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Sample records for bacterial species identification

  1. Broad spectrum microarray for fingerprint-based bacterial species identification

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    Frey Jürg E

    2010-02-01

    Full Text Available Abstract Background Microarrays are powerful tools for DNA-based molecular diagnostics and identification of pathogens. Most target a limited range of organisms and are based on only one or a very few genes for specific identification. Such microarrays are limited to organisms for which specific probes are available, and often have difficulty discriminating closely related taxa. We have developed an alternative broad-spectrum microarray that employs hybridisation fingerprints generated by high-density anonymous markers distributed over the entire genome for identification based on comparison to a reference database. Results A high-density microarray carrying 95,000 unique 13-mer probes was designed. Optimized methods were developed to deliver reproducible hybridisation patterns that enabled confident discrimination of bacteria at the species, subspecies, and strain levels. High correlation coefficients were achieved between replicates. A sub-selection of 12,071 probes, determined by ANOVA and class prediction analysis, enabled the discrimination of all samples in our panel. Mismatch probe hybridisation was observed but was found to have no effect on the discriminatory capacity of our system. Conclusions These results indicate the potential of our genome chip for reliable identification of a wide range of bacterial taxa at the subspecies level without laborious prior sequencing and probe design. With its high resolution capacity, our proof-of-principle chip demonstrates great potential as a tool for molecular diagnostics of broad taxonomic groups.

  2. Identification of bacterial species by untargeted NMR spectroscopy of the exo-metabolome.

    Science.gov (United States)

    Palama, T L; Canard, I; Rautureau, G J P; Mirande, C; Chatellier, S; Elena-Herrmann, B

    2016-08-01

    Identification of bacterial species is a crucial bottleneck for clinical diagnosis of infectious diseases. Quick and reliable identification is a key factor to provide suitable antibiotherapies and avoid the development of multiple-drug resistance. We propose a novel nuclear magnetic resonance (NMR)-based metabolomics strategy for rapid discrimination and identification of several bacterial species that relies on untargeted metabolic profiling of supernatants from bacterial culture media. We show that six bacterial species (Gram negative: Escherichia coli, Pseudomonas aeruginosa, Proteus mirabilis; Gram positive: Enterococcus faecalis, Staphylococcus aureus, and Staphylococcus saprophyticus) can be well discriminated from multivariate statistical analysis, opening new prospects for NMR applications to microbial clinical diagnosis. PMID:27349704

  3. Raman microspectroscopy for species identification and mapping within bacterial biofilms

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    Beier, Brooke D; Quivey, Robert G.; Berger, Andrew J.

    2012-01-01

    A new method of mapping multiple species of oral bacteria in intact biofilms has been developed, using the optical technique of confocal Raman microscopy. A species classification algorithm, developed on dried biofilms, was used to analyze spectra of hydrated biofilms containing two microbial species central to dental health: Streptococcus sanguinis and Streptococcus mutans. The algorithm transferred successfully to the hydrated environment, correctly identifying the species of origin of sing...

  4. Confocal Raman microscopy for identification of bacterial species in biofilms

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    Beier, Brooke D.; Quivey, Robert G.; Berger, Andrew J.

    2011-03-01

    Implemented through a confocal microscope, Raman spectroscopy has been used to distinguish between biofilm samples of two common oral bacteria species, Streptococcus sanguinis and mutans, which are associated with healthy and cariogenic plaque, respectively. Biofilms of these species are studied as a model of dental plaque. A prediction model has been calibrated and validated using pure biofilms. This model has been used to identify the species of transferred and dehydrated samples (much like a plaque scraping) as well as hydrated biofilms in situ. Preliminary results of confocal Raman mapping of species in an intact two-species biofilm will be shown.

  5. Identification of different bacterial species in biofilms using confocal Raman microscopy

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    Beier, Brooke D.; Quivey, Robert G.; Berger, Andrew J.

    2010-11-01

    Confocal Raman microspectroscopy is used to discriminate between different species of bacteria grown in biofilms. Tests are performed using two bacterial species, Streptococcus sanguinis and Streptococcus mutans, which are major components of oral plaque and of particular interest due to their association with healthy and cariogenic plaque, respectively. Dehydrated biofilms of these species are studied as a simplified model of dental plaque. A prediction model based on principal component analysis and logistic regression is calibrated using pure biofilms of each species and validated on pure biofilms grown months later, achieving 96% accuracy in prospective classification. When biofilms of the two species are partially mixed together, Raman-based identifications are achieved within ~2 μm of the boundaries between species with 97% accuracy. This combination of spatial resolution and predication accuracy should be suitable for forming images of species distributions within intact two-species biofilms.

  6. Validation of hierarchical cluster analysis for identification of bacterial species using 42 bacterial isolates

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    Ghebremedhin, Meron; Yesupriya, Shubha; Luka, Janos; Crane, Nicole J.

    2015-03-01

    Recent studies have demonstrated the potential advantages of the use of Raman spectroscopy in the biomedical field due to its rapidity and noninvasive nature. In this study, Raman spectroscopy is applied as a method for differentiating between bacteria isolates for Gram status and Genus species. We created models for identifying 28 bacterial isolates using spectra collected with a 785 nm laser excitation Raman spectroscopic system. In order to investigate the groupings of these samples, partial least squares discriminant analysis (PLSDA) and hierarchical cluster analysis (HCA) was implemented. In addition, cluster analyses of the isolates were performed using various data types consisting of, biochemical tests, gene sequence alignment, high resolution melt (HRM) analysis and antimicrobial susceptibility tests of minimum inhibitory concentration (MIC) and degree of antimicrobial resistance (SIR). In order to evaluate the ability of these models to correctly classify bacterial isolates using solely Raman spectroscopic data, a set of 14 validation samples were tested using the PLSDA models and consequently the HCA models. External cluster evaluation criteria of purity and Rand index were calculated at different taxonomic levels to compare the performance of clustering using Raman spectra as well as the other datasets. Results showed that Raman spectra performed comparably, and in some cases better than, the other data types with Rand index and purity values up to 0.933 and 0.947, respectively. This study clearly demonstrates that the discrimination of bacterial species using Raman spectroscopic data and hierarchical cluster analysis is possible and has the potential to be a powerful point-of-care tool in clinical settings.

