection, WBC, ANC, CXR report and body fluid culture results were collected and analyzed. Results: Thirty-four patients were reviewed in this study, Eight patients (23.5%) had bacterial infection: classified as group (2 patchy pneumonia, 3 Urinary tract infection (UTI), 2 meningitis, 1 Occult bacteremia (OB) and 26 patients (76.5%) had no evidence of bacterial infection, classified as group 2, No significant difference was found between the two groups in respect to age, sex, temperature and WBC P>0.05, while there was a significant difference between the two groups in respect to the ANC P = 0.02, also ANC had better sensitivity (78%) and specificity (89%) than WBC (sensitivity 77%, specificity 62%). Conclusion: ANC is a good predictive test for determining bacterial infection in young febrile children without focus, However there is need for other more reliable rapid cost effective measures in dealing with young febrile children at emergency department. (author)

Significant relationship between soil bacterial community structure and incidence of bacterial wilt disease under continuous cropping system.

Science.gov (United States)

She, Siyuan; Niu, Jiaojiao; Zhang, Chao; Xiao, Yunhua; Chen, Wu; Dai, Linjian; Liu, Xueduan; Yin, Huaqun

2017-03-01

Soil bacteria are very important in biogeochemical cycles and play significant role in soil-borne disease suppression. Although continuous cropping is responsible for soil-borne disease enrichment, its effect on tobacco plant health and how soil bacterial communities change are yet to be elucidated. In this study, soil bacterial communities across tobacco continuous cropping time-series fields were investigated through high-throughput sequencing of 16S ribosomal RNA genes. The results showed that long-term continuous cropping could significantly alter soil microbial communities. Bacterial diversity indices and evenness indices decreased over the monoculture span and obvious variations for community structures across the three time-scale tobacco fields were detected. Compared with the first year, the abundances of Arthrobacter and Lysobacter showed a significant decrease. Besides, the abundance of the pathogen Ralstonia spp. accumulated over the monoculture span and was significantly correlated with tobacco bacterial wilt disease rate. Moreover, Pearson's correlation demonstrated that the abundance of Arthrobacter and Lysobacter, which are considered to be beneficial bacteria had significant negative correlation with tobacco bacterial wilt disease. Therefore, after long-term continuous cropping, tobacco bacterial wilt disease could be ascribed to the alteration of the composition as well as the structure of the soil microbial community.

Nutritional and fermentation parameters of Xaraés grass silage produced with bacterial additive

Directory of Open Access Journals (Sweden)

Erickson Tiago Pinheiro da Silva

2014-07-01

Full Text Available The use of bacterial additives in forage silages with low content of dry matter prevents undesirable fermentation and reduces losses by gases (PG and effluents (PE during the ensiling process. This study aimed to evaluate the fermentation parameters, chemical composition and in vitro digestibility of silage of Urochloa brizantha cv. Xaraés produced with bacterial additive. The inoculant contained the following strains: Propionibacterium acidipropionici + Lactobacillus plantarum; Lactobacillus buchnari; Propionibacterium acipropionici + commercial enzymes and Lactobacillus plantarum and Pediococcus pentosaccus, at 0, 25, 50, 75, 100, and 125% of the recommended level for sugarcane (2 g ton-1. The experiment was a completely randomized design with four replications, and six levels of inoculant (0, 25, 50, 75, 100, and 125%. There was a quadratic relationship between the inoculant addition and the levels of pH, PE, DMIVD, NDF, ADF and LIG of the silage. PG and MM increased linearly with the addition of inoculant. The N-NH3, DM, CP, CEL, HEM and EE were not affected by the inoculant. Bacterial additive at 50% provided increased DMIVD. Appropriate values were found for pH and NH3.

Temperate bacterial viruses as double-edged swords in bacterial warfare.

Science.gov (United States)

Gama, João Alves; Reis, Ana Maria; Domingues, Iolanda; Mendes-Soares, Helena; Matos, Ana Margarida; Dionisio, Francisco

2013-01-01

It has been argued that bacterial cells may use their temperate viruses as biological weapons. For instance, a few bacterial cells among a population of lysogenic cells could release the virus and kill susceptible non-lysogenic competitors, while their clone mates would be immune. Because viruses replicate inside their victims upon infection, this process would amplify their number in the arena. Sometimes, however, temperate viruses spare recipient cells from death by establishing themselves in a dormant state inside cells. This phenomenon is called lysogenization and, for some viruses such as the λ virus, the probability of lysogenization increases with the multiplicity of infection. Therefore, the amplification of viruses leads to conflicting predictions about the efficacy of temperate viruses as biological weapons: amplification can increase the relative advantage of clone mates of lysogens but also the likelihood of saving susceptible cells from death, because the probability of lysogenization is higher. To test the usefulness of viruses as biological weapons, we performed competition experiments between lysogenic Escherichia coli cells carrying the λ virus and susceptible λ-free E. coli cells, either in a structured or unstructured habitat. In structured and sometimes in unstructured habitats, the λ virus qualitatively behaved as a "replicating toxin". However, such toxic effect of λ viruses ceased after a few days of competition. This was due to the fact that many of initially susceptible cells became lysogenic. Massive lysogenization of susceptible cells occurred precisely under the conditions where the amplification of the virus was substantial. From then on, these cells and their descendants became immune to the λ virus. In conclusion, if at short term bacterial cells may use temperate viruses as biological weapons, after a few days only the classical view of temperate bacterial viruses as parasitic agents prevails.

Temperate bacterial viruses as double-edged swords in bacterial warfare.

Directory of Open Access Journals (Sweden)

João Alves Gama

Full Text Available It has been argued that bacterial cells may use their temperate viruses as biological weapons. For instance, a few bacterial cells among a population of lysogenic cells could release the virus and kill susceptible non-lysogenic competitors, while their clone mates would be immune. Because viruses replicate inside their victims upon infection, this process would amplify their number in the arena. Sometimes, however, temperate viruses spare recipient cells from death by establishing themselves in a dormant state inside cells. This phenomenon is called lysogenization and, for some viruses such as the λ virus, the probability of lysogenization increases with the multiplicity of infection. Therefore, the amplification of viruses leads to conflicting predictions about the efficacy of temperate viruses as biological weapons: amplification can increase the relative advantage of clone mates of lysogens but also the likelihood of saving susceptible cells from death, because the probability of lysogenization is higher. To test the usefulness of viruses as biological weapons, we performed competition experiments between lysogenic Escherichia coli cells carrying the λ virus and susceptible λ-free E. coli cells, either in a structured or unstructured habitat. In structured and sometimes in unstructured habitats, the λ virus qualitatively behaved as a "replicating toxin". However, such toxic effect of λ viruses ceased after a few days of competition. This was due to the fact that many of initially susceptible cells became lysogenic. Massive lysogenization of susceptible cells occurred precisely under the conditions where the amplification of the virus was substantial. From then on, these cells and their descendants became immune to the λ virus. In conclusion, if at short term bacterial cells may use temperate viruses as biological weapons, after a few days only the classical view of temperate bacterial viruses as parasitic agents prevails.

Bacterial disease management: challenges, experience, innovation and future prospects: Challenges in Bacterial Molecular Plant Pathology.

Science.gov (United States)

Sundin, George W; Castiblanco, Luisa F; Yuan, Xiaochen; Zeng, Quan; Yang, Ching-Hong

2016-12-01

Plant diseases caused by bacterial pathogens place major constraints on crop production and cause significant annual losses on a global scale. The attainment of consistent effective management of these diseases can be extremely difficult, and management potential is often affected by grower reliance on highly disease-susceptible cultivars because of consumer preferences, and by environmental conditions favouring pathogen development. New and emerging bacterial disease problems (e.g. zebra chip of potato) and established problems in new geographical regions (e.g. bacterial canker of kiwifruit in New Zealand) grab the headlines, but the list of bacterial disease problems with few effective management options is long. The ever-increasing global human population requires the continued stable production of a safe food supply with greater yields because of the shrinking areas of arable land. One major facet in the maintenance of the sustainability of crop production systems with predictable yields involves the identification and deployment of sustainable disease management solutions for bacterial diseases. In addition, the identification of novel management tactics has also come to the fore because of the increasing evolution of resistance to existing bactericides. A number of central research foci, involving basic research to identify critical pathogen targets for control, novel methodologies and methods of delivery, are emerging that will provide a strong basis for bacterial disease management into the future. Near-term solutions are desperately needed. Are there replacement materials for existing bactericides that can provide effective disease management under field conditions? Experience should inform the future. With prior knowledge of bactericide resistance issues evolving in pathogens, how will this affect the deployment of newer compounds and biological controls? Knowledge is critical. A comprehensive understanding of bacterial pathosystems is required to not

Bacterial assemblages differ between compartments within the coral holobiont

Science.gov (United States)

Sweet, M. J.; Croquer, A.; Bythell, J. C.

2011-03-01

It is widely accepted that corals are associated with a diverse and host species-specific microbiota, but how they are organized within their hosts remains poorly understood. Previous sampling techniques (blasted coral tissues, coral swabs and milked mucus) may preferentially sample from different compartments such as mucus, tissue and skeleton, or amalgamate them, making comparisons and generalizations between studies difficult. This study characterized bacterial communities of corals with minimal mechanical disruption and contamination from water, air and sediments from three compartments: surface mucus layer (SML), coral tissue and coral skeleton. A novel apparatus (the `snot sucker') was used to separate the SML from tissues and skeleton, and these three compartments were compared to swab samples and milked mucus along with adjacent environmental samples (water column and sediments). Bacterial 16S rRNA gene diversity was significantly different between the various coral compartments and environmental samples (PERMANOVA, F = 6.9, df = 8, P = 0.001), the only exceptions being the complete crushed coral samples and the coral skeleton, which were similar, because the skeleton represents a proportionally large volume and supports a relatively rich microflora. Milked mucus differed significantly from the SML collected with the `snot sucker' and was contaminated with zooxanthellae, suggesting that it may originate at least partially from the gastrovascular cavity rather than the tissue surface. A common method of sampling the SML, surface swabs, produced a bacterial community profile distinct from the SML sampled using our novel apparatus and also showed contamination from coral tissues. Our results indicate that microbial communities are spatially structured within the coral holobiont, and methods used to describe these need to be standardized to allow comparisons between studies.

Analysis of bacterial communities and bacterial pathogens in a biogas plant by the combination of ethidium monoazide, PCR and Ion Torrent sequencing.

Science.gov (United States)

Luo, Gang; Angelidaki, Irini

2014-09-01

The present study investigated the changes of bacterial community composition including bacterial pathogens along a biogas plant, i.e. from the influent, to the biogas reactor and to the post-digester. The effects of post-digestion temperature and time on the changes of bacterial community composition and bacterial pathogens were also studied. Microbial analysis was made by Ion Torrent sequencing of the PCR amplicons from ethidium monoazide treated samples, and ethidium monoazide was used to cleave DNA from dead cells and exclude it from PCR amplification. Both similarity and taxonomic analysis showed that the bacterial community composition in the influent was changed after anaerobic digestion. Firmicutes were dominant in all the samples, while Proteobacteria decreased in the biogas reactor compared with the influent. Variations of bacterial community composition in the biogas reactor with time were also observed. This could be attributed to varying composition of the influent. Batch experiments showed that the methane recovery from the digested residues (obtained from biogas reactor) was mainly related with post-digestion temperature. However, post-digestion time rather than temperature had a significant effect on the changes of bacterial community composition. The changes of bacterial community composition were also reflected in the changes of relative abundance of bacterial pathogens. The richness and relative abundance of bacterial pathogens were reduced after anaerobic digestion in the biogas reactor. It was found in batch experiments that bacterial pathogens showed the highest relative abundance and richness after 30 days' post-digestion. Streptococcus bovis was found in all the samples. Our results showed that special attention should be paid to the post-digestion since the increase in relative abundance of bacterial pathogens after post-digestion might reflect regrowth of bacterial pathogens and limit biosolids disposal vectors. Copyright © 2014 Elsevier

Non-homogeneous flow profiles in sheared bacterial suspensions

Science.gov (United States)

Samanta, Devranjan; Cheng, Xiang

Bacterial suspensions under shear exhibit interesting rheological behaviors including the remarkable ``superfluidic'' state with vanishing viscosity at low shear rates. Theoretical studies have shown that such ``superfluidic'' state is linked with non-homogeneous shear flows, which are induced by coupling between nematic order of active fluids and hydrodynamics of shear flows. However, although bulk rheology of bacterial suspensions has been experimentally studied, shear profiles within bacterial suspensions have not been explored so far. Here, we experimentally investigate the flow behaviors of E. coli suspensions under planar oscillatory shear. Using confocal microscopy and PIV, we measure velocity profiles across gap between two shear plates. We find that with increasing shear rates, high-concentration bacterial suspensions exhibit an array of non-homogeneous flow behaviors like yield-stress flows and shear banding. We show that these non-homogeneous flows are due to collective motion of bacterial suspensions. The phase diagram of sheared bacterial suspensions is systematically mapped as functions of shear rates an bacterial concentrations. Our experiments provide new insights into rheology of bacterial suspensions and shed light on shear induced dynamics of active fluids. Chemical Engineering and Material Science department.

Bacterial reproductive pathogens of cats and dogs.

Science.gov (United States)

Graham, Elizabeth M; Taylor, David J

2012-05-01

With the notable exception of Brucella canis, exogenous bacterial pathogens are uncommon causes of reproductive disease in cats and dogs. Most bacterial reproductive infections are endogenous, and predisposing factors for infection are important. This article reviews the etiology, pathogenesis, clinical presentation, diagnosis, treatment, and public health significance of bacterial reproductive pathogens in cats and dogs.

Bacterial Community Succession in Pine-Wood Decomposition.

Science.gov (United States)

Kielak, Anna M; Scheublin, Tanja R; Mendes, Lucas W; van Veen, Johannes A; Kuramae, Eiko E

2016-01-01

Though bacteria and fungi are common inhabitants of decaying wood, little is known about the relationship between bacterial and fungal community dynamics during natural wood decay. Based on previous studies involving inoculated wood blocks, strong fungal selection on bacteria abundance and community composition was expected to occur during natural wood decay. Here, we focused on bacterial and fungal community compositions in pine wood samples collected from dead trees in different stages of decomposition. We showed that bacterial communities undergo less drastic changes than fungal communities during wood decay. Furthermore, we found that bacterial community assembly was a stochastic process at initial stage of wood decay and became more deterministic in later stages, likely due to environmental factors. Moreover, composition of bacterial communities did not respond to the changes in the major fungal species present in the wood but rather to the stage of decay reflected by the wood density. We concluded that the shifts in the bacterial communities were a result of the changes in wood properties during decomposition and largely independent of the composition of the wood-decaying fungal communities.

Coral-Associated Bacterial Diversity is Conserved Across Two Deep-Sea Anthothela Species

Directory of Open Access Journals (Sweden)

Stephanie Nichole Lawler

2016-04-01

Full Text Available Cold-water corals, similar to tropical corals, contain diverse and complex microbial assemblages. These bacteria provide essential biological functions within coral holobionts, facilitating increased nutrient utilization and production of antimicrobial compounds. To date, few cold-water octocoral species have been analyzed to explore the diversity and abundance of their microbial associates. For this study, 23 samples of the family Anthothelidae were collected from Norfolk (n = 12 and Baltimore Canyons (n = 11 from the western Atlantic in August 2012 and May 2013. Genetic testing found that these samples comprised two Anthothela species (Anthothela grandiflora and Anthothela sp. and Alcyonium grandiflorum. DNA was extracted and sequenced with primers targeting the V4-V5 variable region of the 16S rRNA gene using 454 pyrosequencing with GS FLX Titanium chemistry. Results demonstrated that the coral host was the primary driver of bacterial community composition. Al. grandiflorum, dominated by Alteromonadales and Pirellulales had much higher species richness, and a distinct bacterial community compared to Anthothela samples. Anthothela species (A. grandiflora and Anthothela sp. had very similar bacterial communities, dominated by Oceanospirillales and Spirochaetes. Additional analysis of core-conserved bacteria at 90% sample coverage revealed genus level conservation across Anthothela samples. This core included unclassified Oceanospirillales, Kiloniellales, Campylobacterales, and genus Spirochaeta. Members of this core were previously recognized for their functional capabilities in nitrogen cycling and suggest the possibility of a nearly complete nitrogen cycle within Anthothela species. Overall, many of the bacterial associates identified in this study have the potential to contribute to the acquisition and cycling of nutrients within the coral holobiont.

Spontaneous Bacterial Peritonitis in Subclinical Hypothyroidism

Directory of Open Access Journals (Sweden)

Dalip Gupta

2013-11-01

Full Text Available Hypothyroidism is an uncommon cause of ascites. Here we describe a case of a 75 year-old female patient with spontaneous bacterial peritonitis and subclinical hypothyroidism that resolved with thyroid replacement and antibiotic therapy respectively. Ascitic fluid analysis revealed a gram-positive bacterium on gram staining. A review of the literature revealed just one other reported case of myxoedema ascites with concomitant spontaneous bacterial peritonitis and no case has till been reported of spontaneous bacterial peritonitis in subclinical hypothyroidism.

Electrical conductivity measurements of bacterial nanowires from Pseudomonas aeruginosa

International Nuclear Information System (INIS)

Maruthupandy, Muthusamy; Anand, Muthusamy; Beevi, Akbar Sait Hameedha; Priya, Radhakrishnan Jeeva; Maduraiveeran, Govindhan

2015-01-01

The extracellular appendages of bacteria (flagella) that transfer electrons to electrodes are called bacterial nanowires. This study focuses on the isolation and separation of nanowires that are attached via Pseudomonas aeruginosa bacterial culture. The size and roughness of separated nanowires were measured using transmission electron microscopy (TEM) and atomic force microscopy (AFM), respectively. The obtained bacterial nanowires indicated a clear image of bacterial nanowires measuring 16 nm in diameter. The formation of bacterial nanowires was confirmed by microscopic studies (AFM and TEM) and the conductivity nature of bacterial nanowire was investigated by electrochemical techniques. Cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS), which are nondestructive voltammetry techniques, suggest that bacterial nanowires could be the source of electrons—which may be used in various applications, for example, microbial fuel cells, biosensors, organic solar cells, and bioelectronic devices. Routine analysis of electron transfer between bacterial nanowires and the electrode was performed, providing insight into the extracellular electron transfer (EET) to the electrode. CV revealed the catalytic electron transferability of bacterial nanowires and electrodes and showed excellent redox activities. CV and EIS studies showed that bacterial nanowires can charge the surface by producing and storing sufficient electrons, behave as a capacitor, and have features consistent with EET. Finally, electrochemical studies confirmed the development of bacterial nanowires with EET. This study suggests that bacterial nanowires can be used to fabricate biomolecular sensors and nanoelectronic devices. (paper)

Bacterial stress

Indian Academy of Sciences (India)

First page Back Continue Last page Graphics. Bacterial stress. Physicochemical and chemical parameters: temperature, pressure, pH, salt concentration, oxygen, irradiation. Nutritional depravation: nutrient starvation, water shortage. Toxic compounds: Antibiotics, heavy metals, toxins, mutagens. Interactions with other cells: ...

Diagnosis and treatment of bacterial prostatitis.

Science.gov (United States)

Videčnik Zorman, Jerneja; Matičič, Mojca; Jeverica, Samo; Smrkolj, Tomaž

2015-01-01

Prostate inflammation is a common syndrome, especially in men under 50. It usually presents with voiding symptoms and pain in the genitourinary area, and sometimes as sexual dysfunction. Based on clinical and laboratory characteristics, prostatitis is classified as acute bacterial prostatitis, chronic bacterial prostatitis, chronic inflammatory and non-inflammatory prostatitis or chronic pelvic pain syndrome, and asymptomatic inflammatory prostatitis. Bacterial prostatitis is most often caused by infection with uropathogens, mainly Gram-negative bacilli, but Gram-positive and atypical microorganisms have also been identified as causative organisms of chronic prostatitis. According to reports by several authors, Chlamydia trachomatis and Trichomonas vaginalis are some of the most common pathogens, making chronic prostatitis a sexually transmitted disease. Diagnosis and treatment of acute and chronic bacterial prostatitis in particular can be challenging.

Bacterial endophytes enhance competition by invasive plants.

Science.gov (United States)

Rout, Marnie E; Chrzanowski, Thomas H; Westlie, Tara K; DeLuca, Thomas H; Callaway, Ragan M; Holben, William E

2013-09-01

Invasive plants can alter soil microbial communities and profoundly alter ecosystem processes. In the invasive grass Sorghum halepense, these disruptions are consequences of rhizome-associated bacterial endophytes. We describe the effects of N2-fixing bacterial strains from S. halepense (Rout and Chrzanowski, 2009) on plant growth and show that bacteria interact with the plant to alter soil nutrient cycles, enabling persistence of the invasive. • We assessed fluxes in soil nutrients for ∼4 yr across a site invaded by S. halepense. We assayed the N2-fixing bacteria in vitro for phosphate solubilization, iron chelation, and production of the plant-growth hormone indole-3-acetic acid (IAA). We assessed the plant's ability to recruit bacterial partners from substrates and vertically transmit endophytes to seeds and used an antibiotic approach to inhibit bacterial activity in planta and assess microbial contributions to plant growth. • We found persistent alterations to eight biogeochemical cycles (including nitrogen, phosphorus, and iron) in soils invaded by S. halepense. In this context, three bacterial isolates solubilized phosphate, and all produced iron siderophores and IAA in vitro. In growth chamber experiments, bacteria were transmitted vertically, and molecular analysis of bacterial community fingerprints from rhizomes indicated that endophytes are also horizontally recruited. Inhibiting bacterial activity with antibiotics resulted in significant declines in plant growth rate and biomass, with pronounced rhizome reductions. • This work suggests a major role of endophytes on growth and resource allocation of an invasive plant. Indeed, bacterial isolate physiology is correlated with invader effects on biogeochemical cycles of nitrogen, phosphate, and iron.

Autophagy and bacterial clearance: a not so clear picture

OpenAIRE

Mostowy, Serge

2012-01-01

Autophagy, an intracellular degradation process highly conserved from yeast to humans, is viewed as an important defence mechanism to clear intracellular bacteria. However, recent work has shown that autophagy may have different roles during different bacterial infections that restrict bacterial replication (antibacterial autophagy), act in cell autonomous signalling (non-bacterial autophagy) or support bacterial replication (pro-bacterial autophagy). This review will focus on newfound intera...

Elucidating Duramycin’s Bacterial Selectivity and Mode of Action on the Bacterial Cell Envelope

Directory of Open Access Journals (Sweden)

Sahar Hasim

2018-02-01

Full Text Available The use of naturally occurring antimicrobial peptides provides a promising route to selectively target pathogenic agents and to shape microbiome structure. Lantibiotics, such as duramycin, are one class of bacterially produced peptidic natural products that can selectively inhibit the growth of other bacteria. However, despite longstanding characterization efforts, the microbial selectivity and mode of action of duramycin are still obscure. We describe here a suite of biological, chemical, and physical characterizations that shed new light on the selective and mechanistic aspects of duramycin activity. Bacterial screening assays have been performed using duramycin and Populus-derived bacterial isolates to determine species selectivity. Lipidomic profiles of selected resistant and sensitive strains show that the sensitivity of Gram-positive bacteria depends on the presence of phosphatidylethanolamine (PE in the cell membrane. Further the surface and interface morphology were studied by high resolution atomic force microscopy and showed a progression of cellular changes in the cell envelope after treatment with duramycin for the susceptible bacterial strains. Together, these molecular and cellular level analyses provide insight into duramycin’s mode of action and a better understanding of its selectivity.

Combined carbon and nitrogen removal from acetonitrile using algal-bacterial bioreactors

Energy Technology Data Exchange (ETDEWEB)

Munoz, R.; Jacinto, M.; Guieysse, B.; Mattiasson, B. [Dept. of Biotechnology, Center for Chemistry and Chemical Engineering, Lund Univ., Lund (Sweden)

2005-06-01

When compared with Chlorella vulgaris, Scenedesmus obliquus and Selenastrum capricornutum, C. sorokiniana presented the highest tolerance to acetonitrile and the highest O{sub 2} production capacity. It also supported the fastest acetonitrile biodegradation when mixed with a suitable acetonitrile-degrading bacterial consortium. Consequently, this microalga was tested in symbiosis with the bacterial culture for the continuous biodegradation of acetonitrile at 2 g l{sup -1} in a stirred tank photobioreactor and in a column photobioreactor under continuous illumination (250 {mu}E m{sup -2} s{sup -1}). Acetonitrile removal rates of up to 2.3 g l{sup -1} day{sup -1} and 1.9 g l{sup -1} day{sup -1} were achieved in the column photobioreactor and the stirred-tank photobioreactor, respectively, when operated at the shortest retention times tested (0.4 days, 0.6 days, respectively). In addition, when the stirred-tank photobioreactor was operated with a retention time of 3.5 days, the microbial culture was capable of assimilating up to 71% and nitrifying up to 12% of the NH{sub 4}{sup +} theoretically released through the biodegradation of acetonitrile, thus reducing the need for subsequent nitrogen removal. This study suggests that complete removal of N-organics can be combined with a significant removal of nitrogen by using algal-bacterial systems and that further residual biomass digestion could pay-back part of the operation costs of the treatment plant. (orig.)

Bacterial meningitis

NARCIS (Netherlands)

Heckenberg, Sebastiaan G. B.; Brouwer, Matthijs C.; van de Beek, Diederik

2014-01-01

Bacterial meningitis is a neurologic emergency. Vaccination against common pathogens has decreased the burden of disease. Early diagnosis and rapid initiation of empiric antimicrobial and adjunctive therapy are vital. Therapy should be initiated as soon as blood cultures have been obtained,

Plasmids foster diversification and adaptation of bacterial populations in soil.

Science.gov (United States)

Heuer, Holger; Smalla, Kornelia

2012-11-01

It is increasingly being recognized that the transfer of conjugative plasmids across species boundaries plays a vital role in the adaptability of bacterial populations in soil. There are specific driving forces and constraints of plasmid transfer within bacterial communities in soils. Plasmid-mediated genetic variation allows bacteria to respond rapidly with adaptive responses to challenges such as irregular antibiotic or metal concentrations, or opportunities such as the utilization of xenobiotic compounds. Cultivation-independent detection and capture of plasmids from soil bacteria, and complete sequencing have provided new insights into the role and ecology of plasmids. Broad host range plasmids such as those belonging to IncP-1 transfer a wealth of accessory functions which are carried by similar plasmid backbones. Plasmids with a narrower host range can be more specifically adapted to particular species and often transfer genes which complement chromosomally encoded functions. Plasmids seem to be an ancient and successful strategy to ensure survival of a soil population in spatial and temporal heterogeneous conditions with various environmental stresses or opportunities that occur irregularly or as a novel challenge in soil. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Antimicrobial susceptibility in community-acquired bacterial ...

African Journals Online (AJOL)

Objectives: To determine the antimicrobial susceptibility patterns of Streptococcus pneumoniae and Haemophilus influenzae, two bacterial pathogens commonly associated with communityacquired pneumonia. Design: Cross-sectional study. Setting: Bacterial isolates were obtained from adults suspected to have ...

Calcium phosphate coating containing silver shows high antibacterial activity and low cytotoxicity and inhibits bacterial adhesion

Energy Technology Data Exchange (ETDEWEB)

Ando, Yoshiki, E-mail: andoy@jmmc.jp [Division of Microbiology, Department of Pathology and Microbiology, Faculty of Medicine, Saga University, 5-1-1 Nabeshima, Saga 849-8501 (Japan); Research Department, Japan Medical Materials Corporation, Uemura Nissei Bldg.9F 3-3-31 Miyahara, Yodogawa-ku, Osaka 532-0003 (Japan); Miyamoto, Hiroshi [Division of Microbiology, Department of Pathology and Microbiology, Faculty of Medicine, Saga University, 5-1-1 Nabeshima, Saga 849-8501 (Japan); Noda, Iwao; Sakurai, Nobuko [Research Department, Japan Medical Materials Corporation, Uemura Nissei Bldg.9F 3-3-31 Miyahara, Yodogawa-ku, Osaka 532-0003 (Japan); Akiyama, Tomonori [Division of Microbiology, Department of Pathology and Microbiology, Faculty of Medicine, Saga University, 5-1-1 Nabeshima, Saga 849-8501 (Japan); Yonekura, Yutaka; Shimazaki, Takafumi; Miyazaki, Masaki; Mawatari, Masaaki; Hotokebuchi, Takao [Department of Orthopaedic Surgery, Faculty of Medicine, Saga University, 5-1-1 Nabeshima, Saga 849-8501 (Japan)

2010-01-01

Surgical site infection is one of the serious complications of orthopedic implants. In order to reduce the incidence of implant-associated infections, we developed a novel coating technology of calcium phosphate (CP) containing silver (Ag), designated Ag-CP coating, using a thermal spraying technique. In this study, we evaluated the antibacterial efficacy and biological safety of this coating. In vitro antibacterial activity tests showed that the growths of Escherichia coli, Staphylococcus aureus and methicillin-resistant S. aureus (MRSA) are completely suppressed on Ag-CP coating. In vitro bacterial adherence tests revealed that the number of adherent bacteria on the surface of this coating is significantly less (p < 0.02) than that on the surface of the CP coating. Moreover, the Ag-CP coating completely inhibits MRSA adhesion [<10 colony-forming units (CFU)] when 10{sup 2} CFU MRSA is inoculated. On the other hand, V79 Chinese hamster lung cells were found to grow on the Ag-CP coating as well as on the CP coating in a cytotoxicity test. These results indicate that the Ag-CP coating on the surface of orthopedic implants exhibits antibacterial activity and inhibits bacterial adhesion without cytotoxicity.

Bovine milk osteopontin - Targeting bacterial adhesion for biofilm control

DEFF Research Database (Denmark)

Kristensen, Mathilde Frost; Meyer, Rikke Louise; Schlafer, Sebastian

2016-01-01

Self-performed mechanical tooth cleaning does usually not result in complete biofilm removal, due to the complex oral anatomy and the strong adhesion of the biofilm to the tooth. Therefore, different supportive measures are employed, most of which aim at the chemical eradication of bacteria...... in dental biofilms. As their bactericidal action impacts the entire oral microflora, agents that inhibit biofilm formation without killing bacteria, such as the bovine milk protein osteopontin, have gained increasing attention. Here, we investigate the adhesion of 8 bacterial species associated with dental...... subsp. paracasei, Streptococcus mitis and Streptococcus oralis with 74.0%, 62.4%, 90.0%, 89.6% and 81.5%, respectively, compared to protein-free saliva. All reductions were statistically significant (p

Recurrent bacterial meningitis in a child with mondini dysplasia.

Science.gov (United States)

Kepenekli-Kadayifci, Eda; Karaaslan, Ayşe; Atıcı, Serkan; Binnetoğlu, Adem; Sarı, Murat; Soysal, Ahmet; Altınkanat, Gülşen; Bakır, Mustafa

2014-01-01

Mondini dysplasia, also known as Mondini malformation, is a developmental abnormality of the inner and middle ears that can cause hearing loss, cerebrospinal fluid (CSF) leakage, and recurrent bacterial meningitis (RBM), which is defined as two or more episodes of meningitis separated by a period of convalescence and the complete resolution of all signs and symptoms. An accurate diagnosis of the underlying pathology is crucial to prevent further episodes from occurring. Herein, we present a three-year-old boy with RBM and unilateral sensorineural hearing loss. During the evaluation to determine the etiology of the RBM, cystic malformation in the cochlea and vestibular dilatation consistent with Mondini dysplasia were detected via computerized tomography (CT) of the temporal bone.

Peritonitis - spontaneous bacterial

Science.gov (United States)

Spontaneous bacterial peritonitis (SBP); Ascites - peritonitis; Cirrhosis - peritonitis ... who are on peritoneal dialysis for kidney failure. Peritonitis may have other causes . These include infection from ...

Bacterial lipases

NARCIS (Netherlands)

Jaeger, Karl-Erich; Ransac, Stéphane; Dijkstra, Bauke W.; Colson, Charles; Heuvel, Margreet van; Misset, Onno

Many different bacterial species produce lipases which hydrolyze esters of glycerol with preferably long-chain fatty acids. They act at the interface generated by a hydrophobic lipid substrate in a hydrophilic aqueous medium. A characteristic property of lipases is called interfacial activation,

Stimulation of bacterial DNA synthesis by algal exudates in attached algal-bacterial consortia

International Nuclear Information System (INIS)

Murray, R.E.; Cooksey, K.E.; Priscu, J.C.

1986-01-01

Algal-bacterial consortia attached to polystyrene surfaces were prepared in the laboratory by using the marine diatom Amphora coffeaeformis and the marine bacterium Vibrio proteolytica (the approved name of this bacterium is Vibrio proteolyticus. The organisms were attached to the surfaces at cell densities of approximately 5 x 10 4 cells cm -2 (diatoms) and 5 x 10 6 cells cm -2 (bacteria). The algal-bacterial consortia consistently exhibited higher rates of [ 3 H]thymidine incorporation than did biofilms composed solely of bacteria. The rates of [ 3 H]thymidine incorporation by the algal-bacterial consortia were fourfold greater than the rates of incorporation by monobacterial biofilms 16 h after biofilm formation and were 16-fold greater 70 h after biofilm formation. Extracellular material released from the attached Amphora cells supported rates of bacterial activity (0.8 x 10 -21 mol to 17.9 x 10 -21 mol of [ 3 H]thymidine incorporated cell -1 h -1 ) and growth (doubling time, 29.5 to 1.4 days) comparable to values reported for a wide variety of marine and freshwater ecosystems. In the presence of sessile diatom populations, DNA synthesis by attached V. proteolytica cells was light dependent and increased with increasing algal abundance. The metabolic activity of diatoms thus appears to be the rate-limiting process in biofilm development on illuminated surfaces under conditions of low bulk-water dissolved organic carbon

Effects of sulfadiazine on soil bacterial communities

DEFF Research Database (Denmark)

Hangler, Martin

as fertilizers on agricultural lands they represent a route for antibiotics into the soil environment where they may persist and affect levels of antibiotic resistance in soil microbial communities over time. In this work the level of tolerance to the antibiotic sulfadiazine (SDZ) was studied in a number......Combating bacterial infections by antibiotic treatment is one of the greatest achievements in medicine. However, once administered antibiotic compounds are often not metabolized completely in humans and animals and are thus excreted, eventually ending up in sewage sludge or manure. As both are used......, whereas only a very weak PICT response was found for unfertilized soil. In conclusion, I show that fertilized soils are more conducive for PICT development, and therefore presumably also for selection of antibiotic resistance in individual bacteria, than unfertilized soil and that SDZ-loaded sludge can...

Bacterial cells with improved tolerance to isobutyric acid

DEFF Research Database (Denmark)

2017-01-01

Bacterial cells genetically modified to improve their tolerance to certain commodity chemicals, such as isobutyric acid and related compounds, and methods of preparing and using such bacterial cells for production of isobutyric acid and related compounds.......Bacterial cells genetically modified to improve their tolerance to certain commodity chemicals, such as isobutyric acid and related compounds, and methods of preparing and using such bacterial cells for production of isobutyric acid and related compounds....

Bacterial community succession in pine-wood decomposition

Directory of Open Access Journals (Sweden)

Anna eKielak

2016-03-01

Full Text Available Though bacteria and fungi are common inhabitants of decaying wood, little is known about the relationship between bacterial and fungal community dynamics during natural wood decay. Based on previous studies involving inoculated wood blocks, strong fungal selection on bacteria abundance and community composition was expected to occur during natural wood decay. Here we focused on bacterial and fungal community compositions in pine wood samples collected from dead trees in different stages of decomposition. We showed that bacterial communities undergo less drastic changes than fungal communities during wood decay. Furthermore, we found that bacterial community assembly was a stochastic process at initial stage of wood decay and became more deterministic in later stages, likely due to environmental factors. Moreover, composition of bacterial communities did not respond to the changes in the major fungal species present in the wood but rather to the stage of decay reflected by the wood density. We concluded that the shifts in the bacterial communities were a result of the changes in wood properties during decomposition and largely independent of the composition of the wood-decaying fungal communities.

First Reported Case of Bacterial Endocarditis Attributable to Actinomyces meyeri

Directory of Open Access Journals (Sweden)

Susan Moffatt

1996-01-01

Full Text Available A 48-year-old man presented to the Victoria General Hospital, Halifax, Nova Scotia in severe congestive heart failure. Echocardiographic studies revealed significant aortic valve insufficiency. Two anaerobic blood cultures performed two weeks apart were both positive for Actinomyces meyeri. The patient was treated with high dose intravenous penicillin. Three weeks after antibiotics were begun, he underwent aortic valve replacement. Intraoperative cultures were negative. Histopathological examination revealed findings in keeping with subacute bacterial endocarditis. The patient completed a six-week course of penicillin and was doing well three months after surgery. This is the first case of endocarditis attributable to A meyeri reported in the literature.

Flow cytometric bacterial cell counts challenge conventional heterotrophic plate counts for routine microbiological drinking water monitoring

KAUST Repository

Van Nevel, S.

2017-02-08

Drinking water utilities and researchers continue to rely on the century-old heterotrophic plate counts (HPC) method for routine assessment of general microbiological water quality. Bacterial cell counting with flow cytometry (FCM) is one of a number of alternative methods that challenge this status quo and provide an opportunity for improved water quality monitoring. After more than a decade of application in drinking water research, FCM methodology is optimised and established for routine application, supported by a considerable amount of data from multiple full-scale studies. Bacterial cell concentrations obtained by FCM enable quantification of the entire bacterial community instead of the minute fraction of cultivable bacteria detected with HPC (typically < 1% of all bacteria). FCM measurements are reproducible with relative standard deviations below 3% and can be available within 15 min of samples arriving in the laboratory. High throughput sample processing and complete automation are feasible and FCM analysis is arguably less expensive than HPC when measuring more than 15 water samples per day, depending on the laboratory and selected staining procedure(s). Moreover, many studies have shown FCM total (TCC) and intact (ICC) cell concentrations to be reliable and robust process variables, responsive to changes in the bacterial abundance and relevant for characterising and monitoring drinking water treatment and distribution systems. The purpose of this critical review is to initiate a constructive discussion on whether FCM could replace HPC in routine water quality monitoring. We argue that FCM provides a faster, more descriptive and more representative quantification of bacterial abundance in drinking water.

Flow cytometric bacterial cell counts challenge conventional heterotrophic plate counts for routine microbiological drinking water monitoring

KAUST Repository

Van Nevel, S.; Koetzsch, S.; Proctor, C.R.; Besmer, M.D.; Prest, E.I.; Vrouwenvelder, Johannes S.; Knezev, A.; Boon, N.; Hammes, F.

2017-01-01

Drinking water utilities and researchers continue to rely on the century-old heterotrophic plate counts (HPC) method for routine assessment of general microbiological water quality. Bacterial cell counting with flow cytometry (FCM) is one of a number of alternative methods that challenge this status quo and provide an opportunity for improved water quality monitoring. After more than a decade of application in drinking water research, FCM methodology is optimised and established for routine application, supported by a considerable amount of data from multiple full-scale studies. Bacterial cell concentrations obtained by FCM enable quantification of the entire bacterial community instead of the minute fraction of cultivable bacteria detected with HPC (typically < 1% of all bacteria). FCM measurements are reproducible with relative standard deviations below 3% and can be available within 15 min of samples arriving in the laboratory. High throughput sample processing and complete automation are feasible and FCM analysis is arguably less expensive than HPC when measuring more than 15 water samples per day, depending on the laboratory and selected staining procedure(s). Moreover, many studies have shown FCM total (TCC) and intact (ICC) cell concentrations to be reliable and robust process variables, responsive to changes in the bacterial abundance and relevant for characterising and monitoring drinking water treatment and distribution systems. The purpose of this critical review is to initiate a constructive discussion on whether FCM could replace HPC in routine water quality monitoring. We argue that FCM provides a faster, more descriptive and more representative quantification of bacterial abundance in drinking water.

Study of soil bacterial and crop quality irrigated with treated municipal wastewater

DEFF Research Database (Denmark)

Alinezhadian, A; Karim, A; Mohammadi, J

2014-01-01

Background and Objectives: In arid and semi-arid regions, wastewater reuse has become an important element in agriculture. However, irrigation with this resource can be either beneficial or harmful, depending on the wastewater characteristics. The aim of this research was to investigate the soil...... bacterial and crops quality irrigated with treated wastewater. Material and Methods: This research was conducted on a maize field near the wastewater treatment plant in Shahr-e-kord in summer,2011. Plots were arranged in a randomized complete block design in 3 replications and 2 treatments, well water (W1...

Endocarditis in adults with bacterial meningitis

NARCIS (Netherlands)

Lucas, Marjolein J.; Brouwer, Matthijs C.; van der Ende, Arie; van de Beek, Diederik

2013-01-01

Endocarditis may precede or complicate bacterial meningitis, but the incidence and impact of endocarditis in bacterial meningitis are unknown. We assessed the incidence and clinical characteristics of patients with meningitis and endocarditis from a nationwide cohort study of adults with

Comparison of topical fixed-combination fortified vancomycin-amikacin (VA solution) to conventional separate therapy in the treatment of bacterial corneal ulcer.

Science.gov (United States)

Chiang, C-C; Lin, J-M; Chen, W-L; Chiu, Y-T; Tsai, Y-Y

2009-02-01

In an in vitro study, fixed-combination fortified vancomycin and amikacin ophthalmic solutions (VA solution) had the same potency and stable physical properties as the separate components. In this retrospective clinical study, we evaluated the efficacy of the topical VA solution in the treatment of bacterial corneal ulcer and comparison with separate topical fortified vancomycin and amikacin. Separate topical fortified eye drops was used prior to January 2004 and switched to the VA solution afterwards in the treatment of bacterial corneal ulcer. The medical records of 223 patients diagnosed with bacterial corneal ulcers between January 2002 and December 2005 were reviewed retrospectively. There were 122 patients in the VA group and 101 in the separate group. Cure was defined as complete healing of the ulcer accompanied by a nonprogressive stromal infiltrate on two consecutive visits. No significant difference was found between the VA and separate therapy group. The mean treatment duration was 15.4 days in the VA group and 16.1 days in the separate therapy group. The average hospital stay was 5.4 days (VA) and 7.2 days (separate antibiotics). Stromal infiltration regressed significantly without further expansion in both groups. All corneal ulcers completely re-epithelialized without complications related to drugs. VA solution provided similar efficacy to the conventional separate therapy in the treatment of bacterial corneal ulcers; however, it is more convenient and tolerable, promotes patient's compliance, avoids the washout effect, and reduces nurse utilization. Hence, VA solution is a good alternative to separate therapy.

Bacterial Degradation of Aromatic Compounds

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Qing X. Li

2009-01-01

Full Text Available Aromatic compounds are among the most prevalent and persistent pollutants in the environment. Petroleum-contaminated soil and sediment commonly contain a mixture of polycyclic aromatic hydrocarbons (PAHs and heterocyclic aromatics. Aromatics derived from industrial activities often have functional groups such as alkyls, halogens and nitro groups. Biodegradation is a major mechanism of removal of organic pollutants from a contaminated site. This review focuses on bacterial degradation pathways of selected aromatic compounds. Catabolic pathways of naphthalene, fluorene, phenanthrene, fluoranthene, pyrene, and benzo[a]pyrene are described in detail. Bacterial catabolism of the heterocycles dibenzofuran, carbazole, dibenzothiophene, and dibenzodioxin is discussed. Bacterial catabolism of alkylated PAHs is summarized, followed by a brief discussion of proteomics and metabolomics as powerful tools for elucidation of biodegradation mechanisms.

Use of prebiotics and probiotics of bacterial and yeast origin for free-range broiler chickens

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K Pelícia

2004-09-01

Full Text Available This study aimed to evaluate the effects of probiotics and prebiotics of bacterial and yeast origin on the performance, development of the digestive system, carcass yield and meat quality of free-range broiler chickens. Five hundred and sixty male chicks of the strain ISA S757-N were reared from one to 84 days old. The birds were distributed in four treatments according to a completely randomized block design: T1 = Control, T2 = Probiotics and Prebiotics of bacterial origin, T3 = Probiotics and prebiotics of yeast origin, T4 = Probiotics and prebiotics of bacterial origin + probiotics and prebiotics of yeast origin. There were four repetitions with 35 birds per repetition, and the birds had access to a pasture area after 35 days of age. Characteristics evaluated were performance, development of the digestive system, carcass and parts yield, abdominal fat, breast meat physical measurements (length, width and height and meat quality parameters (pH from breast and leg meat, cooking loss and shearing force from breast meat. Lower mortality (p<0.05 and higher weight gain from 64 to 77 and 64 to 84 days of age were seen in birds supplemented with probiotics and prebiotics of bacterial origin compared to the non-supplemented birds (control. There were significant differences (p<0.05 among treatments for carcass yield. Birds supplemented with both probiotics and prebiotics of microbial and yeast origin (T4 showed higher carcass yield than control birds. Supplementation with probiotics and prebiotics of bacterial origin (T2 or the supplementation of these together with those of yeast origin (T4 reduced mortality and increased the carcass yield in free-range broiler chickens.

Microbiological and molecular identification of bacterial species isolated from nasal and oropharyngeal mucosa of fuel workers in Riyadh, Saudi Arabia.

Science.gov (United States)

AlWakeel, Suaad S

2017-09-01

This study aimed to determine the bacterial species colonizing the nasal and oropharyngeal mucosa of fuel workers in Central Riyadh, Saudi Arabia on a microbiological and molecular level. Throat and nasal swab samples were obtained from 29 fuel station attendants in the period of time extending from March to May 2014 in Riyadh, Saudi Arabia. Microbiological identification techniques were utilized to identify the bacterial species isolated. Antibiotic sensitivity was assessed for each of the bacterial isolates. Molecular identification techniques based on PCR analysis of specific genomic sequences was conducted and was the basis on which phylogeny representation was done for 10 randomly selected samples of the isolates. Blood was drawn and a complete blood count was conducted to note the hematological indices for each of the study participants. Nineteen bacterial species were isolated from both the nasal cavity and the oropharynx including Streptococcus thoraltensis , alpha-hemolytic streptococci, Staphylococcus hominis , coagulase-negative staphylococci, Leuconostoc mesenteroides , Erysipelothrix rhusiopathiae and several others. We found 100% sensitivity of the isolates to ciprofloxacin, cefuroxime and gentamicin. Whereas cefotaxime and azithromycin posted sensitivities of 85.7% and 91.4%, respectively. Low sensitivities (fuel products may be a contributing factor to bacterial colonization of the respiratory tract in fuel workers.