  7. BOX-PCR-based identification of bacterial species belonging to Pseudomonas syringae: P. viridiflava group

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    Abi S.A. Marques

    2008-01-01

    Full Text Available The phenotypic characteristics and genetic fingerprints of a collection of 120 bacterial strains, belonging to Pseudomonas syringae sensu lato group, P. viridiflava and reference bacteria were evaluated, with the aim of species identification. The numerical analysis of 119 nutritional characteristics did not show patterns that would help with identification. Regarding the genetic fingerprinting, the results of the present study supported the observation that BOX-PCR seems to be able to identify bacterial strains at species level. After numerical analyses of the bar-codes, all pathovars belonging to each one of the nine described genomospecies were clustered together at a distance of 0.72, and could be separated at genomic species level. Two P. syringae strains of unknown pathovars (CFBP 3650 and CFBP 3662 and the three P. syringae pv. actinidiae strains were grouped in two extra clusters and might eventually constitute two new species. This genomic species clustering was particularly evident for genomospecies 4, which gathered P. syringae pvs. atropurpurea, coronafaciens, garçae, oryzae, porri, striafaciens, and zizaniae at a noticeably low distance.

  8. Identification and ecology of bacterial communities associated with necroses of three cactus species.

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    Foster, J. L.; Fogleman, J C

    1993-01-01

    To compare the bacterial communities residing in necrotic tissues of columnar cacti of the Sonoran Desert, isolates from 39 organ pipe, 19 saguaro, and 16 senita cacti were obtained. The isolates were clustered into 28 conspecific groups on the basis of their fatty acid profiles. The distributions of the individual bacterial isolates varied among cactus species. Seven of the 28 species groups were unique to a particular cactus species, whereas 8 species groups were found in all three cacti. T...

  9. Identification of Household Bacterial Community and Analysis of Species Shared with Human Microbiome

    OpenAIRE

    Jeon, Yoon-Seong; Chun, Jongsik; Kim, Bong-Soo

    2013-01-01

    Microbial populations in indoor environments, where we live and eat, are important for public health. Various bacterial species reside in the kitchen, and refrigerators, the major means of food storage within kitchens, can be a direct source of food borne illness. Therefore, the monitoring of microbiota in the refrigerator is important for food safety. We investigated and compared bacterial communities that reside in the vegetable compartment of the refrigerator and on the seat of the toilet,...

  10. Identification of household bacterial community and analysis of species shared with human microbiome.

    Science.gov (United States)

    Jeon, Yoon-Seong; Chun, Jongsik; Kim, Bong-Soo

    2013-11-01

    Microbial populations in indoor environments, where we live and eat, are important for public health. Various bacterial species reside in the kitchen, and refrigerators, the major means of food storage within kitchens, can be a direct source of food borne illness. Therefore, the monitoring of microbiota in the refrigerator is important for food safety. We investigated and compared bacterial communities that reside in the vegetable compartment of the refrigerator and on the seat of the toilet, which is recognized as highly colonized by microorganisms, in ten houses using high-throughput sequencing. Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes were predominant in refrigerator and toilet samples. However, Proteobacteria was more abundant in the refrigerator, and Firmicutes was more abundant in the toilet. These household bacterial communities were compared with those of human skin and gut to identify potential sources of household bacteria. Bacterial communities from refrigerators and toilets shared more species in common with human skin than gut. Opportunistic pathogens, including Propionibacterium acnes, Bacteroides vulgatus, and Staphylococcus epidermidis, were identified as species shared with human skin and gut microbiota. This approach can provide a general background of the household microbiota and a potential method of source-tracking for public health purposes. PMID:23743600

  11. Isolation and identification of bacterial endophytes from pharmaceutical agarwood-producing Aquilaria species

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    Subhash J Bhore

    2013-01-01

    Full Text Available Background: Resins and gums are used in traditional medicine and do have potential applications in pharmacy and medicine. Agarwood is the fragrant resinous wood, which is an important commodity from Aquilaria species and has been used as a sedative, analgesic, and digestive in traditional medicine. Endophytic bacteria are potentially important in producing pharmaceutical compounds found in the plants. Hence, it was important to understand which types of endophytic bacteria are associated with pharmaceutical agarwood-producing Aquilaria species. Objective: This study was undertaken to isolate and identify endophytic bacteria associated with agarwood-producing seven (7 Aquilaria species from Malaysia. Materials and Methods: Botanical samples of seven Aquilaria species were collected, and endophytic bacteria were isolated from surface-sterilized-tissue samples. The 16S rRNA gene fragments were amplified using PCR method, and endophytic bacterial isolates (EBIs were identified based on 16S rRNA gene sequence similarity based method. Results: Culturable, 77 EBIs were analyzed, and results of 16S rRNA gene sequences analysis suggest that 18 different types of endophytic bacteria are associated with (seven Aquilaria species. From 77 EBIs, majority (36.4% of the isolates were of Bacillus pumilus. Conclusion: These findings indicate that agarwood-producing Aquilaria species are harboring 18 different types of culturable endophytic bacteria.

  12. Identification of beta-subunit of bacterial RNA-polymerase--a non-species-specific bacterial protein--as target of antibodies in primary biliary cirrhosis.

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    Roesler, Kai-Wolfgang; Schmider, Wolfgang; Kist, Manfred; Batsford, Stephen; Schiltz, Emile; Oelke, Mathias; Tuczek, Anja; Dettenborn, Therese; Behringer, Dirk; Kreisel, Wolfgang

    2003-03-01

    Several observations suggest that bacteria induce autoimmunity in primary biliary cirrhosis (PBC). Since no PBC-specific bacterial species could be identified, it can be speculated that the triggers are non-species-specific bacterial proteins. This hypothesis would imply that several or even all bacterial species can trigger PBC. Therefore, we investigated whether PBC exhibits immune reactions to non-species-specific bacterial antigens. Yersinia enterocolitica O3 was screened for the presence of proteins that were labeled by immunoblotting using PBC sera. We focused our investigations on a 160-kDa protein, which was further enriched and characterized by partial N-terminal amino acid sequencing. The prevalence of antibodies to this protein was determined by immunoblotting in a variety of diseases. The 160-kDa protein was identified as the beta-subunit of bacterial RNA-polymerase, a highly conserved bacterial protein with a very high degree of sequence identity among all bacterial species. Antibodies to the beta-subunit of bacterial RNA polymerase were specific for this protein. Until now no mammalian protein could be found that cross-reacts with these antibodies. The prevalence of antibodies to the beta-subunit of bacterial RNA polymerase (ARPA) using the protein from Yersinia enterocolitica O3 (serum dilution 1:1000) was: healthy controls (HC, N = 101) 7.9%, primary biliary cirrhosis (PBC, N = 61) 32.8%, autoimmune hepatitis type 1 (AIH, N = 46) 26.1%, alcoholic liver cirrhosis (ALC, N = 44) 9.1%, Crohn's disease (CD, N = 38) 7.9%, ulcerative colitis (UC, N = 24) 8.3%, primary sclerosing cholangitis + UC (PSC/UC, N = 11) 0%, acute yersiniosis (Yers, N = 36) 19.4%, acute infection with Campylobacter jejuni (Camp, N = 10) 0%, acute Q-fever (QF, N = 16) 6.25%, chronic hepatitis C (HCV, N = 39) 7.7%, c-ANCA-positive vasculitis (Vasc, N = 40) 15%, systemic lupus erythematosus (SLE, N = 28) 10.7%, and malaria tropica (MT, N = 24) 16.7%. There was no significant

  13. Isolation and Identification of a New Tetrodotoxin-Producing Bacterial Species, Raoultella terrigena, from Hong Kong Marine Puffer Fish Takifugu niphobles

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    Fred Wang-Fat Lee

    2011-11-01

    Full Text Available Puffer fish, Takifugu niphobles, collected from the Hong Kong coastal waters were screened for tetrodotoxin-producing bacteria. A Gram-negative, non-acid-fast, non-sporing and rod shaped bacterial strain (designated as gutB01 was isolated from the intestine of the puffer fish and was shown to produce tetrodotoxin (TTX. Based on the Microbial Identification (MIDI and 16S-23S rDNA internal transcribed spacer (ITS phylogenetic analysis, the strain was identified as Raoultella terrigena. The TTX production ability of the strain was confirmed by mouse bioassay, ELISA and mass spectrometry (MALDI-TOF. Our results reiterate that the TTX found in puffer fish was likely produced by the associated bacteria and TTX are widely produced amongst a diversity of bacterial species.

  14. Molecular Analysis of Bacterial Species Associated with Childhood Caries

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    Becker, Mitzi R.; Paster, Bruce J.; Leys, Eugene J.; Moeschberger, Melvin L.; Kenyon, Sarah G.; Galvin, Jamie L.; Boches, Susan K.; Dewhirst, Floyd E.; Griffen, Ann L.

    2002-01-01

    Although substantial epidemiologic evidence links Streptococcus mutans to caries, the pathobiology of caries may involve more complex communities of bacterial species. Molecular methods for bacterial identification and enumeration now make it possible to more precisely study the microbiota associated with dental caries. The purpose of this study was to compare the bacteria found in early childhood caries (ECC) to those found in caries-free children by using molecular identification methods. C...

  15. Population Genomics and the Bacterial Species Concept

    OpenAIRE

    Riley, Margaret A.; Lizotte-Waniewski, Michelle

    2009-01-01

    In recent years, the importance of horizontal gene transfer (HGT) in bacterial evolution has been elevated to such a degree that many bacteriologists now question the very existence of bacterial species. If gene transfer is as rampant as comparative genomic studies have suggested, how could bacterial species survive such genomic fluidity? And yet, most bacteriologists recognize, and name, as species, clusters of bacterial isolates that share complex phenotypic properties. The Core Genome Hypo...

  16. Distribution of periodontopathic bacterial species in Japanese children with developmental disabilities

    OpenAIRE

    Nemoto Hirotoshi; Kojima Ayuchi; Fujita Kazuyo; Okawa Rena; Nakano Kazuhiko; Yamana Aki; Naka Shuhei; Nomura Ryota; Matsumoto Michiyo; Ooshima Takashi

    2009-01-01

    Abstract Background Recent developments in molecular biological techniques have enabled rapid detection of periodontopathic bacterial species in clinical specimens. Accumulated evidence suggests that detection of specific bacterial species enables identification of subjects at high risk for the onset of periodontitis. We investigated the distribution of 10 selected periodontopathic bacterial species in dental plaque specimens obtained from children with disabilities who were attending daycare...

  17. Bacteriophage Amplification-Coupled Detection and Identification of Bacterial Pathogens

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    Cox, Christopher R.; Voorhees, Kent J.

    Current methods of species-specific bacterial detection and identification are complex, time-consuming, and often require expensive specialized equipment and highly trained personnel. Numerous biochemical and genotypic identification methods have been applied to bacterial characterization, but all rely on tedious microbiological culturing practices and/or costly sequencing protocols which render them impractical for deployment as rapid, cost-effective point-of-care or field detection and identification methods. With a view towards addressing these shortcomings, we have exploited the evolutionarily conserved interactions between a bacteriophage (phage) and its bacterial host to develop species-specific detection methods. Phage amplification-coupled matrix assisted laser desorption time-of-flight mass spectrometry (MALDI-TOF-MS) was utilized to rapidly detect phage propagation resulting from species-specific in vitro bacterial infection. This novel signal amplification method allowed for bacterial detection and identification in as little as 2 h, and when combined with disulfide bond reduction methods developed in our laboratory to enhance MALDI-TOF-MS resolution, was observed to lower the limit of detection by several orders of magnitude over conventional spectroscopy and phage typing methods. Phage amplification has been combined with lateral flow immunochromatography (LFI) to develop rapid, easy-to-operate, portable, species-specific point-of-care (POC) detection devices. Prototype LFI detectors have been developed and characterized for Yersinia pestis and Bacillus anthracis, the etiologic agents of plague and anthrax, respectively. Comparable sensitivity and rapidity was observed when phage amplification was adapted to a species-specific handheld LFI detector, thus allowing for rapid, simple, POC bacterial detection and identification while eliminating the need for bacterial culturing or DNA isolation and amplification techniques.

  18. Raman spectroscopy for bacterial identification and characterization

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    Bernatová, Silvie; Samek, Ota; Pilát, Zdeněk.; Šerý, Mojmír.; Ježek, Jan; Krzyžánek, Vladislav; Zemánek, Pavel; Ružička, Filip

    2012-01-01

    The main goal of our investigation is to use Raman tweezers technique so that the responce of Raman scattering on microorganisms suspended in liquid media (bacteria, algae and yeast cells in microfluidic chips) can be used to identify different species. The investigations presented here include identification of different bacteria strains (biofilm-positive and biofilm-negative) and yeast cells by using principal component analysis (PCA). The main driving force behind our investigation was a common problem in the clinical microbiology laboratory - how to distinguish between contaminant and invasive isolates. Invasive bacterial/yeast isolates can be assumed to form a biofilm, while isolates which do not form a biofilm can be treated as contaminant. Thus, the latter do not represent an important virulence factor.