Shellfish as reservoirs of bacterial pathogens

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Harry Hariharan

2016-04-01

Full Text Available The objective of this article is to present an overview on bacterial pathogens associated with shellfish in Grenada and other countries including the authors’ experience. Although there have been considerable published work on vibrios, there is a lack of information on Salmonella serovars associated with various shellfish. In Grenada, for instance the blue land crabs collected from their habitats were found to harbor several Salmonella serovars. Also, it is notable that only minimal research has been done on shellfish such as conchs and whelks, which are common in the Caribbean and West Indies. Information on anaerobic bacteria, particularly, non-spore forming bacteria associated with shellfish, in general, is also scanty. This review re-examines this globally important topic based on the recent findings as well as past observations. Strategies for reduction of bacteria in oysters are briefly mentioned because of the fact that oysters are consumed commonly without complete cooking.

Copper effects on bacterial activity of estuarine silty sediments

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Almeida, Adelaide; Cunha, Ângela; Fernandes, Sandra; Sobral, Paula; Alcântara, Fernanda

2007-07-01

Bacteria of silty estuarine sediments were spiked with copper to 200 μg Cu g -1 dry weight sediment in order to assess the impact of copper on bacterial degradation of organic matter and on bacterial biomass production. Bacterial density was determined by direct counting under epifluorescence microscopy and bacterial production by the incorporation of 3H-Leucine. Leucine turnover rate was evaluated by 14C-leucine incorporation and ectoenzymatic activities were estimated as the hydrolysis rate of model substrates for β-glucosidase and leucine-aminopeptidase. The presence of added copper in the microcosms elicited, after 21 days of incubation, generalised anoxia and a decrease in organic matter content. The non-eroded surface of the copper-spiked sediment showed, when compared to the control, a decrease in bacterial abundance and significant lower levels of bacterial production and of leucine turnover rate. Bacterial production and leucine turnover rate decreased to 1.4% and 13% of the control values, respectively. Ectoenzymatic activities were also negatively affected but by smaller factors. After erosion by the water current in laboratory flume conditions, the eroded surface of the control sediment showed a generalised decline in all bacterial activities. The erosion of the copper-spiked sediment showed, however, two types of responses with respect to bacterial activities at the exposed surface: positive responses of bacterial production and leucine turnover rate contrasting with slight negative responses of ectoenzymatic activities. The effects of experimental erosion in the suspended cells were also different in the control and in the copper-spiked sediment. Bacterial cells in the control microcosm exhibited, when compared to the non-eroded sediment cells, decreases in all activities after the 6-h suspension. The response of the average suspended copper-spiked sediment cell differed from the control by a less sharp decrease in ectoenzymatic activities and

Algal-bacterial interactions in metal contaminated floodplain sediments

International Nuclear Information System (INIS)

Boivin, M.E.Y.; Greve, G.D.; Garcia-Meza, J.V.; Massieux, B.; Sprenger, W.; Kraak, M.H.S.; Breure, A.M.; Rutgers, M.; Admiraal, W.

2007-01-01

The aim of the present study was to investigate algal-bacterial interactions in a gradient of metal contaminated natural sediments. By means of multivariate techniques, we related the genetic structure (denaturing gradient gel electrophoresis, DGGE) and the physiological structure (community-level physiological profiling, CLPP) of the bacterial communities to the species composition of the algal communities and to the abiotic environmental variables, including metal contamination. The results revealed that genetic and physiological structure of the bacterial communities correlated with the species composition of the algal community, but hardly to the level of metal pollution. This must be interpreted as an indication for a strong and species-specific linkage of algal and bacterial species in floodplain sediments. Metals were, however, not proven to affect either the algal or the bacterial communities of the Dutch river floodplains. - Algal and bacterial communities in floodplain sediments are interlinked, but are not affected by metal pollution

Neonatal Bacterial Meningitis And Dexamethasone Adjunctive ...

African Journals Online (AJOL)

Methodology: Babies admitted from1992 to 1995 in the Special Care Baby Unit of the University of Maiduguri Teaching Hospital, Maduguri, Nigeria, with bacterial meningitis were studied prospectively. Neonatal bacterial meningitis was confirmed if the cerebrospinal fluid (CSF) microbiological, chemical, immunological and ...

Bacterial fatty acid metabolism in modern antibiotic discovery.

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Yao, Jiangwei; Rock, Charles O

2017-11-01

Bacterial fatty acid synthesis is essential for many pathogens and different from the mammalian counterpart. These features make bacterial fatty acid synthesis a desirable target for antibiotic discovery. The structural divergence of the conserved enzymes and the presence of different isozymes catalyzing the same reactions in the pathway make bacterial fatty acid synthesis a narrow spectrum target rather than the traditional broad spectrum target. Furthermore, bacterial fatty acid synthesis inhibitors are single-targeting, rather than multi-targeting like traditional monotherapeutic, broad-spectrum antibiotics. The single-targeting nature of bacterial fatty acid synthesis inhibitors makes overcoming fast-developing, target-based resistance a necessary consideration for antibiotic development. Target-based resistance can be overcome through multi-targeting inhibitors, a cocktail of single-targeting inhibitors, or by making the single targeting inhibitor sufficiently high affinity through a pathogen selective approach such that target-based mutants are still susceptible to therapeutic concentrations of drug. Many of the pathogens requiring new antibiotic treatment options encode for essential bacterial fatty acid synthesis enzymes. This review will evaluate the most promising targets in bacterial fatty acid metabolism for antibiotic therapeutics development and review the potential and challenges in advancing each of these targets to the clinic and circumventing target-based resistance. This article is part of a Special Issue entitled: Bacterial Lipids edited by Russell E. Bishop. Copyright © 2016 Elsevier B.V. All rights reserved.

Initial insights into bacterial succession during human decomposition.

Science.gov (United States)

Hyde, Embriette R; Haarmann, Daniel P; Petrosino, Joseph F; Lynne, Aaron M; Bucheli, Sibyl R

2015-05-01

Decomposition is a dynamic ecological process dependent upon many factors such as environment, climate, and bacterial, insect, and vertebrate activity in addition to intrinsic properties inherent to individual cadavers. Although largely attributed to microbial metabolism, very little is known about the bacterial basis of human decomposition. To assess the change in bacterial community structure through time, bacterial samples were collected from several sites across two cadavers placed outdoors to decompose and analyzed through 454 pyrosequencing and analysis of variable regions 3-5 of the bacterial 16S ribosomal RNA (16S rRNA) gene. Each cadaver was characterized by a change in bacterial community structure for all sites sampled as time, and decomposition, progressed. Bacteria community structure is variable at placement and before purge for all body sites. At bloat and purge and until tissues began to dehydrate or were removed, bacteria associated with flies, such as Ignatzschineria and Wohlfahrtimonas, were common. After dehydration and skeletonization, bacteria associated with soil, such as Acinetobacter, were common at most body sites sampled. However, more cadavers sampled through multiple seasons are necessary to assess major trends in bacterial succession.

SEXUAL DYSFUNCTION ASSOCIATION WITH THE CHRONIC BACTERIAL PROSTATITIS

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H. S. Ibishev

2013-01-01

Full Text Available The study involved 230 patients aged 20 to 45 years with a diagnosis of chronic bacterial prostatitis. The study found that in patients with chronic bacterial prostatitis clinical picture, in addition to pain, is a lower urinary tract symptoms, neuro-vegetative and sexual dysfunction. In patients with chronic bacterial prostatitis, recorded various sexual disorders, most of which are normalized after antibiotic therapy. Erectile dysfunction, which are recorded in patients with chronic bacterial prostatitis is psychogenic in nature dysfunction.

Getting complete genomes from complex samples using nanopore sequencing

DEFF Research Database (Denmark)

Kirkegaard, Rasmus Hansen; Karst, Søren Michael; Albertsen, Mads

Background Short read DNA sequencing and metagenomic binning workflows have made it possible to extract bacterial genome bins from environmental microbial samples containing hundreds to thousands of different species. However, these genome bins often do not represent complete genomes......, as they are mostly fragmented, incomplete and often contaminated with foreign DNA. The value of these `draft genomes` have limited, lasting value to the scientific community, as gene synteny is broken and there is some uncertainty of what is missing1. The genetic material most often missed is important multi......-copy and/or conserved marker genes such as the 16S rRNA gene, as sequence micro-heterogeneity prevents assembly of these genes in the de novo assembly. However, long read sequencing technologies are emerging promising an end to fragmented genome assemblies2. Experimental design We extracted DNA from a full...

The burden of bacterial vaginosis: women's experience of the physical, emotional, sexual and social impact of living with recurrent bacterial vaginosis.

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Jade E Bilardi

Full Text Available BACKGROUND: Bacterial vaginosis is a common vaginal infection, causing an abnormal vaginal discharge and/or odour in up to 50% of sufferers. Recurrence is common following recommended treatment. There are limited data on women's experience of bacterial vaginosis, and the impact on their self-esteem, sexual relationships and quality of life. The aim of this study was to explore the experiences and impact of recurrent bacterial vaginosis on women. METHODS: A social constructionist approach was chosen as the framework for the study. Thirty five women with male and/or female partners participated in semi-structured interviews face-to-face or by telephone about their experience of recurrent bacterial vaginosis. RESULTS: Recurrent bacterial vaginosis impacted on women to varying degrees, with some women reporting it had little impact on their lives but most reporting it had a moderate to severe impact. The degree to which it impacted on women physically, emotionally, sexually and socially often depended on the frequency of episodes and severity of symptoms. Women commonly reported that symptoms of bacterial vaginosis made them feel embarrassed, ashamed, 'dirty' and very concerned others may detect their malodour and abnormal discharge. The biggest impact of recurrent bacterial vaginosis was on women's self-esteem and sex lives, with women regularly avoiding sexual activity, in particular oral sex, as they were too embarrassed and self-conscious of their symptoms to engage in these activities. Women often felt confused about why they were experiencing recurrent bacterial vaginosis and frustrated at their lack of control over recurrence. CONCLUSION: Women's experience of recurrent bacterial vaginosis varied broadly and significantly in this study. Some women reported little impact on their lives but most reported a moderate to severe impact, mainly on their self-esteem and sex life. Further support and acknowledgement of these impacts are required when

Bacterial flora of conjunctiva after death

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Sagili Chandrasekhara Reddy

2013-10-01

Full Text Available AIM:To evaluate the frequency of bacterial flora of conjunctiva after death (cadaver eyes which will give information about the bacterial contamination of donor eyes, and the in-vitro sensitivity of isolated bacteria to the commonly used antibiotics in ophthalmic practice.METHODS: Conjunctival swabs were taken from the cadavers (motor vehicle accident deaths and patients who died in the hospital, within 6h after death, and sent for culture and sensitivity test. Conjunctival swabs, taken from the healthy conjunctiva of patients admitted for cataract surgery, were sent for culture and sensitivity as controls (eyes in those of living status. The bacterial isolates were tested against the commonly used antibiotics (chloramphenicol, gentamicin, ciprofloxacin in ophthalmology practice.RESULTS: Bacteria were isolated in 41 out of 100 conjunctival swabs (41%, taken from 50 cadavers (study group. Coagulase negative staphylococcus was the most common bacteria isolated (15%, followed by pseudomonas aeruginosa (5%. Gentamicin was effective against majority of the bacterial isolates (82%. Bacteria were isolated from 7 out of 100 conjunctival swabs taken as control group (eyes in living state. Coagulase negative staphylococcus was the most common organism (5% isolated in control group; the others were staphylococcus aureus (1% and beta hemolyticus streptococci (1%.CONCLUSION: Bacteria were isolated from 41% of the cadaver eyes. High percentage sensitivity of the bacterial isolates to gentamicin (82% supports the practice of thorough irrigation of the eyes with gentamicin solution before starting the procedure of enucleation followed by immersion of the enucleated eyeballs in gentamycin solution, to prevent the bacterial contamination.

Does circumcision alter the periurethral uropathogenic bacterial flora

African Journals Online (AJOL)

Background: The aim of this study was to assess the pattern of periurethral bacterial flora in uncircumcised boys and to evaluate the effect of circumcision on alteration of periurethral uropathogenic bacterial flora. Materials and Methods: Pattern of periurethral bacterial flora before and after circumcision was studied ...

Diazotrophic Bacterial Community of Degraded Pastures

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João Tiago Correia Oliveira

2017-01-01

Full Text Available Pasture degradation can cause changes in diazotrophic bacterial communities. Thus, this study aimed to evaluate the culturable and total diazotrophic bacterial community, associated with regions of the rhizosphere and roots of Brachiaria decumbens Stapf. pastures in different stages of degradation. Samples of roots and rhizospheric soil were collected from slightly, partially, and highly degraded pastures. McCrady’s table was used to obtain the Most Probable Number (MPN of bacteria per gram of sample, in order to determine population density and calculate the Shannon-Weaver diversity index. The diversity of total diazotrophic bacterial community was determined by the technique of Denaturing Gradient Gel Electrophoresis (DGGE of the nifH gene, while the diversity of the culturable diazotrophic bacteria was determined by the Polymerase Chain Reaction (BOX-PCR technique. The increase in the degradation stage of the B. decumbens Stapf. pasture did not reduce the population density of the cultivated diazotrophic bacterial community, suggesting that the degradation at any degree of severity was highly harmful to the bacteria. The structure of the total diazotrophic bacterial community associated with B. decumbens Stapf. was altered by the pasture degradation stage, suggesting a high adaptive capacity of the bacteria to altered environments.

Effect of Copper Treatment on the Composition and Function of the Bacterial Community in the Sponge Haliclona cymaeformis

KAUST Repository

Tian, R.-M.

2014-11-04

Marine sponges are the most primitive metazoan and host symbiotic microorganisms. They are crucial components of the marine ecological system and play an essential role in pelagic processes. Copper pollution is currently a widespread problem and poses a threat to marine organisms. Here, we examined the effects of copper treatment on the composition of the sponge-associated bacterial community and the genetic features that facilitate the survival of enriched bacteria under copper stress. The 16S rRNA gene sequencing results showed that the sponge Haliclona cymaeformis harbored symbiotic sulfur-oxidizing Ectothiorhodospiraceae and photosynthetic Cyanobacteria as dominant species. However, these autotrophic bacteria decreased substantially after treatment with a high copper concentration, which enriched for a heterotrophic-bacterium-dominated community. Metagenomic comparison revealed a varied profile of functional genes and enriched functions, including bacterial motility and chemotaxis, extracellular polysaccharide and capsule synthesis, virulence-associated genes, and genes involved in cell signaling and regulation, suggesting short-period mechanisms of the enriched bacterial community for surviving copper stress in the microenvironment of the sponge. Microscopic observation and comparison revealed dynamic bacterial aggregation within the matrix and lysis of sponge cells. The bacteriophage community was also enriched, and the complete genome of a dominant phage was determined, implying that a lytic phage cycle was stimulated by the high copper concentration. This study demonstrated a copper-induced shift in the composition of functional genes of the sponge-associated bacterial community, revealing the selective effect of copper treatment on the functions of the bacterial community in the microenvironment of the sponge. IMPORTANCE This study determined the bacterial community structure of the common sponge Haliclona cymaeformis and examined the effect of copper

The epidemiology of bacterial meningitis in Kosovo.

Science.gov (United States)

Namani, Sadie A; Koci, Remzie A; Qehaja-Buçaj, Emine; Ajazaj-Berisha, Lindita; Mehmeti, Murat

2014-07-14

The purpose of this study was to present the epidemiologic features of bacterial meningitis in the developing country of Kosovo. Data were collected from active surveillance of bacterial meningitis cases treated at the University Clinical Center of Kosovo in the years 2000 (first post-war year) and 2010. Meningitis cases in 2000 compared with 2010 showed a 35.5% decline in incidence (from 4.8 to 3.1 cases per 100,000 population) and a decrease in the case fatality rate from 10% to 5%. In children, there was a lower mortality rate (5% versus 2%) and a lower incidence of neurological complications (13% versus 16%) as compared to adults (32% versus 10% and 16% versus 35%, respectively). Neisseria meningitidis was the most common pathogen of bacterial meningitis in both study periods. Bacterial meningitis was most prevalent in the pediatric population, and showed an increase in the median age, from three years in 2000 to seven years in 2010. A steady number of bacterial meningitis cases in adults throughout last decade (around 20 cases per year) was recorded. During the last decade, gradual changes have been observed in the epidemiology of bacterial meningitis that are unrelated to the introduction of new vaccines, but are partly due to the improvement of living conditions.

The use of 14C-FIAU to predict bacterial thymidine kinase presence: Implications for radiolabeled FIAU bacterial imaging

International Nuclear Information System (INIS)

Peterson, Kristin L.; Reid, William C.; Freeman, Alexandra F.; Holland, Steven M.; Pettigrew, Roderic I.; Gharib, Ahmed M.; Hammoud, Dima A.

2013-01-01

Currently available infectious disease imaging techniques cannot differentiate between infection and sterile inflammation or between different types of infections. Recently, radiolabeled FIAU was found to be a substrate for the thymidine kinase (TK) enzyme of multiple pathogenic bacteria, leading to its translational use in the imaging of bacterial infections. Patients with immunodeficiencies, however, are susceptible to a different group of pathogenic bacteria when compared to immunocompetent subjects. In this study, we wanted to predict the usefulness of radiolabeled FIAU in the detection of bacterial infections commonly occurring in patients with immunodeficiencies, in vitro, prior to attempting in vivo imaging with 124 I-FIAU-PET. Methods: We obtained representative strains of bacterial pathogens isolated from actual patients with genetic immunodeficiencies. We evaluated the bacterial susceptibility of different strains to the effect of incubation with FIAU, which would implicate the presence of the thymidine kinase (TK) enzyme. We also incubated the bacteria with 14 C-FIAU and consequently measured its rate of incorporation in the bacterial DNA using a liquid scintillation counter. Results: Unlike the other bacterial strains, the growth of Pseudomonas aeruginosa was not halted by FIAU at any concentration. All the tested clinical isolates demonstrated different levels of 14 C-FIAU uptake, except for P. aeruginosa. Conclusion: Radiolabeled FIAU has been successful in delineating bacterial infections, both in preclinical and pilot translational studies. In patients with immunodeficiencies, Pseudomonas infections are commonly encountered and are usually difficult to differentiate from fungal infections. The use of radiolabeled FIAU for in vivo imaging of those patients, however, would not be useful, considering the apparent lack of TK enzyme in Pseudomonas. One has to keep in mind that not all pathogenic bacteria possess the TK enzyme and as such will not all

Antibiotic resistance of bacterial biofilms

DEFF Research Database (Denmark)

Hoiby, N.; Bjarnsholt, T.; Givskov, M.

2010-01-01

A biofilm is a structured consortium of bacteria embedded in a self-produced polymer matrix consisting of polysaccharide, protein and DNA. Bacterial biofilms cause chronic infections because they show increased tolerance to antibiotics and disinfectant chemicals as well as resisting phagocytosis...... and other components of the body's defence system. The persistence of, for example, staphylococcal infections related to foreign bodies is due to biofilm formation. Likewise, chronic Pseudomonas aeruginosa lung infection in cystic fibrosis patients is caused by biofilm-growing mucoid strains....... Characteristically, gradients of nutrients and oxygen exist from the top to the bottom of biofilms and these gradients are associated with decreased bacterial metabolic activity and increased doubling times of the bacterial cells; it is these more or less dormant cells that are responsible for some of the tolerance...

Prevalent bacterial species and novel phylotypes in advanced noma lesions.

Science.gov (United States)

Paster, B J; Falkler Jr, W A; Enwonwu, C O; Idigbe, E O; Savage, K O; Levanos, V A; Tamer, M A; Ericson, R L; Lau, C N; Dewhirst, F E

2002-06-01

The purpose of this study was to determine the bacterial diversity in advanced noma lesions using culture-independent molecular methods. 16S ribosomal DNA bacterial genes from DNA isolated from advanced noma lesions of four Nigerian children were PCR amplified with universally conserved primers and spirochetal selective primers and cloned into Escherichia coli. Partial 16S rRNA sequences of approximately 500 bases from 212 cloned inserts were used initially to determine species identity or closest relatives by comparison with sequences of known species or phylotypes. Nearly complete sequences of approximately 1,500 bases were obtained for most of the potentially novel species. A total of 67 bacterial species or phylotypes were detected, 25 of which have not yet been grown in vitro. Nineteen of the species or phylotypes, including Propionibacterium acnes, Staphylococcus spp., and the opportunistic pathogens Stenotrophomonas maltophilia and Ochrobactrum anthropi were detected in more than one subject. Other known species that were detected included Achromobacter spp., Afipia spp., Brevundimonas diminuta, Capnocytophaga spp., Cardiobacterium sp., Eikenella corrodens, Fusobacterium spp., Gemella haemoylsans, and Neisseria spp. Phylotypes that were unique to noma infections included those in the genera Eubacterium, Flavobacterium, Kocuria, Microbacterium, and Porphyromonas and the related Streptococcus salivarius and genera Sphingomonas and TREPONEMA: Since advanced noma lesions are infections open to the environment, it was not surprising to detect species not commonly associated with the oral cavity, e.g., from soil. Several species previously implicated as putative pathogens of noma, such as spirochetes and Fusobacterium spp., were detected in at least one subject. However, due to the limited number of available noma subjects, it was not possible at this time to associate specific species with the disease.

Nest Material Shapes Eggs Bacterial Environment.

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Cristina Ruiz-Castellano

Full Text Available Selective pressures imposed by pathogenic microorganisms to embryos have selected in hosts for a battery of antimicrobial lines of defenses that includes physical and chemical barriers. Due to the antimicrobial properties of volatile compounds of green plants and of chemicals of feather degrading bacteria, the use of aromatic plants and feathers for nest building has been suggested as one of these barriers. However, experimental evidence suggesting such effects is scarce in the literature. During two consecutive years, we explored experimentally the effects of these nest materials on loads of different groups of bacteria (mesophilic bacteria, Enterobacteriaceae, Staphylococcus and Enterococcus of eggshells in nests of spotless starlings (Sturnus unicolor at the beginning and at the end of the incubation period. This was also explored in artificial nests without incubation activity. We also experimentally increased bacterial density of eggs in natural and artificial nests and explored the effects of nest lining treatments on eggshell bacterial load. Support for the hypothetical antimicrobial function of nest materials was mainly detected for the year and location with larger average values of eggshell bacterial density. The beneficial effects of feathers and plants were more easily detected in artificial nests with no incubation activity, suggesting an active role of incubation against bacterial colonization of eggshells. Pigmented and unpigmented feathers reduced eggshell bacterial load in starling nests and artificial nest boxes. Results from artificial nests allowed us to discuss and discard alternative scenarios explaining the detected association, particularly those related to the possible sexual role of feathers and aromatic plants in starling nests. All these results considered together confirm the antimicrobial functionality mainly of feathers but also of plants used as nest materials, and highlight the importance of temporally and

Nest Material Shapes Eggs Bacterial Environment.

Science.gov (United States)

Ruiz-Castellano, Cristina; Tomás, Gustavo; Ruiz-Rodríguez, Magdalena; Martín-Gálvez, David; Soler, Juan José

2016-01-01

Selective pressures imposed by pathogenic microorganisms to embryos have selected in hosts for a battery of antimicrobial lines of defenses that includes physical and chemical barriers. Due to the antimicrobial properties of volatile compounds of green plants and of chemicals of feather degrading bacteria, the use of aromatic plants and feathers for nest building has been suggested as one of these barriers. However, experimental evidence suggesting such effects is scarce in the literature. During two consecutive years, we explored experimentally the effects of these nest materials on loads of different groups of bacteria (mesophilic bacteria, Enterobacteriaceae, Staphylococcus and Enterococcus) of eggshells in nests of spotless starlings (Sturnus unicolor) at the beginning and at the end of the incubation period. This was also explored in artificial nests without incubation activity. We also experimentally increased bacterial density of eggs in natural and artificial nests and explored the effects of nest lining treatments on eggshell bacterial load. Support for the hypothetical antimicrobial function of nest materials was mainly detected for the year and location with larger average values of eggshell bacterial density. The beneficial effects of feathers and plants were more easily detected in artificial nests with no incubation activity, suggesting an active role of incubation against bacterial colonization of eggshells. Pigmented and unpigmented feathers reduced eggshell bacterial load in starling nests and artificial nest boxes. Results from artificial nests allowed us to discuss and discard alternative scenarios explaining the detected association, particularly those related to the possible sexual role of feathers and aromatic plants in starling nests. All these results considered together confirm the antimicrobial functionality mainly of feathers but also of plants used as nest materials, and highlight the importance of temporally and geographically

Detergent-compatible bacterial amylases.

Science.gov (United States)

Niyonzima, Francois N; More, Sunil S

2014-10-01

Proteases, lipases, amylases, and cellulases are enzymes used in detergent formulation to improve the detergency. The amylases are specifically supplemented to the detergent to digest starchy stains. Most of the solid and liquid detergents that are currently manufactured contain alkaline enzymes. The advantages of using alkaline enzymes in the detergent formulation are that they aid in removing tough stains and the process is environmentally friendly since they reduce the use of toxic detergent ingredients. Amylases active at low temperature are preferred as the energy consumption gets reduced, and the whole process becomes cost-effective. Most microbial alkaline amylases are used as detergent ingredients. Various reviews report on the production, purification, characterization, and application of amylases in different industry sectors, but there is no specific review on bacterial or fungal alkaline amylases or detergent-compatible amylases. In this mini-review, an overview on the production and property studies of the detergent bacterial amylases is given, and the stability and compatibility of the alkaline bacterial amylases in the presence of the detergents and the detergent components are highlighted.

Diversity of bacterial communities along a petroleum contamination gradient in desert soils.

Science.gov (United States)

Abed, Raeid M M; Al-Kindi, Sumaiya; Al-Kharusi, Samiha

2015-01-01

Microbial communities in oil-polluted desert soils have been rarely studied compared to their counterparts from freshwater and marine environments. We investigated bacterial diversity and changes therein in five desert soils exposed to different levels of oil pollution. Automated rRNA intergenic spacer (ARISA) analysis profiles showed that the bacterial communities of the five soils were profoundly different (analysis of similarities (ANOSIM), R = 0.45, P pollution levels. Multivariate analyses of ARISA profiles revealed that the microbial communities in the S soil, which contains the highest level of contamination, were different from the other soils and formed a completely separate cluster. A total of 16,657 ribosomal sequences were obtained, with 42-89 % of these sequences belonging to the phylum Proteobacteria. While sequences belonging to Betaproteobacteria, Gammaproteobacteria, Bacilli, and Actinobacteria were encountered in all soils, sequences belonging to anaerobic bacteria from the classes Deltaproteobacteria, Clostridia, and Anaerolineae were only detected in the S soil. Sequences belonging to the genus Terriglobus of the class Acidobacteria were only detected in the B3 soil with the lowest level of contamination. Redundancy analysis (RDA) showed that oil contamination level was the most determinant factor that explained variations in the microbial communities. We conclude that the exposure to different levels of oil contamination exerts a strong selective pressure on bacterial communities and that desert soils are rich in aerobic and anaerobic bacteria that could potentially contribute to the degradation of hydrocarbons.

Effects of chemical and biological pesticides on plant growth parameters and rhizospheric bacterial community structure in Vigna radiata

Energy Technology Data Exchange (ETDEWEB)

Singh, Sunil; Gupta, Rashi; Sharma, Shilpi, E-mail: shilpi@dbeb.iitd.ac.in

2015-06-30

Highlights: • Non-target effects of pesticides employing qualitative and quantitative approaches. • Qualitative shifts in resident and active bacterial community structure. • Abundance of 16S rRNA gene and transcripts were reduced significantly. • Effects of biological pesticide similar to chemical pesticides on rhizospheric bacteria. - Abstract: With increasing application of pesticides in agriculture, their non-target effects on soil microbial communities are critical to soil health maintenance. The present study aimed to evaluate the effects of chemical pesticides (chlorpyrifos and cypermethrin) and a biological pesticide (azadirachtin) on growth parameters and the rhizospheric bacterial community of Vigna radiata. Qualitative and quantitative analysis by PCR-denaturing gradient gel electrophoresis (DGGE) and q-PCR, respectively, of the 16S rRNA gene and transcript were performed to study the impact of these pesticides on the resident and active rhizospheric bacterial community. While plant parameters were not affected significantly by the pesticides, a shift in the bacterial community structure was observed with an adverse effect on the abundance of 16S rRNA gene and transcripts. Chlorpyrifos showed almost complete degradation toward the end of the experiment. These non-target impacts on soil ecosystems and the fact that the effects of the biopesticide mimic those of chemical pesticides raise serious concerns regarding their application in agriculture.

Effects of chemical and biological pesticides on plant growth parameters and rhizospheric bacterial community structure in Vigna radiata

International Nuclear Information System (INIS)

Singh, Sunil; Gupta, Rashi; Sharma, Shilpi

2015-01-01

Highlights: • Non-target effects of pesticides employing qualitative and quantitative approaches. • Qualitative shifts in resident and active bacterial community structure. • Abundance of 16S rRNA gene and transcripts were reduced significantly. • Effects of biological pesticide similar to chemical pesticides on rhizospheric bacteria. - Abstract: With increasing application of pesticides in agriculture, their non-target effects on soil microbial communities are critical to soil health maintenance. The present study aimed to evaluate the effects of chemical pesticides (chlorpyrifos and cypermethrin) and a biological pesticide (azadirachtin) on growth parameters and the rhizospheric bacterial community of Vigna radiata. Qualitative and quantitative analysis by PCR-denaturing gradient gel electrophoresis (DGGE) and q-PCR, respectively, of the 16S rRNA gene and transcript were performed to study the impact of these pesticides on the resident and active rhizospheric bacterial community. While plant parameters were not affected significantly by the pesticides, a shift in the bacterial community structure was observed with an adverse effect on the abundance of 16S rRNA gene and transcripts. Chlorpyrifos showed almost complete degradation toward the end of the experiment. These non-target impacts on soil ecosystems and the fact that the effects of the biopesticide mimic those of chemical pesticides raise serious concerns regarding their application in agriculture

Bacterial pathogen manipulation of host membrane trafficking.

Science.gov (United States)

Asrat, Seblewongel; de Jesús, Dennise A; Hempstead, Andrew D; Ramabhadran, Vinay; Isberg, Ralph R

2014-01-01

Pathogens use a vast number of strategies to alter host membrane dynamics. Targeting the host membrane machinery is important for the survival and pathogenesis of several extracellular, vacuolar, and cytosolic bacteria. Membrane manipulation promotes bacterial replication while suppressing host responses, allowing the bacterium to thrive in a hostile environment. This review provides a comprehensive summary of various strategies used by both extracellular and intracellular bacteria to hijack host membrane trafficking machinery. We start with mechanisms used by bacteria to alter the plasma membrane, delve into the hijacking of various vesicle trafficking pathways, and conclude by summarizing bacterial adaptation to host immune responses. Understanding bacterial manipulation of host membrane trafficking provides insights into bacterial pathogenesis and uncovers the molecular mechanisms behind various processes within a eukaryotic cell.

Grepafloxacin in Patients with Acute Bacterial Exacerbations of Chronic Bronchitis - a Question of Speed in Bacterial Killing

Directory of Open Access Journals (Sweden)

Jerome J Schentag

1998-01-01

Full Text Available OBJECTIVE: To characterize the population pharmacokinetics and pharmacodynamics of oral grepafloxacin in patients with acute bacterial exacerbations of chronic bronchitis (ABECB, with particular attention to the speed of bacterial killing. This was possible because the study design incorporated daily cultures of the patients’ sputum.

Bacterial vaginosis - aftercare

Science.gov (United States)

Bacterial vaginosis (BV) is a type of vaginal infection. The vagina normally contains both healthy bacteria and unhealthy bacteria. BV occurs when more unhealthy bacteria grow than healthy bacteria. No one knows ...

Bacterial lipoprotein delays apoptosis in human neutrophils through inhibition of caspase-3 activity: regulatory roles for CD14 and TLR-2.

LENUS (Irish Health Repository)

Power, Colm P

2012-02-03

The human sepsis syndrome resulting from bacterial infection continues to account for a significant proportion of hospital mortality. Neutralizing strategies aimed at individual bacterial wall products (such as LPS) have enjoyed limited success in this arena. Bacterial lipoprotein (BLP) is a major constituent of the wall of diverse bacterial forms and profoundly influences cellular function in vivo and in vitro, and has been implicated in the etiology of human sepsis. Delayed polymorphonuclear cell (PMN) apoptosis is a characteristic feature of human sepsis arising from Gram-negative or Gram-positive bacterial infection. Bacterial wall product ligation and subsequent receptor-mediated events upstream of caspase inhibition in neutrophils remain incompletely understood. BLP has been shown to exert its cellular effects primarily through TLR-2, and it is now widely accepted that lateral associations with the TLRs represent the means by which CD14 communicates intracellular messages. In this study, we demonstrate that BLP inhibits neutrophil mitochondrial membrane depolarization with a subsequent reduction in caspase-3 processing, ultimately leading to a significant delay in PMN apoptosis. Pretreatment of PMNs with an anti-TLR-2 mAb or anti-CD14 mAb prevented BLP from delaying PMN apoptosis to such a marked degree. Combination blockade using both mAbs completely prevented the effects of BLP (in 1 and 10 ng\\/ml concentrations) on PMN apoptosis. At higher concentrations of BLP, the antiapoptotic effects were observed, but were not as pronounced. Our findings therefore provide the first evidence of a crucial role for both CD14 and TLR-2 in delayed PMN apoptosis arising from bacterial infection.

Composition of Bacterial Assemblages in Different Components of Reed Warbler Nests and a Possible Role of Egg Incubation in Pathogen Regulation.

Directory of Open Access Journals (Sweden)

Hanja B Brandl

Full Text Available Bacteria play a central role in animal health. Yet, little is known about the acquisition of bacteria and the extent to which bacteria are acquired from different environmental sources. For example, bird nests host diverse bacteria associated with the eggs, nestlings and nesting material, but previous research has typically focussed on only a limited number of nest components at a time. It therefore remains unknown to what extent bacteria are transmitted between these components. Using both molecular and culture techniques, we characterised nest-associated bacterial assemblages throughout the entire nesting cycle of reed warblers by sampling bacteria on eggs before and during incubation, within nestling faeces, and on the nesting material of post-breeding nests. We found that bacterial assemblages clustered by nest component. Yet some overlap existed between nest components, suggesting that bacterial transmission across components is likely to occur. Eggs and nestlings from the same nest harboured more similar bacteria than expected by chance, suggesting an influence of environment or genetics on bacterial assemblages. Bacterial loads were not lower on incubated eggs. Instead, incubation was associated with a change in the structure of assemblages, including a decrease in potentially-harmful Gram-negative bacteria. In addition we show for the first time, that incubation is associated with the complete extinction of harmful haemolytic bacteria. Overall, our study appears to be the first to demonstrate differences in bacterial assemblages between bird nest components. In addition, we highlight the complexity of nest bacterial assemblages and provide new insights into the benefits of incubation.

The bacterial meningitis score to distinguish bacterial from aseptic meningitis in children from Sao Paulo, Brazil.

Science.gov (United States)

Mekitarian Filho, Eduardo; Horita, Sérgio Massaru; Gilio, Alfredo Elias; Alves, Anna Cláudia Dominguez; Nigrovic, Lise E

2013-09-01

In a retrospective cohort of 494 children with meningitis in Sao Paulo, Brazil, the Bacterial Meningitis Score identified all the children with bacterial meningitis (sensitivity 100%, 95% confidence interval: 92-100% and negative predictive value 100%, 95% confidence interval: 98-100%). Addition of cerebrospinal fluid lactate to the score did not improve clinical prediction rule performance.

Antimicrobial Nanoparticle for the Treatment of Bacterial Infection

Science.gov (United States)

Pornpattananangkul, Dissaya

Liposomes are spherical lipid vesicles with bilayered membrane structure, which have been recognized as one of the most widely used carriers for delivering a myriad of pharmaceuticals. Liposomes can carry both hydrophilic and hydrophobic agents with high efficiency and protect them from undesired effects of external conditions. However, the applications of liposomes are usually limited by their instability during storage. They are inclined to fuse with one another immediately after preparation, resulting in undesired mixing, increase in size, and payload loss. To overcome this limitation, this dissertation will focus on the technology to stabilize liposomes during storage and destabilize at specific conditions in order to allow controllable therapeutic release, as well as demonstrate their application to treat one of the bacterial infection diseases, acne vulgaris. The first area of this research is stimuli-responsive liposomes development, where the liposomes are stabilized by introducing gold nanoparticles to adsorb to their surface. As a result, the liposomes are prevented from fusing with one another and undesirable payload release during storage or physiological environments. Moreover, therapeutic is controllably released depending on environment conditions, such as acidic pH and bacterial virulence factor. In case of acid-responsive liposomes, the bound gold nanoparticles can effectively prevent liposomes from fusing with one another at neutral pH value, while at acidic environment (e.g. pHhuman skin are typically acidic. Demonstrated by fluorescent and antimicrobial experiments, the bound gold nanoparticles effectively prevent LipoLA from fusing with one another at neutral pH value. However, at acidic condition, the gold particles detatch from LipoLA surface, allowing the fusion with P.acnes membrane and lauric acid delivery, resulting in a complete killing effect. The stimuli-responsive liposomes presented here provide a new, safe, and effective approach to

Molecular cloning of cellulase genes from indigenous bacterial isolates

International Nuclear Information System (INIS)

Jong Bor Chyan; Pauline Liew Woan Ying; Mat Rasol Awang

2006-01-01

Indigenous cellulolytic bacterial isolates having high activities in degrading carboxymethyl cellulose (CMC) were isolated from local environments. Identification of these isolates were performed by molecular techniques. By using polymerase chain reaction (PCR) techniques, PCR products encoding cellulase gene were amplified from the total genomic DNAs. Purified PCR product was successfully cloned and expressed in Escherichia coli host system. The complete nucleotide sequences of the cellulase genes determined. The analysis of amino acid sequences deduced from the genes indicated that the cloned DNA fragments show high homology to those of endoglucanase genes of family GH5. All cloned genes consist of an N-terminal signal peptide, a catalytic domain of family 5 glycosyl hydrolase and a cellulose-binding domain of family III. (Author)

Recurrent Bacterial Meningitis in a Child with Mondini Dysplasia

Directory of Open Access Journals (Sweden)

Eda Kepenekli-Kadayifci

2014-01-01

Full Text Available Mondini dysplasia, also known as Mondini malformation, is a developmental abnormality of the inner and middle ears that can cause hearing loss, cerebrospinal fluid (CSF leakage, and recurrent bacterial meningitis (RBM, which is defined as two or more episodes of meningitis separated by a period of convalescence and the complete resolution of all signs and symptoms. An accurate diagnosis of the underlying pathology is crucial to prevent further episodes from occurring. Herein, we present a three-year-old boy with RBM and unilateral sensorineural hearing loss. During the evaluation to determine the etiology of the RBM, cystic malformation in the cochlea and vestibular dilatation consistent with Mondini dysplasia were detected via computerized tomography (CT of the temporal bone.

[Bacterial biofilms and infection].

Science.gov (United States)

Lasa, I; Del Pozo, J L; Penadés, J R; Leiva, J

2005-01-01

In developed countries we tend to think of heart disease and the numerous forms of cancer as the main causes of mortality, but on a global scale infectious diseases come close, or may even be ahead: 14.9 million deaths in 2002 compared to cardiovascular diseases (16.9 million deaths) and cancer (7.1 million deaths) (WHO report 2004). The infectious agents responsible for human mortality have evolved as medical techniques and hygienic measures have changed. Modern-day acute infectious diseases caused by specialized bacterial pathogens such as diphtheria, tetanus, cholera, plague, which represented the main causes of death at the beginning of XX century, have been effectively controlled with antibiotics and vaccines. In their place, more than half of the infectious diseases that affect mildly immunocompromised patients involve bacterial species that are commensal with the human body; these can produce chronic infections, are resistant to antimicrobial agents and there is no effective vaccine against them. Examples of these infections are the otitis media, native valve endocarditis, chronic urinary infections, bacterial prostatitis, osteomyelitis and all the infections related to medical devices. Direct analysis of the surface of medical devices or of tissues that have been foci of chronic infections shows the presence of large numbers of bacteria surrounded by an exopolysaccharide matrix, which has been named the "biofilm". Inside the biofilm, bacteria grow protected from the action of the antibodies, phagocytic cells and antimicrobial treatments. In this article, we describe the role of bacterial biofilms in human persistent infections.

In vitro effect of Reiki treatment on bacterial cultures: Role of experimental context and practitioner well-being.

Science.gov (United States)

Rubik, Beverly; Brooks, Audrey J; Schwartz, Gary E

2006-01-01

To measure effects of Reiki treatments on growth of heat-shocked bacteria, and to determine the influence of healing context and practitioner well-being. Overnight cultures of Escherichia coli K12 in fresh medium were used. Culture samples were paired with controls to minimize any ordering effects. Samples were heat-shocked prior to Reiki treatment, which was performed by Reiki practitioners for up to 15 minutes, with untreated controls. Plate-count assay using an automated colony counter determined the number of viable bacteria. Fourteen Reiki practitioners each completed 3 runs (n = 42 runs) without healing context, and another 2 runs (n = 28 runs) in which they first treated a pain patient for 30 minutes (healing context). Well-being questionnaires were administered to practitioners pre-post all sessions. No overall difference was found between the Reiki and control plates in the nonhealing context. In the healing context, the Reiki treated cultures overall exhibited significantly more bacteria than controls (p bacterial cultures in the nonhealing context. Practitioner social (p bacterial cultures in the healing context. For practitioners starting with diminished well-being, control counts were likely to be higher than Reiki-treated bacterial counts. For practitioners starting with a higher level of well-being, Reiki counts were likely to be higher than control counts. Reiki improved growth of heat-shocked bacterial cultures in a healing context. The initial level of well-being of the Reiki practitioners correlates with the outcome of Reiki on bacterial culture growth and is key to the results obtained.

Temporal and Spatial Impact of Human Cadaver Decomposition on Soil Bacterial and Arthropod Community Structure and Function

Science.gov (United States)

Singh, Baneshwar; Minick, Kevan J.; Strickland, Michael S.; Wickings, Kyle G.; Crippen, Tawni L.; Tarone, Aaron M.; Benbow, M. Eric; Sufrin, Ness; Tomberlin, Jeffery K.; Pechal, Jennifer L.

2018-01-01

As vertebrate carrion decomposes, there is a release of nutrient-rich fluids into the underlying soil, which can impact associated biological community structure and function. How these changes alter soil biogeochemical cycles is relatively unknown and may prove useful in the identification of carrion decomposition islands that have long lasting, focal ecological effects. This study investigated the spatial (0, 1, and 5 m) and temporal (3–732 days) dynamics of human cadaver decomposition on soil bacterial and arthropod community structure and microbial function. We observed strong evidence of a predictable response to cadaver decomposition that varies over space for soil bacterial and arthropod community structure, carbon (C) mineralization and microbial substrate utilization patterns. In the presence of a cadaver (i.e., 0 m samples), the relative abundance of Bacteroidetes and Firmicutes was greater, while the relative abundance of Acidobacteria, Chloroflexi, Gemmatimonadetes, and Verrucomicrobia was lower when compared to samples at 1 and 5 m. Micro-arthropods were more abundant (15 to 17-fold) in soils collected at 0 m compared to either 1 or 5 m, but overall, micro-arthropod community composition was unrelated to either bacterial community composition or function. Bacterial community structure and microbial function also exhibited temporal relationships, whereas arthropod community structure did not. Cumulative precipitation was more effective in predicting temporal variations in bacterial abundance and microbial activity than accumulated degree days. In the presence of the cadaver (i.e., 0 m samples), the relative abundance of Actinobacteria increased significantly with cumulative precipitation. Furthermore, soil bacterial communities and C mineralization were sensitive to the introduction of human cadavers as they diverged from baseline levels and did not recover completely in approximately 2 years. These data are valuable for understanding ecosystem

Temporal and Spatial Impact of Human Cadaver Decomposition on Soil Bacterial and Arthropod Community Structure and Function

Directory of Open Access Journals (Sweden)

Baneshwar Singh

2018-01-01

Full Text Available As vertebrate carrion decomposes, there is a release of nutrient-rich fluids into the underlying soil, which can impact associated biological community structure and function. How these changes alter soil biogeochemical cycles is relatively unknown and may prove useful in the identification of carrion decomposition islands that have long lasting, focal ecological effects. This study investigated the spatial (0, 1, and 5 m and temporal (3–732 days dynamics of human cadaver decomposition on soil bacterial and arthropod community structure and microbial function. We observed strong evidence of a predictable response to cadaver decomposition that varies over space for soil bacterial and arthropod community structure, carbon (C mineralization and microbial substrate utilization patterns. In the presence of a cadaver (i.e., 0 m samples, the relative abundance of Bacteroidetes and Firmicutes was greater, while the relative abundance of Acidobacteria, Chloroflexi, Gemmatimonadetes, and Verrucomicrobia was lower when compared to samples at 1 and 5 m. Micro-arthropods were more abundant (15 to 17-fold in soils collected at 0 m compared to either 1 or 5 m, but overall, micro-arthropod community composition was unrelated to either bacterial community composition or function. Bacterial community structure and microbial function also exhibited temporal relationships, whereas arthropod community structure did not. Cumulative precipitation was more effective in predicting temporal variations in bacterial abundance and microbial activity than accumulated degree days. In the presence of the cadaver (i.e., 0 m samples, the relative abundance of Actinobacteria increased significantly with cumulative precipitation. Furthermore, soil bacterial communities and C mineralization were sensitive to the introduction of human cadavers as they diverged from baseline levels and did not recover completely in approximately 2 years. These data are valuable for understanding

Abdominal radiation causes bacterial translocation

International Nuclear Information System (INIS)

Guzman-Stein, G.; Bonsack, M.; Liberty, J.; Delaney, J.P.

1989-01-01

The purpose of this study was to determine if a single dose of radiation to the rat abdomen leads to bacterial translocation into the mesenteric lymph nodes (MLN). A second issue addressed was whether translocation correlates with anatomic damage to the mucosa. The radiated group (1100 cGy) which received anesthesia also was compared with a control group and a third group which received anesthesia alone but no abdominal radiation. Abdominal radiation lead to 100% positive cultures of MLN between 12 hr and 4 days postradiation. Bacterial translocation was almost nonexistent in the control and anesthesia group. Signs of inflammation and ulceration of the intestinal mucosa were not seen until Day 3 postradiation. Mucosal damage was maximal by Day 4. Bacterial translocation onto the MLN after a single dose of abdominal radiation was not apparently dependent on anatomical, histologic damage of the mucosa

Presence of bacterial DNA and bacterial peptidoglycans in joints of patients with rheumatoid arthritis and other arthritides

NARCIS (Netherlands)

van der Heijden, I. M.; Wilbrink, B.; Tchetverikov, I.; Schrijver, I. A.; Schouls, L. M.; Hazenberg, M. P.; Breedveld, F. C.; Tak, P. P.