  19. Identification of bacterial cells by chromosomal painting.

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    Lanoil, B. D.; Giovannoni, S J

    1997-01-01

    Chromosomal painting is a technique for the microscopic localization of genetic material. It has been applied at the subcellular level to identify regions of eukaryotic chromosomes. Here we describe the development of bacterial chromosomal painting (BCP), a related technology for the identification of bacterial cells. Purified genomic DNAs from six bacterial strains were labeled by nick translation with the fluorochrome Fluor-X, Cy3, or Cy5. The average size of the labeled fragments was ca. 5...

  20. Isolation and Identification of a New Tetrodotoxin-Producing Bacterial Species, Raoultella terrigena, from Hong Kong Marine Puffer Fish Takifugu niphobles

    OpenAIRE

    Fred Wang-Fat Lee; Peter Hoi-Fu Yu; Vincent Chung-Him Yu; Kin-Chung Ho

    2011-01-01

    Puffer fish, Takifugu niphobles, collected from the Hong Kong coastal waters were screened for tetrodotoxin-producing bacteria. A Gram-negative, non-acid-fast, non-sporing and rod shaped bacterial strain (designated as gutB01) was isolated from the intestine of the puffer fish and was shown to produce tetrodotoxin (TTX). Based on the Microbial Identification (MIDI) and 16S-23S rDNA internal transcribed spacer (ITS) phylogenetic analysis, the strain was identified as Raoultella terrigena. The ...

  1. Multiple bacterial species reside in chronic wounds

    DEFF Research Database (Denmark)

    Gjødsbøl, Kristine; Christensen, Jens Jørgen; Karlsmark, Tonny; Jørgensen, Bo; Klein, Bjarke M; Krogfelt, Karen A

    2006-01-01

    species present were identified. More than one bacterial species were detected in all the ulcers. The most common bacteria found were Staphylococcus aureus (found in 93.5% of the ulcers), Enterococcus faecalis (71.7%), Pseudomonas aeruginosa (52.2%), coagulase-negative staphylococci (45.7%), Proteus...

  2. Bacterial responses to reactive chlorine species.

    Science.gov (United States)

    Gray, Michael J; Wholey, Wei-Yun; Jakob, Ursula

    2013-01-01

    Hypochlorous acid (HOCl), the active ingredient of household bleach, is the most common disinfectant in medical, industrial, and domestic use and plays an important role in microbial killing in the innate immune system. Given the critical importance of the antimicrobial properties of chlorine to public health, it is surprising how little is known about the ways in which bacteria sense and respond to reactive chlorine species (RCS). Although the literature on bacterial responses to reactive oxygen species (ROS) is enormous, work addressing bacterial responses to RCS has begun only recently. Transcriptomic and proteomic studies now provide new insights into how bacteria mount defenses against this important class of antimicrobial compounds. In this review, we summarize the current knowledge, emphasizing the overlaps between RCS stress responses and other more well-characterized bacterial defense systems, and identify outstanding questions that represent productive avenues for future research. PMID:23768204

  3. Rapid Bacterial Identification Using Fourier Transform Infrared Spectroscopy

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    Valentine, Nancy B.; Johnson, Timothy J.; Su, Yin-Fong; Forrester, Joel B.

    2007-02-01

    Recent studies at Pacific Northwest National Laboratory (PNNL) using infrared spectroscopy combined with statistical analysis have shown the ability to identify and discriminate vegetative bacteria, bacterial spores and background interferents from one another. Since the anthrax releases in 2001, rapid identification of unknown powders has become a necessity. Bacterial endospores are formed by some Bacillus species as a result of the vegetative bacteria undergoing environmental stress, e.g. a lack of nutrients. Endospores are formed as a survival mechanism and are extremely resistant to heat, cold, sunlight and some chemicals. They become airborne easily and are thus readily dispersed which was demonstrated in the Hart building. Fourier Transform Infrared (FTIR) spectroscopy is one of several rapid analytical methods used for bacterial endospore identification. The most common means of bacterial identification is culturing, but this is a time-consuming process, taking hours to days. It is difficult to rapidly identify potentially harmful bacterial agents in a highly reproducible way. Various analytical methods, including FTIR, Raman, photoacoustic FTIR and Matrix Assisted Laser Desorption/Ionization (MALDI) have been used to identify vegetative bacteria and bacterial endospores. Each has shown certain areas of promise, but each has shortcomings in terms of sensitivity, measurement time or portability. IR spectroscopy has been successfully used to distinguish between the sporulated and vegetative state. [1,2] It has also shown its utility at distinguishing between the spores of different species. [2-4] There are several Bacillus species that occur commonly in nature, so it is important to be able to distinguish between the many different species versus those that present an imminent health threat. The spectra of the different sporulated species are all quite similar, though there are some subtle yet reproducible spectroscopic differences. Thus, a more robust and

  4. Rapid bacterial identification using evanescent-waveguide oligonucleotide microarray classification.

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    Francois, Patrice; Charbonnier, Yvan; Jacquet, Jean; Utinger, Dominic; Bento, Manuela; Lew, Daniel; Kresbach, Gerhard M; Ehrat, Markus; Schlegel, Werner; Schrenzel, Jacques

    2006-06-01

    Bacterial identification relies primarily on culture-based methodologies and requires 48-72 h to deliver results. We developed and used i) a bioinformatics strategy to select oligonucleotide signature probes, ii) a rapid procedure for RNA labelling and hybridization, iii) an evanescent-waveguide oligoarray with exquisite signal/noise performance, and iv) informatics methods for microarray data analysis. Unique 19-mer signature oligonucleotides were selected in the 5'-end of 16s rDNA genes of human pathogenic bacteria. Oligonucleotides spotted onto a Ta(2)O(5)-coated microarray surface were incubated with chemically labelled total bacterial RNA. Rapid hybridization and stringent washings were performed before scanning and analyzing the slide. In the present paper, the eight most abundant bacterial pathogens representing >54% of positive blood cultures were selected. Hierarchical clustering analysis of hybridization data revealed characteristic patterns, even for closely related species. We then evaluated artificial intelligence-based approaches that outperformed conventional threshold-based identification schemes on cognate probes. At this stage, the complete procedure applied to spiked blood cultures was completed in less than 6 h. In conclusion, when coupled to optimal signal detection strategy, microarrays provide bacterial identification within a few hours post-sampling, allowing targeted antimicrobial prescription. PMID:16216356

  5. Identification of Bacterial Species Associated with the Sheep Scab Mite (Psoroptes ovis) by Using Amplified Genes Coding for 16S rRNA

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    Hogg, J.C.; Lehane, M. J.

    1999-01-01

    This was the first molecular study of the bacterial flora of the sheep scab mite (Psoroptes ovis). A sequence analysis of genes coding for 16S rRNA revealed that Serratia marcescens and bacteria closely related to Staphylococcus intermedius or Staphylococcus chromogens and Alloiococcus otitidis were present. These bacteria were associated with skin lesions, dermatitis, and otitis media caused by P. ovis.

  6. Bacterial Community Diversity Harboured by Interacting Species.

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    Mikaël Bili

    Full Text Available All animals are infected by microbial partners that can be passengers or residents and influence many biological traits of their hosts. Even if important factors that structure the composition and abundance of microbial communities within and among host individuals have been recently described, such as diet, developmental stage or phylogeny, few studies have conducted cross-taxonomic comparisons, especially on host species related by trophic relationships. Here, we describe and compare the microbial communities associated with the cabbage root fly Delia radicum and its three major parasitoids: the two staphylinid beetles Aleochara bilineata and A. bipustulata and the hymenopteran parasitoid Trybliographa rapae. For each species, two populations from Western France were sampled and microbial communities were described through culture independent methods (454 pyrosequencing. Each sample harbored at least 59 to 261 different bacterial phylotypes but was strongly dominated by one or two. Microbial communities differed markedly in terms of composition and abundance, being mainly influenced by phylogenetic proximity but also geography to a minor extent. Surprisingly, despite their strong trophic interaction, parasitoids shared a very low proportion of microbial partners with their insect host. Three vertically transmitted symbionts from the genus Wolbachia, Rickettsia, and Spiroplasma were found in this study. Among them, Wolbachia and Spiroplasma were found in both the cabbage fly and at least one of its parasitoids, which could result from horizontal transfers through trophic interactions. Phylogenetic analysis showed that this hypothesis may explain some but not all cases. More work is needed to understand the dynamics of symbiotic associations within trophic network and the effect of these bacterial communities on the fitness of their hosts.

  7. Culturomics identified 11 new bacterial species from a single anorexia nervosa stool sample

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    Pfleiderer, A.; Lagier, J. C.; Armougom, Fabrice; Robert, C.; Vialettes, B; Raoult, Didier

    2013-01-01

    The rebirth of bacterial culture has been highlighted successively by environmental microbiologists, the design of axenic culture for intracellular bacteria in clinical microbiology, and, more recently, by human gut microbiota studies. Indeed, microbial culturomics (large scale of culture conditions with the identification of colonies by MALDI-TOF or 16S rRNA) allowed to culture 32 new bacterial species from only four stool samples studied. We performed culturomics in comparison with pyrosequ...

  8. MALDI-TOF mass spectrometry proteomic based identification of clinical bacterial isolates

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    Ashutosh Panda

    2014-01-01

    Full Text Available Background & objectives: Pathogenic bacteria often cause life threatening infections especially in immunocompromised individuals. Therefore, rapid and reliable species identification is essential for a successful treatment and disease management. We evaluated a rapid, proteomic based technique for identification of clinical bacterial isolates by protein profiling using matrix-assisted laser desorption-ionization time - of - flight mass spectrometry (MALDI-TOF MS. Methods: Freshly grown bacterial isolates were selected from culture plates. Ethanol/formic acid extraction procedure was carried out, followed by charging of MALDI target plate with the extract and overlaying with α-cyano-4 hydroxy-cinnamic acid matrix solution. Identification was performed using the MALDI BioTyper 1.1, software for microbial identification (Bruker Daltonik GmbH, Bremen, Germany. Results: A comparative analysis of 82 clinical bacterial isolates using MALDI -TOF MS and conventional techniques was carried out. Amongst the clinical isolates, the accuracy at the species level for clinical isolates was 98.78%. One out of 82 isolates was not in accordance with the conventional assays because MALDI-TOF MS established it as Streptococcus pneumoniae and conventional methods as Streptococcus viridans. Interpretation & conclusions: MALDI - TOF MS was found to be an accurate, rapid, cost-effective and robust system for identification of clinical bacterial isolates. This innovative approach holds promise for earlier therapeutic intervention leading to better patient care.

  9. Bacterial species dominance within a binary culture biofilm.

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    Banks, M.K.; Bryers, J.D.

    1991-01-01

    Studies with two species of bacteria, Pseudomonas putida and Hyphomicrobium sp. strain ZV620, were carried out to evaluate the overall net rate of accumulation of biofilm, the biofilm species composition, and individual species shear-related removal rates. Bacterial cells of either or both species were deposited onto glass or biofilm surfaces to initiate multispecies biofilms. Subsequent biofilm development was carried out under known conditions of nutrient concentration and laminar flow. Est...

  10. Coffee species and varietal identification

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    Tornincasa, Patrizia; Furlan, Michela; Pallavicini, Alberto; Graziosi, Giorgio

    2010-01-01

    There are serious economical reasons to pretend warranties in coffee species and varieties authenticity. Arabica adulteration with Robusta coffees, intentional or not, is carried out at different steps of the coffee chain, from plantation to beverage. We present a method based on a real-time PCR technique to perform: a) a qualitative analysis to evaluate the presence/ absence of a species in a sample; b) a quantitative analysis to amplify Robusta samples only, making possibl...

  11. Antibiogram of bacterial species isolated from canine pyometra

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    Madhu Swamy; Varun Bassessar; Yamini Verma

    2013-01-01

    Aim: The aim of the present work was to ascertain the bacterial flora causing pyometra in female dogs and their antibiotic sensitivity. Materials and Methods: A study was conducted to determine the antibiogram of bacterial species isolated from 20 female dogs diagnosed with pyometra. The vaginal discharge was collected by sterile swab and streaked smoothly over Mueller Hinton medium and sensitivity towards antibiotics was determined by measuring the zone of inhibition using a Hi-media scale. ...