2000-01-01

The continuous presence of bacteria or their degraded antigens in the synovium may be involved in the pathogenesis of rheumatoid arthritis (RA). The aim of this study was to determine the presence of bacterial nucleic acids and bacterial cell wall constituents in the joints of patients with RA and

A Bacterial Receptor PcrK Senses the Plant Hormone Cytokinin to Promote Adaptation to Oxidative Stress

Directory of Open Access Journals (Sweden)

Fang-Fang Wang

2017-12-01

Full Text Available Summary: Recognition of the host plant is a prerequisite for infection by pathogenic bacteria. However, how bacterial cells sense plant-derived stimuli, especially chemicals that function in regulating plant development, remains completely unknown. Here, we have identified a membrane-bound histidine kinase of the phytopathogenic bacterium Xanthomonas campestris, PcrK, as a bacterial receptor that specifically detects the plant cytokinin 2-isopentenyladenine (2iP. 2iP binds to the extracytoplasmic region of PcrK to decrease its autokinase activity. Through a four-step phosphorelay, 2iP stimulation decreased the phosphorylation level of PcrR, the cognate response regulator of PcrK, to activate the phosphodiesterase activity of PcrR in degrading the second messenger 3′,5′-cyclic diguanylic acid. 2iP perception by the PcrK-PcrR remarkably improves bacterial tolerance to oxidative stress by regulating the transcription of 56 genes, including the virulence-associated TonB-dependent receptor gene ctrA. Our results reveal an evolutionarily conserved, inter-kingdom signaling by which phytopathogenic bacteria intercept a plant hormone signal to promote adaptation to oxidative stress. : How pathogenic bacteria use receptors to recognize the signals of the host plant is unknown. Wang et al. have identified a bacterial receptor histidine kinase that specifically senses the plant hormone cytokinin. Through a four-step phosphorelay, cytokinin perception triggers degradation of a second messenger, c-di-GMP, to activate the bacterial response to oxidative stress. Keywords: histidine kinase, ligand, cytokinin, autokinase activity, phosphorelay, response regulator, two-component signal transduction system, Xanthomonas campestris pv. campestris, virulence, oxidative stress

Long-term nitrogen amendment alters the diversity and assemblage of soil bacterial communities in tallgrass prairie.

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Joseph D Coolon

Full Text Available Anthropogenic changes are altering the environmental conditions and the biota of ecosystems worldwide. In many temperate grasslands, such as North American tallgrass prairie, these changes include alteration in historically important disturbance regimes (e.g., frequency of fires and enhanced availability of potentially limiting nutrients, particularly nitrogen. Such anthropogenically-driven changes in the environment are known to elicit substantial changes in plant and consumer communities aboveground, but much less is known about their effects on soil microbial communities. Due to the high diversity of soil microbes and methodological challenges associated with assessing microbial community composition, relatively few studies have addressed specific taxonomic changes underlying microbial community-level responses to different fire regimes or nutrient amendments in tallgrass prairie. We used deep sequencing of the V3 region of the 16S rRNA gene to explore the effects of contrasting fire regimes and nutrient enrichment on soil bacterial communities in a long-term (20 yrs experiment in native tallgrass prairie in the eastern Central Plains. We focused on responses to nutrient amendments coupled with two extreme fire regimes (annual prescribed spring burning and complete fire exclusion. The dominant bacterial phyla identified were Proteobacteria, Verrucomicrobia, Bacteriodetes, Acidobacteria, Firmicutes, and Actinobacteria and made up 80% of all taxa quantified. Chronic nitrogen enrichment significantly impacted bacterial community diversity and community structure varied according to nitrogen treatment, but not phosphorus enrichment or fire regime. We also found significant responses of individual bacterial groups including Nitrospira and Gammaproteobacteria to long-term nitrogen enrichment. Our results show that soil nitrogen enrichment can significantly alter bacterial community diversity, structure, and individual taxa abundance, which have

Bacterial community composition and extracellular enzyme activity in temperate streambed sediment during drying and rewetting.

Directory of Open Access Journals (Sweden)

Elisabeth Pohlon

Full Text Available Droughts are among the most important disturbance events for stream ecosystems; they not only affect stream hydrology but also the stream biota. Although desiccation of streams is common in Mediterranean regions, phases of dryness in headwaters have been observed more often and for longer periods in extended temperate regions, including Central Europe, reflecting global climate change and enhanced water withdrawal. The effects of desiccation and rewetting on the bacterial community composition and extracellular enzyme activity, a key process in the carbon flow of streams and rivers, were investigated in a typical Central European stream, the Breitenbach (Hesse, Germany. Wet streambed sediment is an important habitat in streams. It was sampled and exposed in the laboratory to different drying scenarios (fast, intermediate, slow for 13 weeks, followed by rewetting of the sediment from the fast drying scenario via a sediment core perfusion technique for 2 weeks. Bacterial community structure was analyzed using CARD-FISH and TGGE, and extracellular enzyme activity was assessed using fluorogenic model substrates. During desiccation the bacterial community composition shifted toward composition in soil, exhibiting increasing proportions of Actinobacteria and Alphaproteobacteria and decreasing proportions of Bacteroidetes and Betaproteobacteria. Simultaneously the activities of extracellular enzymes decreased, most pronounced with aminopeptidases and less pronounced with enzymes involved in the degradation of polymeric carbohydrates. After rewetting, the general ecosystem functioning, with respect to extracellular enzyme activity, recovered after 10 to 14 days. However, the bacterial community composition had not yet achieved its original composition as in unaffected sediments within this time. Thus, whether the bacterial community eventually recovers completely after these events remains unknown. Perhaps this community undergoes permanent changes

The Burden of Bacterial Vaginosis: Women’s Experience of the Physical, Emotional, Sexual and Social Impact of Living with Recurrent Bacterial Vaginosis

Science.gov (United States)

Bilardi, Jade E.; Walker, Sandra; Temple-Smith, Meredith; McNair, Ruth; Mooney-Somers, Julie; Bellhouse, Clare; Fairley, Christopher K.; Chen, Marcus Y.; Bradshaw, Catriona

2013-01-01

Background Bacterial vaginosis is a common vaginal infection, causing an abnormal vaginal discharge and/or odour in up to 50% of sufferers. Recurrence is common following recommended treatment. There are limited data on women’s experience of bacterial vaginosis, and the impact on their self-esteem, sexual relationships and quality of life. The aim of this study was to explore the experiences and impact of recurrent bacterial vaginosis on women. Methods A social constructionist approach was chosen as the framework for the study. Thirty five women with male and/or female partners participated in semi-structured interviews face-to-face or by telephone about their experience of recurrent bacterial vaginosis. Results Recurrent bacterial vaginosis impacted on women to varying degrees, with some women reporting it had little impact on their lives but most reporting it had a moderate to severe impact. The degree to which it impacted on women physically, emotionally, sexually and socially often depended on the frequency of episodes and severity of symptoms. Women commonly reported that symptoms of bacterial vaginosis made them feel embarrassed, ashamed, ‘dirty’ and very concerned others may detect their malodour and abnormal discharge. The biggest impact of recurrent bacterial vaginosis was on women’s self-esteem and sex lives, with women regularly avoiding sexual activity, in particular oral sex, as they were too embarrassed and self-conscious of their symptoms to engage in these activities. Women often felt confused about why they were experiencing recurrent bacterial vaginosis and frustrated at their lack of control over recurrence. Conclusion Women’s experience of recurrent bacterial vaginosis varied broadly and significantly in this study. Some women reported little impact on their lives but most reported a moderate to severe impact, mainly on their self-esteem and sex life. Further support and acknowledgement of these impacts are required when managing women

Bacterial pyomyositis in a patient with aplastic anaemia.

OpenAIRE

Mitsuyasu, R.; Gale, R. P.

1980-01-01

Bacterial pyomyositis is common in the tropids but is rare in temperate climates. A patient with aplastic anaemia who had never left the continental United States developed bacterial pyomyositis secondary to Staphylococcus aureus which responded to antibiotics and surgical drainage. Bacterial pyomyositis should be considered in the differential diagnosis of fever and myalgias in the immunocompromised patient.

Role of Sulfhydryl Sites on Bacterial Cell Walls in the Biosorption, Mobility and Bioavailability of Mercury and Uranium

Energy Technology Data Exchange (ETDEWEB)

Myneni, Satish C. [Princeton Univ., NJ (United States); Mishra, Bhoopesh [Princeton Univ., NJ (United States); Fein, Jeremy [Princeton Univ., NJ (United States)

2009-04-01

almost complete removal of Hg from the experimental solutions at relatively low bacterial concentrations. Synchrotron based X-ray spectroscopic studies of these samples indicate that the structure and the coordination environment of Hg surface complexes on bacterial cell walls change dramatically- with sulfhydryls as the dominant Hg-binding groups in the micromolar and submicromolar range, and carboxyls and phosphoryls dominating at high micromolar concentrations. Hg interactions change from a trigonal or T-shaped HgS{sub 3} complex to HgS or HgS{sub 2} type complexes as the Hg concentration increases in the submicromolar range. Although all bacterial species studied exhibited the same types of coordination environments for Hg, the relative concentrations of the complexes change as a function of Hg concentration.

Minerals in soil select distinct bacterial communities in their microhabitats.

Science.gov (United States)

Carson, Jennifer K; Campbell, Louise; Rooney, Deirdre; Clipson, Nicholas; Gleeson, Deirdre B

2009-03-01

We tested the hypothesis that different minerals in soil select distinct bacterial communities in their microhabitats. Mica (M), basalt (B) and rock phosphate (RP) were incubated separately in soil planted with Trifolium subterraneum, Lolium rigidum or left unplanted. After 70 days, the mineral and soil fractions were separated by sieving. Automated ribosomal intergenic spacer analysis was used to determine whether the bacterial community structure was affected by the mineral, fraction and plant treatments. Principal coordinate plots showed clustering of bacterial communities from different fraction and mineral treatments, but not from different plant treatments. Permutational multivariate anova (permanova) showed that the microhabitats of M, B and RP selected bacterial communities different from each other in unplanted and L. rigidum, and in T. subterraneum, bacterial communities from M and B differed (Ppermanova also showed that each mineral fraction selected bacterial communities different from the surrounding soil fraction (P<0.05). This study shows that the structure of bacterial communities in soil is influenced by the mineral substrates in their microhabitat and that minerals in soil play a greater role in bacterial ecology than simply providing an inert matrix for bacterial growth. This study suggests that mineral heterogeneity in soil contributes to the spatial variation in bacterial communities.

Bacterial strategies of resistance to antimicrobial peptides.

Science.gov (United States)

Joo, Hwang-Soo; Fu, Chih-Iung; Otto, Michael

2016-05-26

Antimicrobial peptides (AMPs) are a key component of the host's innate immune system, targeting invasive and colonizing bacteria. For successful survival and colonization of the host, bacteria have a series of mechanisms to interfere with AMP activity, and AMP resistance is intimately connected with the virulence potential of bacterial pathogens. In particular, because AMPs are considered as potential novel antimicrobial drugs, it is vital to understand bacterial AMP resistance mechanisms. This review gives a comparative overview of Gram-positive and Gram-negative bacterial strategies of resistance to various AMPs, such as repulsion or sequestration by bacterial surface structures, alteration of membrane charge or fluidity, degradation and removal by efflux pumps.This article is part of the themed issue 'Evolutionary ecology of arthropod antimicrobial peptides'. © 2016 The Author(s).

Bacterial diversity and biogeochemistry of different chemosynthetic habitats of the REGAB cold seep (West African margin, 3160 m water depth

Directory of Open Access Journals (Sweden)

P. Pop Ristova

2012-12-01

Full Text Available The giant pockmark REGAB (West African margin, 3160 m water depth is an active methane-emitting cold seep ecosystem, where the energy derived from microbially mediated oxidation of methane supports high biomass and diversity of chemosynthetic communities. Bare sediments interspersed with heterogeneous chemosynthetic assemblages of mytilid mussels, vesicomyid clams and siboglinid tubeworms form a complex seep ecosystem. To better understand if benthic bacterial communities reflect the patchy distribution of chemosynthetic fauna, all major chemosynthetic habitats at REGAB were investigated using an interdisciplinary approach combining pore water geochemistry, in situ quantification of fluxes and consumption of methane, as well as bacterial community fingerprinting. This study revealed that sediments populated by different fauna assemblages show distinct biogeochemical activities and are associated with distinct sediment bacterial communities. The methane consumption rates and methane effluxes ranged over one to two orders of magnitude across habitats, and reached highest values at the mussel habitat, which hosted a different bacterial community compared to the other habitats. Clam assemblages had a profound impact on the sediment geochemistry, but less so on the bacterial community structure. Moreover, all clam assemblages at REGAB were restricted to sediments characterized by complete methane consumption in the seafloor, and intermediate biogeochemical activity. Overall, variations in the sediment geochemistry were reflected in the distribution of both fauna and microbial communities; and were mostly determined by methane flux.

Probing bacterial adhesion at the single-cell level

DEFF Research Database (Denmark)

Zeng, Guanghong; Müller, Torsten; Meyer, Rikke Louise

be considered. We have developed a simple and versatile method to make single-cell bacterial probes for measuring single cell adhesion by force spectroscopy using atomic force microscopy (AFM). A single-cell probe was readily made by picking up a bacterial cell from a glass surface by approaching a tipless AFM...... cantilever coated with the commercial cell adhesive CellTakTM. We applied the method to study adhesion of living cells to abiotic surfaces at the single-cell level. Immobilisation of single bacterial cells to the cantilever was stable for several hours, and viability was confirmed by Live/Dead staining...... on the adhesion force, we explored the bond formation and adhesive strength of four different bacterial strains towards three abiotic substrates with variable hydrophobicity and surface roughness. The adhesion force and final rupture length were dependent on bacterial strains, surfaces properties, and time...

Contrasting ability to take up leucine and thymidine among freshwater bacterial groups: implications for bacterial production measurements

Science.gov (United States)

Pérez, María Teresa; Hörtnagl, Paul; Sommaruga, Ruben

2010-01-01

We examined the ability of different freshwater bacterial groups to take up leucine and thymidine in two lakes. Utilization of both substrates by freshwater bacteria was examined at the community level by looking at bulk incorporation rates and at the single-cell level by combining fluorescent in situ hybridization and signal amplification by catalysed reporter deposition with microautoradiography. Our results showed that leucine was taken up by 70–80% of Bacteria-positive cells, whereas only 15–43% of Bacteria-positive cells were able to take up thymidine. When a saturating substrate concentration in combination with a short incubation was used, 80–90% of Betaproteobacteria and 67–79% of Actinobacteria were positive for leucine uptake, whereas thymidine was taken up by bacterial group. Bacterial abundance was a good predictor of the relative contribution of bacterial groups to leucine uptake, whereas when thymidine was used Actinobacteria represented the large majority (> 80%) of the cells taking up this substrate. Increasing the substrate concentration to 100 nM did not affect the percentage of R-BT cells taking up leucine (> 90% even at low concentrations), but moderately increased the fraction of thymidine-positive R-BT cells to a maximum of 35% of the hybridized cells. Our results show that even at very high concentrations, thymidine is not taken up by all, otherwise active, bacterial cells. PMID:19725866

9 CFR 113.64 - General requirements for live bacterial vaccines.

Science.gov (United States)

2010-01-01

... bacterial vaccines. 113.64 Section 113.64 Animals and Animal Products ANIMAL AND PLANT HEALTH INSPECTION... STANDARD REQUIREMENTS Live Bacterial Vaccines § 113.64 General requirements for live bacterial vaccines... bacterial vaccine shall meet the requirements in this section. (a) Purity test. Final container samples of...

Effects of chemical and biological pesticides on plant growth parameters and rhizospheric bacterial community structure in Vigna radiata.

Science.gov (United States)

Singh, Sunil; Gupta, Rashi; Sharma, Shilpi

2015-06-30

With increasing application of pesticides in agriculture, their non-target effects on soil microbial communities are critical to soil health maintenance. The present study aimed to evaluate the effects of chemical pesticides (chlorpyrifos and cypermethrin) and a biological pesticide (azadirachtin) on growth parameters and the rhizospheric bacterial community of Vigna radiata. Qualitative and quantitative analysis by PCR-denaturing gradient gel electrophoresis (DGGE) and q-PCR, respectively, of the 16S rRNA gene and transcript were performed to study the impact of these pesticides on the resident and active rhizospheric bacterial community. While plant parameters were not affected significantly by the pesticides, a shift in the bacterial community structure was observed with an adverse effect on the abundance of 16S rRNA gene and transcripts. Chlorpyrifos showed almost complete degradation toward the end of the experiment. These non-target impacts on soil ecosystems and the fact that the effects of the biopesticide mimic those of chemical pesticides raise serious concerns regarding their application in agriculture. Copyright © 2015 Elsevier B.V. All rights reserved.

Phage Therapy Is Effective in a Mouse Model of Bacterial Equine Keratitis.

Science.gov (United States)

Furusawa, Takaaki; Iwano, Hidetomo; Hiyashimizu, Yutaro; Matsubara, Kazuki; Higuchi, Hidetoshi; Nagahata, Hajime; Niwa, Hidekazu; Katayama, Yoshinari; Kinoshita, Yuta; Hagiwara, Katsuro; Iwasaki, Tomohito; Tanji, Yasunori; Yokota, Hiroshi; Tamura, Yutaka

2016-09-01

Bacterial keratitis of the horse is mainly caused by staphylococci, streptococci, and pseudomonads. Of these bacteria, Pseudomonas aeruginosa sometimes causes rapid corneal corruption and, in some cases, blindness. Antimicrobial resistance can make treatment very difficult. Therefore, new strategies to control bacterial infection are required. A bacteriophage (phage) is a virus that specifically infects and kills bacteria. Since phage often can lyse antibiotic-resistant bacteria because the killing mechanism is different, we examined the use of phage to treat horse bacterial keratitis. We isolated Myoviridae or Podoviridae phages, which together have a broad host range. They adsorb efficiently to host bacteria; more than 80% of the ΦR18 phage were adsorbed to host cells after 30 s. In our keratitis mouse model, the administration of phage within 3 h also could kill bacteria and suppress keratitis. A phage multiplicity of infection of 100 times the host bacterial number could kill host bacteria effectively. A cocktail of two phages suppressed bacteria in the keratitis model mouse. These data demonstrated that the phages in this study could completely prevent the keratitis caused by P. aeruginosa in a keratitis mouse model. Furthermore, these results suggest that phage may be a more effective prophylaxis for horse keratitis than the current preventive use of antibiotics. Such treatment may reduce the use of antibiotics and therefore antibiotic resistance. Further studies are required to assess phage therapy as a candidate for treatment of horse keratitis. Antibiotic-resistant bacteria are emerging all over the world. Bacteriophages have great potential for resolution of this problem. A bacteriophage, or phage, is a virus that infects bacteria specifically. As a novel therapeutic strategy against racehorse keratitis caused by Pseudomonas aeruginosa, we propose the application of phages for treatment. Phages isolated in this work had in vitro effectiveness for a broad

The Bacterial Sequential Markov Coalescent.

Science.gov (United States)

De Maio, Nicola; Wilson, Daniel J

2017-05-01

Bacteria can exchange and acquire new genetic material from other organisms directly and via the environment. This process, known as bacterial recombination, has a strong impact on the evolution of bacteria, for example, leading to the spread of antibiotic resistance across clades and species, and to the avoidance of clonal interference. Recombination hinders phylogenetic and transmission inference because it creates patterns of substitutions (homoplasies) inconsistent with the hypothesis of a single evolutionary tree. Bacterial recombination is typically modeled as statistically akin to gene conversion in eukaryotes, i.e. , using the coalescent with gene conversion (CGC). However, this model can be very computationally demanding as it needs to account for the correlations of evolutionary histories of even distant loci. So, with the increasing popularity of whole genome sequencing, the need has emerged for a faster approach to model and simulate bacterial genome evolution. We present a new model that approximates the coalescent with gene conversion: the bacterial sequential Markov coalescent (BSMC). Our approach is based on a similar idea to the sequential Markov coalescent (SMC)-an approximation of the coalescent with crossover recombination. However, bacterial recombination poses hurdles to a sequential Markov approximation, as it leads to strong correlations and linkage disequilibrium across very distant sites in the genome. Our BSMC overcomes these difficulties, and shows a considerable reduction in computational demand compared to the exact CGC, and very similar patterns in simulated data. We implemented our BSMC model within new simulation software FastSimBac. In addition to the decreased computational demand compared to previous bacterial genome evolution simulators, FastSimBac provides more general options for evolutionary scenarios, allowing population structure with migration, speciation, population size changes, and recombination hotspots. FastSimBac is

Bacterial binding to extracellular proteins - in vitro adhesion

DEFF Research Database (Denmark)

Schou, C.; Fiehn, N.-E.

1999-01-01

Viridans streptococci, bacterial adherence, extracellular matrix proteins, surface receptors, endocarditis......Viridans streptococci, bacterial adherence, extracellular matrix proteins, surface receptors, endocarditis...

Bacterial translocation: impact of probiotics

OpenAIRE

Jeppsson, Bengt; Mangell, Peter; Adawi, Diya; Molin, Göran

2004-01-01

There is a considerable amount of data in humans showing that patients who cannot take in nutrients enterally have more organ failure in the intensive care unit, a less favourable prognosis, and a higher frequency of septicaemia, in particular involving bacterial species from the intestinal tract. However, there is little evidence that this is connected with translocation of bacterial species in humans. Animal data more uniformly imply the existence of such a connection. The main focus of thi...

Microbiological analysis after complete or partial removal of carious dentin using two different techniques in primary teeth: A randomized clinical trial

Science.gov (United States)

Singhal, Deepak Kumar; Acharya, Shashidhar; Thakur, Arun Singh

2016-01-01

Background: The management of deep carious lesions can be done by various techniques but residual caries dilemma still persists and bacterial reduction in cavities treated by either partial or complete caries removal techniques is debatable. So the objective of the present randomized clinical trial was to compare microbial counts in cavities submitted to complete caries removal and partial caries removal using either hand instruments or burs before and after 3 weeks of restoration. Materials and Methods: Primary molars with acute carious lesions in inner half of dentine and vital pulp were randomly divided into three groups of 14 each: Group A: Partial caries removal using hand instruments atraumatic restorative treatment (ART) only; Group B: Partial caries removal using bur; Group C: Complete caries removal using bur and caries detector dye. Dentine sample obtained after caries removal and 3 weeks after restoration, were subjected to microbial culture and counting (colony-forming units [CFU]/mg of dentine) for total viable bacterial count, Streptococcus spp., mutans streptococci, Lactobacillus spp. Results: Three techniques of caries removal showed significant (P < 0.05) reduction in all microorganisms studied after 3 weeks of evaluation, but there was no statistically significant difference in percentage reduction of microbial count among three groups. Conclusion: Results suggest the use of partial caries removal in a single session as compared to complete caries removal as a part of treatment of deep lesions in deciduous teeth in order to reduce the risk of pulp exposure. Partial caries removal using ART can be preferred for community settings as public health procedure for caries management. PMID:26962313

Antibiotics promote aggregation within aquatic bacterial communities

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Gianluca eCorno

2014-07-01

Full Text Available The release of antibiotics (AB into the environment poses several threats for human health due to potential development of ABresistant natural bacteria. Even though the use of low-dose antibiotics has been promoted in health care and farming, significant amounts of AB are observed in aquatic environments. Knowledge on the impact of AB on natural bacterial communities is missing both in terms of spread and evolution of resistance mechanisms, and of modifications of community composition and productivity. New approaches are required to study the response of microbial communities rather than individual resistance genes. In this study a chemostat-based experiment with 4 coexisting bacterial strains has been performed to mimicking the response of a freshwater bacterial community to the presence of antibiotics in low and high doses. Bacterial abundance rapidly decreased by 75% in the presence of AB, independently of their concentration, and remained constant until the end of the experiment. The bacterial community was mainly dominated by Aeromonas hydrophila and Brevundimonas intermedia while the other two strains, Micrococcus luteus and Rhodococcus sp. never exceed 10%. Interestingly, the bacterial strains, which were isolated at the end of the experiment, were not AB-resistant, while reassembled communities composed of the 4 strains, isolated from treatments under AB stress, significantly raised their performance (growth rate, abundance in the presence of AB compared to the communities reassembled with strains isolated from the treatment without AB. By investigating the phenotypic adaptations of the communities subjected to the different treatments, we found that the presence of AB significantly increased co-aggregation by 5-6 fold.These results represent the first observation of co-aggregation as a successful strategy of AB resistance based on phenotype in aquatic bacterial communities, and can represent a fundamental step in the understanding of

Photoinactivation of major bacterial pathogens in aquaculture

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Heyong Jin Roh

2016-08-01

Full Text Available Abstract Background Significant increases in the bacterial resistance to various antibiotics have been found in fish farms. Non-antibiotic therapies for infectious diseases in aquaculture are needed. In recent years, light-emitting diode technology has been applied to the inactivation of pathogens, especially those affecting humans. The purpose of this study was to assess the effect of blue light (wavelengths 405 and 465 nm on seven major bacterial pathogens that affect fish and shellfish important in aquaculture. Results We successfully demonstrate inactivation activity of a 405/465-nm LED on selected bacterial pathogens. Although some bacteria were not fully inactivated by the 465-nm light, the 405-nm light had a bactericidal effect against all seven pathogens, indicating that blue light can be effective without the addition of a photosensitizer. Photobacterium damselae, Vibrio anguillarum, and Edwardsiella tarda were the most susceptible to the 405-nm light (36.1, 41.2, and 68.4 J cm−2, respectively, produced one log reduction in the bacterial populations, whereas Streptococcus parauberis was the least susceptible (153.8 J cm−2 per one log reduction. In general, optical density (OD values indicated that higher bacterial densities were associated with lower inactivating efficacy, with the exception of P. damselae and Vibrio harveyi. In conclusion, growth of the bacterial fish and shellfish pathogens evaluated in this study was inactivated by exposure to either the 405- or 465-nm light. In addition, inactivation was dependent on exposure time. Conclusions This study presents that blue LED has potentially alternative therapy for treating fish and shellfish bacterial pathogens. It has great advantages in aspect of eco-friendly treating methods differed from antimicrobial methods.

Does circumcision alter the periurethral uropathogenic bacterial flora

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Mushtaq Ahmad Laway

2012-01-01

Full Text Available Background: The aim of this study was to assess the pattern of periurethral bacterial flora in uncircumcised boys and to evaluate the effect of circumcision on alteration of periurethral uropathogenic bacterial flora. Materials and Methods: Pattern of periurethral bacterial flora before and after circumcision was studied prospectively in 124 boys. The results were analysed to compare change in bacterial colonisation before and after circumcision. Results: The age range was 6 weeks to 96 months. Most (94.3% of the boys had religious indication and 5.7% had medical indication for circumcision. E. coli, Proteus and Klebsiella were most common periurethral bacterial flora in uncircumcised subjects. Coagulase-negative staphylococcus and Staphylococcus aureus was most common periurethral bacterial flora in circumcised subjects. In 66.1% of circumcised subjects, no bacteria were grown from periurethral region. Conclusion: We conclude that presence of prepuce is associated with great quantity of periurethral bacteria, greater likelihood of the presence of high concentration of uropathogens and high incidence of urinary tract infection (UTI. This study provides circumstantial evidence supporting the idea that early circumcision may be beneficial for prevention of UTI.

Metamorphosis of a butterfly-associated bacterial community.

Science.gov (United States)

Hammer, Tobin J; McMillan, W Owen; Fierer, Noah

2014-01-01

Butterflies are charismatic insects that have long been a focus of biological research. They are also habitats for microorganisms, yet these microbial symbionts are little-studied, despite their likely importance to butterfly ecology and evolution. In particular, the diversity and composition of the microbial communities inhabiting adult butterflies remain uncharacterized, and it is unknown how the larval (caterpillar) and adult microbiota compare. To address these knowledge gaps, we used Illumina sequencing of 16S rRNA genes from internal bacterial communities associated with multiple life stages of the neotropical butterfly Heliconius erato. We found that the leaf-chewing larvae and nectar- and pollen-feeding adults of H. erato contain markedly distinct bacterial communities, a pattern presumably rooted in their distinct diets. Larvae and adult butterflies host relatively small and similar numbers of bacterial phylotypes, but few are common to both stages. The larval microbiota clearly simplifies and reorganizes during metamorphosis; thus, structural changes in a butterfly's bacterial community parallel those in its own morphology. We furthermore identify specific bacterial taxa that may mediate larval and adult feeding biology in Heliconius and other butterflies. Although male and female Heliconius adults differ in reproductive physiology and degree of pollen feeding, bacterial communities associated with H. erato are not sexually dimorphic. Lastly, we show that captive and wild individuals host different microbiota, a finding that may have important implications for the relevance of experimental studies using captive butterflies.

Metamorphosis of a butterfly-associated bacterial community.

Directory of Open Access Journals (Sweden)

Tobin J Hammer

Full Text Available Butterflies are charismatic insects that have long been a focus of biological research. They are also habitats for microorganisms, yet these microbial symbionts are little-studied, despite their likely importance to butterfly ecology and evolution. In particular, the diversity and composition of the microbial communities inhabiting adult butterflies remain uncharacterized, and it is unknown how the larval (caterpillar and adult microbiota compare. To address these knowledge gaps, we used Illumina sequencing of 16S rRNA genes from internal bacterial communities associated with multiple life stages of the neotropical butterfly Heliconius erato. We found that the leaf-chewing larvae and nectar- and pollen-feeding adults of H. erato contain markedly distinct bacterial communities, a pattern presumably rooted in their distinct diets. Larvae and adult butterflies host relatively small and similar numbers of bacterial phylotypes, but few are common to both stages. The larval microbiota clearly simplifies and reorganizes during metamorphosis; thus, structural changes in a butterfly's bacterial community parallel those in its own morphology. We furthermore identify specific bacterial taxa that may mediate larval and adult feeding biology in Heliconius and other butterflies. Although male and female Heliconius adults differ in reproductive physiology and degree of pollen feeding, bacterial communities associated with H. erato are not sexually dimorphic. Lastly, we show that captive and wild individuals host different microbiota, a finding that may have important implications for the relevance of experimental studies using captive butterflies.

Concatenated image completion via tensor augmentation and completion

OpenAIRE

Bengua, Johann A.; Tuan, Hoang D.; Phien, Ho N.; Do, Minh N.

2016-01-01

This paper proposes a novel framework called concatenated image completion via tensor augmentation and completion (ICTAC), which recovers missing entries of color images with high accuracy. Typical images are second- or third-order tensors (2D/3D) depending if they are grayscale or color, hence tensor completion algorithms are ideal for their recovery. The proposed framework performs image completion by concatenating copies of a single image that has missing entries into a third-order tensor,...

Identifying Bacterial Immune Evasion Proteins Using Phage Display.

Science.gov (United States)

Fevre, Cindy; Scheepmaker, Lisette; Haas, Pieter-Jan

2017-01-01

Methods aimed at identification of immune evasion proteins are mainly rely on in silico prediction of sequence, structural homology to known evasion proteins or use a proteomics driven approach. Although proven successful these methods are limited by a low efficiency and or lack of functional identification. Here we describe a high-throughput genomic strategy to functionally identify bacterial immune evasion proteins using phage display technology. Genomic bacterial DNA is randomly fragmented and ligated into a phage display vector that is used to create a phage display library expressing bacterial secreted and membrane bound proteins. This library is used to select displayed bacterial secretome proteins that interact with host immune components.

Acute Bacterial Prostatitis: Diagnosis and Management.

Science.gov (United States)

Coker, Timothy J; Dierfeldt, Daniel M

2016-01-15

Acute bacterial prostatitis is an acute infection of the prostate gland that causes pelvic pain and urinary tract symptoms, such as dysuria, urinary frequency, and urinary retention, and may lead to systemic symptoms, such as fevers, chills, nausea, emesis, and malaise. Although the true incidence is unknown, acute bacterial prostatitis is estimated to comprise approximately 10% of all cases of prostatitis. Most acute bacterial prostatitis infections are community acquired, but some occur after transurethral manipulation procedures, such as urethral catheterization and cystoscopy, or after transrectal prostate biopsy. The physical examination should include abdominal, genital, and digital rectal examination to assess for a tender, enlarged, or boggy prostate. Diagnosis is predominantly made based on history and physical examination, but may be aided by urinalysis. Urine cultures should be obtained in all patients who are suspected of having acute bacterial prostatitis to determine the responsible bacteria and its antibiotic sensitivity pattern. Additional laboratory studies can be obtained based on risk factors and severity of illness. Radiography is typically unnecessary. Most patients can be treated as outpatients with oral antibiotics and supportive measures. Hospitalization and broad-spectrum intravenous antibiotics should be considered in patients who are systemically ill, unable to voluntarily urinate, unable to tolerate oral intake, or have risk factors for antibiotic resistance. Typical antibiotic regimens include ceftriaxone and doxycycline, ciprofloxacin, and piperacillin/tazobactam. The risk of nosocomial bacterial prostatitis can be reduced by using antibiotics, such as ciprofloxacin, before transrectal prostate biopsy.

Controlling of bacterial flora contaminating animal diet and its components by gamma irradiation

International Nuclear Information System (INIS)

El-Fouly, M.Z.; El-Zawahry, Y.A.; Helal, G.A.; El-Hady, A.F.

1991-01-01

The total bacterial counts in complete diets were found to range between 10 3 -10 5 cells/g, which they ranged between 10 2 and 10 6 in the main components. One hundred and sixteen bacterial colonies were isolated from the animal diet samples and found to be gram positive belonging to three genera: Staphylococcus, Streptococcus and Bacillus. The most radioresistant bacteria isolated at 7.5 KGy were identified as B. megaterium, B. licheniformis, B. pumilus, B.circulans and B.laterosporus. The D 1 0 values for the bacteria contaminated the diet samples ranged between 928 Gy and 2199 Gy. Meanwhile, the D 1 0 values of staph.aureus and Strapt.faecalis artificially contaminated the diet were 400 Gy and 1136 Gy, respectively. It could be recommended from obtained results that dose level of 10 KGy is quite sufficient to eliminate all pathogens from animal diets or their components. In addition, it decreases the microbial count to minimum counts and hence increases the diet shelf life.1 fig.,4 tab

Dispersal networks for enhancing bacterial degradation in heterogeneous environments

International Nuclear Information System (INIS)

Banitz, Thomas; Wick, Lukas Y.; Fetzer, Ingo; Frank, Karin; Harms, Hauke; Johst, Karin

2011-01-01

Successful biodegradation of organic soil pollutants depends on their bioavailability to catabolically active microorganisms. In particular, environmental heterogeneities often limit bacterial access to pollutants. Experimental and modelling studies revealed that fungal networks can facilitate bacterial dispersal and may thereby improve pollutant bioavailability. Here, we investigate the influence of such bacterial dispersal networks on biodegradation performance under spatially heterogeneous abiotic conditions using a process-based simulation model. To match typical situations in polluted soils, two types of abiotic conditions are studied: heterogeneous bacterial dispersal conditions and heterogeneous initial resource distributions. The model predicts that networks facilitating bacterial dispersal can enhance biodegradation performance for a wide range of these conditions. Additionally, the time horizon over which this performance is assessed and the network's spatial configuration are key factors determining the degree of biodegradation improvement. Our results support the idea of stimulating the establishment of fungal mycelia for enhanced bioremediation of polluted soils. - Highlights: → Bacterial dispersal networks can considerably improve biodegradation performance. → They facilitate bacterial access to dispersal-limited areas and remote resources. → Abiotic conditions, time horizon and network structure govern the improvements. → Stimulating the establishment of fungal mycelia promises enhanced soil remediation. - Simulation modelling demonstrates that fungus-mediated bacterial dispersal can considerably improve the bioavailability of organic pollutants under spatially heterogeneous abiotic conditions typical for water-unsaturated soils.

Dispersal networks for enhancing bacterial degradation in heterogeneous environments

Energy Technology Data Exchange (ETDEWEB)

Banitz, Thomas, E-mail: thomas.banitz@ufz.de [Department of Ecological Modelling, UFZ - Helmholtz Centre for Environmental Research, Permoserstr. 15, 04318 Leipzig (Germany); Wick, Lukas Y.; Fetzer, Ingo [Department of Environmental Microbiology, UFZ - Helmholtz Centre for Environmental Research, Permoserstr. 15, 04318 Leipzig (Germany); Frank, Karin [Department of Ecological Modelling, UFZ - Helmholtz Centre for Environmental Research, Permoserstr. 15, 04318 Leipzig (Germany); Harms, Hauke [Department of Environmental Microbiology, UFZ - Helmholtz Centre for Environmental Research, Permoserstr. 15, 04318 Leipzig (Germany); Johst, Karin [Department of Ecological Modelling, UFZ - Helmholtz Centre for Environmental Research, Permoserstr. 15, 04318 Leipzig (Germany)

2011-10-15

Successful biodegradation of organic soil pollutants depends on their bioavailability to catabolically active microorganisms. In particular, environmental heterogeneities often limit bacterial access to pollutants. Experimental and modelling studies revealed that fungal networks can facilitate bacterial dispersal and may thereby improve pollutant bioavailability. Here, we investigate the influence of such bacterial dispersal networks on biodegradation performance under spatially heterogeneous abiotic conditions using a process-based simulation model. To match typical situations in polluted soils, two types of abiotic conditions are studied: heterogeneous bacterial dispersal conditions and heterogeneous initial resource distributions. The model predicts that networks facilitating bacterial dispersal can enhance biodegradation performance for a wide range of these conditions. Additionally, the time horizon over which this performance is assessed and the network's spatial configuration are key factors determining the degree of biodegradation improvement. Our results support the idea of stimulating the establishment of fungal mycelia for enhanced bioremediation of polluted soils. - Highlights: > Bacterial dispersal networks can considerably improve biodegradation performance. > They facilitate bacterial access to dispersal-limited areas and remote resources. > Abiotic conditions, time horizon and network structure govern the improvements. > Stimulating the establishment of fungal mycelia promises enhanced soil remediation. - Simulation modelling demonstrates that fungus-mediated bacterial dispersal can considerably improve the bioavailability of organic pollutants under spatially heterogeneous abiotic conditions typical for water-unsaturated soils.

Effects of octreotide and a-tocopherol on bacterial translocation in experimental intestinal obstruction: a microbiological, light and electronmicroscopical study.

Science.gov (United States)

Reis, E; Kama, N A; Coskun, T; Korkusuz, P; Ors, U; Aksoy, M; Kulaçoglu, S

1997-01-01

Bacterial translocation induced by intestinal obstruction is suggested to be due to increased intestinal luminal volume, leading to intestinal overgrowth with certain enteric microorganisms and intestinal mucosal damage. If this suggestion is true, maintenance of intestinal mucosal integrity by a cytoprotective agent, a-tocopherol, and inhibition of gastrointestinal secretions by octreotide should decrease the incidence of bacterial translocation and extent of mucosal injury due to intestinal obstruction. Complete intestinal obstruction was created in the distal ileum of male Wistar Albino rats by a single 3-0 silk suture. The animals received subcutaneous injections of 1 ml of physiologic saline (group 1) (PS 24) and 1 ml of saline containing octreotide acetate (100 micrograms/kg) (group 2) (OC 24), at 0, 12 and 24 hours of obstruction. In group 3 (PS 48) and group 4 (OC 48), the rats were treated with subcutaneous physiologic saline (1 ml) and octreotide acetate (100 micrograms/kg), respectively, beginning at the time of obstruction and every 12 hours for 48 hours. The rats in group 5 (Toc 24), were pretreated with intramuscular a-tocopherol 500 mg/kg on day 1 and 8, and underwent laparotomy on day 9. A third dose of a-tocopherol was injected at the time of obstruction on day 9 and no treatment was given thereafter. We tested the incidence of bacterial translocation in systemic organs and circulation and evaluated the histopathological changes in all groups. Treatment with octreotide acetate was found to be ineffective in reducing the incidence of translocation, with no histopathological improvement. Mucosal damage scores, on the other hand, in the a-tocopherol group were statistically less than those in the octreotide and control groups (p < 0.05). Additionally, a-tocopherol treatment decreased the incidence of organ invasion with translocating bacteria, although this difference did not reach statistical significance. Octreotide acetate treatment in complete

Exploring the Bacterial Microbiota of Colombian Fermented Maize Dough "Masa Agria" (Maiz Añejo).

Science.gov (United States)

Chaves-Lopez, Clemencia; Serio, Annalisa; Delgado-Ospina, Johannes; Rossi, Chiara; Grande-Tovar, Carlos D; Paparella, Antonello

2016-01-01

Masa Agria is a naturally fermented maize dough produced in Colombia, very common in the traditional gastronomy. In this study we used culture-dependent and RNA-based pyrosequencing to investigate the bacterial community structure of Masa Agria samples produced in the south west of Colombia. The mean value of cell density was 7.6 log CFU/g of presumptive lactic acid bacteria, 5.4 log cfu/g for presumptive acetic bacteria and 5.6 og CFU/g for yeasts. The abundance of these microorganisms is also responsible for the low pH (3.1-3.7) registered. Although the 16S rRNA pyrosequencing revealed that the analyzed samples were different in bacteria richness and diversity, the genera Lactobacillus, Weissella, and Acetobacter were predominant. In particular, the most common species were Lactobacillus plantarum and Acetobacter fabarum, followed by L. fermentum, L. vaccinostercus, and Pediococcus argentinicus. Several microorganisms of environmental origin, such as Dechloromonas and most of all Sphingobium spp., revealed in each sample, were detected, and also bacteria related to maize, such as Phytoplasma. In conclusion, our results elucidated for the first time the structures of the bacterial communities of Masa Agria samples obtained from different producers, identifying the specific dominant species and revealing a complete picture of the bacterial consortium in this specific niche. The selective pressure of tropical environments may favor microbial biodiversity characterized by a useful technological potential.

Adjunctive Corticosteroids in Adults with Bacterial Meningitis

NARCIS (Netherlands)

van de Beek, Diederik; de Gans, Jan

2005-01-01

Bacterial meningitis is a complex disorder in which neurologic injury is caused, in part, by the causative organism and, in part, by the host's own inflammatory response. In studies of experimental bacterial meningitis, adjuvant treatment with corticosteroids, specifically dexamethasone, has

Bacterial Communities in Women with Bacterial Vaginosis: High Resolution Phylogenetic Analyses Reveal Relationships of Microbiota to Clinical Criteria

Science.gov (United States)

Srinivasan, Sujatha; Hoffman, Noah G.; Morgan, Martin T.; Matsen, Frederick A.; Fiedler, Tina L.; Hall, Robert W.; Ross, Frederick J.; McCoy, Connor O.; Bumgarner, Roger; Marrazzo, Jeanne M.; Fredricks, David N.

2012-01-01

Background Bacterial vaginosis (BV) is a common condition that is associated with numerous adverse health outcomes and is characterized by poorly understood changes in the vaginal microbiota. We sought to describe the composition and diversity of the vaginal bacterial biota in women with BV using deep sequencing of the 16S rRNA gene coupled with species-level taxonomic identification. We investigated the associations between the presence of individual bacterial species and clinical diagnostic characteristics of BV. Methodology/Principal Findings Broad-range 16S rRNA gene PCR and pyrosequencing were performed on vaginal swabs from 220 women with and without BV. BV was assessed by Amsel’s clinical criteria and confirmed by Gram stain. Taxonomic classification was performed using phylogenetic placement tools that assigned 99% of query sequence reads to the species level. Women with BV had heterogeneous vaginal bacterial communities that were usually not dominated by a single taxon. In the absence of BV, vaginal bacterial communities were dominated by either Lactobacillus crispatus or Lactobacillus iners. Leptotrichia amnionii and Eggerthella sp. were the only two BV-associated bacteria (BVABs) significantly associated with each of the four Amsel’s criteria. Co-occurrence analysis revealed the presence of several sub-groups of BVABs suggesting metabolic co-dependencies. Greater abundance of several BVABs was observed in Black women without BV. Conclusions/Significance The human vaginal bacterial biota is heterogeneous and marked by greater species richness and diversity in women with BV; no species is universally present. Different bacterial species have different associations with the four clinical criteria, which may account for discrepancies often observed between Amsel and Nugent (Gram stain) diagnostic criteria. Several BVABs exhibited race-dependent prevalence when analyzed in separate groups by BV status which may contribute to increased incidence of BV in

Microbiological and molecular identification of bacterial species isolated from nasal and oropharyngeal mucosa of fuel workers in Riyadh,

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Suaad S. AlWakeel

2017-09-01

Full Text Available This study aimed to determine the bacterial species colonizing the nasal and oropharyngeal mucosa of fuel workers in Central Riyadh, Saudi Arabia on a microbiological and molecular level. Throat and nasal swab samples were obtained from 29 fuel station attendants in the period of time extending from March to May 2014 in Riyadh, Saudi Arabia. Microbiological identification techniques were utilized to identify the bacterial species isolated. Antibiotic sensitivity was assessed for each of the bacterial isolates. Molecular identification techniques based on PCR analysis of specific genomic sequences was conducted and was the basis on which phylogeny representation was done for 10 randomly selected samples of the isolates. Blood was drawn and a complete blood count was conducted to note the hematological indices for each of the study participants. Nineteen bacterial species were isolated from both the nasal cavity and the oropharynx including Streptococcus thoraltensis, alpha-hemolytic streptococci, Staphylococcus hominis, coagulase-negative staphylococci, Leuconostoc mesenteroides, Erysipelothrix rhusiopathiae and several others. We found 100% sensitivity of the isolates to ciprofloxacin, cefuroxime and gentamicin. Whereas cefotaxime and azithromycin posted sensitivities of 85.7% and 91.4%, respectively. Low sensitivities (<60% sensitivity to the antibiotics ampicillin, erythromycin, clarithromycin and norfloxacin were observed. Ninety-seven percent similarity to the microbial bank species was noted when the isolates were compared to it. Most hematological indices recorded were within the normal range. In conclusion, exposure to toxic fumes and compounds within fuel products may be a contributing factor to bacterial colonization of the respiratory tract in fuel workers.

Distinct Habitats Select Particular Bacterial Communities in Mangrove Sediments

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Lidianne L. Rocha

2016-01-01

Full Text Available We investigated the relationship among environmental variables, composition, and structure of bacterial communities in different habitats in a mangrove located nearby to an oil exploitation area, aiming to retrieve the natural pattern of bacterial communities in this ecosystem. The T-RFLP analysis showed a high diversity of bacterial populations and an increase in the bacterial richness from habitats closer to the sea and without vegetation (S1 to habitats covered by Avicennia schaueriana (S2 and Rhizophora mangle (S3. Environmental variables in S1 and S2 were more similar than in S3; however, when comparing the bacterial compositions, S2 and S3 shared more OTUs between them, suggesting that the presence of vegetation is an important factor in shaping these bacterial communities. In silico analyses of the fragments revealed a high diversity of the class Gammaproteobacteria in the 3 sites, although in general they presented quite different bacterial composition, which is probably shaped by the specificities of each habitat. This study shows that microhabitats inside of a mangrove ecosystem harbor diverse and distinct microbiota, reinforcing the need to conserve these ecosystems as a whole.