  12. Defining pathogenic bacterial species in the genomic era

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    DidierRaoult

    2011-01-01

    Actual definitions of bacterial species are limited due to the current criteria of definition and the use of restrictive genetic tools. The 16S rRNA sequence, for example, has been widely used as a marker for phylogenetic analyses; however, its use often leads to misleading species definitions. According to the first genetic studies, removing a certain number of genes from pathogenic bacteria removes their capacity to infect hosts. However, more recent studies have demonstrated that the speci...

  13. Bacterial acquisition in juveniles of several broadcast spawning coral species.

    Directory of Open Access Journals (Sweden)

    Koty H Sharp

    Full Text Available Coral animals harbor diverse microorganisms in their tissues, including archaea, bacteria, viruses, and zooxanthellae. The extent to which coral-bacterial associations are specific and the mechanisms for their maintenance across generations in the environment are unknown. The high diversity of bacteria in adult coral colonies has made it challenging to identify species-specific patterns. Localization of bacteria in gametes and larvae of corals presents an opportunity for determining when bacterial-coral associations are initiated and whether they are dynamic throughout early development. This study focuses on the early onset of bacterial associations in the mass spawning corals Montastraea annularis, M. franksi, M. faveolata, Acropora palmata, A. cervicornis, Diploria strigosa, and A. humilis. The presence of bacteria and timing of bacterial colonization was evaluated in gametes, swimming planulae, and newly settled polyps by fluorescence in situ hybridization (FISH using general eubacterial probes and laser-scanning confocal microscopy. The coral species investigated in this study do not appear to transmit bacteria via their gametes, and bacteria are not detectable in or on the corals until after settlement and metamorphosis. This study suggests that mass-spawning corals do not acquire, or are not colonized by, detectable numbers of bacteria until after larval settlement and development of the juvenile polyp. This timing lays the groundwork for developing and testing new hypotheses regarding general regulatory mechanisms that control bacterial colonization and infection of corals, and how interactions among bacteria and juvenile polyps influence the structure of bacterial assemblages in corals.

  14. Identification of ligands for bacterial sensor proteins.

    Science.gov (United States)

    Fernández, Matilde; Morel, Bertrand; Corral-Lugo, Andrés; Rico-Jiménez, Miriam; Martín-Mora, David; López-Farfán, Diana; Reyes-Darias, José Antonio; Matilla, Miguel A; Ortega, Álvaro; Krell, Tino

    2016-02-01

    Bacteria have evolved a variety of different signal transduction mechanisms. However, the cognate signal molecule for the very large amount of corresponding sensor proteins is unknown and their functional annotation represents a major bottleneck in the field of signal transduction. The knowledge of the signal molecule is an essential prerequisite to understand the signalling mechanisms. Recently, the identification of signal molecules by the high-throughput protein screening of commercially available ligand collections using differential scanning fluorimetry has shown promise to resolve this bottleneck. Based on the analysis of a significant number of different ligand binding domains (LBDs) in our laboratory, we identified two issues that need to be taken into account in the experimental design. Since a number of LBDs require the dimeric state for ligand recognition, it has to be assured that the protein analysed is indeed in the dimeric form. A number of other examples demonstrate that purified LBDs can contain bound ligand which prevents further binding. In such cases, the apo-form can be generated by denaturation and subsequent refolding. We are convinced that this approach will accelerate the functional annotation of sensor proteins which will help to understand regulatory circuits in bacteria. PMID:26511375

  15. Antibiogram of bacterial species isolated from canine pyometra

    Directory of Open Access Journals (Sweden)

    Madhu Swamy

    2013-06-01

    Full Text Available Aim: The aim of the present work was to ascertain the bacterial flora causing pyometra in female dogs and their antibiotic sensitivity. Materials and Methods: A study was conducted to determine the antibiogram of bacterial species isolated from 20 female dogs diagnosed with pyometra. The vaginal discharge was collected by sterile swab and streaked smoothly over Mueller Hinton medium and sensitivity towards antibiotics was determined by measuring the zone of inhibition using a Hi-media scale. Results: The antobiogram showed that Gentamicin was the most sensitive (85% antibiotic followed by Enrofloxacin, Ciprofloxacin and Amoxicillin (65%, 65% and 55%, respectively. The isolates were most resistant to Oxytetracycline (85% followed by Tetracycline, Ampicillin, Chloramphenicol, Cloxacillin and Erythromycin (80%, 80%, 75%, 70% and 70%, respectively. Conclusion: Gentamicin was found to be most effective antibiotic against the bacterial species isolated from canine pyometra. [Vet World 2013; 6(8.000: 546-549

  16. SPECIES IDENTIFICATION OF MEAT BY ELECTROPHORETIC METHODS

    Directory of Open Access Journals (Sweden)

    Edward Pospiech

    2007-03-01

    Full Text Available Electrophoretic methods can be used to identify meat of various animal species. The protein electrophoresis, especially the IEF of the sarcoplasmic proteins, is a well-established technique for species identification of raw fish and is used in the control of seafood authenticity. However, in the case of the analysis of heat-processed fish, the method is applicable only to those species which possess characteristic patterns of the heat-stable parvalbumins. Heat-denatured fish muscle proteins may be solubilised by urea or sodium dodecylsulfate (SDS and separated by urea-IEF or SDS-PAGE, respectively. The comparison of these two methods allowed to conclude that, basically, each of them can be used for species identification of heated fishery products. However, extensively washed products may be preferentially analysed by the SDS-PAGE, because most of the parvalbumins are washed out leaving mainly myosins. On the other hand, the IEF method may be preferred for the differentiation of closely related species rich in parvalbumins isoforms. It is evident from the literature data that species-specific protein separations yield proteins of low molecular weight made up of three light chains of myosin (14-23 kDa, troponin (19-30 kDa and parvalbumin (about 12 kDa. Investigations showed that the SDS-PAGE method can be used to identify meats of: cattle, sheep, lambs, goats, red deer and rabbits. The technique allowed researchers to identify the following myofibrillar and sarcoplasmic muscle proteins: myosin and actin, α-actinin, tropomyosin, troponin. SDS-PAGE allowed the identification of myofibrillar proteins taking into account their molecular weights which was not possible with the assistance of the PAGIF because too many protein bands were obtained. It was possible to obtain differences in the separation of proteins characteristic for certain species, e.g. beef, resulting from the presence of sin-gle myofibrillar proteins.