Distinct Habitats Select Particular Bacterial Communities in Mangrove Sediments

Science.gov (United States)

Rocha, Lidianne L.; Colares, Geórgia B.; Nogueira, Vanessa L. R.; Paes, Fernanda A.; Melo, Vânia M. M.

2016-01-01

We investigated the relationship among environmental variables, composition, and structure of bacterial communities in different habitats in a mangrove located nearby to an oil exploitation area, aiming to retrieve the natural pattern of bacterial communities in this ecosystem. The T-RFLP analysis showed a high diversity of bacterial populations and an increase in the bacterial richness from habitats closer to the sea and without vegetation (S1) to habitats covered by Avicennia schaueriana (S2) and Rhizophora mangle (S3). Environmental variables in S1 and S2 were more similar than in S3; however, when comparing the bacterial compositions, S2 and S3 shared more OTUs between them, suggesting that the presence of vegetation is an important factor in shaping these bacterial communities. In silico analyses of the fragments revealed a high diversity of the class Gammaproteobacteria in the 3 sites, although in general they presented quite different bacterial composition, which is probably shaped by the specificities of each habitat. This study shows that microhabitats inside of a mangrove ecosystem harbor diverse and distinct microbiota, reinforcing the need to conserve these ecosystems as a whole. PMID:26989418

Cytosolic Access of Intracellular Bacterial Pathogens: The Shigella Paradigm.

Science.gov (United States)

Mellouk, Nora; Enninga, Jost

2016-01-01

Shigella is a Gram-negative bacterial pathogen, which causes bacillary dysentery in humans. A crucial step of Shigella infection is its invasion of epithelial cells. Using a type III secretion system, Shigella injects several bacterial effectors ultimately leading to bacterial internalization within a vacuole. Then, Shigella escapes rapidly from the vacuole, it replicates within the cytosol and spreads from cell-to-cell. The molecular mechanism of vacuolar rupture used by Shigella has been studied in some detail during the recent years and new paradigms are emerging about the underlying molecular events. For decades, bacterial effector proteins were portrayed as main actors inducing vacuolar rupture. This includes the effector/translocators IpaB and IpaC. More recently, this has been challenged and an implication of the host cell in the process of vacuolar rupture has been put forward. This includes the bacterial subversion of host trafficking regulators, such as the Rab GTPase Rab11. The involvement of the host in determining bacterial vacuolar integrity has also been found for other bacterial pathogens, particularly for Salmonella. Here, we will discuss our current view of host factor and pathogen effector implications during Shigella vacuolar rupture and the steps leading to it.

Bacterial intermediate filaments

DEFF Research Database (Denmark)

Charbon, Godefroid; Cabeen, M.; Jacobs-Wagner, C.

2009-01-01

Crescentin, which is the founding member of a rapidly growing family of bacterial cytoskeletal proteins, was previously proposed to resemble eukaryotic intermediate filament (IF) proteins based on structural prediction and in vitro polymerization properties. Here, we demonstrate that crescentin...

Analysis of bacterial communities and bacterial pathogens in a biogas plant by the combination of ethidium monoazide, PCR and Ion Torrent sequencing

DEFF Research Database (Denmark)

Luo, Gang; Angelidaki, Irini

2014-01-01

with time were also observed. This could be attributed to varying composition of the influent. Batch experiments showed that the methane recovery from the digested residues (obtained from biogas reactor) was mainly related with post-digestion temperature. However, post-digestion time rather than temperature......The present study investigated the changes of bacterial community composition including bacterial pathogens along a biogas plant, i.e. from the influent, to the biogas reactor and to the post-digester. The effects of post-digestion temperature and time on the changes of bacterial community...... showed that the bacterial community composition in the influent was changed after anaerobic digestion. Firmicutes were dominant in all the samples, while Proteobacteria decreased in the biogas reactor compared with the influent. Variations of bacterial community composition in the biogas reactor...

Evaluation of acute bacterial rhino sinusitis in asthma patients based on clinical parameters and imaging studies, together with ear, nose and throat examination

Energy Technology Data Exchange (ETDEWEB)

Faure, Alecsandra Calil Moises; Santoro, Ilka Lopes; Lederman, Henrique Manoel; Fernandes, Ana Luisa Godoy [Federal University of Sao Paulo (UNIFESP/EPM), SP (Brazil). School of Medicine from Sao Paulo. Dept. of Internal Medicine]. E-mail: analgf@terra.com.br; analuisa@pneumo.epm.br; Weckx, Luc Louis Maurice [Federal University of Sao Paulo (UNIFESP/EPM), SP (Brazil). School of Medicine from Sao Paulo. Otorhinolaryngology; Fernandes, Artur da Rocha Correa [Federal University of Sao Paulo (UNIFESP/EPM), SP (Brazil). School of Medicine from Sao Paulo. Dept. of Diagnostic Imaging

2008-06-15

Objective: To evaluate paranasal sinuses in patients with stable or acute asthma in order to determine the prevalence of acute bacterial rhinosinusitis. Methods: A cross-sectional study including 30 patients with acute asthma (73% females) treated in the emergency room and 30 patients with stable asthma (80% females) regularly monitored as outpatients. All patients completed a questionnaire on respiratory signs and symptoms and were submitted to ear, nose and throat (ENT) examination, as well as to X-ray and computed tomography (CT) imaging of the sinuses. Results: Based on the clinical diagnosis, the prevalence of acute bacterial rhinosinusitis was 40% in the patients with acute asthma and 3% in those with stable asthma. The ENT examination findings and the imaging findings in isolation were not useful to confirm the diagnosis. Conclusions: In themselves, ENT examination findings, X-ray findings and CT findings were not useful for the diagnosis of acute bacterial rhinosinusitis. Our results provide further evidence that a clinical diagnosis of bacterial rhinosinusitis should be made with caution. (author)

Evaluation of acute bacterial rhino sinusitis in asthma patients based on clinical parameters and imaging studies, together with ear, nose and throat examination

International Nuclear Information System (INIS)

Faure, Alecsandra Calil Moises; Santoro, Ilka Lopes; Lederman, Henrique Manoel; Fernandes, Ana Luisa Godoy; Weckx, Luc Louis Maurice; Fernandes, Artur da Rocha Correa

2008-01-01

Objective: To evaluate paranasal sinuses in patients with stable or acute asthma in order to determine the prevalence of acute bacterial rhinosinusitis. Methods: A cross-sectional study including 30 patients with acute asthma (73% females) treated in the emergency room and 30 patients with stable asthma (80% females) regularly monitored as outpatients. All patients completed a questionnaire on respiratory signs and symptoms and were submitted to ear, nose and throat (ENT) examination, as well as to X-ray and computed tomography (CT) imaging of the sinuses. Results: Based on the clinical diagnosis, the prevalence of acute bacterial rhinosinusitis was 40% in the patients with acute asthma and 3% in those with stable asthma. The ENT examination findings and the imaging findings in isolation were not useful to confirm the diagnosis. Conclusions: In themselves, ENT examination findings, X-ray findings and CT findings were not useful for the diagnosis of acute bacterial rhinosinusitis. Our results provide further evidence that a clinical diagnosis of bacterial rhinosinusitis should be made with caution. (author)

Bacterial microbiota of Kazakhstan cheese revealed by single molecule real time (SMRT) sequencing and its comparison with Belgian, Kalmykian and Italian artisanal cheeses.

Science.gov (United States)

Li, Jing; Zheng, Yi; Xu, Haiyan; Xi, Xiaoxia; Hou, Qiangchuan; Feng, Shuzhen; Wuri, Laga; Bian, Yanfei; Yu, Zhongjie; Kwok, Lai-Yu; Sun, Zhihong; Sun, Tiansong

2017-01-09

In Kazakhstan, traditional artisanal cheeses have a long history and are widely consumed. The unique characteristics of local artisanal cheeses are almost completely preserved. However, their microbial communities have rarely been reported. The current study firstly generated the Single Molecule, Real-Time (SMRT) sequencing bacterial diversity profiles of 6 traditional artisanal cheese samples of Kazakhstan origin, followed by comparatively analyzed the microbiota composition between the current dataset and those from cheeses originated from Belgium, Russian Republic of Kalmykia (Kalmykia) and Italy. Across the Kazakhstan cheese samples, a total of 238 bacterial species belonging to 14 phyla and 140 genera were identified. Lactococcus lactis (28.93%), Lactobacillus helveticus (26.43%), Streptococcus thermophilus (12.18%) and Lactobacillus delbrueckii (12.15%) were the dominant bacterial species for these samples. To further evaluate the cheese bacterial diversity of Kazakhstan cheeses in comparison with those from other geographic origins, 16S rRNA datasets of 36 artisanal cheeses from Belgium, Russian Republic of Kalmykia (Kalmykia) and Italy were retrieved from public databases. The cheese bacterial microbiota communities were largely different across sample origins. By principal coordinate analysis (PCoA) and multivariate analysis of variance (MANOVA), the structure of the Kazakhstan artisanal cheese samples was found to be different from those of the other geographic origins. Furthermore, the redundancy analysis (RDA) identified 16 bacterial OTUs as the key variables responsible for such microbiota structural difference. Our results together suggest that the diversity of bacterial communities in different groups is stratified by geographic region. This study does not only provide novel information on the bacterial microbiota of traditional artisanal cheese of Kazakhstan at species level, but also interesting insights into the bacterial diversity of artisanal

Molecular Analysis of Bacterial Microbiota on Brazilian Currency Note Surfaces

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Tairacan Augusto Pereira da Fonseca

2015-10-01

Full Text Available Currency notes have been implicated as a vehicle for transmitting community-acquired bacterial infections. However, the overall diversity of the bacterial population residing on banknotes is still unknown in Brazil. In this study, we aimed to investigate the overall bacterial population from 150 different Brazilian Rial (R$ notes in circulation using a culture-independent Illumina massively parallel sequencing approach of the 16S rRNA genes. Samples were randomly collected from three different street markets or “feiras” in the metropolitan region of São Paulo. Taxonomical composition revealed the abundance of Proteobacteria phyla, followed by Firmicutes and Streptophyta, with a total of 1193 bacterial families and 3310 bacterial genera. Most of these bacterial genera are of human, animal, and environmental origins. Also, our analysis revealed the presence of some potential pathogenic bacterial genera including Salmonella, Staphylococcus, and Klebsiella. The results demonstrate that there is a tremendous diversity of bacterial contamination on currency notes, including organisms known to be opportunistic pathogens. One of the factors that may contribute to the richness of bacterial diversity in currency notes is personal hygiene. Thus, our results underscore the need to increase public awareness of the importance of personal hygiene of money handlers who also handle food.

Molecular Analysis of Bacterial Microbiota on Brazilian Currency Note Surfaces.

Science.gov (United States)

Pereira da Fonseca, Tairacan Augusto; Pessôa, Rodrigo; Sanabani, Sabri Saeed

2015-10-22

Currency notes have been implicated as a vehicle for transmitting community-acquired bacterial infections. However, the overall diversity of the bacterial population residing on banknotes is still unknown in Brazil. In this study, we aimed to investigate the overall bacterial population from 150 different Brazilian Rial (R$) notes in circulation using a culture-independent Illumina massively parallel sequencing approach of the 16S rRNA genes. Samples were randomly collected from three different street markets or "feiras" in the metropolitan region of São Paulo. Taxonomical composition revealed the abundance of Proteobacteria phyla, followed by Firmicutes and Streptophyta, with a total of 1193 bacterial families and 3310 bacterial genera. Most of these bacterial genera are of human, animal, and environmental origins. Also, our analysis revealed the presence of some potential pathogenic bacterial genera including Salmonella, Staphylococcus, and Klebsiella. The results demonstrate that there is a tremendous diversity of bacterial contamination on currency notes, including organisms known to be opportunistic pathogens. One of the factors that may contribute to the richness of bacterial diversity in currency notes is personal hygiene. Thus, our results underscore the need to increase public awareness of the importance of personal hygiene of money handlers who also handle food.

Bacterial biofilms: prokaryotic adventures in multicellularity

DEFF Research Database (Denmark)

Webb, J.S.; Givskov, Michael Christian; Kjelleberg, S.

2003-01-01

The development of bacterial biofilms includes both the initial social behavior of undifferentiated cells, as well as cell death and differentiation in the mature biofilm, and displays several striking similarities with higher organisms. Recent advances in the field provide new insight...... into differentiation and cell death events in bacterial biofilm development and propose that biofilms have an unexpected level of multicellularity....

Enzymatic hydrolysis of biomimetic bacterial cellulose-hemicellulose composites.

Science.gov (United States)

Penttilä, Paavo A; Imai, Tomoya; Hemming, Jarl; Willför, Stefan; Sugiyama, Junji

2018-06-15

The production of biofuels and other chemicals from lignocellulosic biomass is limited by the inefficiency of enzymatic hydrolysis. Here a biomimetic composite material consisting of bacterial cellulose and wood-based hemicelluloses was used to study the effects of hemicelluloses on the enzymatic hydrolysis with a commercial cellulase mixture. Bacterial cellulose synthesized in the presence of hemicelluloses, especially xylan, was found to be more susceptible to enzymatic hydrolysis than hemicellulose-free bacterial cellulose. The reason for the easier hydrolysis could be related to the nanoscale structure of the substrate, particularly the packing of cellulose microfibrils into ribbons or bundles. In addition, small-angle X-ray scattering was used to show that the average nanoscale morphology of bacterial cellulose remained unchanged during the enzymatic hydrolysis. The reported easier enzymatic hydrolysis of bacterial cellulose produced in the presence of wood-based xylan offers new insights to overcome biomass recalcitrance through genetic engineering. Copyright © 2018 Elsevier Ltd. All rights reserved.

Bacterial desorption from food container and food processing surfaces.

Science.gov (United States)

McEldowney, S; Fletcher, M

1988-03-01

The desorption ofStaphylococcus aureus, Acinetobacter calcoaceticus, and a coryneform from the surfaces of materials used for manufacturing food containers (glass, tin plate, and polypropylene) or postprocess canning factory conveyor belts (stainless steel and nylon) was investigated. The effect of time, pH, temperature, and adsorbed organic layers on desorption was studied.S. aureus did not detach from the substrata at any pH investigated (between pH 5 and 9).A. calcoaceticus and the coryneform in some cases detached, depending upon pH and substratum composition. The degree of bacterial detachment from the substrata was not related to bacterial respiration at experimental pH values. Bacterial desorption was not affected by temperature (4-30°C) nor by an adsorbed layer of peptone and yeast extract on the substrata. The results indicate that bacterial desorption, hence bacterial removal during cleaning or their transfer via liquids flowing over colonized surfaces, is likely to vary with the surface composition and the bacterial species colonizing the surfaces.

Community-acquired multidrug-resistant Gram-negative bacterial infective endocarditis.

Science.gov (United States)

Naha, Sowjanya; Naha, Kushal; Acharya, Vasudev; Hande, H Manjunath; Vivek, G

2014-08-05

We describe two cases of bacterial endocarditis secondary to multidrug-resistant Gram-negative organisms. In both cases, the diagnosis was made in accordance with the modified Duke's criteria and confirmed by histopathological analysis. Furthermore, in both instances there were no identifiable sources of bacteraemia and no history of contact with hospital or other medical services prior to the onset of symptoms. The patients were managed in similar fashion with prolonged broad-spectrum antibiotic therapy and surgical intervention and made complete recoveries. These cases highlight Gram-negative organisms as potential agents for endocarditis, as well as expose the dissemination of such multidrug-resistant bacteria into the community. The application of an integrated medical and surgical approach and therapeutic dilemmas encountered in managing these cases are described. 2014 BMJ Publishing Group Ltd.

Phage “delay” towards enhancing bacterial escape from biofilms: a more comprehensive way of viewing resistance to bacteriophages

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Stephen T. Abedon

2017-03-01

Full Text Available In exploring bacterial resistance to bacteriophages, emphasis typically is placed on those mechanisms which completely prevent phage replication. Such resistance can be detected as extensive reductions in phage ability to form plaques, that is, reduced efficiency of plating. Mechanisms include restriction-modification systems, CRISPR/Cas systems, and abortive infection systems. Alternatively, phages may be reduced in their “vigor” when infecting certain bacterial hosts, that is, with phages displaying smaller burst sizes or extended latent periods rather than being outright inactivated. It is well known, as well, that most phages poorly infect bacteria that are less metabolically active. Extracellular polymers such as biofilm matrix material also may at least slow phage penetration to bacterial surfaces. Here I suggest that such “less-robust” mechanisms of resistance to bacteriophages could serve bacteria by slowing phage propagation within bacterial biofilms, that is, delaying phage impact on multiple bacteria rather than necessarily outright preventing such impact. Related bacteria, ones that are relatively near to infected bacteria, e.g., roughly 10+ µm away, consequently may be able to escape from biofilms with greater likelihood via standard dissemination-initiating mechanisms including erosion from biofilm surfaces or seeding dispersal/central hollowing. That is, given localized areas of phage infection, so long as phage spread can be reduced in rate from initial points of contact with susceptible bacteria, then bacterial survival may be enhanced due to bacteria metaphorically “running away” to more phage-free locations. Delay mechanisms—to the extent that they are less specific in terms of what phages are targeted—collectively could represent broader bacterial strategies of phage resistance versus outright phage killing, the latter especially as require specific, evolved molecular recognition of phage presence. The

Bacterial Exposures and Associations with Atopy and Asthma in Children.

Directory of Open Access Journals (Sweden)

Maria Valkonen

Full Text Available The increase in prevalence of asthma and atopic diseases in Western countries has been linked to aspects of microbial exposure patterns of people. It remains unclear which microbial aspects contribute to the protective farm effect.The objective of this study was to identify bacterial groups associated with prevalence of asthma and atopy, and to quantify indoor exposure to some of these bacterial groups.A DNA fingerprinting technique, denaturing gradient gel electrophoresis (DGGE, was applied to mattress dust samples of farm children and control children in the context of the GABRIEL Advanced study. Associations between signals in DGGE and atopy, asthma and other allergic health outcomes were analyzed. Quantitative DNA based assays (qPCR for four bacterial groups were applied on the dust samples to seek quantitative confirmation of associations indicated in DNA fingerprinting.Several statistically significant associations between individual bacterial signals and also bacterial diversity in DGGE and health outcomes in children were observed. The majority of these associations showed inverse relationships with atopy, less so with asthma. Also, in a subsequent confirmation study using a quantitative method (qPCR, higher mattress levels of specifically targeted bacterial groups - Mycobacterium spp., Bifidobacteriaceae spp. and two different clusters of Clostridium spp. - were associated with a lower prevalence of atopy.DNA fingerprinting proved useful in identifying bacterial signals that were associated with atopy in particular. These findings were quantitatively confirmed for selected bacterial groups with a second method. High correlations between the different bacterial exposures impede a clear attribution of protective effects to one specific bacterial group. More diverse bacterial flora in mattress dust may link to microbial exposure patterns that protect against development of atopic diseases.

Bacterial contaminations of informally marketed raw milk in Ghana ...

African Journals Online (AJOL)

Background: Milk has an outstanding nutritional quality but is also an excellent medium for bacterial growth and an important source of bacterial infection when consumed without pasteurization. Objective: To estimate the bacterial health risk of milk consumption in Accra and Kumasi, the twomajor cities in Ghana. Method: A ...

Community-acquired bacterial meningitis in alcoholic patients.

Directory of Open Access Journals (Sweden)

Martijn Weisfelt

2010-02-01

Full Text Available Alcoholism is associated with susceptibility to infectious disease, particularly bacterial pneumonia. In the present study we described characteristics in alcoholic patients with bacterial meningitis and delineate the differences with findings in non-alcoholic adults with bacterial meningitis.This was a prospective nationwide observational cohort study including patients aged >16 years who had bacterial meningitis confirmed by culture of cerebrospinal fluid (696 episodes of bacterial meningitis occurring in 671 patients. Alcoholism was present in 27 of 686 recorded episodes of bacterial meningitis (4% and alcoholics were more often male than non-alcoholics (82% vs 48%, P = 0.001. A higher proportion of alcoholics had underlying pneumonia (41% vs 11% P<0.001. Alcoholics were more likely to have meningitis due to infection with Streptococcus pneumoniae (70% vs 50%, P = 0.01 and Listeria monocytogenes (19% vs 4%, P = 0.005, whereas Neisseria meningitidis was more common in non-alcoholic patients (39% vs 4%, P = 0.01. A large proportion of alcoholics developed complications during clinical course (82% vs 62%, as compared with non-alcoholics; P = 0.04, often cardiorespiratory failure (52% vs 28%, as compared with non-alcoholics; P = 0.01. Alcoholic patients were at risk for unfavourable outcome (67% vs 33%, as compared with non-alcoholics; P<0.001.Alcoholic patients are at high risk for complications resulting in high morbidity and mortality. They are especially at risk for cardiorespiratory failure due to underlying pneumonia, and therefore, aggressive supportive care may be crucial in the treatment of these patients.

Determinants of bacterial communities in Canadian agroforestry systems.

Science.gov (United States)

Banerjee, Samiran; Baah-Acheamfour, Mark; Carlyle, Cameron N; Bissett, Andrew; Richardson, Alan E; Siddique, Tariq; Bork, Edward W; Chang, Scott X

2016-06-01

Land-use change is one of the most important factors influencing soil microbial communities, which play a pivotal role in most biogeochemical and ecological processes. Using agroforestry systems as a model, this study examined the effects of land uses and edaphic properties on bacterial communities in three agroforestry types covering a 270 km soil-climate gradient in Alberta, Canada. Our results demonstrate that land-use patterns exert stronger effects on soil bacterial communities than soil zones in these agroforestry systems. Plots with trees in agroforestry systems promoted greater bacterial abundance and to some extent species richness, which was associated with more nutrient-rich soil resources. While Acidobacteria, Actinobacteria and Alphaproteobacteria were the dominant bacterial phyla and subphyla across land uses, Arthrobacter, Acidobacteria_Gp16, Burkholderia, Rhodanobacter and Rhizobium were the keystone taxa in these agroforestry systems. Soil pH and carbon contents emerged as the major determinants of bacterial community characteristics. We found non-random co-occurrence and modular patterns of soil bacterial communities, and these patterns were controlled by edaphic factors and not their taxonomy. Overall, this study highlights the drivers and co-occurrence patterns of soil microbial communities in agroforestry systems. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

Bacterial successions in the Broiler Gastrointestinal tract

DEFF Research Database (Denmark)

Ranjitkar, Samir; Lawley, Blair; Tannock, Gerald

2016-01-01

diversity, data were pooled for downstream analysis. With increasing age, a clear succession of bacterial communities and an increased bacterial diversity was observed. Lactobacillaceae (mainly Lactobacillus) represented most of the Firmicutes at all ages and in all segments of the gut except the ceca...

neonatal bacterial meningitis in Cape Town children

African Journals Online (AJOL)

neonatal bacterial meningitis in Cape Town children. Bacterial meningitis is a major cause of childhood morbidity and mortality in South Africa. However, comprehensive regional or national epidemiological data, essential for rational public health interventions, are lacking. The purpose of this 1-year prospective study, from.

Specific amplification of bacterial DNA by optimized so-called universal bacterial primers in samples rich of plant DNA.

Science.gov (United States)

Dorn-In, Samart; Bassitta, Rupert; Schwaiger, Karin; Bauer, Johann; Hölzel, Christina S

2015-06-01

Universal primers targeting the bacterial 16S-rRNA-gene allow quantification of the total bacterial load in variable sample types by qPCR. However, many universal primer pairs also amplify DNA of plants or even of archaea and other eukaryotic cells. By using these primers, the total bacterial load might be misevaluated, whenever samples contain high amounts of non-target DNA. Thus, this study aimed to provide primer pairs which are suitable for quantification and identification of bacterial DNA in samples such as feed, spices and sample material from digesters. For 42 primers, mismatches to the sequence of chloroplasts and mitochondria of plants were evaluated. Six primer pairs were further analyzed with regard to the question whether they anneal to DNA of archaea, animal tissue and fungi. Subsequently they were tested with sample matrix such as plants, feed, feces, soil and environmental samples. To this purpose, the target DNA in the samples was quantified by qPCR. The PCR products of plant and feed samples were further processed for the Single Strand Conformation Polymorphism method followed by sequence analysis. The sequencing results revealed that primer pair 335F/769R amplified only bacterial DNA in samples such as plants and animal feed, in which the DNA of plants prevailed. Copyright © 2015 Elsevier B.V. All rights reserved.

Temporal relationships exist between cecum, ileum and litter bacterial microbiomes in a commercial turkey flock, and subtherapeutic penicillin treatment impacts ileum bacterial community establishment

Directory of Open Access Journals (Sweden)

Jessica L Danzeisen

2015-11-01

Full Text Available Gut health is paramount for commercial poultry production, and improved methods to assess gut health are critically needed to better understand how the avian gastrointestinal tract matures over time. One important aspect of gut health is the totality of bacterial populations inhabiting different sites of the avian gastrointestinal tract, and associations of these populations with the poultry farm environment, since these bacteria are thought to drive metabolism and prime the developing host immune system. In this study, a single flock of commercial turkeys was followed over the course of twelve weeks to examine bacterial microbiome inhabiting the ceca, ileum, and corresponding poultry litter. Furthermore, the effects of low-dose, growth-promoting penicillin treatment (50 g/ton in feed on the ileum bacterial microbiome were also examined during the early brood period. The cecum and ileum bacterial communities of turkeys were distinct, yet shifted in parallel to one another over time during bird maturation. Corresponding poultry litter was also distinct yet more closely represented the ileal bacterial populations than cecal bacterial populations, and also changed parallel to ileum bacterial populations over time. Penicillin applied at low dose in feed significantly enhanced early weight gain in commercial poults, and this correlated with predictable shifts in the ileum bacterial populations in control versus treatment groups. Overall, this study identified the dynamics of the turkey gastrointestinal microbiome during development, correlations between bacterial populations in the gastrointestinal tract and the litter environment, and the impact of low-dose penicillin on modulation of bacterial communities in the ileum. Such modulations provide a target for alternatives to low-dose antibiotics.

Structure of bacterial lipopolysaccharides.

Science.gov (United States)

Caroff, Martine; Karibian, Doris

2003-11-14

Bacterial lipopolysaccharides are the major components of the outer surface of Gram-negative bacteria They are often of interest in medicine for their immunomodulatory properties. In small amounts they can be beneficial, but in larger amounts they may cause endotoxic shock. Although they share a common architecture, their structural details exert a strong influence on their activity. These molecules comprise: a lipid moiety, called lipid A, which is considered to be the endotoxic component, a glycosidic part consisting of a core of approximately 10 monosaccharides and, in "smooth-type" lipopolysaccharides, a third region, named O-chain, consisting of repetitive subunits of one to eight monosaccharides responsible for much of the immunospecificity of the bacterial cell.

Simplified and representative bacterial community of maize roots.

Science.gov (United States)

Niu, Ben; Paulson, Joseph Nathaniel; Zheng, Xiaoqi; Kolter, Roberto

2017-03-21

Plant-associated microbes are important for the growth and health of their hosts. As a result of numerous prior studies, we know that host genotypes and abiotic factors influence the composition of plant microbiomes. However, the high complexity of these communities challenges detailed studies to define experimentally the mechanisms underlying the dynamics of community assembly and the beneficial effects of such microbiomes on plant hosts. In this work, from the distinctive microbiota assembled by maize roots, through host-mediated selection, we obtained a greatly simplified synthetic bacterial community consisting of seven strains ( Enterobacter cloacae , Stenotrophomonas maltophilia, Ochrobactrum pituitosum, Herbaspirillum frisingense, Pseudomonas putida, Curtobacterium pusillum , and Chryseobacterium indologenes ) representing three of the four most dominant phyla found in maize roots. By using a selective culture-dependent method to track the abundance of each strain, we investigated the role that each plays in community assembly on roots of axenic maize seedlings. Only the removal of E. cloacae led to the complete loss of the community, and C. pusillum took over. This result suggests that E. cloacae plays the role of keystone species in this model ecosystem. In planta and in vitro, this model community inhibited the phytopathogenic fungus Fusarium verticillioides , indicating a clear benefit to the host. Thus, combined with the selective culture-dependent quantification method, our synthetic seven-species community representing the root microbiome has the potential to serve as a useful system to explore how bacterial interspecies interactions affect root microbiome assembly and to dissect the beneficial effects of the root microbiota on hosts under laboratory conditions in the future.

Compatible bacterial mixture, tolerant to desiccation, improves maize plant growth.

Science.gov (United States)

Molina-Romero, Dalia; Baez, Antonino; Quintero-Hernández, Verónica; Castañeda-Lucio, Miguel; Fuentes-Ramírez, Luis Ernesto; Bustillos-Cristales, María Del Rocío; Rodríguez-Andrade, Osvaldo; Morales-García, Yolanda Elizabeth; Munive, Antonio; Muñoz-Rojas, Jesús

2017-01-01

Plant growth-promoting rhizobacteria (PGPR) increase plant growth and crop productivity. The inoculation of plants with a bacterial mixture (consortium) apparently provides greater benefits to plant growth than inoculation with a single bacterial strain. In the present work, a bacterial consortium was formulated containing four compatible and desiccation-tolerant strains with potential as PGPR. The formulation had one moderately (Pseudomonas putida KT2440) and three highly desiccation-tolerant (Sphingomonas sp. OF178, Azospirillum brasilense Sp7 and Acinetobacter sp. EMM02) strains. The four bacterial strains were able to adhere to seeds and colonize the rhizosphere of plants when applied in both mono-inoculation and multi-inoculation treatments, showing that they can also coexist without antagonistic effects in association with plants. The effects of the bacterial consortium on the growth of blue maize were evaluated. Seeds inoculated with either individual bacterial strains or the bacterial consortium were subjected to two experimental conditions before sowing: normal hydration or desiccation. In general, inoculation with the bacterial consortium increased the shoot and root dry weight, plant height and plant diameter compared to the non-inoculated control or mono-inoculation treatments. The bacterial consortium formulated in this work had greater benefits for blue maize plants even when the inoculated seeds underwent desiccation stress before germination, making this formulation attractive for future field applications.

Compatible bacterial mixture, tolerant to desiccation, improves maize plant growth.

Directory of Open Access Journals (Sweden)

Dalia Molina-Romero

Full Text Available Plant growth-promoting rhizobacteria (PGPR increase plant growth and crop productivity. The inoculation of plants with a bacterial mixture (consortium apparently provides greater benefits to plant growth than inoculation with a single bacterial strain. In the present work, a bacterial consortium was formulated containing four compatible and desiccation-tolerant strains with potential as PGPR. The formulation had one moderately (Pseudomonas putida KT2440 and three highly desiccation-tolerant (Sphingomonas sp. OF178, Azospirillum brasilense Sp7 and Acinetobacter sp. EMM02 strains. The four bacterial strains were able to adhere to seeds and colonize the rhizosphere of plants when applied in both mono-inoculation and multi-inoculation treatments, showing that they can also coexist without antagonistic effects in association with plants. The effects of the bacterial consortium on the growth of blue maize were evaluated. Seeds inoculated with either individual bacterial strains or the bacterial consortium were subjected to two experimental conditions before sowing: normal hydration or desiccation. In general, inoculation with the bacterial consortium increased the shoot and root dry weight, plant height and plant diameter compared to the non-inoculated control or mono-inoculation treatments. The bacterial consortium formulated in this work had greater benefits for blue maize plants even when the inoculated seeds underwent desiccation stress before germination, making this formulation attractive for future field applications.

Normal bacterial flora from vaginas of Criollo Limonero cows.

Science.gov (United States)

Zambrano-Nava, Sunny; Boscán-Ocando, Julio; Nava, Jexenia

2011-02-01

In order to describe the normal bacterial flora in vaginas of Criollo Limonero cows, 51 healthy multiparous cows, at least 90-day postpartum, were selected. Duplicated swabs (N = 102) were taken from the vaginal fornix of cows to perform aerobic and anaerobic cultures as well as conventional biochemical tests. Out of 102 swabs, bacterial growth was obtained in 55 (53.9%) while the remaining 47 (46.1%) did not exhibited any bacterial growth. Of the 55 bacterial growths, 23 (41.8%) were aerobic whereas 32 (58.1%) were anaerobic. Likewise, 29 (52.72%) of bacterial growths were pure and 26 (47.27%) were mixed. Under both aerobic and anaerobic conditions, Gram positive bacteria were predominant (81.82% and 73.08%, respectively) over Gram negative bacteria (18.18% and 26.92%, respectively). Isolated bacteria were Arcanobacterium pyogenes (22.92%), Staphylococcus aureus (15.63%), Staphylococcus coagulase negative (17.71%), Erysipelothrix rhusiopathiae (6.25%), Bacteroides spp. (13.54%), and Peptostreptococcus spp. (7.29%). In conclusion, normal vaginal bacterial flora of Criollo Limonero cows was predominantly Gram positive and included A. pyogenes, S. aureus, coagulase negative Staphylococcus, E. rhusiopathiae, Bacteroides spp., and Peptostreptococcus spp. In Criollo Limonero cattle, adaptive aspects such as development of humoral and physical mechanisms for defense, and bacterial adaptation to host deserve research attention.

Applications of bacterial cellulose and its composites in biomedicine.

Science.gov (United States)

Rajwade, J M; Paknikar, K M; Kumbhar, J V

2015-03-01

Bacterial cellulose produced by few but specific microbial genera is an extremely pure natural exopolysaccharide. Besides providing adhesive properties and a competitive advantage to the cellulose over-producer, bacterial cellulose confers UV protection, ensures maintenance of an aerobic environment, retains moisture, protects against heavy metal stress, etc. This unique nanostructured matrix is being widely explored for various medical and nonmedical applications. It can be produced in various shapes and forms because of which it finds varied uses in biomedicine. The attributes of bacterial cellulose such as biocompatibility, haemocompatibility, mechanical strength, microporosity and biodegradability with its unique surface chemistry make it ideally suited for a plethora of biomedical applications. This review highlights these qualities of bacterial cellulose in detail with emphasis on reports that prove its utility in biomedicine. It also gives an in-depth account of various biomedical applications ranging from implants and scaffolds for tissue engineering, carriers for drug delivery, wound-dressing materials, etc. that are reported until date. Besides, perspectives on limitations of commercialisation of bacterial cellulose have been presented. This review is also an update on the variety of low-cost substrates used for production of bacterial cellulose and its nonmedical applications and includes patents and commercial products based on bacterial cellulose.

Bacterial carbon utilization in vertical subsurface flow constructed wetlands.

Science.gov (United States)

Tietz, Alexandra; Langergraber, Günter; Watzinger, Andrea; Haberl, Raimund; Kirschner, Alexander K T

2008-03-01

Subsurface vertical flow constructed wetlands with intermittent loading are considered as state of the art and can comply with stringent effluent requirements. It is usually assumed that microbial activity in the filter body of constructed wetlands, responsible for the removal of carbon and nitrogen, relies mainly on bacterially mediated transformations. However, little quantitative information is available on the distribution of bacterial biomass and production in the "black-box" constructed wetland. The spatial distribution of bacterial carbon utilization, based on bacterial (14)C-leucine incorporation measurements, was investigated for the filter body of planted and unplanted indoor pilot-scale constructed wetlands, as well as for a planted outdoor constructed wetland. A simple mass-balance approach was applied to explain the bacterially catalysed organic matter degradation in this system by comparing estimated bacterial carbon utilization rates with simultaneously measured carbon reduction values. The pilot-scale constructed wetlands proved to be a suitable model system for investigating microbial carbon utilization in constructed wetlands. Under an ideal operating mode, the bulk of bacterial productivity occurred within the first 10cm of the filter body. Plants seemed to have no significant influence on productivity and biomass of bacteria, as well as on wastewater total organic carbon removal.

Cytosolic access of intracellular bacterial pathogens: the Shigella paradigm

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Nora eMellouk

2016-04-01

Full Text Available Shigella is a Gram-negative bacterial pathogen, which causes bacillary dysentery in humans. A crucial step of Shigella infection is its invasion of epithelial cells. Using a type III secretion system, Shigella injects several bacterial effectors ultimately leading to bacterial internalization within a vacuole. Then, Shigella escapes rapidly from the vacuole, it replicates within the cytosol and spreads from cell-to-cell. The molecular mechanism of vacuolar rupture used by Shigella has been studied in some detail during the recent years and new paradigms are emerging about the underlying molecular events. For decades, bacterial effector proteins were portrayed as main actors inducing vacuolar rupture. This includes the effector/translocators IpaB and IpaC. More recently, this has been challenged and an implication of the host cell in the process of vacuolar rupture has been put forward. This includes the bacterial subversion of host trafficking regulators, such as the Rab GTPase Rab11. The involvement of the host in determining bacterial vacuolar integrity has also been found for other bacterial pathogens, particularly for Salmonella. Here, we will discuss our current view of host factor and pathogen effector implications during Shigella vacuolar rupture and the steps leading to it.

Effects of the antibiotic ciprofloxacin on the bacterial community structure and degradation of pyrene in marine sediment

International Nuclear Information System (INIS)

Naeslund, Johan; Hedman, Jenny E.; Agestrand, Cecilia

2008-01-01

The ecological consequences of antibiotics in the aquatic environment have been an issue of concern over the past years due to the potential risk for negative effects on indigenous microorganisms. Microorganisms provide important ecosystem services, such as nutrient recycling, organic matter mineralization and degradation of pollutants. In this study, effects of exposure to the antibiotic ciprofloxacin on the bacterial diversity and pollutant degradation in natural marine sediments were studied using molecular methods (T-RFLP) in combination with radiorespirometry. In a microcosm experiment, sediment spiked with 14 C-labelled pyrene was exposed to five concentrations of ciprofloxacin (0, 20, 200, 1000 and 2000 μg L -1 ) in a single dose to the overlying water. The production of 14 CO 2 (i.e. complete mineralization of pyrene) was measured during 11 weeks. Sediment samples for bacterial community structure analysis were taken after 7 weeks. Results showed a significant dose-dependent inhibition of pyrene mineralization measured as the total 14 CO 2 production. The nominal EC 50 was calculated to 560 μg L -1 , corresponding to 0.4 μg/kg d.w. sediment. The lowest effect concentration on the bacterial community structure was 200 μg L -1 , which corresponds to 0.1 μg/kg d.w. sediment. Our results show that antibiotic pollution can be a potential threat to both bacterial diversity and an essential ecosystem service they perform in marine sediment

Adaptive Bacterial Foraging Optimization

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Hanning Chen

2011-01-01

Full Text Available Bacterial Foraging Optimization (BFO is a recently developed nature-inspired optimization algorithm, which is based on the foraging behavior of E. coli bacteria. Up to now, BFO has been applied successfully to some engineering problems due to its simplicity and ease of implementation. However, BFO possesses a poor convergence behavior over complex optimization problems as compared to other nature-inspired optimization techniques. This paper first analyzes how the run-length unit parameter of BFO controls the exploration of the whole search space and the exploitation of the promising areas. Then it presents a variation on the original BFO, called the adaptive bacterial foraging optimization (ABFO, employing the adaptive foraging strategies to improve the performance of the original BFO. This improvement is achieved by enabling the bacterial foraging algorithm to adjust the run-length unit parameter dynamically during algorithm execution in order to balance the exploration/exploitation tradeoff. The experiments compare the performance of two versions of ABFO with the original BFO, the standard particle swarm optimization (PSO and a real-coded genetic algorithm (GA on four widely-used benchmark functions. The proposed ABFO shows a marked improvement in performance over the original BFO and appears to be comparable with the PSO and GA.

Vaginal epithelial cells regulate membrane adhesiveness to co-ordinate bacterial adhesion

NARCIS (Netherlands)

Younes, Jessica A.; Klappe, Karin; Kok, Jan Willem; Busscher, Henk J.; Reid, Gregor; van der Mei, Henny C.

Vaginal epithelium is colonized by different bacterial strains and species. The bacterial composition of vaginal biofilms controls the balance between health and disease. Little is known about the relative contribution of the epithelial and bacterial cell surfaces to bacterial adhesion and whether

Isolation of cell-free bacterial inclusion bodies.

Science.gov (United States)

Rodríguez-Carmona, Escarlata; Cano-Garrido, Olivia; Seras-Franzoso, Joaquin; Villaverde, Antonio; García-Fruitós, Elena

2010-09-17

Bacterial inclusion bodies are submicron protein clusters usually found in recombinant bacteria that have been traditionally considered as undesirable products from protein production processes. However, being fully biocompatible, they have been recently characterized as nanoparticulate inert materials useful as scaffolds for tissue engineering, with potentially wider applicability in biomedicine and material sciences. Current protocols for inclusion body isolation from Escherichia coli usually offer between 95 to 99% of protein recovery, what in practical terms, might imply extensive bacterial cell contamination, not compatible with the use of inclusion bodies in biological interfaces. Using an appropriate combination of chemical and mechanical cell disruption methods we have established a convenient procedure for the recovery of bacterial inclusion bodies with undetectable levels of viable cell contamination, below 10⁻¹ cfu/ml, keeping the particulate organization of these aggregates regarding size and protein folding features. The application of the developed protocol allows obtaining bacterial free inclusion bodies suitable for use in mammalian cell cultures and other biological interfaces.

Identification and Characterization of Novel Biocontrol Bacterial

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Young Cheol Kim

2014-09-01

Full Text Available Because bacterial isolates from only a few genera have been developed commercially as biopesticides, discovery and characterization of novel bacterial strains will be a key to market expansion. Our previous screen using plant bioassays identified 24 novel biocontrol isolates representing 12 different genera. In this study, we characterized the 3 isolates showing the best biocontrol activities. The isolates were Pantoea dispersa WCU35, Proteus myxofaciens WCU244, and Exiguobacterium acetylicum WCU292 based on 16S rRNA sequence analysis. The isolates showed differential production of extracellular enzymes, antimicrobial activity against various fungal or bacterial plant pathogens, and induced systemic resistance activity against tomato gray mold disease caused by Botrytis cinerea. E. acetylicum WCU292 lacked strong in vitro antimicrobial activity against plant pathogens, but induced systemic resistance against tomato gray mold disease. These results confirm that the trait of biological control is found in a wide variety of bacterial genera

Endolymphatic sac involvement in bacterial meningitis

DEFF Research Database (Denmark)

Møller, Martin Nue; Brandt, Christian; Østergaard, Christian

2015-01-01

The commonest sequelae of bacterial meningitis are related to the inner ear. Little is known about the inner ear immune defense. Evidence suggests that the endolymphatic sac provides some protection against infection. A potential involvement of the endolymphatic sac in bacterial meningitis...... is largely unaccounted for, and thus the object of the present study. A well-established adult rat model of Streptococcus pneumoniae meningitis was employed. Thirty adult rats were inoculated intrathecally with Streptococcus pneumoniae and received no additional treatment. Six rats were sham...... days. Bacteria invaded the inner ear through the cochlear aquaduct. On days 5-6, the bacteria invaded the endolymphatic sac through the endolymphatic duct subsequent to invasion of the vestibular endolymphatic compartment. No evidence of direct bacterial invasion of the sac through the meninges...

Completely continuous and weakly completely continuous abstract ...

Indian Academy of Sciences (India)

An algebra A is called right completely continuous (right weakly completely continuous) ... Moreover, some applications of these results in group algebras are .... A linear subspace S(G) of L1(G) is said to be a Segal algebra, if it satisfies the.

Bacterial community changes in an industrial algae production system.

Science.gov (United States)

Fulbright, Scott P; Robbins-Pianka, Adam; Berg-Lyons, Donna; Knight, Rob; Reardon, Kenneth F; Chisholm, Stephen T

2018-04-01

While microalgae are a promising feedstock for production of fuels and other chemicals, a challenge for the algal bioproducts industry is obtaining consistent, robust algae growth. Algal cultures include complex bacterial communities and can be difficult to manage because specific bacteria can promote or reduce algae growth. To overcome bacterial contamination, algae growers may use closed photobioreactors designed to reduce the number of contaminant organisms. Even with closed systems, bacteria are known to enter and cohabitate, but little is known about these communities. Therefore, the richness, structure, and composition of bacterial communities were characterized in closed photobioreactor cultivations of Nannochloropsis salina in F/2 medium at different scales, across nine months spanning late summer-early spring, and during a sequence of serially inoculated cultivations. Using 16S rRNA sequence data from 275 samples, bacterial communities in small, medium, and large cultures were shown to be significantly different. Larger systems contained richer bacterial communities compared to smaller systems. Relationships between bacterial communities and algae growth were complex. On one hand, blooms of a specific bacterial type were observed in three abnormal, poorly performing replicate cultivations, while on the other, notable changes in the bacterial community structures were observed in a series of serial large-scale batch cultivations that had similar growth rates. Bacteria common to the majority of samples were identified, including a single OTU within the class Saprospirae that was found in all samples. This study contributes important information for crop protection in algae systems, and demonstrates the complex ecosystems that need to be understood for consistent, successful industrial algae cultivation. This is the first study to profile bacterial communities during the scale-up process of industrial algae systems.

Hydrodebridement of wounds: effectiveness in reducing wound bacterial contamination and potential for air bacterial contamination.

Science.gov (United States)

Bowling, Frank L; Stickings, Daryl S; Edwards-Jones, Valerie; Armstrong, David G; Boulton, Andrew Jm

2009-05-08

The purpose of this study was to assess the level of air contamination with bacteria after surgical hydrodebridement and to determine the effectiveness of hydro surgery on bacterial reduction of a simulated infected wound. Four porcine samples were scored then infected with a broth culture containing a variety of organisms and incubated at 37 degrees C for 24 hours. The infected samples were then debrided with the hydro surgery tool (Versajet, Smith and Nephew, Largo, Florida, USA). Samples were taken for microbiology, histology and scanning electron microscopy pre-infection, post infection and post debridement. Air bacterial contamination was evaluated before, during and after debridement by using active and passive methods; for active sampling the SAS-Super 90 air sampler was used, for passive sampling settle plates were located at set distances around the clinic room. There was no statistically significant reduction in bacterial contamination of the porcine samples post hydrodebridement. Analysis of the passive sampling showed a significant (p air whilst using hydro surgery equipment compared with a basal count of 582 CFUs/m3. During removal of the wound dressing, a significant increase was observed relative to basal counts (p air samples was still significantly raised 1 hour post-therapy. The results suggest a significant increase in bacterial air contamination both by active sampling and passive sampling. We believe that action might be taken to mitigate fallout in the settings in which this technique is used.