  17. Identification and characterisation of potential biofertilizer bacterial strains

    Science.gov (United States)

    Karagöz, Kenan; Kotan, Recep; Dadaşoǧlu, Fatih; Dadaşoǧlu, Esin

    2016-04-01

    In this study we aimed that isolation, identification and characterizations of PGPR strains from rhizosphere of legume plants. 188 bacterial strains isolated from different legume plants like clover, sainfoin and vetch in Erzurum province of Turkey. These three plants are cultivated commonly in the Erzurum province. It was screen that 50 out of 188 strains can fix nitrogen and solubilize phosphate. These strains were identified via MIS (Microbial identification system). According to MIS identification results, 40 out of 50 strains were identified as Bacillus, 5 as Pseudomonas, 3 as Paenibacillus, 1 as Acinetobacter, 1 as Brevibacterium. According to classical test results, while the catalase test result of all isolates are positive, oxidase, KOH and starch hydrolysis rest results are variable.

  18. Panamanian frog species host unique skin bacterial communities.

    Science.gov (United States)

    Belden, Lisa K; Hughey, Myra C; Rebollar, Eria A; Umile, Thomas P; Loftus, Stephen C; Burzynski, Elizabeth A; Minbiole, Kevin P C; House, Leanna L; Jensen, Roderick V; Becker, Matthew H; Walke, Jenifer B; Medina, Daniel; Ibáñez, Roberto; Harris, Reid N

    2015-01-01

    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 these skin symbiont

  19. Printed Identification Key or Web-Based Identification Guide: An Effective Tool for Species Identification?

    OpenAIRE

    THOMAS EDISON E. DELA CRUZ; Pangilinan, Ma. Victoria B.; Rodrigo A. Litao

    2012-01-01

    Species identification is often done with the aid of traditional dichotomous keys. This printed material is based on one’s decision between two alternatives, which is followed by another pair of alternatives until the final species name is reached. With the advent of internet technology, the use of an online database offers an updatable and accumulative approach to species identification. It can also be accessed anytime, and this is very useful for fast-changing groups of organisms. In this p...

  20. Progress of DNA-based Methods for Species Identification

    Institute of Scientific and Technical Information of China (English)

    HU Zhen; ZHANG Su-hua; WANG Zheng; BIAN Ying-nan; LI Cheng-tao

    2015-01-01

    Species identification of biological samples is widely used in such fields as forensic science and food industry. A variety of accurate and reliable methods have been developed in recent years. The cur-rent reviewshows common target genes and screening criteria suitable for species identification, and de-scribed various DNA-based molecular biology methods about species identification. Additionally, it dis-cusses the future development of species identification combined with real-time PCR and sequencing technologies.

  1. Molecular genetic strategies for species identification

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    This paper probes into the molecular genetic mechanism of the formation of species, subspecies and variety in evolving progression, and brings forward 5 criteria of an ideal strategy in species identification: stating the specific characteristics at species, subspecies and variety level without any interference of too high polymorphism at individual or population level; keys should be distributed as 0 or 1, e. g. yes or no; satisfying re-peatability and simple operation; high veracity and reliability; adaptability to widely various specimen. Respec-tively, this paper reviews two strategies focusing on detecting the fragment length polymorphism and base re-placement and lays out some detail methods under above strategies. It demonstrates that it is not possible to solve all species problems by pursuing identification with only a single gene or DNA fragment. Only based on thorough consideration of all strategies, a method or combined several methods could bring satisfying reliability. For advanced focuses, it requires not only development and optimization of methods under above strategies, but also new originality of creative strategies.

  2. Bacterial species involved in the conversion of dietary flavonoids in the human gut.

    Science.gov (United States)

    Braune, Annett; Blaut, Michael

    2016-05-01

    The gut microbiota plays a crucial role in the conversion of dietary flavonoids and thereby affects their health-promoting effects in the human host. The identification of the bacteria involved in intestinal flavonoid conversion has gained increasing interest. This review summarizes available information on the so far identified human intestinal flavonoid-converting bacterial species and strains as well as their enzymes catalyzing the underlying reactions. The majority of described species involved in flavonoid transformation are capable of carrying out the O-deglycosylation of flavonoids. Other bacteria cleave the less common flavonoid-C-glucosides and/or further degrade the aglycones of flavonols, flavanonols, flavones, flavanones, dihydrochalcones, isoflavones and monomeric flavan-3-ols. To increase the currently limited knowledge in this field, identification of flavonoid-converting bacteria should be continued using culture-dependent screening or isolation procedures and molecular approaches based on sequence information of the involved enzymes. PMID:26963713

  3. VULVO VAGINAL CANDIDIASIS : IMPORTANCE OF SPECIES IDENTIFICATION

    Directory of Open Access Journals (Sweden)

    Swarajya Lakshmi

    2014-01-01

    Full Text Available OBJECTIVES : Vulvo Vaginal Candidiasis is a common nagging problem faced by 75% of women in reproductive age group. Present study was undertaken to determine the prevalence of Candida in patients suffering from vaginitis , to assess predisposing factors and correlate the symptoms with gram stain for presumptive diagnosis of Candidiasis. METHODS : A prospective study of the laboratory diagnosis of vulvovaginal candidiasis (VVC was carried out in 100 women presenting with symptoms suggestive of vaginosis in the reproductive age group. Investigation s included microscopy and culture for yeast. Candida is identified, based on growth on SDA, corn meal agar and Saba raud’s Triphenyl tetrazolium agar, and assimilation and fermentation of sugars. RESULTS : Candida was isolated in 33% of women. Clue cells on gram stain suggestive of bacterial vaginosis was seen in equal number of women, whereas mixed infection was found in 9%. Candida albicans accounted for 15% and nonalbicans species for 85% . O f the non albicans species, Candida glabrata was the commonest (4 2%. Pruritus with or without vaginal discharge and vaginal erythema were the most common symptoms and signs in women with positive Candida culture. CONCLUSION : On comparing the significance of gram stain and culture for presumptive diagnosis of candidiasi s, culture was more significant than gram stain alone. In present study, the rate of culture positivity was 33% and C. glabrata was the predominant species. VVC cannot be diagnosed by clinical criteria alone and requires confirmation by culture including i dentification of species.