Predicted Bacterial Interactions Affect in Vivo Microbial Colonization Dynamics in Nematostella

Science.gov (United States)

Domin, Hanna; Zurita-Gutiérrez, Yazmín H.; Scotti, Marco; Buttlar, Jann; Hentschel Humeida, Ute; Fraune, Sebastian

2018-01-01

The maintenance and resilience of host-associated microbiota during development is a fundamental process influencing the fitness of many organisms. Several host properties were identified as influencing factors on bacterial colonization, including the innate immune system, mucus composition, and diet. In contrast, the importance of bacteria–bacteria interactions on host colonization is less understood. Here, we use bacterial abundance data of the marine model organism Nematostella vectensis to reconstruct potential bacteria–bacteria interactions through co-occurrence networks. The analysis indicates that bacteria–bacteria interactions are dynamic during host colonization and change according to the host’s developmental stage. To assess the predictive power of inferred interactions, we tested bacterial isolates with predicted cooperative or competitive behavior for their ability to influence bacterial recolonization dynamics. Within 3 days of recolonization, all tested bacterial isolates affected bacterial community structure, while only competitive bacteria increased bacterial diversity. Only 1 week after recolonization, almost no differences in bacterial community structure could be observed between control and treatments. These results show that predicted competitive bacteria can influence community structure for a short period of time, verifying the in silico predictions. However, within 1 week, the effects of the bacterial isolates are neutralized, indicating a high degree of resilience of the bacterial community. PMID:29740401

Predicted Bacterial Interactions Affect in Vivo Microbial Colonization Dynamics in Nematostella

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Hanna Domin

2018-04-01

Full Text Available The maintenance and resilience of host-associated microbiota during development is a fundamental process influencing the fitness of many organisms. Several host properties were identified as influencing factors on bacterial colonization, including the innate immune system, mucus composition, and diet. In contrast, the importance of bacteria–bacteria interactions on host colonization is less understood. Here, we use bacterial abundance data of the marine model organism Nematostella vectensis to reconstruct potential bacteria–bacteria interactions through co-occurrence networks. The analysis indicates that bacteria–bacteria interactions are dynamic during host colonization and change according to the host’s developmental stage. To assess the predictive power of inferred interactions, we tested bacterial isolates with predicted cooperative or competitive behavior for their ability to influence bacterial recolonization dynamics. Within 3 days of recolonization, all tested bacterial isolates affected bacterial community structure, while only competitive bacteria increased bacterial diversity. Only 1 week after recolonization, almost no differences in bacterial community structure could be observed between control and treatments. These results show that predicted competitive bacteria can influence community structure for a short period of time, verifying the in silico predictions. However, within 1 week, the effects of the bacterial isolates are neutralized, indicating a high degree of resilience of the bacterial community.

Microbial activity of soil with sulfentrazone associated with phytoremediator species and inoculation with a bacterial consortium

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Christiane Augusta Diniz Melo

Full Text Available ABSTRACT Phytostimulation plays a key role in the process of rhizodegradation of herbicides in soil. Additionally, bio-enhancement associated with phytoremediation may increase the efficiency of the decontamination process of soils with herbicides. Therefore, the objective of this study was to evaluate the biomass and microbial activity of soil contaminated with sulfentrazone and cultivated with phytoremediator species plus a bacterial consortium. The experiment was conducted in a greenhouse, carried out with a 2 × 4 × 4 completely randomized factorial design with 4 replications. The first factor consisted of the presence or absence of bio-enhancement with a bacterial consortium composed of Pseudomonas bacteria; the second factor consisted of a monoculture or mixed cultivation of 2 phytoremediator species Canavalia ensiformis and Helianthus annuus, besides the absence of cultivation; the third factor was made up by the bio-remediation time (25, 45, 65, and 85 days after thinning. Uncultivated soils displayed low values of microbial biomass carbon and microbial quotient as well as high values of metabolic quotient throughout the bio-remediation time, indicating the importance of cultivating phytoremediator species for the stimulation of soil microbiota. Bio-enhancement with the bacterial consortium, in general, promoted an increase in the microbial biomass and activity of soil contaminated with sulfentrazone. In the presence of the bacterial consortium, Canavalia ensiformis stimulated a greater activity of associated microbiota and supported a higher microbial biomass. Phytoremediation associated with microbial bio-enhancement are thus promising techniques for the bio-remediation for soils contaminated with sulfentrazone. This technique enhances the biomass and activity of soil microorganisms.

[Combination therapy of chronic bacterial prostatitis].

Science.gov (United States)

Khryanin, A A; Reshetnikov, O V

2016-08-01

The article discusses the possible etiological factors in the development of chronic bacterial prostatitis. The authors presented a comparative long-term analysis of morbidity from non-viral sexually transmitted infections (STIs) in Russia. Against the background of general decline in STIs incidence, a significant percentage of them is made up by urogenital trichomoniasis. The findings substantiated the advantages of combination therapy (ornidazole and ofloxacin) for bacterial urinary tract infections.

Fundamental principles in bacterial physiology—history, recent progress, and the future with focus on cell size control: a review

Science.gov (United States)

Jun, Suckjoon; Si, Fangwei; Pugatch, Rami; Scott, Matthew

2018-05-01

Bacterial physiology is a branch of biology that aims to understand overarching principles of cellular reproduction. Many important issues in bacterial physiology are inherently quantitative, and major contributors to the field have often brought together tools and ways of thinking from multiple disciplines. This article presents a comprehensive overview of major ideas and approaches developed since the early 20th century for anyone who is interested in the fundamental problems in bacterial physiology. This article is divided into two parts. In the first part (sections 1–3), we review the first ‘golden era’ of bacterial physiology from the 1940s to early 1970s and provide a complete list of major references from that period. In the second part (sections 4–7), we explain how the pioneering work from the first golden era has influenced various rediscoveries of general quantitative principles and significant further development in modern bacterial physiology. Specifically, section 4 presents the history and current progress of the ‘adder’ principle of cell size homeostasis. Section 5 discusses the implications of coarse-graining the cellular protein composition, and how the coarse-grained proteome ‘sectors’ re-balance under different growth conditions. Section 6 focuses on physiological invariants, and explains how they are the key to understanding the coordination between growth and the cell cycle underlying cell size control in steady-state growth. Section 7 overviews how the temporal organization of all the internal processes enables balanced growth. In the final section 8, we conclude by discussing the remaining challenges for the future in the field.

S1PR3 Signaling Drives Bacterial Killing and Is Required for Survival in Bacterial Sepsis.

Science.gov (United States)

Hou, JinChao; Chen, QiXing; Wu, XiaoLiang; Zhao, DongYan; Reuveni, Hadas; Licht, Tamar; Xu, MengLong; Hu, Hu; Hoeft, Andreas; Ben-Sasson, Shmuel A; Shu, Qiang; Fang, XiangMing

2017-12-15

Efficient elimination of pathogenic bacteria is a critical determinant in the outcome of sepsis. Sphingosine-1-phosphate receptor 3 (S1PR3) mediates multiple aspects of the inflammatory response during sepsis, but whether S1PR3 signaling is necessary for eliminating the invading pathogens remains unknown. To investigate the role of S1PR3 in antibacterial immunity during sepsis. Loss- and gain-of-function experiments were performed using cell and murine models. S1PR3 levels were determined in patients with sepsis and healthy volunteers. S1PR3 protein levels were up-regulated in macrophages upon bacterial stimulation. S1pr3 -/- mice showed increased mortality and increased bacterial burden in multiple models of sepsis. The transfer of wild-type bone marrow-derived macrophages rescued S1pr3 -/- mice from lethal sepsis. S1PR3-overexpressing macrophages further ameliorated the mortality rate of sepsis. Loss of S1PR3 led to markedly decreased bacterial killing in macrophages. Enhancing endogenous S1PR3 activity using a peptide agonist potentiated the macrophage bactericidal function and improved survival rates in multiple models of sepsis. Mechanically, the reactive oxygen species levels were decreased and phagosome maturation was delayed in S1pr3 -/- macrophages due to impaired recruitment of vacuolar protein-sorting 34 to the phagosomes. In addition, S1RP3 expression levels were elevated in monocytes from patients with sepsis. Higher levels of monocytic S1PR3 were associated with efficient intracellular bactericidal activity, better immune status, and preferable outcomes. S1PR3 signaling drives bacterial killing and is essential for survival in bacterial sepsis. Interventions targeting S1PR3 signaling could have translational implications for manipulating the innate immune response to combat pathogens.

Bacterial leaching of uranium ores - a review

International Nuclear Information System (INIS)

Lowson, R.T.

1975-11-01

The bacterial leaching of uranium ores involves the bacterially catalysed oxidation of associated pyrite to sulphuric acid and Fe 3+ by autotrophic bacteria and the leaching of the uranium by the resulting acidic, oxidising solution. Industrial application has been limited to Thiobacillus thiooxidans and Thiobacillus ferrooxidans at pH 2 to 3, and examples of these are described. The bacterial catalysis can be improved with nutrients or prevented with poisons. The kinetics of leaching are controlled by the bed depth, particle size, percolation rate, mineralogy and temperature. Current work is aimed at quantitatively defining the parameters controlling the kinetics and extending the method to alkaline conditions with other autotrophic bacteria. (author)

Deciphering the Bacterial Microbiome in Huanglongbing-Affected Citrus Treated with Thermotherapy and Sulfonamide Antibiotics.

Directory of Open Access Journals (Sweden)

Chuanyu Yang

Full Text Available Huanglongbing (HLB is a serious citrus disease that threatens the citrus industry. In previous studies, sulfonamide antibiotics and heat treatment suppressed 'Candidatus Liberibacter asiaticus' (Las, but did not completely eliminate the Las. Furthermore, there are few reports studying the bacterial microbiome of HLB-affected citrus treated by heat and sulfonamide antibiotics. In this study, combinations of heat (45°C or 40°C and sulfonamide treatment (sulfathiazole sodium-STZ, or sulfadimethoxine sodium-SDX were applied to HLB-affected citrus. The bacterial microbiome of HLB-affected citrus following thermotherapy and/or chemotherapy was characterized by PhyloChipTMG3-based metagenomics. Our results showed that the combination of thermotherapy at 45°C and chemotherapy with STZ and SDX was more effective against HLB than thermotherapy alone, chemotherapy alone, or a combination of thermotherapy at 40°C and chemotherapy. The PhyloChipTMG3-based results indicated that 311 empirical Operational Taxonomic Units (eOTUs were detected in 26 phyla. Cyanobacteria (18.01% were dominant after thermo-chemotherapy. Thermotherapy at 45°C decreased eOTUs (64.43% in leaf samples, compared with thermotherapy at 40°C (73.96% or without thermotherapy (90.68% and it also reduced bacterial family biodiversity. The eOTU in phylum Proteobacteria was reduced significantly and eOTU_28, representing "Candidatus Liberibacter," was not detected following thermotherapy at 45°C. Following antibiotic treatment with SDX and STZ, there was enhanced abundance of specific eOTUs belonging to the families Streptomycetaceae, Desulfobacteraceae, Chitinophagaceae, and Xanthomonadaceae, which may be implicated in increased resistance to plant pathogens. Our study further develops an integrated strategy for combating HLB, and also provides new insight into the bacterial microbiome of HLB-affected citrus treated by heat and sulfonamide antibiotics.

Bacterial growth and DOC consumption in a tropical coastal lagoon

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V. F. Farjalla

Full Text Available The aims of this research were to determine the main limiting nutrient to bacterial growth in Imboassica lagoon, southeastern Brazil, to estimate the percentage of dissolved organic carbon (DOC available for bacterial growth, and to determine the bacterial growth efficiency (BGE of natural assemblages. Bacterial growth and DOC consumption were determined in batch culture experiments, in which water samples were supplemented with nitrogen and phosphorus together or separately, or incubated without nutrient additions. When added together, N and P stimulated higher bacterial growth rates and production, as well as higher DOC consumption. The BGEs and DOC consumption rates were strongly dependent on the method used to determine bacterial production. The BGE ranged from 11 to 72%. However, only a minor fraction of bulk DOC was consumed by the planktonic bacteria (from 0.7 to 3.4%. The results suggest that low availability of phosphorus and nitrogen coupled with excess organic carbon was the main factor responsible for the relatively low bacterial utilization of DOC in Imboassica lagoon.

Bacterial sex in dental plaque.

Science.gov (United States)

Olsen, Ingar; Tribble, Gena D; Fiehn, Nils-Erik; Wang, Bing-Yan

2013-01-01

Genes are transferred between bacteria in dental plaque by transduction, conjugation, and transformation. Membrane vesicles can also provide a mechanism for horizontal gene transfer. DNA transfer is considered bacterial sex, but the transfer is not parallel to processes that we associate with sex in higher organisms. Several examples of bacterial gene transfer in the oral cavity are given in this review. How frequently this occurs in dental plaque is not clear, but evidence suggests that it affects a number of the major genera present. It has been estimated that new sequences in genomes established through horizontal gene transfer can constitute up to 30% of bacterial genomes. Gene transfer can be both inter- and intrageneric, and it can also affect transient organisms. The transferred DNA can be integrated or recombined in the recipient's chromosome or remain as an extrachromosomal inheritable element. This can make dental plaque a reservoir for antimicrobial resistance genes. The ability to transfer DNA is important for bacteria, making them better adapted to the harsh environment of the human mouth, and promoting their survival, virulence, and pathogenicity.

Bacterial sex in dental plaque

Directory of Open Access Journals (Sweden)

Ingar Olsen

2013-06-01

Full Text Available Genes are transferred between bacteria in dental plaque by transduction, conjugation, and transformation. Membrane vesicles can also provide a mechanism for horizontal gene transfer. DNA transfer is considered bacterial sex, but the transfer is not parallel to processes that we associate with sex in higher organisms. Several examples of bacterial gene transfer in the oral cavity are given in this review. How frequently this occurs in dental plaque is not clear, but evidence suggests that it affects a number of the major genera present. It has been estimated that new sequences in genomes established through horizontal gene transfer can constitute up to 30% of bacterial genomes. Gene transfer can be both inter- and intrageneric, and it can also affect transient organisms. The transferred DNA can be integrated or recombined in the recipient's chromosome or remain as an extrachromosomal inheritable element. This can make dental plaque a reservoir for antimicrobial resistance genes. The ability to transfer DNA is important for bacteria, making them better adapted to the harsh environment of the human mouth, and promoting their survival, virulence, and pathogenicity.

Isolation and screening of azo dye decolorizing bacterial isolates from dye-contaminated textile wastewater

Directory of Open Access Journals (Sweden)

Shahid Mahmood

2011-04-01

Full Text Available Azo dyes are released into wastewater streams without any pretreatment and pollute water and soilenvironments. To prevent contamination of our vulnerable resources, removal of these dye pollutants is of greatimportance. For this purpose, wastewater samples were collected from dye-contaminated sites of Faisalabad. About200 bacterial isolates were isolated through enrichment and then tested for their potential to remove RemazolBlack-B azo dye in liquid medium. Five bacterial isolates capable of degrading Remazol Black-B azo dye efficientlywere screened through experimentation on modified mineral salt medium. Isolate SS1 (collected from wastewater ofSupreme Textile Industry was able to completely remove the Remazol Black-B dye from the liquid medium in 18 h.Further, the isolate showed the best performance at the dye concentration of 100 mg L-1 medium (pH 7 and attemperature 35oC. Similarly, yeast extract proved to be the best carbon source for decolorization purpose. Theresults imply that the isolate SS1 could be used for the removal of the reactive dyes from textile effluents.

Gain and loss of phototrophic genes revealed by comparison of two Citromicrobium bacterial genomes.

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Qiang Zheng

Full Text Available Proteobacteria are thought to have diverged from a phototrophic ancestor, according to the scattered distribution of phototrophy throughout the proteobacterial clade, and so the occurrence of numerous closely related phototrophic and chemotrophic microorganisms may be the result of the loss of genes for phototrophy. A widespread form of bacterial phototrophy is based on the photochemical reaction center, encoded by puf and puh operons that typically are in a 'photosynthesis gene cluster' (abbreviated as the PGC with pigment biosynthesis genes. Comparison of two closely related Citromicrobial genomes (98.1% sequence identity of complete 16S rRNA genes, Citromicrobium sp. JL354, which contains two copies of reaction center genes, and Citromicrobium strain JLT1363, which is chemotrophic, revealed evidence for the loss of phototrophic genes. However, evidence of horizontal gene transfer was found in these two bacterial genomes. An incomplete PGC (pufLMC-puhCBA in strain JL354 was located within an integrating conjugative element, which indicates a potential mechanism for the horizontal transfer of genes for phototrophy.

Pediatric bacterial meningitis in French Guiana.

Science.gov (United States)

Elenga, N; Sicard, S; Cuadro-Alvarez, E; Long, L; Njuieyon, F; Martin, E; Kom-Tchameni, R; Balcaen, J; Moreau, B; Boukhari, R

2015-01-01

Controlling vaccine-preventable infectious diseases is a public health priority in French Guiana but there is currently no epidemiological data on pediatric bacterial meningitis in this overseas department. Our aim was to describe data related to pediatric bacterial meningitis in French Guiana and compare it with that of metropolitan France. We conducted a multicenter retrospective study from 2000 to 2010 to describe the clinical picture, biological data, epidemiology, and outcome of pediatric bacterial meningitis case patients in French Guiana. The median age of bacterial meningitis patients was 6months [0-15] and the sex ratio 1.06. We observed a total of 60 bacterial meningitis case patients. Most presented with pneumococcal meningitis (24 patients; 40%); 11 with Haemophilus influenzae type b meningitis (23%), five with group B streptococcal meningitis (8.5%), and five others (8.5%) with staphylococcal meningitis (three patients presented with coagulase-negative staphylococci and two with Staphylococcus aureus). Only one patient presented with group B meningococcal meningitis, an 18-month-old infant. We recorded 14 deaths (overall case fatality: 23%); eight were due to Streptococcus pneumoniae (case fatality: 33%). The overall sequelae rate was 28%. It was 32% for patients presenting with pneumococcal meningitis. We observed that 38% of children who had never been vaccinated were infected by a vaccine-preventable bacterium. We observed many differences in the distribution of the bacteria and in the patients' prognosis when comparing the French Guiana data with that of metropolitan France. Improving vaccination coverage would decrease the incidence of H. influenzae meningitis. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

Biosensors for Whole-Cell Bacterial Detection

Science.gov (United States)

Rushworth, Jo V.; Hirst, Natalie A.; Millner, Paul A.

2014-01-01

SUMMARY Bacterial pathogens are important targets for detection and identification in medicine, food safety, public health, and security. Bacterial infection is a common cause of morbidity and mortality worldwide. In spite of the availability of antibiotics, these infections are often misdiagnosed or there is an unacceptable delay in diagnosis. Current methods of bacterial detection rely upon laboratory-based techniques such as cell culture, microscopic analysis, and biochemical assays. These procedures are time-consuming and costly and require specialist equipment and trained users. Portable stand-alone biosensors can facilitate rapid detection and diagnosis at the point of care. Biosensors will be particularly useful where a clear diagnosis informs treatment, in critical illness (e.g., meningitis) or to prevent further disease spread (e.g., in case of food-borne pathogens or sexually transmitted diseases). Detection of bacteria is also becoming increasingly important in antibioterrorism measures (e.g., anthrax detection). In this review, we discuss recent progress in the use of biosensors for the detection of whole bacterial cells for sensitive and earlier identification of bacteria without the need for sample processing. There is a particular focus on electrochemical biosensors, especially impedance-based systems, as these present key advantages in terms of ease of miniaturization, lack of reagents, sensitivity, and low cost. PMID:24982325

Bacterial leaching of pyritic gold ores

International Nuclear Information System (INIS)

Gagliardi, F.M.; Cashion, J.D.; Brown, J.; Jay, W.H.

1998-01-01

Full text: Pyritic ores (pyrite and arsenopyrite) containing gold concentrations in excess of 50g Au/t can be processed to recover the gold by the removal of the sulphur from the ore. This may be achieved by roasting (producing sulphur dioxide emissions), pressure oxidation (expensive and suitable for large high grade deposits), pressure leaching (still currently being developed) or bacterial oxidation. The bacterial oxidation process is a well known process in nature but has only recently come under investigation as a economically viable and relatively clean method of gold recovery from deep low grade sulphidic ores. Samples were obtained from the Wiluna Gold Mine in Western Australia consisting of the original ore, six successive bacterial reactors and the final products. Moessbauer experiments have been performed at room temperature, liquid nitrogen and liquid helium temperatures, and in applied magnetic fields. The main components of the iron phases which were present during the bacterial treatment were pyrite and arsenopyrite which were readily oxidised by the bacteria. Ferric sulfates and ferric arsenates were identified as by-products of the process with a small amount of the oxyhydroxide goethite. These results are in contrast to the similar study of the Fairview Mine in South Africa where principally Fe(II) species were observed

Bacterial leaching of pyritic gold ores

Energy Technology Data Exchange (ETDEWEB)

Gagliardi, F.M.; Cashion, J.D.; Brown, L.J. [Monash Univ., Clayton, VIC (Australia). Dept. of Physics; Jay, W.H. [Monash Univ., Clayton, VIC (Australia). Chemical Engineering Department

1996-12-31

The bacterial oxidation process is well known in nature but has only recently come under investigation as a viable and relatively clean method of gold recovery from ores. However there is currently little information about the process at an atomic scale. It is known that the bacterial attack progresses preferentially along grain boundaries which is precisely where the gold has been deposited from aqueous infiltration. Samples have been obtained from the Wiluna mine in Western Australia consisting of the original ore, 2 pre-treatments, and from six successive bacterial reactors. {sup 57}Fe Moessbauer spectra taken at room temperature show only two quadrupole split doublets which can be ascribed to pyrite, FeS{sub 2}, and arsenopyrite, FeAsS. However, the presence of any superparamagnetic oxide or oxyhydroxide species would be expected to give a spectrum very similar to that of pyrite and would be undetectable in small quantities. At a temperature of 5K, a broad magnetically split sextet is observable with a mean hyperfine field of approximately 50T. This field is characteristic of magnetically ordered ferric iron surrounded by an octahedron of oxygens. The intensity and characteristics of this subspectrum alters through the series and interpretations will be given on the oxidation products of the bacterial leaching

Bacterial leaching of pyritic gold ores

International Nuclear Information System (INIS)

Gagliardi, F.M.; Cashion, J.D.; Brown, L.J.; Jay, W.H.

1996-01-01

The bacterial oxidation process is well known in nature but has only recently come under investigation as a viable and relatively clean method of gold recovery from ores. However there is currently little information about the process at an atomic scale. It is known that the bacterial attack progresses preferentially along grain boundaries which is precisely where the gold has been deposited from aqueous infiltration. Samples have been obtained from the Wiluna mine in Western Australia consisting of the original ore, 2 pre-treatments, and from six successive bacterial reactors. 57 Fe Moessbauer spectra taken at room temperature show only two quadrupole split doublets which can be ascribed to pyrite, FeS 2 , and arsenopyrite, FeAsS. However, the presence of any superparamagnetic oxide or oxyhydroxide species would be expected to give a spectrum very similar to that of pyrite and would be undetectable in small quantities. At a temperature of 5K, a broad magnetically split sextet is observable with a mean hyperfine field of approximately 50T. This field is characteristic of magnetically ordered ferric iron surrounded by an octahedron of oxygens. The intensity and characteristics of this subspectrum alters through the series and interpretations will be given on the oxidation products of the bacterial leaching

Characterization of TEMPO-oxidized bacterial cellulose

International Nuclear Information System (INIS)

Nascimento, Eligenes S.; Pereira, Andre L.S.; Lima, Helder L.; Barroso, Maria K. de A.; Barros, Matheus de O.; Morais, Joao P.S.; Borges, Maria de F.; Rosa, Morsyleide de F.

2015-01-01

The aim of this study was to characterize the TEMPO-oxidized bacterial cellulose, as a preliminary research for further application in nanocomposites. Bacterial cellulose (BC) was selectively oxidized at C-6 carbon by TEMPO radical. Oxidized bacterial cellulose (BCOX) was characterized by TGA, FTIR, XRD, and zeta potential. BCOX suspension was stable at pH 7.0, presented a crystallinity index of 83%, in spite of 92% of BC, because of decrease in the free hydroxyl number. FTIR spectra showed characteristic BC bands and, in addition, band of carboxylic group, proving the oxidation. BCOX DTG showed, in addition to characteristic BC thermal events, a maximum degradation peak at 233 °C, related to sodium anhydro-glucuronate groups formed during the cellulose oxidation. Thus, BC can be TEMPO-oxidized without great loss in its structure and properties. (author)

Composition and variation of sediment bacterial and nirS-harboring bacterial communities at representative sites of the Bohai Gulf coastal zone, China.

Science.gov (United States)

Guan, Xiangyu; Zhu, Lingling; Li, Youxun; Xie, Yuxuan; Zhao, Mingzhang; Luo, Ximing

2014-04-01

With rapid urbanization, anthropogenic activities are increasingly influencing the natural environment of the Bohai Bay. In this study, the composition and variation of bacterial and nirS-harboring bacterial communities in the coastal zone sediments of the Bohai Gulf were analyzed using PCR-based clone libraries. A total of 95 genera were detected in the bacterial communities, with Proteobacteria (72.1 %), Acidobacteria (10.5 %), Firmicutes (1.7 %), Bacteroidetes (1.4 %), Chloroflexi (0.7 %) and Planctomycetes (0.7 %) being the dominated phyla. The NirS sequences were divided into nine Clusters (A-I). Canonical correlation analysis showed that the bacterial or denitrifying communities were correlated with different environmental factors, such as total organic carbon, total nitrogen, ammonium, sulfate, etc. Furthermore, bacterial communities' composition and diversity are influenced by oil exploration, sewage discharge and other anthropogenic activities in the coastal area of the Bohai Sea. Thus, this study provided useful information on further research on regional or global environmental control and restore.

Emerging antibiotic resistant enteric bacterial flora among food ...

African Journals Online (AJOL)

Emerging antibiotic resistant enteric bacterial flora among food animals in Abeokuta, Nigeria. ... Nigerian Journal of Animal Production ... Bacterial resistance to antibiotic in food animals is an emerging public health concern as a result of ...

Diagnosis of bacterial infection

African Journals Online (AJOL)

direct or indirect evidence of a compatible bacterial pathogen. Inflammation may be .... cardinal features (fever, confusion, headache and neck stiffness). .... specificity, inappropriate indications or poor sampling technique may diminish this ...

Characterization of the vaginal microbiota among sexual risk behavior groups of women with bacterial vaginosis.

Science.gov (United States)

Muzny, Christina A; Sunesara, Imran R; Kumar, Ranjit; Mena, Leandro A; Griswold, Michael E; Martin, David H; Lefkowitz, Elliot J; Schwebke, Jane R; Swiatlo, Edwin

2013-01-01

The pathogenesis of bacterial vaginosis (BV) remains elusive. BV may be more common among women who have sex with women (WSW). The objective of this study was to use 454 pyrosequencing to investigate the vaginal microbiome of WSW, women who have sex with women and men (WSWM), and women who have sex with men (WSM) with BV to determine if there are differences in organism composition between groups that may inform new hypotheses regarding the pathogenesis of BV. Vaginal swab specimens from eligible women with BV at the Mississippi State Department of Health STD Clinic were used. After DNA extraction, 454 pyrosequencing of PCR-amplified 16S rRNA gene sequences was performed. Sequence data was classified using the Ribosomal Database Program classifer. Complete linkage clustering analysis was performed to compare bacterial community composition among samples. Differences in operational taxonomic units with an abundance of ≥ 2% between risk behavior groups were determined. Alpha and beta diversity were measured using Shannon's Index implemented in QIIME and Unifrac analysis, respectively. 33 WSW, 35 WSWM, and 44 WSM were included. The vaginal bacterial communities of all women clustered into four taxonomic groups with the dominant taxonomic group in each being Lactobacillus, Lachnospiraceae, Prevotella, and Sneathia. Regarding differences in organism composition between risk behavior groups, the abundance of Atopobium (relative ratio (RR)=0.24; 95%CI 0.11-0.54) and Parvimonas (RR=0.33; 95%CI 0.11-0.93) were significantly lower in WSW than WSM, the abundance of Prevotella was significantly higher in WSW than WSWM (RR=1.77; 95%CI 1.10-2.86), and the abundance of Atopobium (RR=0.41; 95%CI 0.18-0.88) was significantly lower in WSWM than WSM. Overall, WSM had the highest diversity of bacterial taxa. The microbiology of BV among women in different risk behavior groups is heterogeneous. WSM in this study had the highest diversity of bacterial taxa. Additional studies are

Characterization of the vaginal microbiota among sexual risk behavior groups of women with bacterial vaginosis.

Directory of Open Access Journals (Sweden)

Christina A Muzny

Full Text Available The pathogenesis of bacterial vaginosis (BV remains elusive. BV may be more common among women who have sex with women (WSW. The objective of this study was to use 454 pyrosequencing to investigate the vaginal microbiome of WSW, women who have sex with women and men (WSWM, and women who have sex with men (WSM with BV to determine if there are differences in organism composition between groups that may inform new hypotheses regarding the pathogenesis of BV.Vaginal swab specimens from eligible women with BV at the Mississippi State Department of Health STD Clinic were used. After DNA extraction, 454 pyrosequencing of PCR-amplified 16S rRNA gene sequences was performed. Sequence data was classified using the Ribosomal Database Program classifer. Complete linkage clustering analysis was performed to compare bacterial community composition among samples. Differences in operational taxonomic units with an abundance of ≥ 2% between risk behavior groups were determined. Alpha and beta diversity were measured using Shannon's Index implemented in QIIME and Unifrac analysis, respectively.33 WSW, 35 WSWM, and 44 WSM were included. The vaginal bacterial communities of all women clustered into four taxonomic groups with the dominant taxonomic group in each being Lactobacillus, Lachnospiraceae, Prevotella, and Sneathia. Regarding differences in organism composition between risk behavior groups, the abundance of Atopobium (relative ratio (RR=0.24; 95%CI 0.11-0.54 and Parvimonas (RR=0.33; 95%CI 0.11-0.93 were significantly lower in WSW than WSM, the abundance of Prevotella was significantly higher in WSW than WSWM (RR=1.77; 95%CI 1.10-2.86, and the abundance of Atopobium (RR=0.41; 95%CI 0.18-0.88 was significantly lower in WSWM than WSM. Overall, WSM had the highest diversity of bacterial taxa.The microbiology of BV among women in different risk behavior groups is heterogeneous. WSM in this study had the highest diversity of bacterial taxa. Additional studies

A census of membrane-bound and intracellular signal transduction proteins in bacteria: bacterial IQ, extroverts and introverts.

Science.gov (United States)

Galperin, Michael Y

2005-06-14

Analysis of complete microbial genomes showed that intracellular parasites and other microorganisms that inhabit stable ecological niches encode relatively primitive signaling systems, whereas environmental microorganisms typically have sophisticated systems of environmental sensing and signal transduction. This paper presents results of a comprehensive census of signal transduction proteins--histidine kinases, methyl-accepting chemotaxis receptors, Ser/Thr/Tyr protein kinases, adenylate and diguanylate cyclases and c-di-GMP phosphodiesterases--encoded in 167 bacterial and archaeal genomes, sequenced by the end of 2004. The data have been manually checked to avoid false-negative and false-positive hits that commonly arise during large-scale automated analyses and compared against other available resources. The census data show uneven distribution of most signaling proteins among bacterial and archaeal phyla. The total number of signal transduction proteins grows approximately as a square of genome size. While histidine kinases are found in representatives of all phyla and are distributed according to the power law, other signal transducers are abundant in certain phylogenetic groups but virtually absent in others. The complexity of signaling systems differs even among closely related organisms. Still, it usually can be correlated with the phylogenetic position of the organism, its lifestyle, and typical environmental challenges it encounters. The number of encoded signal transducers (or their fraction in the total protein set) can be used as a measure of the organism's ability to adapt to diverse conditions, the 'bacterial IQ', while the ratio of transmembrane receptors to intracellular sensors can be used to define whether the organism is an 'extrovert', actively sensing the environmental parameters, or an 'introvert', more concerned about its internal homeostasis. Some of the microorganisms with the highest IQ, including the current leader Wolinella succinogenes

A census of membrane-bound and intracellular signal transduction proteins in bacteria: Bacterial IQ, extroverts and introverts

Directory of Open Access Journals (Sweden)

Galperin Michael Y

2005-06-01

Full Text Available Abstract Background Analysis of complete microbial genomes showed that intracellular parasites and other microorganisms that inhabit stable ecological niches encode relatively primitive signaling systems, whereas environmental microorganisms typically have sophisticated systems of environmental sensing and signal transduction. Results This paper presents results of a comprehensive census of signal transduction proteins – histidine kinases, methyl-accepting chemotaxis receptors, Ser/Thr/Tyr protein kinases, adenylate and diguanylate cyclases and c-di-GMP phosphodiesterases – encoded in 167 bacterial and archaeal genomes, sequenced by the end of 2004. The data have been manually checked to avoid false-negative and false-positive hits that commonly arise during large-scale automated analyses and compared against other available resources. The census data show uneven distribution of most signaling proteins among bacterial and archaeal phyla. The total number of signal transduction proteins grows approximately as a square of genome size. While histidine kinases are found in representatives of all phyla and are distributed according to the power law, other signal transducers are abundant in certain phylogenetic groups but virtually absent in others. Conclusion The complexity of signaling systems differs even among closely related organisms. Still, it usually can be correlated with the phylogenetic position of the organism, its lifestyle, and typical environmental challenges it encounters. The number of encoded signal transducers (or their fraction in the total protein set can be used as a measure of the organism's ability to adapt to diverse conditions, the 'bacterial IQ', while the ratio of transmembrane receptors to intracellular sensors can be used to define whether the organism is an 'extrovert', actively sensing the environmental parameters, or an 'introvert', more concerned about its internal homeostasis. Some of the microorganisms with the

Influence of hydraulic regimes on bacterial community structure and composition in an experimental drinking water distribution system.

Science.gov (United States)

Douterelo, I; Sharpe, R L; Boxall, J B

2013-02-01

Microbial biofilms formed on the inner-pipe surfaces of drinking water distribution systems (DWDS) can alter drinking water quality, particularly if they are mechanically detached from the pipe wall to the bulk water, such as due to changes in hydraulic conditions. Results are presented here from applying 454 pyrosequencing of the 16S ribosomal RNA (rRNA) gene to investigate the influence of different hydrological regimes on bacterial community structure and to study the potential mobilisation of material from the pipe walls to the network using a full scale, temperature-controlled experimental pipeline facility accurately representative of live DWDS. Analysis of pyrosequencing and water physico-chemical data showed that habitat type (water vs. biofilm) and hydraulic conditions influenced bacterial community structure and composition in our experimental DWDS. Bacterial community composition clearly differed between biofilms and bulk water samples. Gammaproteobacteria and Betaproteobacteria were the most abundant phyla in biofilms while Alphaproteobacteria was predominant in bulk water samples. This suggests that bacteria inhabiting biofilms, predominantly species belonging to genera Pseudomonas, Zooglea and Janthinobacterium, have an enhanced ability to express extracellular polymeric substances to adhere to surfaces and to favour co-aggregation between cells than those found in the bulk water. Highest species richness and diversity were detected in 28 days old biofilms with this being accentuated at highly varied flow conditions. Flushing altered the pipe-wall bacterial community structure but did not completely remove bacteria from the pipe walls, particularly under highly varied flow conditions, suggesting that under these conditions more compact biofilms were generated. This research brings new knowledge regarding the influence of different hydraulic regimes on the composition and structure of bacterial communities within DWDS and the implication that this

Diazotrophic Bacterial Community of Degraded Pastures

OpenAIRE

João Tiago Correia Oliveira; Everthon Fernandes Figueredo; Williane Patrícia da Silva Diniz; Lucianne Ferreira Paes de Oliveira; Pedro Avelino Maia de Andrade; Fernando Dini Andreote; Júlia Kuklinsky-Sobral; Danúbia Ramos de Lima; Fernando José Freire

2017-01-01

Pasture degradation can cause changes in diazotrophic bacterial communities. Thus, this study aimed to evaluate the culturable and total diazotrophic bacterial community, associated with regions of the rhizosphere and roots of Brachiaria decumbens Stapf. pastures in different stages of degradation. Samples of roots and rhizospheric soil were collected from slightly, partially, and highly degraded pastures. McCrady’s table was used to obtain the Most Probable Number (MPN) of bacteria per gram ...

A study of bacterial contamination of rattlesnake venom

Directory of Open Access Journals (Sweden)

E. Garcia-Lima

1987-03-01

Full Text Available The authors studied the bacterial contamination of rattlesnake venom isolated from snakes in captivity and wild snakes caught recently. The captive snakes showed a relatively high incidence of bacterial contamination of their venom.

Metallization of bacterial cellulose for electrical and electronic device manufacture

Science.gov (United States)

Evans, Barbara R [Oak Ridge, TN; O'Neill, Hugh M [Knoxville, TN; Jansen, Valerie Malyvanh [Memphis, TN; Woodward, Jonathan [Knoxville, TN

2010-09-28

A method for the deposition of metals in bacterial cellulose and for the employment of the metallized bacterial cellulose in the construction of fuel cells and other electronic devices is disclosed. The method for impregnating bacterial cellulose with a metal comprises placing a bacterial cellulose matrix in a solution of a metal salt such that the metal salt is reduced to metallic form and the metal precipitates in or on the matrix. The method for the construction of a fuel cell comprises placing a hydrated bacterial cellulose support structure in a solution of a metal salt such that the metal precipitates in or on the support structure, inserting contact wires into two pieces of the metal impregnated support structure, placing the two pieces of metal impregnated support structure on opposite sides of a layer of hydrated bacterial cellulose, and dehydrating the three layer structure to create a fuel cell.

Functional recovery of biofilm bacterial communities after copper exposure

International Nuclear Information System (INIS)

Boivin, Marie-Elene Y.; Massieux, Boris; Breure, Anton M.; Greve, Gerdit D.; Rutgers, Michiel; Admiraal, Wim

2006-01-01

Potential of bacterial communities in biofilms to recover after copper exposure was investigated. Biofilms grown outdoor in shallow water on glass dishes were exposed in the laboratory to 0.6, 2.1, 6.8 μmol/l copper amended surface water and a reference and subsequently to un-amended surface water. Transitions of bacterial communities were characterised with denaturing gradient gel electrophoresis (DGGE) and community-level physiological profiles (CLPP). Exposure to 6.8 μmol/l copper provoked distinct changes in DGGE profiles of bacterial consortia, which did not reverse upon copper depuration. Exposure to 2.1 and 6.8 μmol/l copper was found to induce marked changes in CLPP of bacterial communities that proved to be reversible during copper depuration. Furthermore, copper exposure induced the development of copper-tolerance, which was partially lost during depuration. It is concluded that bacterial communities exposed to copper contaminated water for a period of 26 days are capable to restore their metabolic attributes after introduction of unpolluted water in aquaria for 28 days. - Genetically different bacterial communities can have similar functions and tolerance to copper

Visual outcomes in treated bacterial keratitis: four years of prospective follow-up.

Science.gov (United States)

McClintic, Scott M; Prajna, Namperumalsamy V; Srinivasan, Muthiah; Mascarenhas, Jeena; Lalitha, Prajna; Rajaraman, Revathi; Oldenburg, Catherine E; O'Brien, Kieran S; Ray, Kathryn J; Acharya, Nisha R; Lietman, Thomas M; Keenan, Jeremy D

2014-05-02

We described the change in visual acuity experienced by eyes successfully treated for bacterial keratitis. This was a prospective cohort study of a subset of study participants who had previously enrolled in the Steroids for Corneal Ulcers Trial (SCUT). All study participants had been diagnosed with culture-proven bacterial keratitis before enrollment in SCUT and subsequently were randomized to adjunctive topical corticosteroids or placebo. During SCUT, we monitored study participants at enrollment, 3 weeks, 3 months, and 12 months. We invited a subset to complete a comprehensive eye examination approximately 4 years after enrollment in SCUT. Certified refractionists assessed best spectacle-corrected visual acuity (BSCVA) using the same protocol at each study visit. We examined 50 SCUT participants at 4 years after enrollment. Among those in this cohort, mean logMAR BSCVA at enrollment was 0.85 (Snellen equivalent, 20/160; 95% confidence interval [CI], 0.71-0.99). On average, visual acuity improved by 2.9 logMAR lines from enrollment to 3 weeks (P < 0.001), 1.2 lines from 3 weeks to 3 months (P = 0.002), and 0.8 lines from 3 to 12 months (P = 0.01). The BSCVA did not change significantly between 12 months and 4 years (0.04-line improvement, P = 0.88). After controlling for visual acuity at enrollment, BSCVA was not significantly different between the corticosteroid and placebo groups at 4 years (P = 0.53). Cases of bacterial keratitis may continue to demonstrate improvements in visual acuity up to 12 months following diagnosis, but further improvements are unlikely. These findings may guide the appropriate timing of surgical intervention in these patients. (ClinicalTrials.gov number, NCT00324168.).

Circulating Chemokine Levels in Febrile Infants With Serious Bacterial Infections

Directory of Open Access Journals (Sweden)

Hsiu-Lin Chen

2009-12-01

Full Text Available Early diagnosis of serious bacterial infections (SBI in febrile young infants based on clinical symptoms and signs is difficult. This study aimed to evaluate the diagnostic values of circulating chemokines and C-reactive protein (CRP levels in febrile young infants < 3 months of age with suspected SBI. We enrolled 43 febrile young infants < 3 months of age with clinically suspected SBI who were admitted to the neonatal intensive care unit or complete nursing unit of the pediatric department of Kaohsiung Medical University Hospital between December 2006 and July 2007. Blood was drawn from the patients at admission, and complete blood counts, plasma levels of CRP, granulocyte colony-stimulating factor (G-CSF, and chemokines, including interleukin-8 (IL-8, macrophage inflammatory protein-1α, macrophage inflammatory protein-1β, monokine induced by interferon-γ, and monocyte chemotactic protein-1 were measured. Patients’ symptoms and signs, length of hospital stay, main diagnosis, and results of routine blood tests and microbiological culture results were recorded. Twenty-six infants (60.5% were diagnosed with SBI, while 17 (39.5% had no evidence of SBI based on the results of bacterial cultures. CRP, IL-8 and G-CSF levels were significantly higher in the infants with SBI than in those without SBI. Plasma levels of other chemokines were not significantly different between the groups. The area under the receiver-operating characteristic (ROC curve for differentiating between the presence and absence of SBI was 0.79 for CRP level. Diagnostic accuracy was further improved by combining CRP and IL-8, when the area under the ROC curve increased to 0.91. CRP levels were superior to IL-8 and G-CSF levels for predicting SBI in febrile infants at initial survey. IL-8 levels could be used as an additional diagnostic tool in the initial evaluation of febrile young infants, allowing clinicians to treat these patients more appropriately.

Biomimicry of quorum sensing using bacterial lifecycle model.

Science.gov (United States)

Niu, Ben; Wang, Hong; Duan, Qiqi; Li, Li

2013-01-01

Recent microbiologic studies have shown that quorum sensing mechanisms, which serve as one of the fundamental requirements for bacterial survival, exist widely in bacterial intra- and inter-species cell-cell communication. Many simulation models, inspired by the social behavior of natural organisms, are presented to provide new approaches for solving realistic optimization problems. Most of these simulation models follow population-based modelling approaches, where all the individuals are updated according to the same rules. Therefore, it is difficult to maintain the diversity of the population. In this paper, we present a computational model termed LCM-QS, which simulates the bacterial quorum-sensing (QS) mechanism using an individual-based modelling approach under the framework of Agent-Environment-Rule (AER) scheme, i.e. bacterial lifecycle model (LCM). LCM-QS model can be classified into three main sub-models: chemotaxis with QS sub-model, reproduction and elimination sub-model and migration sub-model. The proposed model is used to not only imitate the bacterial evolution process at the single-cell level, but also concentrate on the study of bacterial macroscopic behaviour. Comparative experiments under four different scenarios have been conducted in an artificial 3-D environment with nutrients and noxious distribution. Detailed study on bacterial chemotatic processes with quorum sensing and without quorum sensing are compared. By using quorum sensing mechanisms, artificial bacteria working together can find the nutrient concentration (or global optimum) quickly in the artificial environment. Biomimicry of quorum sensing mechanisms using the lifecycle model allows the artificial bacteria endowed with the communication abilities, which are essential to obtain more valuable information to guide their search cooperatively towards the preferred nutrient concentrations. It can also provide an inspiration for designing new swarm intelligence optimization algorithms

Hijacking Complement Regulatory Proteins for Bacterial Immune Evasion.

Science.gov (United States)

Hovingh, Elise S; van den Broek, Bryan; Jongerius, Ilse

2016-01-01

The human complement system plays an important role in the defense against invading pathogens, inflammation and homeostasis. Invading microbes, such as bacteria, directly activate the complement system resulting in the formation of chemoattractants and in effective labeling of the bacteria for phagocytosis. In addition, formation of the membrane attack complex is responsible for direct killing of Gram-negative bacteria. In turn, bacteria have evolved several ways to evade complement activation on their surface in order to be able to colonize and invade the human host. One important mechanism of bacterial escape is attraction of complement regulatory proteins to the microbial surface. These molecules are present in the human body for tight regulation of the complement system to prevent damage to host self-surfaces. Therefore, recruitment of complement regulatory proteins to the bacterial surface results in decreased complement activation on the microbial surface which favors bacterial survival. This review will discuss recent advances in understanding the binding of complement regulatory proteins to the bacterial surface at the molecular level. This includes, new insights that have become available concerning specific conserved motives on complement regulatory proteins that are favorable for microbial binding. Finally, complement evasion molecules are of high importance for vaccine development due to their dominant role in bacterial survival, high immunogenicity and homology as well as their presence on the bacterial surface. Here, the use of complement evasion molecules for vaccine development will be discussed.

Determination of Bacterial Growth in Culture Media

International Nuclear Information System (INIS)

Elly Ellyna Rashid; Shariza Hanim Zainal Abidin; Mok, P.S.

2015-01-01

Bacteria is one of the important microorganism in our daily life. Bacteria provides human beings with products in the field of medical, industry, food, agriculture and others. Determination of bacteria growth is important so that we can enjoy the most benefit from it. Spread-plate method is one of the methods to obtain the bacterial counts. Agar plates, such as Nutrient Agar or Plate Count Agar are usually used for this purpose. Bacterial culture will be diluted first before being spread on the agar plate and incubated at specific temperature. The number of bacteria in colony-forming unit (CFU) will be counted the next day. The count will be used to determine the bacterial growth. (author)

[Etiology of bacterial vaginosis (non-specific vaginitis)].

Science.gov (United States)

Lefèvre, J C; Jean, M; Averous, S; Viraben, R; Blanc, C; Bauriaud, R; Lareng, M B

1985-01-01

56 women who were diagnosed bioclinically as having a bacterial vaginal infection were studied, as were 35 women as a control group. The study was a semi-quantitative analysis of the vaginal bacterial flora, both aerobic and anaerobic. It shows that Gardnerella vaginalis and anaerobic bacteria such as Peptococcus, Peptostreptococcus, Bacteroïdes, Veillonella and Mobiluncus were associated in a statistically significant way with bacterial vaginitis. On the other hand Lactobacilli were less frequently found (p less than 0.001) than in the control group of women. The way in which the microbial flora is changed has been observed during attacks of vaginitis and is discussed, as is the importance of making the diagnosis and of treating this syndrome.

Cholinesterase modulations in patients with acute bacterial meningitis

DEFF Research Database (Denmark)

Berg, Ronan M G; Ofek, Keren; Qvist, Tavs

2011-01-01

The circulating cholinesterases acetyl- and butyrylcholinesterase may be suppressed and subsequently released from the brain in acute bacterial meningitis.......The circulating cholinesterases acetyl- and butyrylcholinesterase may be suppressed and subsequently released from the brain in acute bacterial meningitis....

Reconstruction of a Bacterial Genome from DNA Cassettes

Energy Technology Data Exchange (ETDEWEB)

Christopher Dupont; John Glass; Laura Sheahan; Shibu Yooseph; Lisa Zeigler Allen; Mathangi Thiagarajan; Andrew Allen; Robert Friedman; J. Craig Venter

2011-12-31

This basic research program comprised two major areas: (1) acquisition and analysis of marine microbial metagenomic data and development of genomic analysis tools for broad, external community use; (2) development of a minimal bacterial genome. Our Marine Metagenomic Diversity effort generated and analyzed shotgun sequencing data from microbial communities sampled from over 250 sites around the world. About 40% of the 26 Gbp of sequence data has been made publicly available to date with a complete release anticipated in six months. Our results and those mining the deposited data have revealed a vast diversity of genes coding for critical metabolic processes whose phylogenetic and geographic distributions will enable a deeper understanding of carbon and nutrient cycling, microbial ecology, and rapid rate evolutionary processes such as horizontal gene transfer by viruses and plasmids. A global assembly of the generated dataset resulted in a massive set (5Gbp) of genome fragments that provide context to the majority of the generated data that originated from uncultivated organisms. Our Synthetic Biology team has made significant progress towards the goal of synthesizing a minimal mycoplasma genome that will have all of the machinery for independent life. This project, once completed, will provide fundamentally new knowledge about requirements for microbial life and help to lay a basic research foundation for developing microbiological approaches to bioenergy.

Morphomechanics of bacterial biofilms undergoing anisotropic differential growth

Science.gov (United States)

Zhang, Cheng; Li, Bo; Huang, Xiao; Ni, Yong; Feng, Xi-Qiao

2016-10-01

Growing bacterial biofilms exhibit a number of surface morphologies, e.g., concentric wrinkles, radial ridges, and labyrinthine networks, depending on their physiological status and nutrient access. We explore the mechanisms underlying the emergence of these greatly different morphologies. Ginzburg-Landau kinetic method and Fourier spectral method are integrated to simulate the morphological evolution of bacterial biofilms. It is shown that the morphological instability of biofilms is triggered by the stresses induced by anisotropic and heterogeneous bacterial expansion, and involves the competition between membrane energy and bending energy. Local interfacial delamination further enriches the morphologies of biofilms. Phase diagrams are established to reveal how the anisotropy and spatial heterogeneity of growth modulate the surface patterns. The mechanics of three-dimensional microbial morphogenesis may also underpin self-organization in other development systems and provide a potential strategy for engineering microscopic structures from bacterial aggregates.

Benthic bacterial diversity in submerged sinkhole ecosystems.

Science.gov (United States)

Nold, Stephen C; Pangborn, Joseph B; Zajack, Heidi A; Kendall, Scott T; Rediske, Richard R; Biddanda, Bopaiah A

2010-01-01

Physicochemical characterization, automated ribosomal intergenic spacer analysis (ARISA) community profiling, and 16S rRNA gene sequencing approaches were used to study bacterial communities inhabiting submerged Lake Huron sinkholes inundated with hypoxic, sulfate-rich groundwater. Photosynthetic cyanobacterial mats on the sediment surface were dominated by Phormidium autumnale, while deeper, organically rich sediments contained diverse and active bacterial communities.

Interspecies chemical communication in bacterial development.

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Straight, Paul D; Kolter, Roberto

2009-01-01

Our view of bacteria, from the earliest observations through the heyday of antibiotic discovery, has shifted dramatically. We recognize communities of bacteria as integral and functionally important components of diverse habitats, ranging from soil collectives to the human microbiome. To function as productive communities, bacteria coordinate metabolic functions, often requiring shifts in growth and development. The hallmark of cellular development, which we characterize as physiological change in response to environmental stimuli, is a defining feature of many bacterial interspecies interactions. Bacterial communities rely on chemical exchanges to provide the cues for developmental change. Traditional methods in microbiology focus on isolation and characterization of bacteria in monoculture, separating the organisms from the surroundings in which interspecies chemical communication has relevance. Developing multispecies experimental systems that incorporate knowledge of bacterial physiology and metabolism with insights from biodiversity and metagenomics shows great promise for understanding interspecies chemical communication in the microbial world.

Prevalence of asymptomatic infections in sexually transmitted diseases attendees diagnosed with bacterial vaginosis, vaginal candidiasis, and trichomoniasis.

Science.gov (United States)

Rajalakshmi, R; Kalaivani, S

2016-01-01

Sexually transmitted diseases (STD) are a major health problem affecting mostly young people in both developing and developed countries. STD in women causes both acute morbidity and complications such as infertility, ectopic pregnancy, low-birth weight, and prematurity. The aim of the study is to assess the prevalence of bacterial vaginosis, vaginal candidiasis, and trichomoniasis among asymptomatic females attending STD outpatient department in a tertiary care hospital in South India. A retrospective analysis of data collected from clinical records of 3000 female patients of age 18 to 49 over a period of 12 months (July 2014 to June 2015) was carried out at the Institute of Venereology, Madras Medical College. Complete epidemiological, clinical, and investigational data were recorded and analyzed for the prevalence of bacterial vaginosis, vaginal candidiasis, and trichomoniasis among asymptomatic patients. About 48.37% (228/470) of bacterial vaginosis patients were asymptomatic. Nearly 45.38% (116/235) of vaginal candidiasis patients were asymptomatic and 30.35% (26/87) of trichomoniasis patients were asymptomatic. The above infections were common in the age group 25-35. Holistic screening protocol was incorporated for all female patients attending STD clinic even if asymptomatic and should be treated accordingly to prevent the acquisition of other serious sexually transmitted infections.

The Prevalence of Bacterial Vaginosis among Pregnant Women ...

African Journals Online (AJOL)

60.4%) were asymptomatic. There were 92 out of 250 pregnant women (36.8%) that had three or more of the Amsel's criteria for the diagnosis of bacterial vaginosis. The associated risk factors for developing bacterial vaginosis in the study ...

Bacterial colonization and gut development in preterm neonates

DEFF Research Database (Denmark)

Cilieborg, Malene S.; Boye, Mette; Sangild, Per Torp

2012-01-01

Necrotizing enterocolitis (NEC) develops in 5–10% of preterm infants in association with enteral feeding and bacterial colonization. It remains unclear how diet and bacteria interact to protect or provoke the immature gastrointestinal tract. Understanding the factors that control bacterial...

Bacterial contamination of platelet concentrates: pathogen detection and inactivation methods

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Dana Védy

2009-04-01

Full Text Available Whereas the reduction of transfusion related viral transmission has been a priority during the last decade, bacterial infection transmitted by transfusion still remains associated to a high morbidity and mortality, and constitutes the most frequent infectious risk of transfusion. This problem especially concerns platelet concentrates because of their favorable bacterial growth conditions. This review gives an overview of platelet transfusion-related bacterial contamination as well as on the different strategies to reduce this problem by using either bacterial detection or inactivation methods.

Altered Bacterial Profiles in Saliva from Adults with Caries Lesions

DEFF Research Database (Denmark)

Belstrøm, D; Fiehn, N-E; Nielsen, C H

2014-01-01

-Whitney's test with Benjamini-Hochberg correction for multiple comparisons. Principal component analysis was used to visualize bacterial community profiles. A reduced bacterial diversity was observed in samples from subjects with dental caries. Five bacterial taxa (Veillonella parvula, Veillonella atypica......, Megasphaera micronuciformis, Fusobacterium periodontium and Achromobacter xylosoxidans) and one bacterial cluster (Leptotrichia sp. clones C3MKM102 and GT018_ot417/462) were less frequently found in the caries group (adjusted p value ... salivarius) and three bacterial clusters (Streptococcus parasanguinis I and II and sp. clone BE024_ot057/411/721, Streptococcus parasanguinis I and II and sinensis_ot411/721/767, Streptococcus salivarius and sp. clone FO042_ot067/755) were present at significantly higher levels (adjusted p value

Bacterial Acclimation Inside an Aqueous Battery.

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Dong, Dexian; Chen, Baoling; Chen, P

2015-01-01

Specific environmental stresses may lead to induced genomic instability in bacteria, generating beneficial mutants and potentially accelerating the breeding of industrial microorganisms. The environmental stresses inside the aqueous battery may be derived from such conditions as ion shuttle, pH gradient, free radical reaction and electric field. In most industrial and medical applications, electric fields and direct currents are used to kill bacteria and yeast. However, the present study focused on increasing bacterial survival inside an operating battery. Using a bacterial acclimation strategy, both Escherichia coli and Bacillus subtilis were acclimated for 10 battery operation cycles and survived in the battery for over 3 days. The acclimated bacteria changed in cell shape, growth rate and colony color. Further analysis indicated that electrolyte concentration could be one of the major factors determining bacterial survival inside an aqueous battery. The acclimation process significantly improved the viability of both bacteria E. coli and B. subtilis. The viability of acclimated strains was not affected under battery cycle conditions of 0.18-0.80 mA cm(-2) and 1.4-2.1 V. Bacterial addition within 1.0×10(10) cells mL(-1) did not significantly affect battery performance. Because the environmental stress inside the aqueous battery is specific, the use of this battery acclimation strategy may be of great potential for the breeding of industrial microorganisms.

Belowground Interactions Impact the Soil Bacterial Community, Soil Fertility, and Crop Yield in Maize/Peanut Intercropping Systems

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Qisong Li

2018-02-01

Full Text Available Intercropping has been widely used to control disease and improve yield in agriculture. In this study, maize and peanut were used for non-separation intercropping (NS, semi-separation intercropping (SS using a nylon net, and complete separation intercropping (CS using a plastic sheet. In field experiments, two-year land equivalent ratios (LERs showed yield advantages due to belowground interactions when using NS and SS patterns as compared to monoculture. In contrast, intercropping without belowground interactions (CS showed a yield disadvantage. Meanwhile, in pot experiments, belowground interactions (found in NS and SS improved levels of soil-available nutrients (nitrogen (N and phosphorus (P and enzymes (urease and acid phosphomonoesterase as compared to intercropping without belowground interactions (CS. Soil bacterial community assay showed that soil bacterial communities in the NS and SS crops clustered together and were considerably different from the CS crops. The diversity of bacterial communities was significantly improved in soils with NS and SS. The abundance of beneficial bacteria, which have the functions of P-solubilization, pathogen suppression, and N-cycling, was improved in maize and peanut soils due to belowground interactions through intercropping. Among these bacteria, numbers of Bacillus, Brevibacillus brevis, and Paenibacillus were mainly increased in the maize rhizosphere. Burkholderia, Pseudomonas, and Rhizobium were mainly increased in the peanut rhizosphere. In conclusion, using maize and peanut intercropping, belowground interactions increased the numbers of beneficial bacteria in the soil and improved the diversity of the bacterial community, which was conducive to improving soil nutrient (N and P supply capacity and soil microecosystem stability.

Vaginal epithelial cells regulate membrane adhesiveness to co-ordinate bacterial adhesion.

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Younes, Jessica A; Klappe, Karin; Kok, Jan Willem; Busscher, Henk J; Reid, Gregor; van der Mei, Henny C

2016-04-01

Vaginal epithelium is colonized by different bacterial strains and species. The bacterial composition of vaginal biofilms controls the balance between health and disease. Little is known about the relative contribution of the epithelial and bacterial cell surfaces to bacterial adhesion and whether and how adhesion is regulated over cell membrane regions. Here, we show that bacterial adhesion forces with cell membrane regions not located above the nucleus are stronger than with regions above the nucleus both for vaginal pathogens and different commensal and probiotic lactobacillus strains involved in health. Importantly, adhesion force ratios over membrane regions away from and above the nucleus coincided with the ratios between numbers of adhering bacteria over both regions. Bacterial adhesion forces were dramatically decreased by depleting the epithelial cell membrane of cholesterol or sub-membrane cortical actin. Thus, epithelial cells can regulate membrane regions to which bacterial adhesion is discouraged, possibly to protect the nucleus. © 2015 John Wiley & Sons Ltd.

Molecular methods for bacterial genotyping and analyzed gene regions

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İbrahim Halil Yıldırım1, Seval Cing Yıldırım2, Nadir Koçak3

2011-06-01

Full Text Available Bacterial strain typing is an important process for diagnosis, treatment and epidemiological investigations. Current bacterial strain typing methods may be classified into two main categories: phenotyping and genotyping. Phenotypic characters are the reflection of genetic contents. Genotyping, which refers discrimination of bacterial strains based on their genetic content, has recently become widely used for bacterial strain typing. The methods already used in genotypingof bacteria are quite different from each other. In this review we tried to summarize the basic principles of DNA-based methods used in genotyping of bacteria and describe some important DNA regions that are used in genotyping of bacteria. J Microbiol Infect Dis 2011;1(1:42-46.

Bacterial Cell Surface Damage Due to Centrifugal Compaction

NARCIS (Netherlands)

Peterson, Brandon W.; Sharma, Prashant K.; van der Mei, Henny C.; Busscher, Henk J.

Centrifugal damage has been known to alter bacterial cell surface properties and interior structures, including DNA. Very few studies exist on bacterial damage caused by centrifugation because of the difficulty in relating centrifugation speed and container geometry to the damage caused. Here, we

Bacterial Carriers for Glioblastoma Therapy

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Nalini Mehta

2017-03-01

Full Text Available Treatment of aggressive glioblastoma brain tumors is challenging, largely due to diffusion barriers preventing efficient drug dosing to tumors. To overcome these barriers, bacterial carriers that are actively motile and programmed to migrate and localize to tumor zones were designed. These carriers can induce apoptosis via hypoxia-controlled expression of a tumor suppressor protein p53 and a pro-apoptotic drug, Azurin. In a xenograft model of human glioblastoma in rats, bacterial carrier therapy conferred a significant survival benefit with 19% overall long-term survival of >100 days in treated animals relative to a median survival of 26 days in control untreated animals. Histological and proteomic analyses were performed to elucidate the safety and efficacy of these carriers, showing an absence of systemic toxicity and a restored neural environment in treated responders. In the treated non-responders, proteomic analysis revealed competing mechanisms of pro-apoptotic and drug-resistant activity. This bacterial carrier opens a versatile avenue to overcome diffusion barriers in glioblastoma by virtue of its active motility in extracellular space and can lead to tailored therapies via tumor-specific expression of tumoricidal proteins.

Bacterial identification and subtyping using DNA microarray and DNA sequencing.

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Al-Khaldi, Sufian F; Mossoba, Magdi M; Allard, Marc M; Lienau, E Kurt; Brown, Eric D

2012-01-01

The era of fast and accurate discovery of biological sequence motifs in prokaryotic and eukaryotic cells is here. The co-evolution of direct genome sequencing and DNA microarray strategies not only will identify, isotype, and serotype pathogenic bacteria, but also it will aid in the discovery of new gene functions by detecting gene expressions in different diseases and environmental conditions. Microarray bacterial identification has made great advances in working with pure and mixed bacterial samples. The technological advances have moved beyond bacterial gene expression to include bacterial identification and isotyping. Application of new tools such as mid-infrared chemical imaging improves detection of hybridization in DNA microarrays. The research in this field is promising and future work will reveal the potential of infrared technology in bacterial identification. On the other hand, DNA sequencing by using 454 pyrosequencing is so cost effective that the promise of $1,000 per bacterial genome sequence is becoming a reality. Pyrosequencing technology is a simple to use technique that can produce accurate and quantitative analysis of DNA sequences with a great speed. The deposition of massive amounts of bacterial genomic information in databanks is creating fingerprint phylogenetic analysis that will ultimately replace several technologies such as Pulsed Field Gel Electrophoresis. In this chapter, we will review (1) the use of DNA microarray using fluorescence and infrared imaging detection for identification of pathogenic bacteria, and (2) use of pyrosequencing in DNA cluster analysis to fingerprint bacterial phylogenetic trees.

Complete urinary tract infection (UTI) diagnosis and antibiogram using surface enhanced Raman spectroscopy (SERS)

Science.gov (United States)

Hadjigeorgiou, Katerina; Kastanos, Evdokia; Kyriakides, Alexandros; Pitris, Costas

2012-03-01

There are three stages to a complete UTI diagnosis: (1) identification of a urine sample as positive/negative for an infection, (2) identification of the responsible bacterium, (3) antibiogram to determine the antibiotic to which the bacteria are most sensitive to. Using conventional methods, all three stages require bacterial cultures in order to provide results. This long delay in diagnosis causes a rise in ineffective treatments, chronic infections, health care costs and antibiotic resistance. In this work, SERS is used to identify a sample as positive/negative for a UTI as well as to obtain an antibiogram against different antibiotics. SERS spectra of serial dilutions of E. coli bacteria mixed with silver nanoparticles, showed a linear correlation between spectral intensity and concentration. For antibiotic sensitivity testing, SERS spectra of three species of gram negative bacteria were collected four hours after exposure to the antibiotics ciprofloxacin and amoxicillin. Spectral analysis revealed clear separation between bacterial samples exposed to antibiotics to which they were sensitive and samples exposed to antibiotics to which they were resistant. With the enhancement provided by SERS, the technique can be applied directly to urine samples leading to the development of a new, rapid method for UTI diagnosis and antibiogram.

Bacterial nucleotide-based second messengers.

Science.gov (United States)

Pesavento, Christina; Hengge, Regine

2009-04-01

In all domains of life nucleotide-based second messengers transduce signals originating from changes in the environment or in intracellular conditions into appropriate cellular responses. In prokaryotes cyclic di-GMP has emerged as an important and ubiquitous second messenger regulating bacterial life-style transitions relevant for biofilm formation, virulence, and many other bacterial functions. This review describes similarities and differences in the architecture of the cAMP, (p)ppGpp, and c-di-GMP signaling systems and their underlying signaling principles. Moreover, recent advances in c-di-GMP-mediated signaling will be presented and the integration of c-di-GMP signaling with other nucleotide-based signaling systems will be discussed.

Validity of bacterial pneumonia score for predicting bacteremia in children with pneumonia

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Rosalia Theodosia Daten Beyeng

2011-12-01

Full Text Available Background Bacteremia in children with pneumonia reflects a severe condition, with longer duration of hospital care and potentially lethal complications. Early detection of bacteremia in patients with pneumonia may reduce serious complications. Few bacteremia screening tools have been widely used in chidren with pneumonia. One of those tools is the bacterial pneumonia score (BPS. Objective To assess the validity of the bacterial pneumonia score for predicting bacteremia in pediatric patients with pneumonia. Methods A diagnostic test was conducted on children aged 1 to 60 months hospitalized with pneumonia from December 2009 to August 2010. Subjects were collected consecutively. Pneumonia was diagnosed using the World Healt Organization (WHO criteria. Subjects underwent complete blood counts and blood culture examinations at admission. Statistical analyses included sensitivity, specificity, positive and negative predictive value (PPV/NPV, positive and negative likelihood ratio (PLR/NLR, and post-test probability. Results Our study included 229 children. Based on BPS with a cut-off score of ≥ 4, the sensitivity was 83.3%, specificity 49.7%, PPV 8.4%, NPV 98.2%, PLR 1.66, NLR 0.31, and post-test probability 8.4% for detecting bacteremia in pediatric pneumonia patients. Conclusion BPS can not be used for predicting bacteremia in pediatric patients with pneumonia.

Role of Autophagy and Apoptosis in the Postinfluenza Bacterial Pneumonia

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Zhen Qin

2016-01-01

Full Text Available The risk of influenza A virus (IAV is more likely caused by secondary bacterial infections. During the past decades, a great amount of studies have been conducted on increased morbidity from secondary bacterial infections following influenza and provide an increasing number of explanations for the mechanisms underlying the infections. In this paper, we first review the recent research progress that IAV infection increased susceptibility to bacterial infection. We then propose an assumption that autophagy and apoptosis manipulation are beneficial to antagonize post-IAV bacterial infection and discuss the clinical significance.

Bacterial Multidrug Efflux Pumps: Much More Than Antibiotic Resistance Determinants.

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Blanco, Paula; Hernando-Amado, Sara; Reales-Calderon, Jose Antonio; Corona, Fernando; Lira, Felipe; Alcalde-Rico, Manuel; Bernardini, Alejandra; Sanchez, Maria Blanca; Martinez, Jose Luis

2016-02-16

Bacterial multidrug efflux pumps are antibiotic resistance determinants present in all microorganisms. With few exceptions, they are chromosomally encoded and present a conserved organization both at the genetic and at the protein levels. In addition, most, if not all, strains of a given bacterial species present the same chromosomally-encoded efflux pumps. Altogether this indicates that multidrug efflux pumps are ancient elements encoded in bacterial genomes long before the recent use of antibiotics for human and animal therapy. In this regard, it is worth mentioning that efflux pumps can extrude a wide range of substrates that include, besides antibiotics, heavy metals, organic pollutants, plant-produced compounds, quorum sensing signals or bacterial metabolites, among others. In the current review, we present information on the different functions that multidrug efflux pumps may have for the bacterial behaviour in different habitats as well as on their regulation by specific signals. Since, in addition to their function in non-clinical ecosystems, multidrug efflux pumps contribute to intrinsic, acquired, and phenotypic resistance of bacterial pathogens, the review also presents information on the search for inhibitors of multidrug efflux pumps, which are currently under development, in the aim of increasing the susceptibility of bacterial pathogens to antibiotics.

Bacterial degradation of monocyclic aromatic amines

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Pankaj Kumar Arora

2015-08-01

Full Text Available Aromatic amines are an important group of industrial chemicals, which are widely used for manufacturing of dyes, pesticides, drugs, pigments, and other industrial products. These compounds have been considered highly toxic to human beings due to their carcinogenic nature. Three groups of aromatic amines have been recognized: monocyclic, polycyclic and heterocyclic aromatic amines. Bacterial degradation of several monocyclic aromatic compounds has been studied in a variety of bacteria, which utilizes monocyclic aromatic amines as their sole source of carbon and energy. Several degradation pathways have been proposed and the related enzymes and genes have also been characterized. Many reviews have been reviewed toxicity of monocyclic aromatic amines; however, there is lack of review on biodegradation of monocyclic aromatic amines. The aim of this review is to summarize bacterial degradation of monocyclic aromatic amines. This review will increase our current understanding of biochemical and molecular basis of bacterial degradation of monocyclic aromatic amines.

Mineral phosphate solubilizing bacterial community in agro-ecosystem

African Journals Online (AJOL)

Mineral phosphate solubilizing bacterial community in agro-ecosystem. N Saha, S Biswas. Abstract. The present communication deals with the assessment of phosphate solubilizing bacterial community structure across artificially created fertility gradient with regards to N, P and K status of soil in the experimental site.

Partial drying accelerates bacterial growth recovery to rewetting

DEFF Research Database (Denmark)

Meisner, Annelein; Leizeaga, Ainara; Rousk, Johannes

2017-01-01

, bacterial growth rates increase immediately in a linear fashion. In the Type 2 pattern, bacterial growth rates increase exponentially after a lag period. However, soils are often only partially dried. Partial drying (higher remaining moisture content before rewetting) may be considered a less harsh...

Extensive Identification of Bacterial Riboflavin Transporters and Their Distribution across Bacterial Species

Science.gov (United States)

Merino, Enrique; Bonomi, Hernán Ruy; Goldbaum, Fernando Alberto; García-Angulo, Víctor Antonio

2015-01-01

Riboflavin, the precursor for the cofactors flavin mononucleotide (FMN) and flavin adenine dinucleotide, is an essential metabolite in all organisms. While the functions for de novo riboflavin biosynthesis and riboflavin import may coexist in bacteria, the extent of this co-occurrence is undetermined. The RibM, RibN, RfuABCD and the energy-coupling factor-RibU bacterial riboflavin transporters have been experimentally characterized. In addition, ImpX, RfnT and RibXY are proposed as riboflavin transporters based on positional clustering with riboflavin biosynthetic pathway (RBP) genes or conservation of the FMN riboswitch regulatory element. Here, we searched for the FMN riboswitch in bacterial genomes to identify genes encoding riboflavin transporters and assessed their distribution among bacteria. Two new putative riboflavin transporters were identified: RibZ in Clostridium and RibV in Mesoplasma florum. Trans-complementation of an Escherichia coli riboflavin auxotroph strain confirmed the riboflavin transport activity of RibZ from Clostridium difficile, RibXY from Chloroflexus aurantiacus, ImpX from Fusobacterium nucleatum and RfnT from Ochrobactrum anthropi. The analysis of the genomic distribution of all known bacterial riboflavin transporters revealed that most occur in species possessing the RBP and that some bacteria may even encode functional riboflavin transporters from two different families. Our results indicate that some species possess ancestral riboflavin transporters, while others possess transporters that appear to have evolved recently. Moreover, our data suggest that unidentified riboflavin transporters also exist. The present study doubles the number of experimentally characterized riboflavin transporters and suggests a specific, non-accessory role for these proteins in riboflavin-prototrophic bacteria. PMID:25938806

Complete genome sequence of community-associated methicillin-resistant Staphylococcus aureus (strain USA400-0051, a prototype of the USA400 clone

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Marina Farrel Côrtes

Full Text Available Staphylococcus aureus subsp. aureus, commonly referred as S. aureus, is an important bacterial pathogen frequently involved in hospital- and community-acquired infections in humans, ranging from skin infections to more severe diseases such as pneumonia, bacteraemia, endocarditis, osteomyelitis, and disseminated infections. Here, we report the complete closed genome sequence of a community-acquired methicillin-resistant S. aureus strain, USA400-0051, which is a prototype of the USA400 clone.

Dynamic Computational Model of Symptomatic Bacteremia to Inform Bacterial Separation Treatment Requirements.

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Sinead E Miller

Full Text Available The rise of multi-drug resistance has decreased the effectiveness of antibiotics, which has led to increased mortality rates associated with symptomatic bacteremia, or bacterial sepsis. To combat decreasing antibiotic effectiveness, extracorporeal bacterial separation approaches have been proposed to capture and separate bacteria from blood. However, bacteremia is dynamic and involves host-pathogen interactions across various anatomical sites. We developed a mathematical model that quantitatively describes the kinetics of pathogenesis and progression of symptomatic bacteremia under various conditions, including bacterial separation therapy, to better understand disease mechanisms and quantitatively assess the biological impact of bacterial separation therapy. Model validity was tested against experimental data from published studies. This is the first multi-compartment model of symptomatic bacteremia in mammals that includes extracorporeal bacterial separation and antibiotic treatment, separately and in combination. The addition of an extracorporeal bacterial separation circuit reduced the predicted time of total bacteria clearance from the blood of an immunocompromised rodent by 49%, compared to antibiotic treatment alone. Implementation of bacterial separation therapy resulted in predicted multi-drug resistant bacterial clearance from the blood of a human in 97% less time than antibiotic treatment alone. The model also proposes a quantitative correlation between time-dependent bacterial load among tissues and bacteremia severity, analogous to the well-known 'area under the curve' for characterization of drug efficacy. The engineering-based mathematical model developed may be useful for informing the design of extracorporeal bacterial separation devices. This work enables the quantitative identification of the characteristics required of an extracorporeal bacteria separation device to provide biological benefit. These devices will potentially

Particle surface area and bacterial activity in recirculating aquaculture systems

DEFF Research Database (Denmark)

Pedersen, Per Bovbjerg; von Ahnen, Mathis; Fernandes, Paulo

2017-01-01

Suspended particles in recirculating aquaculture systems (RAS) provide surface area that can be colonized by bacteria. More particles accumulate as the intensity of recirculation increases thus potentially increasing the bacterial carrying capacity of the systems. Applying a recent, rapid, culture...... but may provide significant surface area. Hence, the study substantiates that particles in RAS provide surface area supporting bacterial activity, and that particles play a key role in controlling the bacterial carrying capacity at least in less intensive RAS. Applying fast, culture-independent techniques......-independent fluorometric detection method (Bactiquant®) for measuring bacterial activity, the current study explored the relationship between total particle surface area (TSA, derived from the size distribution of particles >5 μm) and bacterial activity in freshwater RAS operated at increasing intensity of recirculation...

Optimized bacterial expression and purification of the c-Src catalytic domain for solution NMR studies

International Nuclear Information System (INIS)

Piserchio, Andrea; Ghose, Ranajeet; Cowburn, David

2009-01-01

Progression of a host of human cancers is associated with elevated levels of expression and catalytic activity of the Src family of tyrosine kinases (SFKs), making them key therapeutic targets. Even with the availability of multiple crystal structures of active and inactive forms of the SFK catalytic domain (CD), a complete understanding of its catalytic regulation is unavailable. Also unavailable are atomic or near-atomic resolution information about their interactions, often weak or transient, with regulating phosphatases and downstream targets. Solution NMR, the biophysical method best suited to tackle this problem, was previously hindered by difficulties in bacterial expression and purification of sufficient quantities of soluble, properly folded protein for economically viable labeling with NMR-active isotopes. Through a choice of optimal constructs, co-expression with chaperones and optimization of the purification protocol, we have achieved the ability to bacterially produce large quantities of the isotopically-labeled CD of c-Src, the prototypical SFK, and of its activating Tyr-phosphorylated form. All constructs produce excellent spectra allowing solution NMR studies of this family in an efficient manner

Parallel reaction monitoring on a Q Exactive mass spectrometer increases reproducibility of phosphopeptide detection in bacterial phosphoproteomics measurements.

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Taumer, Christoph; Griesbaum, Lena; Kovacevic, Alen; Soufi, Boumediene; Nalpas, Nicolas C; Macek, Boris

2018-03-29

Increasing number of studies report the relevance of protein Ser/Thr/Tyr phosphorylation in bacterial physiology, yet the analysis of this type of modification in bacteria still presents a considerable challenge. Unlike in eukaryotes, where tens of thousands of phosphorylation events likely occupy more than two thirds of the proteome, the abundance of protein phosphorylation is much lower in bacteria. Even the state-of-the-art phosphopeptide enrichment protocols fail to remove the high background of abundant unmodified peptides, leading to low signal intensity and undersampling of phosphopeptide precursor ions in consecutive data-dependent MS runs. Consequently, large-scale bacterial phosphoproteomic datasets often suffer from poor reproducibility and a high number of missing values. Here we explore the application of parallel reaction monitoring (PRM) on a Q Exactive mass spectrometer in bacterial phosphoproteome analysis, focusing especially on run-to-run sampling reproducibility. In multiple measurements of identical phosphopeptide-enriched samples, we show that PRM outperforms data-dependent acquisition (DDA) in terms of detection frequency, reaching almost complete sampling efficiency, compared to 20% in DDA. We observe a similar trend over multiple heterogeneous phosphopeptide-enriched samples and conclude that PRM shows a great promise in bacterial phosphoproteomics analyses where reproducible detection and quantification of a relatively small set of phosphopeptides is desired. Bacterial phosphorylated peptides occur in low abundance compared to their unmodified counterparts, and are therefore rarely reproducibly detected in shotgun (DDA) proteomics measurements. Here we show that parallel reaction monitoring complements DDA analyses and makes detection of known, targeted phosphopeptides more reproducible. This will be of significance in replicated MS measurements that have a goal to reproducibly detect and quantify phosphopeptides of interest. Copyright �

Soil bacterial community shifts associated with sugarcane straw removal

Science.gov (United States)

Pimentel, Laisa; Gumiere, Thiago; Andreote, Fernando; Cerri, Carlos

2017-04-01

In Brazil, the adoption of the mechanical unburned sugarcane harvest potentially increase the quantity of residue left in the field after harvesting. Economically, this material has a high potential for second generation ethanol (2G) production. However, crop residues have an essential role in diverse properties and processes in the soil. The greater part of the uncertainties about straw removal for 2G ethanol production is based on its effects in soil microbial community. In this sense, it is important to identify the main impacts of sugarcane straw removal on soil microbial community. Therefore, we conducted a field study, during one year, in Valparaíso (São Paulo state - Brazil) to evaluate the effects of straw decomposition on soil bacterial community. Specifically, we wanted: i) to compare the rates of straw removal and ii) to evaluate the effects of straw decomposition on soil bacterial groups over one year. The experiment was in a randomized block design with treatments arranged in strip plot. The treatments are different rates of sugarcane straw removal, namely: no removal, 50, 75 and 100% of straw removal. Soil sampling was carried out at 0, 4, 8 and 12 months after the sugarcane harvest (August 2015). Total DNA was extracted from soil using the PowersoilTM DNA Isolation kit. And the abundance of bacterial in each soil sample was estimated via quantification of 16S rRNA gene. The composition of the bacterial communities was estimated via terminal restriction fragment length polymorphism (T-RFLP) analysis, and the T-RF sizes were performed on a 3500 Genetic Analyzer. Finally, the results were examined with GeneMapper 4.1 software. There was bacterial community shifts through the time and among the rates of sugarcane straw removal. Bacterial community was firstly determined by the time scale, which explained 29.16% of total variation. Rates of straw removal explained 11.55% of shifts on bacterial community. Distribution through the time is an important

Skin bacterial flora as a potential risk factor predisposing to late bacterial infection after cross-linked hyaluronic acid gel augmentation.

Science.gov (United States)

Netsvyetayeva, Irina; Marusza, Wojciech; Olszanski, Romuald; Szyller, Kamila; Krolak-Ulinska, Aneta; Swoboda-Kopec, Ewa; Sierdzinski, Janusz; Szymonski, Zachary; Mlynarczyk, Grazyna

2018-01-01

Cross-linked hyaluronic acid (HA) gel is widely used in esthetic medicine. Late bacterial infection (LBI) is a rare, but severe complication after HA augmentation. The aim of this study was to determine whether patients who underwent the HA injection procedure and developed LBI had qualitatively different bacterial flora on the skin compared to patients who underwent the procedure without any complications. The study group comprised 10 previously healthy women with recently diagnosed, untreated LBI after HA augmentation. The control group comprised 17 healthy women who had a similar amount of HA injected with no complications. To assess the difference between the two groups, their skin flora was cultured from nasal swabs, both before and after antibiotic treatment in the study group. A significant increase in the incidence of Staphylococcus epidermidis was detected in the control group ( P =0.000) compared to the study group. The study group showed a significantly higher incidence of Staphylococcus aureus ( P =0.005), Klebsiella pneumoniae ( P =0.006), Klebsiella oxytoca ( P =0.048), and Staphylococcus haemolyticus ( P =0.048) compared to the control group. The bacterial flora on the skin differed in patients with LBI from the control group. The control group's bacterial skin flora was dominated by S. epidermidis . Patients with LBI had a bacterial skin flora dominated by potentially pathogenic bacteria.

Factors influencing bacterial adhesion to contact lenses.

Science.gov (United States)

Dutta, Debarun; Cole, Nerida; Willcox, Mark

2012-01-01

The process of any contact lens related keratitis generally starts with the adhesion of opportunistic pathogens to contact lens surface. This article focuses on identifying the factors which have been reported to affect bacterial adhesion to contact lenses. Adhesion to lenses differs between various genera/species/strains of bacteria. Pseudomonas aeruginosa, which is the predominant causative organism, adheres in the highest numbers to both hydrogel and silicone hydrogel lenses in vitro. The adhesion of this strain reaches maximum numbers within 1h in most in vitro studies and a biofilm has generally formed within 24 h of cells adhering to the lens surface. Physical and chemical properties of contact lens material affect bacterial adhesion. The water content of hydroxyethylmethacrylate (HEMA)-based lenses and their iconicity affect the ability of bacteria to adhere. The higher hydrophobicity of silicone hydrogel lenses compared to HEMA-based lenses has been implicated in the higher numbers of bacteria that can adhere to their surfaces. Lens wear has different effects on bacterial adhesion, partly due to differences between wearers, responses of bacterial strains and the ability of certain tear film proteins when bound to a lens surface to kill certain types of bacteria.

Demodex-associated bacterial proteins induce neutrophil activation.

LENUS (Irish Health Repository)

2012-02-01

Background: Patients with rosacea demonstrate a higher density of Demodex mites in their skin than controls. A bacterium isolated from a Demodex mite from a patient with papulopustular rosacea (PPR) was previously shown to provoke an immune response in patients with PPR or ocular rosacea thus suggesting a possible role for bacterial proteins in the etiology of this condition. Objectives: To examine the response of neutrophils to proteins derived from a bacterium isolated from a Demodex mite. Methods: Bacterial cells were lysed and proteins were partially purified by AKTA-FPLC. Isolated neutrophils were exposed to bacterial proteins and monitored for alterations in migration, degranulation and cytokine production. Results: Neutrophils exposed to proteins from Bacillus cells demonstrated increased levels of migration and elevated release of MMP-9, an enzyme known to degrade collagen and cathelicidin, an antimicrobial peptide. In addition neutrophils exposed to the bacterial proteins demonstrated elevated rates of Il-8 and TNF-alpha production. Conclusions: Proteins produced by a bacterium isolated from a Demodex mite have the ability to increase the migration, degranulation and cytokine production abilities of neutrophils. These results suggest that bacteria may play a role in the inflammatory erythema associated with rosacea.

Complete Microbiota Engraftment Is Not Essential for Recovery from Recurrent Clostridium difficile Infection following Fecal Microbiota Transplantation

Directory of Open Access Journals (Sweden)

Christopher Staley

2016-12-01

Full Text Available Bacterial communities from subjects treated for recurrent Clostridium difficile infection (rCDI by fecal microbiota transplantation (FMT, using either heterologous donor stool samples or autologous stool samples, were characterized by Illumina next-generation sequencing. As previously reported, the success of heterologous FMT (90% was superior to that of autologous FMT (43% (P = 0.019, and post-FMT intestinal bacterial communities differed significantly between treatment arms (P < 0.001. Subjects cured by autologous FMT typically had greater abundances of the Clostridium XIVa clade and Holdemania bacteria prior to treatment, and the relative abundances of these groups increased significantly after FMT compared to heterologous FMT and pre-FMT samples. The typical shift to post-FMT, donor-like assemblages, featuring high relative abundances of genera within the Bacteroidetes and Firmicutes phyla, was not observed in the autologous FMT subjects. Autologous FMT patient bacterial communities were significantly different in composition than those for heterologous FMT patients and donors (P < 0.001. The SourceTracker program, which employs a Bayesian algorithm to determine source contributions to sink communities, showed that patients initially treated by heterologous FMT had significantly higher percentages of engraftment (i.e., similarity to donor communities, mean value of 74% compared to those who suffered recurrence following autologous FMT (1% (P ≤ 0.013. The findings of this study suggest that complete donor engraftment may be not necessary if functionally critical taxa are present in subjects following antibiotic therapy.

Bacterial biosynthesis and maturation of the didemnin anti-cancer agents

KAUST Repository

Xü , Ying; Kersten, Roland D.; Nam, Sang Jip; Lu, Liang; Al-Suwailem, Abdulaziz M.; Zheng, Huajun; Fenical, William H.; Dorrestein, Pieter C.; Moore, Bradley S.; Qian, Peiyuan

2012-01-01

The anti-neoplastic agent didemnin B from the Caribbean tunicate Trididemnum solidum was the first marine drug to be clinically tested in humans. Because of its limited supply and its complex cyclic depsipeptide structure, considerable challenges were encountered during didemnin B's development that continue to limit aplidine (dehydrodidemnin B), which is currently being evaluated in numerous clinical trials. Herein we show that the didemnins are bacterial products produced by the marine α-proteobacteria Tistrella mobilis and Tistrella bauzanensis via a unique post-assembly line maturation process. Complete genome sequence analysis of the 6,513,401 bp T. mobilis strain KA081020-065 with its five circular replicons revealed the putative didemnin biosynthetic gene cluster (did) on the 1,126,962 bp megaplasmid pTM3. The did locus encodes a 13-module hybrid non-ribosomal peptide synthetase-polyketide synthase enzyme complex organized in a collinear arrangement for the synthesis of the fatty acylglutamine ester derivatives didemnins X and Y rather than didemnin B as first anticipated. Imaging mass spectrometry of T. mobilis bacterial colonies captured the time-dependent extracellular conversion of the didemnin X and Y precursors to didemnin B, in support of an unusual post-synthetase activation mechanism. Significantly, the discovery of the didemnin biosynthetic gene cluster may provide a long-term solution to the supply problem that presently hinders this group of marine natural products and pave the way for the genetic engineering of new didemnin congeners. © 2012 American Chemical Society.

Bacterial biosynthesis and maturation of the didemnin anti-cancer agents

KAUST Repository

Xü, Ying

2012-05-23

The anti-neoplastic agent didemnin B from the Caribbean tunicate Trididemnum solidum was the first marine drug to be clinically tested in humans. Because of its limited supply and its complex cyclic depsipeptide structure, considerable challenges were encountered during didemnin B\\'s development that continue to limit aplidine (dehydrodidemnin B), which is currently being evaluated in numerous clinical trials. Herein we show that the didemnins are bacterial products produced by the marine α-proteobacteria Tistrella mobilis and Tistrella bauzanensis via a unique post-assembly line maturation process. Complete genome sequence analysis of the 6,513,401 bp T. mobilis strain KA081020-065 with its five circular replicons revealed the putative didemnin biosynthetic gene cluster (did) on the 1,126,962 bp megaplasmid pTM3. The did locus encodes a 13-module hybrid non-ribosomal peptide synthetase-polyketide synthase enzyme complex organized in a collinear arrangement for the synthesis of the fatty acylglutamine ester derivatives didemnins X and Y rather than didemnin B as first anticipated. Imaging mass spectrometry of T. mobilis bacterial colonies captured the time-dependent extracellular conversion of the didemnin X and Y precursors to didemnin B, in support of an unusual post-synthetase activation mechanism. Significantly, the discovery of the didemnin biosynthetic gene cluster may provide a long-term solution to the supply problem that presently hinders this group of marine natural products and pave the way for the genetic engineering of new didemnin congeners. © 2012 American Chemical Society.

Cooperative Bacterial Foraging Optimization

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Hanning Chen

2009-01-01

Full Text Available Bacterial Foraging Optimization (BFO is a novel optimization algorithm based on the social foraging behavior of E. coli bacteria. This paper presents a variation on the original BFO algorithm, namely, the Cooperative Bacterial Foraging Optimization (CBFO, which significantly improve the original BFO in solving complex optimization problems. This significant improvement is achieved by applying two cooperative approaches to the original BFO, namely, the serial heterogeneous cooperation on the implicit space decomposition level and the serial heterogeneous cooperation on the hybrid space decomposition level. The experiments compare the performance of two CBFO variants with the original BFO, the standard PSO and a real-coded GA on four widely used benchmark functions. The new method shows a marked improvement in performance over the original BFO and appears to be comparable with the PSO and GA.

Mathematical Modelling of Bacterial Populations in Bio-remediation Processes

Science.gov (United States)

Vasiliadou, Ioanna A.; Vayenas, Dimitris V.; Chrysikopoulos, Constantinos V.

2011-09-01

An understanding of bacterial behaviour concerns many field applications, such as the enhancement of water, wastewater and subsurface bio-remediation, the prevention of environmental pollution and the protection of human health. Numerous microorganisms have been identified to be able to degrade chemical pollutants, thus, a variety of bacteria are known that can be used in bio-remediation processes. In this study the development of mathematical models capable of describing bacterial behaviour considered in bio-augmentation plans, such as bacterial growth, consumption of nutrients, removal of pollutants, bacterial transport and attachment in porous media, is presented. The mathematical models may be used as a guide in designing and assessing the conditions under which areas contaminated with pollutants can be better remediated.

Bacterial community structure in the Cerasus sachalinensis Kom ...

African Journals Online (AJOL)

Jane

2011-07-21

Jul 21, 2011 ... The bacterial community structures of the Cerasus sachalinensis Kom. rhizosphere in wild and cultivated soil were studied and the community changes in different growth stages were analyzed by the PCR-denaturing gradient gel electrophoresis (PCR-DGGE) method. The results showed that the bacterial ...

Interference in Bacterial Quorum Sensing: A Biopharmaceutical Perspective

Directory of Open Access Journals (Sweden)

Benjamin Rémy

2018-03-01

Full Text Available Numerous bacteria utilize molecular communication systems referred to as quorum sensing (QS to synchronize the expression of certain genes regulating, among other aspects, the expression of virulence factors and the synthesis of biofilm. To achieve this process, bacteria use signaling molecules, known as autoinducers (AIs, as chemical messengers to share information. Naturally occurring strategies that interfere with bacterial signaling have been extensively studied in recent years, examining their potential to control bacteria. To interfere with QS, bacteria use quorum sensing inhibitors (QSIs to block the action of AIs and quorum quenching (QQ enzymes to degrade signaling molecules. Recent studies have shown that these strategies are promising routes to decrease bacterial pathogenicity and decrease biofilms, potentially enhancing bacterial susceptibility to antimicrobial agents including antibiotics and bacteriophages. The efficacy of QSIs and QQ enzymes has been demonstrated in various animal models and are now considered in the development of new medical devices against bacterial infections, including dressings, and catheters for enlarging the therapeutic arsenal against bacteria.

Towards revealing the structure of bacterial inclusion bodies.

Science.gov (United States)

Wang, Lei

2009-01-01

Protein aggregation is a widely observed phenomenon in human diseases, biopharmaceutical production, and biological research. Protein aggregates are generally classified as highly ordered, such as amyloid fibrils, or amorphous, such as bacterial inclusion bodies. Amyloid fibrils are elongated filaments with diameters of 6-12 nm, they are comprised of residue-specific cross-beta structure, and display characteristic properties, such as binding with amyloid-specific dyes. Amyloid fibrils are associated with dozens of human pathological conditions, including Alzheimer disease and prion diseases. Distinguished from amyloid fibrils, bacterial inclusion bodies display apparent amorphous morphology. Inclusion bodies are formed during high-level recombinant protein production, and formation of inclusion bodies is a major concern in biotechnology. Despite of the distinctive morphological difference, bacterial inclusion bodies have been found to have some amyloid-like properties, suggesting that they might contain structures similar to amyloid-like fibrils. Recent structural data further support this hypothesis, and this review summarizes the latest progress towards revealing the structural details of bacterial inclusion bodies.

Shifts in bacterial and archaeal community structures during the batch biomethanation of Ulva biomass under mesophilic conditions.

Science.gov (United States)

Kim, Jaai; Jung, Heejung; Lee, Changsoo

2014-10-01

Mesophilic biomethanation of Ulva biomass was performed in a batch bioreactor, and a high organic removal of 77% was obtained on the basis of chemical oxygen demand (COD) after a month of operation. The estimated methane yield was 0.43 ± 0.02 L CH4/g COD(removed) which is close to the theoretical methane potential. Transitions of bacterial and archaeal community structures, associated with process performance data, were investigated using a combination of molecular fingerprinting and biostatistical tools. During the operation, archaeal community structure had no significant changes while bacterial community structure shifted continuously and dynamically. The reactor completely stabilized volatile fatty acids (primarily acetate and propionate) accumulated from the acidogenesis phase, with Methanosaeta- and Methanolinea-related microbes respectively being the main aceticlastic and hydrogenotrophic methanogens. Methanolinea- and Syntrophobacter-related populations were likely the key members to form a syntrophic propionate-degrading consortium. A Methanolinea-related population was likely the dominant methane producer in the experimental reactor. Copyright © 2014 Elsevier Ltd. All rights reserved.

Temperature adaptation of bacterial communities in experimentally warmed forest soils.

Science.gov (United States)

Rousk, Johannes; Frey, Serita D; Bååth, Erland

2012-10-01

A detailed understanding of the influence of temperature on soil microbial activity is critical to predict future atmospheric CO 2 concentrations and feedbacks to anthropogenic warming. We investigated soils exposed to 3-4 years of continuous 5 °C-warming in a field experiment in a temperate forest. We found that an index for the temperature adaptation of the microbial community, T min for bacterial growth, increased by 0.19 °C per 1 °C rise in temperature, showing a community shift towards one adapted to higher temperature with a higher temperature sensitivity (Q 10(5-15 °C) increased by 0.08 units per 1 °C). Using continuously measured temperature data from the field experiment we modelled in situ bacterial growth. Assuming that warming did not affect resource availability, bacterial growth was modelled to become 60% higher in warmed compared to the control plots, with the effect of temperature adaptation of the community only having a small effect on overall bacterial growth (bacterial growth, most likely due to substrate depletion because of the initially higher growth in warmed plots. When this was factored in, the result was similar rates of modelled in situ bacterial growth in warmed and control plots after 3 years, despite the temperature difference. We conclude that although temperature adaptation for bacterial growth to higher temperatures was detectable, its influence on annual bacterial growth was minor, and overshadowed by the direct temperature effect on growth rates. © 2012 Blackwell Publishing Ltd.

Investigation of multimodal forward scatter phenotyping from bacterial colonies

Science.gov (United States)

Kim, Huisung

A rapid, label-free, and elastic light scattering (ELS) based bacterial colony phenotyping technology, bacterial rapid detection using optical scattering technology (BARDOT) provides a successful classification of several bacterial genus and species. For a thorough understanding of the phenomena and overcoming the limitations of the previous design, five additional modalities from a bacterial colony: 3D morphology, spatial optical density (OD) distribution, spectral forward scattering pattern, spectral OD, and surface backward reflection pattern are proposed to enhance the classification/identification ratio, and the feasibilities of each modality are verified. For the verification, three different instruments: integrated colony morphology analyzer (ICMA), multi-spectral BARDOT (MS-BARDOT) , and multi-modal BARDOT (MM-BARDOT) are proposed and developed. The ICMA can measure 3D morphology and spatial OD distribution of the colony simultaneously. A commercialized confocal displacement meter is used to measure the profiles of the bacterial colonies, together with a custom built optical density measurement unit to interrogate the biophysics behind the collective behavior of a bacterial colony. The system delivers essential information related to the quantitative growth dynamics (height, diameter, aspect ratio, optical density) of the bacterial colony, as well as, a relationship in between the morphological characteristics of the bacterial colony and its forward scattering pattern. Two different genera: Escherichia coli O157:H7 EDL933, and Staphylococcus aureus ATCC 25923 are selected for the analysis of the spatially resolved growth dynamics, while, Bacillus spp. such as B. subtilis ATCC 6633, B. cereus ATCC 14579, B. thuringiensis DUP6044, B. polymyxa B719W, and B. megaterium DSP 81319, are interrogated since some of the Bacillus spp. provides strikingly different characteristics of ELS patterns, and the origin of the speckle patterns are successfully correlated with

Bacterial contamination of platelet components not detected by BacT/ALERT®.

Science.gov (United States)

Abela, M A; Fenning, S; Maguire, K A; Morris, K G

2018-02-01

To investigate the possible causes for false negative results in BacT/ALERT ® 3D Signature System despite bacterial contamination of platelet units. The Northern Ireland Blood Transfusion Service (NIBTS) routinely extends platelet component shelf life to 7 days. Components are sampled and screened for bacterial contamination using an automated microbial detection system, the BacT/ALERT ® 3D Signature System. We report on three platelet components with confirmed bacterial contamination, which represent false negative BacT/ALERT ® results and near-miss serious adverse events. NIBTS protocols for risk reduction of bacterial contamination of platelet components are described. The methodology for bacterial detection using BacT/ALERT ® is outlined. Laboratory tests, relevant patient details and relevant follow-up information are analysed. In all three cases, Staphylococcus aureus was isolated from the platelet residue and confirmed on terminal sub-culture using BacT/ALERT ® . In two cases, S. aureus with similar genetic makeup was isolated from the donors. Risk reduction measures for bacterial contamination of platelet components are not always effective. Automated bacterial culture detection does not eliminate the risk of bacterial contamination. Visual inspection of platelet components prior to release, issue and administration remains an important last line of defence. © 2017 British Blood Transfusion Society.

C-reactive protein velocity to distinguish febrile bacterial infections from non-bacterial febrile illnesses in the emergency department

OpenAIRE

Paran, Yael; Yablecovitch, Doron; Choshen, Guy; Zeitlin, Ina; Rogowski, Ori; Ben-Ami, Ronen; Katzir, Michal; Saranga, Hila; Rosenzweig, Tovit; Justo, Dan; Orbach, Yaffa; Halpern, Pinhas; Berliner, Shlomo

2009-01-01

Introduction C-reactive protein (CRP) is a real-time and low-cost biomarker to distinguish febrile bacterial infections from non-bacterial febrile illnesses. We hypothesised that measuring the velocity of the biomarker instead of its absolute serum concentration could enhance its ability to differentiate between these two conditions. Methods We prospectively recruited adult patients (age ? 18 years) who presented to the emergency department with fever. We recorded their data regarding the ons...

Exploring the Bacterial Microbiota of Colombian Fermented Maize Dough “Masa Agria” (Maiz Añejo)

Science.gov (United States)

Chaves-Lopez, Clemencia; Serio, Annalisa; Delgado-Ospina, Johannes; Rossi, Chiara; Grande-Tovar, Carlos D.; Paparella, Antonello

2016-01-01

Masa Agria is a naturally fermented maize dough produced in Colombia, very common in the traditional gastronomy. In this study we used culture-dependent and RNA-based pyrosequencing to investigate the bacterial community structure of Masa Agria samples produced in the south west of Colombia. The mean value of cell density was 7.6 log CFU/g of presumptive lactic acid bacteria, 5.4 log cfu/g for presumptive acetic bacteria and 5.6 og CFU/g for yeasts. The abundance of these microorganisms is also responsible for the low pH (3.1–3.7) registered. Although the 16S rRNA pyrosequencing revealed that the analyzed samples were different in bacteria richness and diversity, the genera Lactobacillus, Weissella, and Acetobacter were predominant. In particular, the most common species were Lactobacillus plantarum and Acetobacter fabarum, followed by L. fermentum, L. vaccinostercus, and Pediococcus argentinicus. Several microorganisms of environmental origin, such as Dechloromonas and most of all Sphingobium spp., revealed in each sample, were detected, and also bacteria related to maize, such as Phytoplasma. In conclusion, our results elucidated for the first time the structures of the bacterial communities of Masa Agria samples obtained from different producers, identifying the specific dominant species and revealing a complete picture of the bacterial consortium in this specific niche. The selective pressure of tropical environments may favor microbial biodiversity characterized by a useful technological potential. PMID:27524979

Exploring the bacterial microbiota of Colombian fermented maize dough “Masa Agria” (Maiz Añejo

Directory of Open Access Journals (Sweden)

Clemencia Chaves

2016-07-01

Full Text Available Masa Agria is a naturally fermented maize dough produced in Colombia, very common in the traditional gastronomy. In this study we used culture-dependent and RNA-based pyrosequencing to investigate the bacterial community structure of Masa Agria samples produced in the south west of Colombia. The mean value of cell density was 7.6 Log CFU/g of presumptive lactic acid bacteria (LAB, 5.4 Log cfu/g for presumptive acetic bacteria and 5.6 Log CFU/g for yeasts. The abundance of these microorganisms is also responsible for the low pH (3.1-3.7 registered. Although the 16S rRNA pyrosequencing revealed that the analyzed samples were different in bacteria richness and diversity, the genera Lactobacillus, Weissella and Acetobacter were predominant. In particular, the most common species were Lactobacillus plantarum and Acetobacter fabarum, followed by Lb. fermentum, Lb. vaccinostercus and Pediococcus argentinicus. Several microorganisms of environmental origin, such as Dechloromonas and most of all Sphingobium spp., revealed in each sample, were detected, and also bacteria related to maize, such as Phytoplasma. In conclusion, our results elucidated for the first time the structures of the bacterial communities of Masa Agria samples obtained from different producers, identifying the specific dominant species and revealing a complete picture of the bacterial consortium in this specific niche. The selective pressure of tropical environments may favour microbial biodiversity characterized by a useful technological potential.

Childhood asthma after bacterial colonization of the airway in neonates

DEFF Research Database (Denmark)

Bisgaard, Hans; Hermansen, Mette Northman; Buchvald, Frederik

2007-01-01

Pathological features of the airway in young children with severe recurrent wheeze suggest an association between bacterial colonization and the initiating events of early asthma. We conducted a study to investigate a possible association between bacterial colonization of the hypopharynx in asymp......Pathological features of the airway in young children with severe recurrent wheeze suggest an association between bacterial colonization and the initiating events of early asthma. We conducted a study to investigate a possible association between bacterial colonization of the hypopharynx...... in asymptomatic neonates and later development of recurrent wheeze, asthma, and allergy during the first 5 years of life....

Carbon nanomaterials alter plant physiology and soil bacterial community composition in a rice-soil-bacterial ecosystem.

Science.gov (United States)

Hao, Yi; Ma, Chuanxin; Zhang, Zetian; Song, Youhong; Cao, Weidong; Guo, Jing; Zhou, Guopeng; Rui, Yukui; Liu, Liming; Xing, Baoshan

2018-01-01

The aim of this study was to compare the toxicity effects of carbon nanomaterials (CNMs), namely fullerene (C 60 ), reduced graphene oxide (rGO) and multi-walled carbon nanotubes (MWCNTs), on a mini-ecosystem of rice grown in a loamy potted soil. We measured plant physiological and biochemical parameters and examined bacterial community composition in the CNMs-treated plant-soil system. After 30 days of exposure, all the three CNMs negatively affected the shoot height and root length of rice, significantly decreased root cortical cells diameter and resulted in shrinkage and deformation of cells, regardless of exposure doses (50 or 500 mg/kg). Additionally, at the high exposure dose of CNM, the concentrations of four phytohormones, including auxin, indoleacetic acid, brassinosteroid and gibberellin acid 4 in rice roots significantly increased as compared to the control. At the high exposure dose of MWCNTs and C 60 , activities of the antioxidant enzymes superoxide dismutase (SOD) and peroxidase (POD) in roots increased significantly. High-throughput sequencing showed that three typical CNMs had little effect on shifting the predominant soil bacterial species, but the presence of CNMs significantly altered the composition of the bacterial community. Our results indicate that different CNMs indeed resulted in environmental toxicity to rice and soil bacterial community in the rhizosphere and suggest that CNMs themselves and their incorporated products should be reasonably used to control their release/discharge into the environment to prevent their toxic effects on living organisms and the potential risks to food safety. Copyright © 2017 Elsevier Ltd. All rights reserved.

Heme Synthesis and Acquisition in Bacterial Pathogens.

Science.gov (United States)

Choby, Jacob E; Skaar, Eric P

2016-08-28

Bacterial pathogens require the iron-containing cofactor heme to cause disease. Heme is essential to the function of hemoproteins, which are involved in energy generation by the electron transport chain, detoxification of host immune effectors, and other processes. During infection, bacterial pathogens must synthesize heme or acquire heme from the host; however, host heme is sequestered in high-affinity hemoproteins. Pathogens have evolved elaborate strategies to acquire heme from host sources, particularly hemoglobin, and both heme acquisition and synthesis are important for pathogenesis. Paradoxically, excess heme is toxic to bacteria and pathogens must rely on heme detoxification strategies. Heme is a key nutrient in the struggle for survival between host and pathogen, and its study has offered significant insight into the molecular mechanisms of bacterial pathogenesis. Copyright © 2016 Elsevier Ltd. All rights reserved.

Counterimmunoelectrophoresis in the diagnosis of bacterial meningitis

DEFF Research Database (Denmark)

Colding, H; Lind, I

1977-01-01

The aim of the present study was to investigate whether counterimmunoelectrophoresis (CIE) would facilitate the rapid, etiological diagnosis of bacterial meningitis when used in parallel with other routine methods in a medical bacteriological laboratory. Of 3,674 consecutive specimens of cerebros......The aim of the present study was to investigate whether counterimmunoelectrophoresis (CIE) would facilitate the rapid, etiological diagnosis of bacterial meningitis when used in parallel with other routine methods in a medical bacteriological laboratory. Of 3,674 consecutive specimens....../139) of the culture-negative specimens. CSF specimens from 21 patients with bacterial meningitis caused by other species were all negative in CIE, except four, three of which contained Escherichia coli antigen reacting with antiserum to N. meningitidis group B and one E. coli antigen reacting with antiserum to H...

Bacterial colonization of psoriasis plaques. Is it relevant?

Directory of Open Access Journals (Sweden)

Eva Marcus

2011-08-01

Full Text Available Bacterial colonization was investigated retrospectively in patients with plaque psoriasis (n=98 inpatient treatments, n=73 patients. At least one pathogen was found in 46% of all cases. Staphylococcus aureus was the most frequent bacterium. Bacterial colonization of psoriasis plaques could be relevant in individual cases.

Engineering nanoparticles to silence bacterial communication

Directory of Open Access Journals (Sweden)

Kristen Publicover Miller

2015-03-01

Full Text Available The alarming spread of bacterial resistance to traditional antibiotics has warranted the study of alternative antimicrobial agents. Quorum sensing is a chemical cell-to-cell communication mechanism utilized by bacteria to coordinate group behaviors and establish infections. Quorum sensing is integral to bacterial survival, and therefore provides a unique target for antimicrobial therapy. In this study, silicon dioxide nanoparticles (Si-NP were engineered to target the signaling molecules (i.e. acylhomoserine lactones (HSL used for quorum sensing in order to halt bacterial communication. Specifically, when Si-NP were surface functionalized with beta-cyclodextrin (beta-CD, then added to cultures of bacteria (Vibrio fischeri, whose luminous output depends upon HSL-mediated quorum sensing, the cell-to-cell communication was dramatically reduced. Reductions in luminescence were further verified by quantitative polymerase chain reaction (qPCR analyses of luminescence genes. Binding of AHLs to Si-NPs was examined using nuclear magnetic resonance (NMR spectroscopy. The results indicated that by delivering high concentrations of engineered NPs with associated quenching compounds, the chemical signals were removed from the immediate bacterial environment. In actively-metabolizing cultures, this treatment blocked the ability of bacteria to communicate and regulate quorum sensing, effectively silencing and isolating the cells. Si-NPs provide a scaffold and critical stepping-stone for more pointed developments in antimicrobial therapy, especially with regard to quorum sensing – a target that will reduce resistance pressures imposed by traditional antibiotics.

Bacterial fingerprints across Europe

NARCIS (Netherlands)

Glasner, Corinna

2014-01-01

Bacterial pathogens, such as Staphylococcus aureus and carbapenemase-producing Enterobacteriaceae (CPE), impose major threats to human health worldwide. Both have a ‘Jekyll & Hyde’ character, since they can be present as human commensals, but can also become harmful invasive pathogens especially

Modeling of scale-dependent bacterial growth by chemical kinetics approach.

Science.gov (United States)

Martínez, Haydee; Sánchez, Joaquín; Cruz, José-Manuel; Ayala, Guadalupe; Rivera, Marco; Buhse, Thomas

2014-01-01

We applied the so-called chemical kinetics approach to complex bacterial growth patterns that were dependent on the liquid-surface-area-to-volume ratio (SA/V) of the bacterial cultures. The kinetic modeling was based on current experimental knowledge in terms of autocatalytic bacterial growth, its inhibition by the metabolite CO2, and the relief of inhibition through the physical escape of the inhibitor. The model quantitatively reproduces kinetic data of SA/V-dependent bacterial growth and can discriminate between differences in the growth dynamics of enteropathogenic E. coli, E. coli JM83, and Salmonella typhimurium on one hand and Vibrio cholerae on the other hand. Furthermore, the data fitting procedures allowed predictions about the velocities of the involved key processes and the potential behavior in an open-flow bacterial chemostat, revealing an oscillatory approach to the stationary states.

Modeling of Scale-Dependent Bacterial Growth by Chemical Kinetics Approach

Directory of Open Access Journals (Sweden)

Haydee Martínez

2014-01-01

Full Text Available We applied the so-called chemical kinetics approach to complex bacterial growth patterns that were dependent on the liquid-surface-area-to-volume ratio (SA/V of the bacterial cultures. The kinetic modeling was based on current experimental knowledge in terms of autocatalytic bacterial growth, its inhibition by the metabolite CO2, and the relief of inhibition through the physical escape of the inhibitor. The model quantitatively reproduces kinetic data of SA/V-dependent bacterial growth and can discriminate between differences in the growth dynamics of enteropathogenic E. coli, E. coli  JM83, and Salmonella typhimurium on one hand and Vibrio cholerae on the other hand. Furthermore, the data fitting procedures allowed predictions about the velocities of the involved key processes and the potential behavior in an open-flow bacterial chemostat, revealing an oscillatory approach to the stationary states.

More than 9,000,000 unique genes in human gut bacterial community: estimating gene numbers inside a human body.

Science.gov (United States)

Yang, Xing; Xie, Lu; Li, Yixue; Wei, Chaochun

2009-06-29

Estimating the number of genes in human genome has been long an important problem in computational biology. With the new conception of considering human as a super-organism, it is also interesting to estimate the number of genes in this human super-organism. We presented our estimation of gene numbers in the human gut bacterial community, the largest microbial community inside the human super-organism. We got 552,700 unique genes from 202 complete human gut bacteria genomes. Then, a novel gene counting model was built to check the total number of genes by combining culture-independent sequence data and those complete genomes. 16S rRNAs were used to construct a three-level tree and different counting methods were introduced for the three levels: strain-to-species, species-to-genus, and genus-and-up. The model estimates that the total number of genes is about 9,000,000 after those with identity percentage of 97% or up were merged. By combining completed genomes currently available and culture-independent sequencing data, we built a model to estimate the number of genes in human gut bacterial community. The total number of genes is estimated to be about 9 million. Although this number is huge, we believe it is underestimated. This is an initial step to tackle this gene counting problem for the human super-organism. It will still be an open problem in the near future. The list of genomes used in this paper can be found in the supplementary table.

Ice formation and growth shape bacterial community structure in Baltic Sea drift ice.

Science.gov (United States)

Eronen-Rasimus, Eeva; Lyra, Christina; Rintala, Janne-Markus; Jürgens, Klaus; Ikonen, Vilma; Kaartokallio, Hermanni

2015-02-01

Drift ice, open water and under-ice water bacterial communities covering several developmental stages from open water to thick ice were studied in the northern Baltic Sea. The bacterial communities were assessed with 16S rRNA gene terminal-restriction fragment length polymorphism and cloning, together with bacterial abundance and production measurements. In the early stages, open water and pancake ice were dominated by Alphaproteobacteria and Actinobacteria, which are common bacterial groups in Baltic Sea wintertime surface waters. The pancake ice bacterial communities were similar to the open-water communities, suggesting that the parent water determines the sea-ice bacterial community in the early stages of sea-ice formation. In consolidated young and thick ice, the bacterial communities were significantly different from water bacterial communities as well as from each other, indicating community development in Baltic Sea drift ice along with ice-type changes. The thick ice was dominated by typical sea-ice genera from classes Flavobacteria and Gammaproteobacteria, similar to those in polar sea-ice bacterial communities. Since the thick ice bacterial community was remarkably different from that of the parent seawater, results indicate that thick ice bacterial communities were recruited from the rarer members of the seawater bacterial community. © FEMS 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Bacterial Cellulose Production from Industrial Waste and by-Product Streams.

Science.gov (United States)

Tsouko, Erminda; Kourmentza, Constantina; Ladakis, Dimitrios; Kopsahelis, Nikolaos; Mandala, Ioanna; Papanikolaou, Seraphim; Paloukis, Fotis; Alves, Vitor; Koutinas, Apostolis

2015-07-01

The utilization of fermentation media derived from waste and by-product streams from biodiesel and confectionery industries could lead to highly efficient production of bacterial cellulose. Batch fermentations with the bacterial strain Komagataeibacter sucrofermentans DSM (Deutsche Sammlung von Mikroorganismen) 15973 were initially carried out in synthetic media using commercial sugars and crude glycerol. The highest bacterial cellulose concentration was achieved when crude glycerol (3.2 g/L) and commercial sucrose (4.9 g/L) were used. The combination of crude glycerol and sunflower meal hydrolysates as the sole fermentation media resulted in bacterial cellulose production of 13.3 g/L. Similar results (13 g/L) were obtained when flour-rich hydrolysates produced from confectionery industry waste streams were used. The properties of bacterial celluloses developed when different fermentation media were used showed water holding capacities of 102-138 g · water/g · dry bacterial cellulose, viscosities of 4.7-9.3 dL/g, degree of polymerization of 1889.1-2672.8, stress at break of 72.3-139.5 MPa and Young's modulus of 0.97-1.64 GPa. This study demonstrated that by-product streams from the biodiesel industry and waste streams from confectionery industries could be used as the sole sources of nutrients for the production of bacterial cellulose with similar properties as those produced with commercial sources of nutrients.

High level bacterial contamination of secondary school students' mobile phones.

Science.gov (United States)

Kõljalg, Siiri; Mändar, Rando; Sõber, Tiina; Rööp, Tiiu; Mändar, Reet

2017-06-01

While contamination of mobile phones in the hospital has been found to be common in several studies, little information about bacterial abundance on phones used in the community is available. Our aim was to quantitatively determine the bacterial contamination of secondary school students' mobile phones. Altogether 27 mobile phones were studied. The contact plate method and microbial identification using MALDI-TOF mass spectrometer were used for culture studies. Quantitative PCR reaction for detection of universal 16S rRNA, Enterococcus faecalis 16S rRNA and Escherichia coli allantoin permease were performed, and the presence of tetracycline ( tet A, tet B, tet M), erythromycin ( erm B) and sulphonamide ( sul 1) resistance genes was assessed. We found a high median bacterial count on secondary school students' mobile phones (10.5 CFU/cm 2 ) and a median of 17,032 bacterial 16S rRNA gene copies per phone. Potentially pathogenic microbes ( Staphylococcus aureus , Acinetobacter spp. , Pseudomonas spp., Bacillus cereus and Neisseria flavescens ) were found among dominant microbes more often on phones with higher percentage of E. faecalis in total bacterial 16S rRNA. No differences in contamination level or dominating bacterial species between phone owner's gender and between phone types (touch screen/keypad) were found. No antibiotic resistance genes were detected on mobile phone surfaces. Quantitative study methods revealed high level bacterial contamination of secondary school students' mobile phones.

Bacterial diversity at different stages of the composting process

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Paulin Lars

2010-03-01

Full Text Available Abstract Background Composting is an aerobic microbiological process that is facilitated by bacteria and fungi. Composting is also a method to produce fertilizer or soil conditioner. Tightened EU legislation now requires treatment of the continuously growing quantities of organic municipal waste before final disposal. However, some full-scale composting plants experience difficulties with the efficiency of biowaste degradation and with the emission of noxious odours. In this study we examine the bacterial species richness and community structure of an optimally working pilot-scale compost plant, as well as a full-scale composting plant experiencing typical problems. Bacterial species composition was determined by isolating total DNA followed by amplifying and sequencing the gene encoding the 16S ribosomal RNA. Results Over 1500 almost full-length 16S rRNA gene sequences were analysed and of these, over 500 were present only as singletons. Most of the sequences observed in either one or both of the composting processes studied here were similar to the bacterial species reported earlier in composts, including bacteria from the phyla Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria and Deinococcus-Thermus. In addition, a number of previously undetected bacterial phylotypes were observed. Statistical calculations estimated a total bacterial diversity of over 2000 different phylotypes in the studied composts. Conclusions Interestingly, locally enriched or evolved bacterial variants of familiar compost species were observed in both composts. A detailed comparison of the bacterial diversity revealed a large difference in composts at the species and strain level from the different composting plants. However, at the genus level, the difference was much smaller and illustrated a delay of the composting process in the full-scale, sub-optimally performing plants.

Combination of therapeutic ultrasound with antibiotics interfere with the growth of bacterial culture that colonizes skin ulcers: An in-vitro study.

Science.gov (United States)

Guirro, Elaine Caldeira de Oliveira; Angelis, Dejanira de Franceschi de; Sousa, Natanael Teixeira Alves de; Guirro, Rinaldo Roberto de Jesus

2016-09-01

Staphylococcus aureus and Escherichia coli are among the major bacterial species that colonize skin ulcers. Therapeutic ultrasound (TUS) produces biophysical effects that are relevant to wound healing; however, its application over a contaminated injury is not evidence-based. The objective of this research was to analyze the effect of TUS on in vitro-isolated S. aureus and E. coli, including the combination of ultrasound and antibiotics, in order to assess their antibiotic action on bacterial susceptibility. For the experiments, the bacterial strains were suspended in saline, then diluted (10(4)CFU/mL) for irradiation (at 1 and 3MHz, 0.5 and 0.8W/cm(2) for 0 and 15min) and the combination treatment of ultrasonication and antibiotics was administered by adding nalidixic acid (S. aureus) and tetracycline (E. coli) at concentrations equivalent to 50% of the minimum inhibitory concentration (MIC). The experiments were carried out in duplicate with six repetitions. The suspensions were inoculated on to Petri plates and incubated at 37°C and the colony forming units (CFUs) were counted after 24h. The results were subjected to the Shapiro-Wilk normality test, followed by parametric ANOVA and Tukey's post hoc test at a significance level of 1%. The results demonstrated that the action of TUS at 1MHz inhibited bacterial growth while at 3MHz, bacterial growth was observed in both species. However, the synergistic combination of ultrasound and antibiotics was able to inhibit the growth of both bacteria completely after 15min of ultrasonication. The results suggest that the action of ultrasound on S. aureus and E. coli are dependent on the oscillation frequency as well as the intensity and time of application. The combination of ultrasound with antibiotics was able to inhibit bacterial growth fully at all frequencies and doses in both species. Copyright © 2016 Elsevier B.V. All rights reserved.

New Parameters to Quantitatively Express the Invasiveness of Bacterial Strains from Implant-Related Orthopaedic Infections into Osteoblast Cells.

Science.gov (United States)

Campoccia, Davide; Montanaro, Lucio; Ravaioli, Stefano; Cangini, Ilaria; Testoni, Francesca; Visai, Livia; Arciola, Carla Renata

2018-04-03

Complete eradication of bacterial infections is often a challenging task, especially in presence of prosthetic devices. Invasion of non-phagocytic host cells appears to be a critical mechanism of microbial persistence in host tissues. Hidden within host cells, bacteria elude host defences and antibiotic treatments that are intracellularly inactive. The intracellular invasiveness of bacteria is generally measured by conventional gentamicin protection assays. The efficiency of invasion, however, markedly differs across bacterial species and adjustments to the titre of the microbial inocula used in the assays are often needed to enumerate intracellular bacteria. Such changes affect the standardisation of the method and hamper a direct comparison of bacteria on a same scale. This study aims at investigating the precise relation between inoculum, in terms of multiplicity of infection (MOI), and internalised bacteria. The investigation included nine Staphylococcus aureus , seven Staphylococcus epidermidis , five Staphylococcus lugdunensis and two Enterococcus faecalis clinical strains, which are co-cultured with MG63 human osteoblasts. Unprecedented insights are offered on the relations existing between MOI, number of internalised bacteria and per cent of internalised bacteria. New parameters are identified that are of potential use for qualifying the efficiency of internalization and compare the behaviour of bacterial strains.

New Parameters to Quantitatively Express the Invasiveness of Bacterial Strains from Implant-Related Orthopaedic Infections into Osteoblast Cells

Directory of Open Access Journals (Sweden)

Davide Campoccia

2018-04-01

Full Text Available Complete eradication of bacterial infections is often a challenging task, especially in presence of prosthetic devices. Invasion of non-phagocytic host cells appears to be a critical mechanism of microbial persistence in host tissues. Hidden within host cells, bacteria elude host defences and antibiotic treatments that are intracellularly inactive. The intracellular invasiveness of bacteria is generally measured by conventional gentamicin protection assays. The efficiency of invasion, however, markedly differs across bacterial species and adjustments to the titre of the microbial inocula used in the assays are often needed to enumerate intracellular bacteria. Such changes affect the standardisation of the method and hamper a direct comparison of bacteria on a same scale. This study aims at investigating the precise relation between inoculum, in terms of multiplicity of infection (MOI, and internalised bacteria. The investigation included nine Staphylococcus aureus, seven Staphylococcus epidermidis, five Staphylococcus lugdunensis and two Enterococcus faecalis clinical strains, which are co-cultured with MG63 human osteoblasts. Unprecedented insights are offered on the relations existing between MOI, number of internalised bacteria and per cent of internalised bacteria. New parameters are identified that are of potential use for qualifying the efficiency of internalization and compare the behaviour of bacterial strains.

Novel Bacterial Proteins and Lipids Reveal the Diversity of Triterpenoid Biomarker Synthesis

Science.gov (United States)

Wei, J. H.; Banta, A. B.; Gill, C. C. C.; Giner, J. L.; Welander, P. V.

2017-12-01

Lipids preserved in sediments and rocks function as organic biomarkers providing evidence for the types of organisms that lived in ancient environments. We use a combined approach utilizing comparative genomics, molecular biology, and lipid analysis to discover novel cyclic triteprenoid lipids and their biosynthetic pathways in bacteria. Here, we present two cases of bacterial synthesis of pentacylic triterpenols previously thought to be indicative of eukaryotes, which address current incongruities in the fossil record. Cyclic triterpenoid lipids, such as hopanoids and sterols, are generally associated with bacteria and eukaryotes, respectively. The pentacyclic triterpenoid tetrahymanol, first discovered in the ciliate Tetrahymena pyriformis, and its diagenetic product gammacerane, have been previously interpreted as markers for eukaryotes and linked to water column stratification. Yet the occurrence of tetrahymanol in bacteria implies our knowledge of extant tetrahymanol producers is not complete. Through comparative genomics we identified a new gene required for tetrahymanol synthesis in the bacterium Methylomicrobium alcaliphilum. This gene encodes a novel enzyme, Tetrahymanol synthase (THS), that synthesizes tetrahymanol from the hopanoid diploptene demonstrating a pathway for tetrahymanol production in bacteria distinct from that in eukaryotes. We bionformatically identified THS homologs in 104 bacterial genomes and 472 metagenomes, implying a great diversity of tetrahymanol producers. Lipids of the arborane class, such as iso-arborinol, are commonly found in modern angiosperms. Arobranes are synthesized by the enzyme oxidosqualene cyclase (OSC), which in plants can form both tetra and pentacyclic molecules. While bacteria are known to produce tetracyclic sterol compounds, bacterial synthesis of pentacyclic arborane class triterpenols of this class were previously undiscovered. We have identified a bacterium, Eudoraea adriatica, whose OSC synthesizes

Alternatives to overcoming bacterial resistances: State-of-the-art.

Science.gov (United States)

Rios, Alessandra C; Moutinho, Carla G; Pinto, Flávio C; Del Fiol, Fernando S; Jozala, Angela; Chaud, Marco V; Vila, Marta M D C; Teixeira, José A; Balcão, Victor M

2016-10-01

Worldwide, bacterial resistance to chemical antibiotics has reached such a high level that endangers public health. Presently, the adoption of alternative strategies that promote the elimination of resistant microbial strains from the environment is of utmost importance. This review discusses and analyses several (potential) alternative strategies to current chemical antibiotics. Bacteriophage (or phage) therapy, although not new, makes use of strictly lytic phage particles as an alternative, or a complement, in the antimicrobial treatment of bacterial infections. It is being rediscovered as a safe method, because these biological entities devoid of any metabolic machinery do not possess any affinity whatsoever to eukaryotic cells. Lysin therapy is also recognized as an innovative antimicrobial therapeutic option, since the topical administration of preparations containing purified recombinant lysins with amounts in the order of nanograms, in infections caused by Gram-positive bacteria, demonstrated a high therapeutic potential by causing immediate lysis of the target bacterial cells. Additionally, this therapy exhibits the potential to act synergistically when combined with certain chemical antibiotics already available on the market. Another potential alternative antimicrobial therapy is based on the use of antimicrobial peptides (AMPs), amphiphilic polypeptides that cause disruption of the bacterial membrane and can be used in the treatment of bacterial, fungal and viral infections, in the prevention of biofilm formation, and as antitumoral agents. Interestingly, bacteriocins are a common strategy of bacterial defense against other bacterial agents, eliminating the potential opponents of the former and increasing the number of available nutrients in the environment for their own growth. They can be applied in the food industry as biopreservatives and as probiotics, and also in fighting multi-resistant bacterial strains. The use of antibacterial antibodies

Carbon nanotubes as anti-bacterial agents.

Science.gov (United States)

Mocan, Teodora; Matea, Cristian T; Pop, Teodora; Mosteanu, Ofelia; Buzoianu, Anca Dana; Suciu, Soimita; Puia, Cosmin; Zdrehus, Claudiu; Iancu, Cornel; Mocan, Lucian

2017-10-01

Multidrug-resistant bacterial infections that have evolved via natural selection have increased alarmingly at a global level. Thus, there is a strong need for the development of novel antibiotics for the treatment of these infections. Functionalized carbon nanotubes through their unique properties hold great promise in the fight against multidrug-resistant bacterial infections. This new family of nanovectors for therapeutic delivery proved to be innovative and efficient for the transport and cellular translocation of therapeutic molecules. The current review examines the latest progress in the antibacterial activity of carbon nanotubes and their composites.

21 CFR 868.5260 - Breathing circuit bacterial filter.

Science.gov (United States)

2010-04-01

... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Breathing circuit bacterial filter. 868.5260 Section 868.5260 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES... filter. (a) Identification. A breathing circuit bacterial filter is a device that is intended to remove...

Binding and entry of DNA in bacterial transformation

Energy Technology Data Exchange (ETDEWEB)

Lacks, S.A.

1976-01-01

Bacterial transformation in relation to DNA transport and competence in Streptococcus pneumoniae (also called Diplococcus pneumoniae) is discussed. This species will serve as a model with which to compare transformation in other bacterial species, particularly Bacillus subtilis and Haemophilus influenzae, with emphasis on the many similarities as well as differences.

Heme Synthesis and Acquisition in Bacterial Pathogens

OpenAIRE

Choby, Jacob E.; Skaar, Eric P.

2016-01-01

Bacterial pathogens require the iron-containing cofactor heme to cause disease. Heme is essential to the function of hemoproteins, which are involved in energy generation by the electron transport chain, detoxification of host immune effectors, and other processes. During infection, bacterial pathogens must synthesize heme or acquire heme from the host; however, host heme is sequestered in high-affinity hemoproteins. Pathogens have evolved elaborate strategies to acquire heme from host source...

Bacterial Vaginosis Presence in Sexually Active Women in Tuzla Canton Area

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Fatima Numanović

2008-11-01

Full Text Available The goal of our research was to determine the presence of bacterial vaginosis in sexually active women in Tuzla Canton area. Diagnosis determination for bacterial vaginosis was conducted on the basis of three out of four internationally accepted criteria according to Amsel and isolation and identification of Gard- nerella vaginalis (G. vaginalis by standard microbiological procedures. Bacterial vaginosis was diagnosed in 20,5 % (41/200 women who asked for gynaecologist’s help due to their personal discomfort, since significantly higher percentage of diagnosed bacterial vaginosis of 48,80% (41/84 was determined in women with personal discomfort typical for this disease. All relevant factors, according to available literature, for genesis of bacterial vaginosis were processed in this research. In respect to the obtained outputs, bacterial vaginosis is significantly more frequent occurrence in women who are not married, since the number of sexual partners, the time of the first sexual intercourse, the use of intrauterine contraceptive device and smoking do not cause the genesis of bacterial vaginosis. According to Nugent, an increased vaginal discharge with unpleasant odour after sexual discourse, its pH>4,5, a positive amino odour test, an occurrence of clue cells in a direct microscopic concoction of vaginal discharge and assessment of the state of vaginal flora for bacterial vaginosis are significantly more frequent occurrences in women with individual discomforts. It was proved that G. vaginalisis a dominant micro organism in 95% of women with clinical signs of vaginosis although it was isolated from vaginal discharge in 40 to 50% of healthy women. In our research, G. vaginalis was isolated in 63,41% of examined women with all signs of bacterial vaginosis, in 36,59% of examined women with one or more clinical signs of bacterial vaginosis and in 2,58% of examined women of control group without clinical signs.

Polymorphism in Bacterial Flagella Suspensions

Science.gov (United States)

Schwenger, Walter J.

Bacterial flagella are a type of biological polymer studied for its role in bacterial motility and the polymorphic transitions undertaken to facilitate the run and tumble behavior. The naturally rigid, helical shape of flagella gives rise to novel colloidal dynamics and material properties. This thesis studies methods in which the shape of bacterial flagella can be controlled using in vitro methods and the changes the shape of the flagella have on both single particle dynamics and bulk material properties. We observe individual flagellum in both the dilute and semidilute regimes to observe the effects of solvent condition on the shape of the filament as well as the effect the filament morphology has on reptation through a network of flagella. In addition, we present rheological measurements showing how the shape of filaments effects the bulk material properties of flagellar suspensions. We find that the individual particle dynamics in suspensions of flagella can vary with geometry from needing to reptate linearly via rotation for helical filaments to the prevention of long range diffusion for block copolymer filaments. Similarly, for bulk material properties of flagella suspensions, helical geometries show a dramatic enhancement in elasticity over straight filaments while block copolymers form an elastic gel without the aid of crosslinking agents.

Bacterial Communities Associated with the Lichen Symbiosis▿ †

Science.gov (United States)

Bates, Scott T.; Cropsey, Garrett W. G.; Caporaso, J. Gregory; Knight, Rob; Fierer, Noah

2011-01-01

Lichens are commonly described as a mutualistic symbiosis between fungi and “algae” (Chlorophyta or Cyanobacteria); however, they also have internal bacterial communities. Recent research suggests that lichen-associated microbes are an integral component of lichen thalli and that the classical view of this symbiotic relationship should be expanded to include bacteria. However, we still have a limited understanding of the phylogenetic structure of these communities and their variability across lichen species. To address these knowledge gaps, we used bar-coded pyrosequencing to survey the bacterial communities associated with lichens. Bacterial sequences obtained from four lichen species at multiple locations on rock outcrops suggested that each lichen species harbored a distinct community and that all communities were dominated by Alphaproteobacteria. Across all samples, we recovered numerous bacterial phylotypes that were closely related to sequences isolated from lichens in prior investigations, including those from a lichen-associated Rhizobiales lineage (LAR1; putative N2 fixers). LAR1-related phylotypes were relatively abundant and were found in all four lichen species, and many sequences closely related to other known N2 fixers (e.g., Azospirillum, Bradyrhizobium, and Frankia) were recovered. Our findings confirm the presence of highly structured bacterial communities within lichens and provide additional evidence that these bacteria may serve distinct functional roles within lichen symbioses. PMID:21169444

Diversity and abundance of the bacterial community of the red Macroalga Porphyra umbilicalis: did bacterial farmers produce macroalgae?

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Lilibeth N Miranda

Full Text Available Macroalgae harbor microbial communities whose bacterial biodiversity remains largely uncharacterized. The goals of this study were 1 to examine the composition of the bacterial community associated with Porphyra umbilicalis Kützing from Schoodic Point, ME, 2 determine whether there are seasonal trends in species diversity but a core group of bacteria that are always present, and 3 to determine how the microbial community associated with a laboratory strain (P.um.1 established in the presence of antibiotics has changed. P. umbilicalis blades (n = 5, fall 2010; n = 5, winter 2011; n = 2, clonal P.um.1 were analyzed by pyrosequencing over two variable regions of the 16 S rDNA (V5-V6 and V8; 147,880 total reads. The bacterial taxa present were classified at an 80% confidence threshold into eight phyla (Bacteroidetes, Proteobacteria, Planctomycetes, Chloroflexi, Actinobacteria, Deinococcus-Thermus, Firmicutes, and the candidate division TM7. The Bacteroidetes comprised the majority of bacterial sequences on both field and lab blades, but the Proteobacteria (Alphaproteobacteria, Gammaproteobacteria were also abundant. Sphingobacteria (Bacteroidetes and Flavobacteria (Bacteroidetes had inverse abundances on natural versus P.um.1 blades. Bacterial communities were richer and more diverse on blades sampled in fall compared to winter. Significant differences were observed between microbial communities among all three groups of blades examined. Only two OTUs were found on all 12 blades, and only one of these, belonging to the Saprospiraceae (Bacteroidetes, was abundant. Lewinella (as 66 OTUs was found on all field blades and was the most abundant genus. Bacteria from the Bacteroidetes, Proteobacteria and Planctomycetes that are known to digest the galactan sulfates of red algal cell walls were well-represented. Some of these taxa likely provide essential morphogenetic and beneficial nutritive factors to P. umbilicalis and may have had

Do Honeybees Shape the Bacterial Community Composition in Floral Nectar?

Science.gov (United States)

Aizenberg-Gershtein, Yana; Izhaki, Ido; Halpern, Malka

2013-01-01

Floral nectar is considered the most important reward animal-pollinated plants offer to attract pollinators. Here we explore whether honeybees, which act as pollinators, affect the composition of bacterial communities in the nectar. Nectar and honeybees were sampled from two plant species: Amygdalus communis and Citrus paradisi. To prevent the contact of nectar with pollinators, C. paradisi flowers were covered with net bags before blooming (covered flowers). Comparative analysis of bacterial communities in the nectar and on the honeybees was performed by the 454-pyrosequencing technique. No significant differences were found among bacterial communities in honeybees captured on the two different plant species. This resemblance may be due to the presence of dominant bacterial OTUs, closely related to the Arsenophonus genus. The bacterial communities of the nectar from the covered and uncovered C. paradisi flowers differed significantly; the bacterial communities on the honeybees differed significantly from those in the covered flowers’ nectar, but not from those in the uncovered flowers’ nectar. We conclude that the honeybees may introduce bacteria into the nectar and/or may be contaminated by bacteria introduced into the nectar by other sources such as other pollinators and nectar thieves. PMID:23844027

Bacteriophage-Based Bacterial Wilt Biocontrol for an Environmentally Sustainable Agriculture

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Belén Álvarez

2017-07-01

Full Text Available Bacterial wilt diseases caused by Ralstonia solanacearum, R. pseudosolanacearum, and R. syzygii subsp. indonesiensis (former R. solanacearum species complex are among the most important plant diseases worldwide, severely affecting a high number of crops and ornamentals. Difficulties of bacterial wilt control by non-biological methods are related to effectiveness, bacterial resistance and environmental impact. Alternatively, a great many biocontrol strategies have been carried out, with the advantage of being environmentally friendly. Advances in bacterial wilt biocontrol include an increasing interest in bacteriophage-based treatments as a promising re-emerging strategy. Bacteriophages against the bacterial wilt pathogens have been described with either lytic or lysogenic effect but, they were proved to be active against strains belonging to R. pseudosolanacearum and/or R. syzygii subsp. indonesiensis, not to the present R. solanacearum species, and only two of them demonstrated successful biocontrol potential in planta. Despite the publication of three patents on the topic, until now no bacteriophage-based product is commercially available. Therefore, there is still much to be done to incorporate valid bacteriophages in an integrated management program to effectively fight bacterial wilt in the field.

Bacteriophage-Based Bacterial Wilt Biocontrol for an Environmentally Sustainable Agriculture.

Science.gov (United States)

Álvarez, Belén; Biosca, Elena G

2017-01-01

Bacterial wilt diseases caused by Ralstonia solanacearum , R. pseudosolanacearum , and R. syzygii subsp. indonesiensis (former R. solanacearum species complex) are among the most important plant diseases worldwide, severely affecting a high number of crops and ornamentals. Difficulties of bacterial wilt control by non-biological methods are related to effectiveness, bacterial resistance and environmental impact. Alternatively, a great many biocontrol strategies have been carried out, with the advantage of being environmentally friendly. Advances in bacterial wilt biocontrol include an increasing interest in bacteriophage-based treatments as a promising re-emerging strategy. Bacteriophages against the bacterial wilt pathogens have been described with either lytic or lysogenic effect but, they were proved to be active against strains belonging to R. pseudosolanacearum and/or R. syzygii subsp. indonesiensis , not to the present R. solanacearum species, and only two of them demonstrated successful biocontrol potential in planta . Despite the publication of three patents on the topic, until now no bacteriophage-based product is commercially available. Therefore, there is still much to be done to incorporate valid bacteriophages in an integrated management program to effectively fight bacterial wilt in the field.

Isolation of the bacterial causes of tonsillitis in dogs

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B. Al-Mufti

2014-06-01

Full Text Available The study was performed to identify the bacterial causes of tonsillitis in dogs. Twelve clinical cases of dogs (5 males and 7 females of different ages and breeds were observed. Tonsils swabs were taken from all the dogs, then cultured on different agars and bacterial smears prepared from all cultures and Gram stains were done. The study confirmed that the most bacterial causes of tonsillitis in dogs were Escherichia coli, Staphylococcus aureus, Staphylococcus intermedius, Staphylococcus albus, Streptococcus pyogenes, Klebsiella spp. and Pasteurella spp.

Bacterial infection increases risk of carcinogenesis by targeting mitochondria

DEFF Research Database (Denmark)

Strickertsson, Jesper A.B.; Desler, Claus; Rasmussen, Lene Juel

2017-01-01

pathways, and compares the impact of the bacterial alteration of mitochondrial function to that of cancer. Bacterial virulence factors have been demonstrated to induce mutations of mitochondrial DNA (mtDNA) and to modulate DNA repair pathways of the mitochondria. Furthermore, virulence factors can induce...... or impair the intrinsic apoptotic pathway. The effect of bacterial targeting of mitochondria is analogous to behavior of mitochondria in a wide array of tumours, and this strongly suggests that mitochondrial targeting of bacteria is a risk factor for carcinogenesis....

Soil bacterial diversity in degraded and restored lands of Northeast Brazil.

Science.gov (United States)

Araújo, Ademir Sérgio Ferreira; Borges, Clovis Daniel; Tsai, Siu Mui; Cesarz, Simone; Eisenhauer, Nico

2014-11-01

Land degradation deteriorates biological productivity and affects environmental, social, and economic sustainability, particularly so in the semi-arid region of Northeast Brazil. Although some studies exist reporting gross measures of soil microbial parameters and processes, limited information is available on how land degradation and restoration strategies influence the diversity and composition of soil microbial communities. In this study we compare the structure and diversity of bacterial communities in degraded and restored lands in Northeast Brazil and determine the soil biological and chemical properties influencing bacterial communities. We found that land degradation decreased the diversity of soil bacteria as indicated by both reduced operational taxonomic unit (OTU) richness and Shannon index. Soils under native vegetation and restoration had significantly higher bacterial richness and diversity than degraded soils. Redundancy analysis revealed that low soil bacterial diversity correlated with a high respiratory quotient, indicating stressed microbial communities. By contrast, soil bacterial communities in restored land positively correlated with high soil P levels. Importantly, however, we found significant differences in the soil bacterial community composition under native vegetation and in restored land, which may indicate differences in their functioning despite equal levels of bacterial diversity.

Removal of Triphenylmethane Dyes by Bacterial Consortium

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Jihane Cheriaa

2012-01-01

Full Text Available A new consortium of four bacterial isolates (Agrobacterium radiobacter; Bacillus spp.; Sphingomonas paucimobilis, and Aeromonas hydrophila-(CM-4 was used to degrade and to decolorize triphenylmethane dyes. All bacteria were isolated from activated sludge extracted from a wastewater treatment station of a dyeing industry plant. Individual bacterial isolates exhibited a remarkable color-removal capability against crystal violet (50 mg/L and malachite green (50 mg/L dyes within 24 h. Interestingly, the microbial consortium CM-4 shows a high decolorizing percentage for crystal violet and malachite green, respectively, 91% and 99% within 2 h. The rate of chemical oxygen demand (COD removal increases after 24 h, reaching 61.5% and 84.2% for crystal violet and malachite green, respectively. UV-Visible absorption spectra, FTIR analysis and the inspection of bacterial cells growth indicated that color removal by the CM-4 was due to biodegradation. Evaluation of mutagenicity by using Salmonella typhimurium test strains, TA98 and TA100 studies revealed that the degradation of crystal violet and malachite green by CM-4 did not lead to mutagenic products. Altogether, these results demonstrated the usefulness of the bacterial consortium in the treatment of the textile dyes.

Assessing Bacterial Interactions Using Carbohydrate-Based Microarrays

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Andrea Flannery

2015-12-01

Full Text Available Carbohydrates play a crucial role in host-microorganism interactions and many host glycoconjugates are receptors or co-receptors for microbial binding. Host glycosylation varies with species and location in the body, and this contributes to species specificity and tropism of commensal and pathogenic bacteria. Additionally, bacterial glycosylation is often the first bacterial molecular species encountered and responded to by the host system. Accordingly, characterising and identifying the exact structures involved in these critical interactions is an important priority in deciphering microbial pathogenesis. Carbohydrate-based microarray platforms have been an underused tool for screening bacterial interactions with specific carbohydrate structures, but they are growing in popularity in recent years. In this review, we discuss carbohydrate-based microarrays that have been profiled with whole bacteria, recombinantly expressed adhesins or serum antibodies. Three main types of carbohydrate-based microarray platform are considered; (i conventional carbohydrate or glycan microarrays; (ii whole mucin microarrays; and (iii microarrays constructed from bacterial polysaccharides or their components. Determining the nature of the interactions between bacteria and host can help clarify the molecular mechanisms of carbohydrate-mediated interactions in microbial pathogenesis, infectious disease and host immune response and may lead to new strategies to boost therapeutic treatments.

Bacteriophage-Based Bacterial Wilt Biocontrol for an Environmentally Sustainable Agriculture

OpenAIRE

?lvarez, Bel?n; Biosca, Elena G.

2017-01-01

Bacterial wilt diseases caused by Ralstonia solanacearum, R. pseudosolanacearum, and R. syzygii subsp. indonesiensis (former R. solanacearum species complex) are among the most important plant diseases worldwide, severely affecting a high number of crops and ornamentals. Difficulties of bacterial wilt control by non-biological methods are related to effectiveness, bacterial resistance and environmental impact. Alternatively, a great many biocontrol strategies have been carried out, with the a...

Community-acquired bacterial meningitis

NARCIS (Netherlands)

van de Beek, Diederik; Brouwer, Matthijs; Hasbun, Rodrigo; Koedel, Uwe; Whitney, Cynthia G.; Wijdicks, Eelco

2016-01-01

Meningitis is an inflammation of the meninges and subarachnoid space that can also involve the brain cortex and parenchyma. It can be acquired spontaneously in the community - community-acquired bacterial meningitis - or in the hospital as a complication of invasive procedures or head trauma

Bacterial Cellulose Production from Industrial Waste and by-Product Streams

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Erminda Tsouko

2015-07-01

Full Text Available The utilization of fermentation media derived from waste and by-product streams from biodiesel and confectionery industries could lead to highly efficient production of bacterial cellulose. Batch fermentations with the bacterial strain Komagataeibacter sucrofermentans DSM (Deutsche Sammlung von Mikroorganismen 15973 were initially carried out in synthetic media using commercial sugars and crude glycerol. The highest bacterial cellulose concentration was achieved when crude glycerol (3.2 g/L and commercial sucrose (4.9 g/L were used. The combination of crude glycerol and sunflower meal hydrolysates as the sole fermentation media resulted in bacterial cellulose production of 13.3 g/L. Similar results (13 g/L were obtained when flour-rich hydrolysates produced from confectionery industry waste streams were used. The properties of bacterial celluloses developed when different fermentation media were used showed water holding capacities of 102–138 g·water/g·dry bacterial cellulose, viscosities of 4.7–9.3 dL/g, degree of polymerization of 1889.1–2672.8, stress at break of 72.3–139.5 MPa and Young’s modulus of 0.97–1.64 GPa. This study demonstrated that by-product streams from the biodiesel industry and waste streams from confectionery industries could be used as the sole sources of nutrients for the production of bacterial cellulose with similar properties as those produced with commercial sources of nutrients.

Bacterial contribution to iodine volatilization in the environment

Energy Technology Data Exchange (ETDEWEB)

Amachi, S; Kasahara, M; Fujii, T [Chiba Univ., Dept. of Bioresources Chemistry, Matsudo, Chiba (Japan); Muramatsu, Y [National Inst. of Radiological Sciences, Chiba (Japan)

2003-09-01

The roles of microorganisms in iodine volatilization from the environment were studied. More than 100 bacterial strains were isolated from various environments such as soils, seawater and marine sediments, and were examined their capacities for volatilizing iodine. Approximately 40% of these bacteria showed significant capacities for volatilizing iodine. Gas chromatographic determinations revealed that the chemical species of gaseous iodine is methyl iodide (CH{sub 3}I). Phylogenetic analysis based on 16S ribosomal DNA showed that these 'iodine-volatilizing bacteria' are widely distributed through the bacterial domain. The iodide-methylating reaction was mediated by an enzyme protein with S-adenosyl-L-methionine (SAM) as the methyl donor. We then estimated bacterial contribution to iodine volatilization from soils. Iodine in soils was volatilized mainly as CH{sub 3}I. CH{sub 3}I emission was enhanced in the presence of glucose or yeast extract, but was inhibited by autoclaving of soils. Little CH{sub 3}I was produced under anaerobic conditions. Furthermore, the addition of streptomycin and tetracycline, antibiotics which inhibit bacterial growth, strongly inhibited CH{sub 3}I emission, while a fungal inhibitor cycloheximide caused little effect. These results suggest that iodine in soils is volatilized as CH{sub 3}I mainly by the action of aerobic soil bacteria. Similar experiment was carried out by using sea water samples. The emission of iodine from sea waters occurred biologically, and bacterial (and also other microbial) contribution was confirmed. Our results suggest that iodine is methylated and volatilized into the atmosphere as a result of bacterial activities. Since bacteria are so abundant and widespread in the environments, they may significantly contribute to global iodine volatilization. This indicates that if {sup 129}I would be released from nuclear facilities, weapons testing or ground storage of nuclear wastes, the pathway of volatilization by

[Congenital skull base defect causing recurrent bacterial meningitis].

Science.gov (United States)

Berliner, Elihay; Bar Meir, Maskit; Megged, Orli

2012-08-01

Bacterial meningitis is a life threatening disease. Most patients will experience only one episode throughout life. Children who experience bacterial meningitis more than once, require further immunologic or anatomic evaluation. We report a 9 year old child with five episodes of bacterial meningitis due to a congenital defect of the skull base. A two and a half year old boy first presented to our medical center with pneumococcal meningitis. He was treated with antibiotics and fully recovered. Two months later he presented again with a similar clinical picture. Streptococcus pneumoniae grew in cerebrospinal fluid (CSF) culture. CT scan and later MRI of the brain revealed a defect in the anterior middle fossa floor, with protrusion of brain tissue into the sphenoidal sinus. Corrective surgery was recommended but the parents refused. Three months later, a third episode of pneumococcal meningitis occurred. The child again recovered with antibiotics and this time corrective surgery was performed. Five years later, the boy presented once again with clinical signs and symptoms consistent with bacterial meningitis. CSF culture was positive, but the final identification of the bacteria was conducted by broad spectrum 16S ribosomal RNA PCR (16S rRNA PCR) which revealed a sequence of Neisseria lactamica. CT and MRI showed recurrence of the skull base defect with encephalocele in the sphenoid sinus. The parents again refused neurosurgical intervention. A year later the patient presented with bacterial meningitis. CSF culture obtained after initiation of antibiotics was negative, but actinobacillus was identified in the CSF by 16S rRNA PCR. The patient is scheduled for neurosurgical intervention. In patients with recurrent bacterial meningitis caused by organisms colonizing the oropharynx or nasopharynx, an anatomical defect should be carefully sought and surgically repaired.

Bacterial Meningitis in Adults After Splenectomy and Hyposplenic States

NARCIS (Netherlands)

Adriani, Kirsten S.; Brouwer, Matthijs C.; van der Ende, Arie; van de Beek, Diederik

2013-01-01

Objective: To examine the occurrence, disease course, prognosis, and vaccination status of patients with community-acquired bacterial meningitis with a history of splenectomy or functional hyposplenia. Patients and Methods: Patients with bacterial meningitis proven by cerebrospinal fluid culture

Bacterial communities in the fruit bodies of ground basidiomycetes

Science.gov (United States)

Zagryadskaya, Yu. A.; Lysak, L. V.; Chernov, I. Yu.

2015-06-01

Fruit bodies of basidiomycetes at different stages of decomposition serve as specific habitats in forest biocenoses for bacteria and differ significantly with respect to the total bacterial population and abundance of particular bacterial genera. A significant increase in the total bacterial population estimated by the direct microscopic method with acridine orange staining and in the population of saprotrophic bacteria (inoculation of glucose peptone yeast agar) in fruit bodies of basidiomycetes Armillaria mellea and Coprinus comatus was recorded at the final stage of their decomposition in comparison with the initial stage. Gramnegative bacteria predominated in the tissues of fruit bodies at all the stages of decomposition and were represented at the final stage by the Aeromonas, Vibrio, and Pseudomonas genera (for fruit bodies of A. mellea) the Pseudomonas genus (for fruit bodies of C. comatus). The potential influence of bacterial communities in the fruit bodies of soil basidiomycetes on the formation of bacterial communities in the upper soil horizons in forest biocenoses is discussed. The loci connected with the development and decomposition of fruit bodies of basidiomycetes on the soil surface are promising for targeted search of Gram-negative bacteria, the important objects of biotechnology.

Bacterial growth in solar heating prepared and traditional tanks

International Nuclear Information System (INIS)

Bagh, L.K.

2000-01-01

In Denmark it has been put forward that the introduction of solar heating prepared tanks into the building regulation can cause increased nuisance with respect to bacterial growth in hot water for domestic use. The reason is that solar heating prepared tanks have a larger volume and another form of operation than traditional tanks. In this investigation the difference between bacterial growth in solar heating prepared and traditional tanks was measured by heterotrophic plate counts as a general parameter for microbiological growth. There was no significant difference between the bacterial number in the solar heating prepared tanks and in the traditional tanks, either for bacteria determined at 37 deg. C, 44 deg. C, 55 deg. C or at 65 deg. C. The hot water for domestic use from the solar heating prepared tanks and the traditional tanks had in most cases a bacterial number below 1.000 CFU/ml, and all tests had a bacterial number below 10.000 CFU/ml. The number of bacteria must be considered low seen in relation to the other measurements of bacteria in hot water for domestic use, particularly in larger block of flats. (au)

TBK1 protects vacuolar integrity during intracellular bacterial infection.

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Andrea L Radtke

2007-03-01

Full Text Available TANK-binding kinase-1 (TBK1 is an integral component of Type I interferon induction by microbial infection. The importance of TBK1 and Type I interferon in antiviral immunity is well established, but the function of TBK1 in bacterial infection is unclear. Upon infection of murine embryonic fibroblasts with Salmonella enterica serovar Typhimurium (Salmonella, more extensive bacterial proliferation was observed in tbk1(-/- than tbk1(+/+ cells. TBK1 kinase activity was required for restriction of bacterial infection, but interferon regulatory factor-3 or Type I interferon did not contribute to this TBK1-dependent function. In tbk1(-/-cells, Salmonella, enteropathogenic Escherichia coli, and Streptococcus pyogenes escaped from vacuoles into the cytosol where increased replication occurred, which suggests that TBK1 regulates the integrity of pathogen-containing vacuoles. Knockdown of tbk1 in macrophages and epithelial cells also resulted in increased bacterial localization in the cytosol, indicating that the role of TBK1 in maintaining vacuolar integrity is relevant in different cell types. Taken together, these data demonstrate a requirement for TBK1 in control of bacterial infection distinct from its established role in antiviral immunity.

TBK1 Protects Vacuolar Integrity during Intracellular Bacterial Infection

Science.gov (United States)

Radtke, Andrea L; Delbridge, Laura M; Balachandran, Siddharth; Barber, Glen N; O'Riordan, Mary X. D

2007-01-01

TANK-binding kinase-1 (TBK1) is an integral component of Type I interferon induction by microbial infection. The importance of TBK1 and Type I interferon in antiviral immunity is well established, but the function of TBK1 in bacterial infection is unclear. Upon infection of murine embryonic fibroblasts with Salmonella enterica serovar Typhimurium (Salmonella), more extensive bacterial proliferation was observed in tbk1−/− than tbk1+/+ cells. TBK1 kinase activity was required for restriction of bacterial infection, but interferon regulatory factor-3 or Type I interferon did not contribute to this TBK1-dependent function. In tbk1−/−cells, Salmonella, enteropathogenic Escherichia coli, and Streptococcus pyogenes escaped from vacuoles into the cytosol where increased replication occurred, which suggests that TBK1 regulates the integrity of pathogen-containing vacuoles. Knockdown of tbk1 in macrophages and epithelial cells also resulted in increased bacterial localization in the cytosol, indicating that the role of TBK1 in maintaining vacuolar integrity is relevant in different cell types. Taken together, these data demonstrate a requirement for TBK1 in control of bacterial infection distinct from its established role in antiviral immunity. PMID:17335348

Bacterial strain changes during chronic otitis media surgery.

Science.gov (United States)

Kim, G J; Yoo, S; Han, S; Bu, J; Hong, Y; Kim, D-K

2017-09-01

Cultures obtained from pre-operative middle-ear swabs from patients with chronic otitis media have traditionally been used to guide antibiotic selection. This study investigated changes in the bacterial strains of the middle ear during chronic otitis media surgery. Pre-operative bacterial cultures of otorrhoea, and peri-operative cultures of the granulation tissue in either the middle ear or mastoid cavity, were obtained. Post-operative cultures were selectively obtained when otorrhoea developed after surgery. Bacterial growth was observed in 45.5 per cent of pre-operative cultures, 13.5 per cent of peri-operative cultures and 4.5 per cent of post-operative cultures. Methicillin-resistant Staphylococcus aureus was identified as the most common bacteria in all pre-operative (32.4 per cent), peri-operative (52.4 per cent) and post-operative (71.4 per cent) tests, and the percentage of Methicillin-resistant S aureus increased from the pre- to the post-operative period. The bacterial culture results for post-operative otorrhoea showed low agreement with those for pre-operative or peri-operative culture, and strain re-identification was required.

A precise, efficient radiometric assay for bacterial growth

International Nuclear Information System (INIS)

Boonkitticharoen, V.; Ehrhardt, C.; Kirchner, P.T.

1984-01-01

The two-compartment radiometric assay for bacterial growth promised major advantages over systems in clinical use, but poor reproducibility and counting efficiency limited its application. In this method, 14-CO/sub 2/ produced by bacterial metabolism of C-14-glucose is trapped and counted on filter paper impregnated with NaOH and fluors. The authors sought to improve assay efficiency and precision through a systematic study of relevant physical and chemical factors. Improvements in efficiency (88% vs. 10%) and in precision (relative S.D. 5% vs. 40%) were produced by a) reversing growth medium and scintillator chambers to permit vigorous agitation, b) increasing NaOH quantity and using a supersaturated PPO solution and c) adding detergent to improve uniformity of NaOH-PPO mixture. Inoculum size, substrate concentration and O/sub 2/ transfer rate affected assay sensitivity but not bacterial growth rate. The authors' assay reliably detects bacterial growth for inocula of 10,000 organisms in 1 hour and for 25 organisms within 4 1/2 hours, thus surpassing other existing clinical and research methods

Evaluation of localized bacterial infection using radioisotope-labeled nucleosides imaging modality

Energy Technology Data Exchange (ETDEWEB)

Jang, Su Jin; Kang, Joo Hyun; Lee, Yong Jin; Lee, Tae Sup; Kim, Kwang Il; Lee, Kyo Chul; An, Gwang II; Cheon, Gi Jeong; Lim, Sang Moo [KIRAMS, Seoul (Korea, Republic of); Lim, Sang Yong [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

2011-10-15

Conventional diagnostic methods for infections are difficult to distinguish localized bacterial infections from sites of sterile inflammation. For this reason, the importance of developing methods to image bacterial infections is widely recognized. In this study to acquire bacterial infection imaging with radiolabeled nucleosides, in vitro bacterial thymidine kinase (tk) activities of Salmonella typhimurium with [{sup 18}F]FLT and [{sup 125}I]IVDU were measured and localized infections model in BALB/c mice was imaged with [{sup 18}F]FLT or [{sup 125}I]FIAU

Characterization of Halophilic Bacterial Communities in Turda Salt Mine (Romania)

Science.gov (United States)

Carpa, Rahela; Keul, Anca; Muntean, Vasile; Dobrotă, Cristina

2014-09-01

Halophilic organisms are having adaptations to extreme salinity, the majority of them being Archaean, which have the ability to grow at extremely high salt concentrations, (from 3 % to 35 %). Level of salinity causes natural fluctuations in the halophilic populations that inhabit this particular habitat, raising problems in maintaining homeostasis of the osmotic pressure. Samples such as salt and water taken from Turda Salt Mine were analyzed in order to identify the eco-physiological bacterial groups. Considering the number of bacteria of each eco-physiological group, the bacterial indicators of salt quality (BISQ) were calculated and studied for each sample. The phosphatase, catalase and dehydrogenases enzymatic activities were quantitatively determined and the enzymatic indicators of salt quality (EISQ) were calculated. Bacterial isolates were analyzed using 16S rRNA gene sequence analysis. Universal bacterial primers, targeting the consensus region of the bacterial 16S rRNA gene were used. Analysis of a large fragment, of 1499 bp was performed to improve discrimination at the species level.

Lateral Gene Transfer Dynamics in the Ancient Bacterial Genus Streptomyces

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Bradon R. McDonald

2017-06-01

Full Text Available Lateral gene transfer (LGT profoundly shapes the evolution of bacterial lineages. LGT across disparate phylogenetic groups and genome content diversity between related organisms suggest a model of bacterial evolution that views LGT as rampant and promiscuous. It has even driven the argument that species concepts and tree-based phylogenetics cannot be applied to bacteria. Here, we show that acquisition and retention of genes through LGT are surprisingly rare in the ubiquitous and biomedically important bacterial genus Streptomyces. Using a molecular clock, we estimate that the Streptomyces bacteria are ~380 million years old, indicating that this bacterial genus is as ancient as land vertebrates. Calibrating LGT rate to this geologic time span, we find that on average only 10 genes per million years were acquired and subsequently maintained. Over that same time span, Streptomyces accumulated thousands of point mutations. By explicitly incorporating evolutionary timescale into our analyses, we provide a dramatically different view on the dynamics of LGT and its impact on bacterial evolution.

Bacterial Communities in the Groundwater of Xikuangshan Antimony Mine, China

Science.gov (United States)

Wu, M.; Wang, H.; Wang, N.; Wang, M.

2017-12-01

Xikuangshan (XKS) is the biggest antimony (Sb) mine around the word, which causes serious environmental contamination due to the mining actives. To fully understand the bacterial compositions in the groundwater around the mining area in XKS and their correlation with environmental factors, groundwater samples were collected and subject to 16S rDNA high throughput sequencing. Results indicated that Proteobacteria (especially Gamma-Proteobacteria) dominated bacterial communities in high-Sb groundwater samples, whereas Bacteroidetes predominated in low-Sb groundwater. Furthermore, antimony concentration was found to be the most significant factor shaping bacterial communities (P=0.002) with an explanation of 9.16% of the variation. Other factors such as pH, contents of Mg, Ca and orthophosphate were also observed to significantly correlate with bacterial communities. This was the first report to show the important impact of Sb concentration on bacterial community structure in the groundwater in the mining area. Our results will enhance the understanding of subsurface biogeochemical processes mediated by microbes.

Airway fungal colonization compromises the immune system allowing bacterial pneumonia to prevail.

Science.gov (United States)

Roux, Damien; Gaudry, Stéphane; Khoy-Ear, Linda; Aloulou, Meryem; Phillips-Houlbracq, Mathilde; Bex, Julie; Skurnik, David; Denamur, Erick; Monteiro, Renato C; Dreyfuss, Didier; Ricard, Jean-Damien

2013-09-01

To study the correlation between fungal colonization and bacterial pneumonia and to test the effect of antifungal treatments on the development of bacterial pneumonia in colonized rats. Experimental animal investigation. University research laboratory. Pathogen-free male Wistar rats weighing 250-275 g. Rats were colonized by intratracheal instillation of Candida albicans. Fungal clearance from the lungs and immune response were measured. Both colonized and noncolonized animals were secondarily instilled with different bacterial species (Pseudomonas aeruginosa, Escherichia coli, or Staphylococcus aureus). Bacterial phagocytosis by alveolar macrophages was evaluated in the presence of interferon-gamma, the main cytokine produced during fungal colonization. The effect of antifungal treatments on fungal colonization and its immune response were assessed. The prevalence of P. aeruginosa pneumonia was compared in antifungal treated and control colonized rats. C. albicans was slowly cleared and induced a Th1-Th17 immune response with very high interferon-gamma concentrations. Airway fungal colonization favored the development of bacterial pneumonia. Interferon-gamma was able to inhibit the phagocytosis of unopsonized bacteria by alveolar macrophages. Antifungal treatment decreased airway fungal colonization, lung interferon-gamma levels and, consequently, the prevalence of subsequent bacterial pneumonia. C. albicans airway colonization elicited a Th1-Th17 immune response that favored the development of bacterial pneumonia via the inhibition of bacterial phagocytosis by alveolar macrophages. Antifungal treatment decreased the risk of bacterial pneumonia in colonized rats.

Incidence and Predictors of Bacterial infection in Febrile Children with Sickle Cell Disease.

Science.gov (United States)

Morrissey, Benita J; Bycroft, Thomas P; Almossawi, Ofran; Wilkey, Olufunke B; Daniels, Justin G

2015-01-01

Children with sickle cell disease are at increased risk of developing bacteremia and other serious bacterial infections. Fever is a common symptom in sickle cell disease and can also occur with sickle cell crises and viral infections. We aimed to evaluate the incidence and predictors of bacteremia and bacterial infection in children with sickle cell disease presenting with fever to a district hospital and sickle cell center in London. A retrospective analysis was performed on all attendances of children (aged under 16 years) with sickle cell disease presenting with a fever of 38.5 °C or higher over a 1-year period. Confirmed bacterial infection was defined as bacteremia, bacterial meningitis, urinary tract infection (UTI), pneumonia, osteomyelitis or other bacterial infection with positive identification of organism. Children were defined as having a suspected bacterial infection if a bacterial infection was suspected clinically, but no organism was identified. Over a 1-year period there were 88 episodes analyzed in 59 children. Bacteremia occurred in 3.4% of episodes and confirmed bacterial infection in 7.0%. Suspected bacterial infection occurred in 33.0%. One death occurred from Salmonella typhirium septicemia. C-reactive protein (CRP) level and white blood cell (WBC) count were both significantly associated with bacterial infection (p = 0.004 and 0.02, respectively.) In conclusion, bacterial infections continue to be a significant problem in children with sickle cell disease. C-reactive protein was significantly associated with bacterial infections, and could be included in clinical risk criteria for febrile children with sickle cell disease.

Automated DNA extraction from genetically modified maize using aminosilane-modified bacterial magnetic particles.

Science.gov (United States)

Ota, Hiroyuki; Lim, Tae-Kyu; Tanaka, Tsuyoshi; Yoshino, Tomoko; Harada, Manabu; Matsunaga, Tadashi

2006-09-18

A novel, automated system, PNE-1080, equipped with eight automated pestle units and a spectrophotometer was developed for genomic DNA extraction from maize using aminosilane-modified bacterial magnetic particles (BMPs). The use of aminosilane-modified BMPs allowed highly accurate DNA recovery. The (A(260)-A(320)):(A(280)-A(320)) ratio of the extracted DNA was 1.9+/-0.1. The DNA quality was sufficiently pure for PCR analysis. The PNE-1080 offered rapid assay completion (30 min) with high accuracy. Furthermore, the results of real-time PCR confirmed that our proposed method permitted the accurate determination of genetically modified DNA composition and correlated well with results obtained by conventional cetyltrimethylammonium bromide (CTAB)-based methods.

Drug Insight: adjunctive therapies in adults with bacterial meningitis

NARCIS (Netherlands)

van de Beek, Diederik; Weisfelt, Martijn; de Gans, Jan; Tunkel, Allan R.; Wijdicks, Eelco F. M.

2006-01-01

Despite the availability of effective antibiotics, mortality and morbidity rates associated with bacterial meningitis are high. Studies in animals have shown that bacterial lysis, induced by treatment with antibiotics, leads to inflammation in the subarachnoid space, which might contribute to an

In Situ Hydrocarbon Degradation by Indigenous Nearshore Bacterial Populations

International Nuclear Information System (INIS)

Cherrier, J.

2005-01-01

Potential episodic hydrocarbon inputs associated with oil mining and transportation together with chronic introduction of hydrocarbons via urban runoff into the relatively pristine coastal Florida waters poses a significant threat to Florida's fragile marine environment. It is therefore important to understand the extent to which indigenous bacterial populations are able to degrade hydrocarbon compounds and also determine factors that could potentially control and promote the rate at which these compounds are broken down in situ. Previous controlled laboratory experiments carried out by our research group demonstrated that separately both photo-oxidation and cometabolism stimulate bacterial hydrocarbon degradation by natural bacterial assemblages collected from a chronically petroleum contaminated site in Bayboro Bay, Florida. Additionally, we also demonstrated that stable carbon and radiocarbon abundances of respired CO 2 could be used to trace in situ hydrocarbon degradation by indigenous bacterial populations at this same site. This current proposal had two main objectives: (a) to evaluate the cumulative impact of cometabolism and photo-oxidation on hydrocarbon degradation by natural bacterial assemblages collected the same site in Bayboro Bay, Florida and (b) to determine if in situ hydrocarbon degradation by indigenous bacterial populations this site could be traced using natural radiocarbon and stable carbon abundances of assimilated bacterial carbon. Funds were used for 2 years of full support for one ESI Ph.D. student, April Croxton. To address our first objective a series of closed system bacterial incubations were carried out using photo-oxidized petroleum and pinfish (i.e. cometabolite). Bacterial production of CO 2 was used as the indicator of hydrocarbon degradation and (delta) 13 C analysis of the resultant CO 2 was used to evaluate the source of the respired CO 2 (i.e. petroleum hydrocarbons or the pinfish cometabolite). Results from these time

Changes of Bacterial Diversity Depend on the Spoilage of Fresh Vegetables

Directory of Open Access Journals (Sweden)

Dong Hwan Lee

2011-04-01

Full Text Available Almost 10~30% of vegetables were discarded by the spoilage from farms to tables. After harvest, vegetables are often spoiled by a wide variety of microorganisms including many bacterial and fungal species. This investigation was conducted to extent the knowledge of relationship the spoilage of vegetables and the diversity of microbes. The total aerobic bacterial numbers in fresh lettuce, perilla leaf, and chicory were 2.6~2.7×106, 4.6×105, 1.2×106 CFU/g of fresh weight, respectively. The most common bacterial species were Pseudomonas spp., Alysiella spp., and Burkholderia spp., and other 18 more genera were involved in. After one week of incubation of those vegetables at 28℃, the microbial diversity had been changed. The total aerobic bacterial numbers increased to 1.1~4.6×108, 4.9×107, and 7.6×108 CFU/g of fresh weight for lettuce, perilla leaf, and chicory that is about 102 times increased bacterial numbers than that before spoilage. However, the diversity of microbes isolated had been simplified and fewer bacterial species had been isolated. The most bacterial population (~48% was taken up by Pseudomonas spp., and followed by Arthrobacter spp. and Bacillus spp. The spoilage activity of individual bacterial isolates had been tested using axenic lettuce plants. Among tested isolates, Pseudomonas fluorescence and Pantoea agglomerans caused severe spoilage on lettuce.

Evaluating the effects of variable water chemistry on bacterial transport during infiltration.

Science.gov (United States)

Zhang, Haibo; Nordin, Nahjan Amer; Olson, Mira S

2013-07-01

Bacterial infiltration through the subsurface has been studied experimentally under different conditions of interest and is dependent on a variety of physical, chemical and biological factors. However, most bacterial transport studies fail to adequately represent the complex processes occurring in natural systems. Bacteria are frequently detected in stormwater runoff, and may present risk of microbial contamination during stormwater recharge into groundwater. Mixing of stormwater runoff with groundwater during infiltration results in changes in local solution chemistry, which may lead to changes in both bacterial and collector surface properties and subsequent bacterial attachment rates. This study focuses on quantifying changes in bacterial transport behavior under variable solution chemistry, and on comparing the influences of chemical variability and physical variability on bacterial attachment rates. Bacterial attachment rate at the soil-water interface was predicted analytically using a combined rate equation, which varies temporally and spatially with respect to changes in solution chemistry. Two-phase Monte Carlo analysis was conducted and an overall input-output correlation coefficient was calculated to quantitatively describe the importance of physiochemical variation on the estimates of attachment rate. Among physical variables, soil particle size has the highest correlation coefficient, followed by porosity of the soil media, bacterial size and flow velocity. Among chemical variables, ionic strength has the highest correlation coefficient. A semi-reactive microbial transport model was developed within HP1 (HYDRUS1D-PHREEQC) and applied to column transport experiments with constant and variable solution chemistries. Bacterial attachment rates varied from 9.10×10(-3)min(-1) to 3.71×10(-3)min(-1) due to mixing of synthetic stormwater (SSW) with artificial groundwater (AGW), while bacterial attachment remained constant at 9.10×10(-3)min(-1) in a constant

Interfering with bacterial gossip

DEFF Research Database (Denmark)

Bjarnsholt, Thomas; Tolker-Nielsen, Tim; Givskov, Michael

2011-01-01

that appropriately target bacteria in their relevant habitat with the aim of mitigating their destructive impact on patients. In this review we describe molecular mechanisms involved in “bacterial gossip” (more scientifically referred to as quorum sensing (QS) and c-di-GMP signaling), virulence, biofilm formation...

Vizantin inhibits bacterial adhesion without affecting bacterial growth and causes Streptococcus mutans biofilm to detach by altering its internal architecture.

Science.gov (United States)

Takenaka, Shoji; Oda, Masataka; Domon, Hisanori; Ohsumi, Tatsuya; Suzuki, Yuki; Ohshima, Hayato; Yamamoto, Hirofumi; Terao, Yutaka; Noiri, Yuichiro

2016-11-11

An ideal antibiofilm strategy is to control both in the quality and quantity of biofilm while maintaining the benefits derived from resident microflora. Vizantin, a recently developed immunostimulating compound, has also been found to have antibiofilm property. This study evaluated the influence on biofilm formation of Streptococcus mutans in the presence of sulfated vizantin and biofilm development following bacterial adhesion on a hydroxyapatite disc coated with sulfated vizantin. Supplementation with sulfated vizantin up to 50 μM did not affect either bacterial growth or biofilm formation, whereas 50 μM sulfated vizantin caused the biofilm to readily detach from the surface. Sulfated vizantin at the concentration of 50 μM upregulated the expression of the gtfB and gtfC genes, but downregulated the expression of the gtfD gene, suggesting altered architecture in the biofilm. Biofilm development on the surface coated with sulfated vizantin was inhibited depending on the concentration, suggesting prevention from bacterial adhesion. Among eight genes related to bacterial adherence in S. mutans, expression of gtfB and gtfC was significantly upregulated, whereas the expression of gtfD, GbpA and GbpC was downregulated according to the concentration of vizantin, especially with 50 μM vizantin by 0.8-, 0.4-, and 0.4-fold, respectively. These findings suggest that sulfated vizantin may cause structural degradation as a result of changing gene regulation related to bacterial adhesion and glucan production of S. mutans. Copyright © 2016 Elsevier Inc. All rights reserved.

Bacterial cellulose–kaolin nanocomposites for application as biomedical wound healing materials

International Nuclear Information System (INIS)

Wanna, Dwi; Alam, Parvez; Alam, Catharina; Toivola, Diana M

2013-01-01

This short communication provides preliminary experimental details on the structure–property relationships of novel biomedical kaolin–bacterial cellulose nanocomposites. Bacterial cellulose is an effective binding agent for kaolin particles forming reticulated structures at kaolin–cellulose interfaces and entanglements when the cellulose fraction is sufficiently high. The mechanical performance of these materials hence improves with an increased fraction of bacterial cellulose, though this also causes the rate of blood clotting to decrease. These composites have combined potential as both short-term (kaolin) and long-term (bacterial cellulose) wound healing materials. (paper)

Bacterial community diversity of the deep-sea octocoral Paramuricea placomus

Directory of Open Access Journals (Sweden)

Christina A. Kellogg

2016-09-01

Full Text Available Compared to tropical corals, much less is known about deep-sea coral biology and ecology. Although the microbial communities of some deep-sea corals have been described, this is the first study to characterize the bacterial community associated with the deep-sea octocoral, Paramuricea placomus. Samples from five colonies of P. placomus were collected from Baltimore Canyon (379–382 m depth in the Atlantic Ocean off the east coast of the United States of America. DNA was extracted from the coral samples and 16S rRNA gene amplicons were pyrosequenced using V4-V5 primers. Three samples sequenced deeply (>4,000 sequences each and were further analyzed. The dominant microbial phylum was Proteobacteria, but other major phyla included Firmicutes and Planctomycetes. A conserved community of bacterial taxa held in common across the three P. placomus colonies was identified, comprising 68–90% of the total bacterial community depending on the coral individual. The bacterial community of P. placomus does not appear to include the genus Endozoicomonas, which has been found previously to be the dominant bacterial associate in several temperate and tropical gorgonians. Inferred functionality suggests the possibility of nitrogen cycling by the core bacterial community.

Mapping and predictive variations of soil bacterial richness across France.

Science.gov (United States)

Terrat, Sébastien; Horrigue, Walid; Dequiedt, Samuel; Saby, Nicolas P A; Lelièvre, Mélanie; Nowak, Virginie; Tripied, Julie; Régnier, Tiffanie; Jolivet, Claudy; Arrouays, Dominique; Wincker, Patrick; Cruaud, Corinne; Karimi, Battle; Bispo, Antonio; Maron, Pierre Alain; Chemidlin Prévost-Bouré, Nicolas; Ranjard, Lionel

2017-01-01

Although numerous studies have demonstrated the key role of bacterial diversity in soil functions and ecosystem services, little is known about the variations and determinants of such diversity on a nationwide scale. The overall objectives of this study were i) to describe the bacterial taxonomic richness variations across France, ii) to identify the ecological processes (i.e. selection by the environment and dispersal limitation) influencing this distribution, and iii) to develop a statistical predictive model of soil bacterial richness. We used the French Soil Quality Monitoring Network (RMQS), which covers all of France with 2,173 sites. The soil bacterial richness (i.e. OTU number) was determined by pyrosequencing 16S rRNA genes and related to the soil characteristics, climatic conditions, geomorphology, land use and space. Mapping of bacterial richness revealed a heterogeneous spatial distribution, structured into patches of about 111km, where the main drivers were the soil physico-chemical properties (18% of explained variance), the spatial descriptors (5.25%, 1.89% and 1.02% for the fine, medium and coarse scales, respectively), and the land use (1.4%). Based on these drivers, a predictive model was developed, which allows a good prediction of the bacterial richness (R2adj of 0.56) and provides a reference value for a given pedoclimatic condition.

Plant innate immunity against human bacterial pathogens

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Maeli eMelotto

2014-08-01

Full Text Available Certain human bacterial pathogens such as the enterohemorrhagic Escherichia coli and Salmonella enterica are not proven to be plant pathogens yet. Nonetheless, under certain conditions they can survive on, penetrate into, and colonize internal plant tissues causing serious food borne disease outbreaks. In this review, we highlight current understanding on the molecular mechanisms of plant responses against human bacterial pathogens and discuss salient common and contrasting themes of plant interactions with phytopathogens or human pathogens.

Bacterial filamentation accelerates colonization of adhesive spots embedded in biopassive surfaces

International Nuclear Information System (INIS)

Möller, Jens; Emge, Philippe; Vizcarra, Ima Avalos; Kollmannsberger, Philip; Vogel, Viola

2013-01-01

Sessile bacteria adhere to engineered surfaces and host tissues and pose a substantial clinical and economical risk when growing into biofilms. Most engineered and biological interfaces are of chemically heterogeneous nature and provide adhesive islands for bacterial attachment and growth. To mimic either defects in a surface coating of biomedical implants or heterogeneities within mucosal layers (Peyer's patches), we embedded micrometre-sized adhesive islands in a poly(ethylene glycol) biopassive background. We show experimentally and computationally that filamentation of Escherichia coli can significantly accelerate the bacterial surface colonization under physiological flow conditions. Filamentation can thus provide an advantage to a bacterial population to bridge non-adhesive distances exceeding 5 μm. Bacterial filamentation, caused by blocking of bacterial division, is common among bacterial species and can be triggered by environmental conditions or antibiotic treatment. While great awareness exists that the build-up of antibiotic resistance serves as intrinsic survival strategy, we show here that antibiotic treatment can actually promote surface colonization by triggering filamentation, which in turn prevents daughter cells from being washed away. Our combined microfabrication and computational approaches provide quantitative insights into mechanisms that enable biofouling of biopassive surfaces with embedded adhesive spots, even for spot distances that are multiples of the bacterial length. (paper)

Bacterial filamentation accelerates colonization of adhesive spots embedded in biopassive surfaces

Science.gov (United States)

Möller, Jens; Emge, Philippe; Avalos Vizcarra, Ima; Kollmannsberger, Philip; Vogel, Viola

2013-12-01

Sessile bacteria adhere to engineered surfaces and host tissues and pose a substantial clinical and economical risk when growing into biofilms. Most engineered and biological interfaces are of chemically heterogeneous nature and provide adhesive islands for bacterial attachment and growth. To mimic either defects in a surface coating of biomedical implants or heterogeneities within mucosal layers (Peyer's patches), we embedded micrometre-sized adhesive islands in a poly(ethylene glycol) biopassive background. We show experimentally and computationally that filamentation of Escherichia coli can significantly accelerate the bacterial surface colonization under physiological flow conditions. Filamentation can thus provide an advantage to a bacterial population to bridge non-adhesive distances exceeding 5 μm. Bacterial filamentation, caused by blocking of bacterial division, is common among bacterial species and can be triggered by environmental conditions or antibiotic treatment. While great awareness exists that the build-up of antibiotic resistance serves as intrinsic survival strategy, we show here that antibiotic treatment can actually promote surface colonization by triggering filamentation, which in turn prevents daughter cells from being washed away. Our combined microfabrication and computational approaches provide quantitative insights into mechanisms that enable biofouling of biopassive surfaces with embedded adhesive spots, even for spot distances that are multiples of the bacterial length.

MIPS bacterial genomes functional annotation benchmark dataset.

Science.gov (United States)

Tetko, Igor V; Brauner, Barbara; Dunger-Kaltenbach, Irmtraud; Frishman, Goar; Montrone, Corinna; Fobo, Gisela; Ruepp, Andreas; Antonov, Alexey V; Surmeli, Dimitrij; Mewes, Hans-Wernen

2005-05-15

Any development of new methods for automatic functional annotation of proteins according to their sequences requires high-quality data (as benchmark) as well as tedious preparatory work to generate sequence parameters required as input data for the machine learning methods. Different program settings and incompatible protocols make a comparison of the analyzed methods difficult. The MIPS Bacterial Functional Annotation Benchmark dataset (MIPS-BFAB) is a new, high-quality resource comprising four bacterial genomes manually annotated according to the MIPS functional catalogue (FunCat). These resources include precalculated sequence parameters, such as sequence similarity scores, InterPro domain composition and other parameters that could be used to develop and benchmark methods for functional annotation of bacterial protein sequences. These data are provided in XML format and can be used by scientists who are not necessarily experts in genome annotation. BFAB is available at http://mips.gsf.de/proj/bfab

Spatial variation of bacterial community composition near the Luzon ...

African Journals Online (AJOL)

Spatial variation of bacterial community composition near the Luzon strait assessed by polymerase chain reaction-denaturing gradient gel electrophoresis ... chain reaction (PCR)-amplified bacterial 16S ribosomal deoxyribonucleic acid (DNA) gene fragments and interpreted the results; its relationship with physical and ...

Strategies for managing rival bacterial communities: Lessons from burying beetles.

Science.gov (United States)

Duarte, Ana; Welch, Martin; Swannack, Chris; Wagner, Josef; Kilner, Rebecca M

2018-03-01

The role of bacteria in animal development, ecology and evolution is increasingly well understood, yet little is known of how animal behaviour affects bacterial communities. Animals that benefit from defending a key resource from microbial competitors are likely to evolve behaviours to control or manipulate the animal's associated external microbiota. We describe four possible mechanisms by which animals could gain a competitive edge by disrupting a rival bacterial community: "weeding," "seeding," "replanting" and "preserving." By combining detailed behavioural observations with molecular and bioinformatic analyses, we then test which of these mechanisms best explains how burying beetles, Nicrophorus vespilloides, manipulate the bacterial communities on their carcass breeding resource. Burying beetles are a suitable species to study how animals manage external microbiota because reproduction revolves around a small vertebrate carcass. Parents shave a carcass and apply antimicrobial exudates on its surface, shaping it into an edible nest for their offspring. We compared bacterial communities in mice carcasses that were either fresh, prepared by beetles or unprepared but buried underground for the same length of time. We also analysed bacterial communities in the burying beetle's gut, during and after breeding, to understand whether beetles could be "seeding" the carcass with particular microbes. We show that burying beetles do not "preserve" the carcass by reducing bacterial load, as is commonly supposed. Instead, our results suggest they "seed" the carcass with bacterial groups which are part of the Nicrophorus core microbiome. They may also "replant" other bacteria from the carcass gut onto the surface of their carrion nest. Both these processes may lead to the observed increase in bacterial load on the carcass surface in the presence of beetles. Beetles may also "weed" the bacterial community by eliminating some groups of bacteria on the carcass, perhaps through

De novo generation of infectious prions with bacterially expressed recombinant prion protein.

Science.gov (United States)

Zhang, Zhihong; Zhang, Yi; Wang, Fei; Wang, Xinhe; Xu, Yuanyuan; Yang, Huaiyi; Yu, Guohua; Yuan, Chonggang; Ma, Jiyan

2013-12-01

The prion hypothesis is strongly supported by the fact that prion infectivity and the pathogenic conformer of prion protein (PrP) are simultaneously propagated in vitro by the serial protein misfolding cyclic amplification (sPMCA). However, due to sPMCA's enormous amplification power, whether an infectious prion can be formed de novo with bacterially expressed recombinant PrP (rPrP) remains to be satisfactorily resolved. To address this question, we performed unseeded sPMCA with rPrP in a laboratory that has never been exposed to any native prions. Two types of proteinase K (PK)-resistant and self-perpetuating recombinant PrP conformers (rPrP-res) with PK-resistant cores of 17 or 14 kDa were generated. A bioassay revealed that rPrP-res(17kDa) was highly infectious, causing prion disease in wild-type mice with an average survival time of about 172 d. In contrast, rPrP-res(14kDa) completely failed to induce any disease. Our findings reveal that sPMCA is sufficient to initiate various self-perpetuating PK-resistant rPrP conformers, but not all of them possess in vivo infectivity. Moreover, generating an infectious prion in a prion-free environment establishes that an infectious prion can be formed de novo with bacterially expressed rPrP.

p-topological Cauchy completions

Directory of Open Access Journals (Sweden)

J. Wig

1999-01-01

Full Text Available The duality between “regular” and “topological” as convergence space properties extends in a natural way to the more general properties “p-regular” and “p-topological.” Since earlier papers have investigated regular, p-regular, and topological Cauchy completions, we hereby initiate a study of p-topological Cauchy completions. A p-topological Cauchy space has a p-topological completion if and only if it is “cushioned,” meaning that each equivalence class of nonconvergent Cauchy filters contains a smallest filter. For a Cauchy space allowing a p-topological completion, it is shown that a certain class of Reed completions preserve the p-topological property, including the Wyler and Kowalsky completions, which are, respectively, the finest and the coarsest p-topological completions. However, not all p-topological completions are Reed completions. Several extension theorems for p-topological completions are obtained. The most interesting of these states that any Cauchy-continuous map between Cauchy spaces allowing p-topological and p′-topological completions, respectively, can always be extended to a θ-continuous map between any p-topological completion of the first space and any p′-topological completion of the second.