  4. Cutaneous bacterial species from Lithobates catesbeianus can inhibit pathogenic dermatophytes.

    Science.gov (United States)

    Lauer, Antje; Hernandez, Trang

    2015-04-01

    Antibiotics are being successfully used to fight many infectious diseases caused by pathogenic microorganisms. However, new infectious diseases are continuously being identified, and some known pathogens are becoming resistant against known antibiotics. Furthermore, many antifungals are causing serious side effects in long-term treatments of patients, and many skin infections caused by dermatophytes are difficult to cure. The beneficial roles of resident cutaneous microbiota to inhibit pathogenic microorganisms have been shown for many vertebrate species. Microbial symbionts on the amphibian skin for example can be a source of powerful antimicrobial metabolites that can protect amphibians against diseases, such as chytridiomycosis, caused by a fungal pathogen. In this research, we investigated whether cutaneous bacterial species isolated from Lithobates catesbeianus (North American bullfrog), an invasive amphibian species that is resistant to chytridiomycosis, produce secondary metabolites that can be used to inhibit the growth of three species of dermatophytes (Microsporum gypseum, Epidermophyton floccosum, and Trichophyton mentagrophytes) which are known to cause topical or subdermal skin infections in humans. Strongly anti-dermatophyte bacterial species that belonged to the Bacillaceae, Streptomycetaceae, Pseudomonadaceae, Xanthomonadaceae, Aeromonadaceae, and Enterobacteriaceae were identified. This research has provided evidence of the presence of cutaneous anti-dermatophyte bacteria from L. catesbeianus which might provide a basis for health care providers to experiment with new antifungals in the future. PMID:25431089

  5. Bacterial communities and species-specific associations with the mucus of Brazilian coral species

    OpenAIRE

    Camila Carlos; Tatiana T. Torres; Ottoboni, Laura M.M.

    2013-01-01

    We investigated the existence of species-specific associations between Brazilian coral species and bacteria. Pyrosequencing of the V3 region of the 16S rDNA was used to analyze the taxonomic composition of bacterial communities associated with the mucus of four coral species (Madracis decactis, Mussismilia hispida, Palythoa caribaeorum, and Tubastraea coccinea) in two seasons (winter and summer), which were compared with the surrounding water and sediment. The microbial communities found in s...

  6. Novel Perspectives on the Characterization of Species-Dependent Optical Signatures of Bacterial Colonies by Digital Holography.

    Science.gov (United States)

    Buzalewicz, Igor; Kujawińska, Małgorzata; Krauze, Wojciech; Podbielska, Halina

    2016-01-01

    The use of light diffraction for the microbiological diagnosis of bacterial colonies was a significant breakthrough with widespread implications for the food industry and clinical practice. We previously confirmed that optical sensors for bacterial colony light diffraction can be used for bacterial identification. This paper is focused on the novel perspectives of this method based on digital in-line holography (DIH), which is able to reconstruct the amplitude and phase properties of examined objects, as well as the amplitude and phase patterns of the optical field scattered/diffracted by the bacterial colony in any chosen observation plane behind the object from single digital hologram. Analysis of the amplitude and phase patterns inside a colony revealed its unique optical properties, which are associated with the internal structure and geometry of the bacterial colony. Moreover, on a computational level, it is possible to select the desired scattered/diffracted pattern within the entire observation volume that exhibits the largest amount of unique, differentiating bacterial features. These properties distinguish this method from the already proposed sensing techniques based on light diffraction/scattering of bacterial colonies. The reconstructed diffraction patterns have a similar spatial distribution as the recorded Fresnel patterns, previously applied for bacterial identification with over 98% accuracy, but they are characterized by both intensity and phase distributions. Our results using digital holography provide new optical discriminators of bacterial species revealed in one single step in form of new optical signatures of bacterial colonies: digital holograms, reconstructed amplitude and phase patterns, as well as diffraction patterns from all observation space, which exhibit species-dependent features. To the best of our knowledge, this is the first report on bacterial colony analysis via digital holography and our study represents an innovative approach

  7. Novel Perspectives on the Characterization of Species-Dependent Optical Signatures of Bacterial Colonies by Digital Holography.

    Directory of Open Access Journals (Sweden)

    Igor Buzalewicz

    Full Text Available The use of light diffraction for the microbiological diagnosis of bacterial colonies was a significant breakthrough with widespread implications for the food industry and clinical practice. We previously confirmed that optical sensors for bacterial colony light diffraction can be used for bacterial identification. This paper is focused on the novel perspectives of this method based on digital in-line holography (DIH, which is able to reconstruct the amplitude and phase properties of examined objects, as well as the amplitude and phase patterns of the optical field scattered/diffracted by the bacterial colony in any chosen observation plane behind the object from single digital hologram. Analysis of the amplitude and phase patterns inside a colony revealed its unique optical properties, which are associated with the internal structure and geometry of the bacterial colony. Moreover, on a computational level, it is possible to select the desired scattered/diffracted pattern within the entire observation volume that exhibits the largest amount of unique, differentiating bacterial features. These properties distinguish this method from the already proposed sensing techniques based on light diffraction/scattering of bacterial colonies. The reconstructed diffraction patterns have a similar spatial distribution as the recorded Fresnel patterns, previously applied for bacterial identification with over 98% accuracy, but they are characterized by both intensity and phase distributions. Our results using digital holography provide new optical discriminators of bacterial species revealed in one single step in form of new optical signatures of bacterial colonies: digital holograms, reconstructed amplitude and phase patterns, as well as diffraction patterns from all observation space, which exhibit species-dependent features. To the best of our knowledge, this is the first report on bacterial colony analysis via digital holography and our study represents an

  8. Novel Perspectives on the Characterization of Species-Dependent Optical Signatures of Bacterial Colonies by Digital Holography

    Science.gov (United States)

    Buzalewicz, Igor; Kujawińska, Małgorzata; Krauze, Wojciech; Podbielska, Halina

    2016-01-01

    The use of light diffraction for the microbiological diagnosis of bacterial colonies was a significant breakthrough with widespread implications for the food industry and clinical practice. We previously confirmed that optical sensors for bacterial colony light diffraction can be used for bacterial identification. This paper is focused on the novel perspectives of this method based on digital in-line holography (DIH), which is able to reconstruct the amplitude and phase properties of examined objects, as well as the amplitude and phase patterns of the optical field scattered/diffracted by the bacterial colony in any chosen observation plane behind the object from single digital hologram. Analysis of the amplitude and phase patterns inside a colony revealed its unique optical properties, which are associated with the internal structure and geometry of the bacterial colony. Moreover, on a computational level, it is possible to select the desired scattered/diffracted pattern within the entire observation volume that exhibits the largest amount of unique, differentiating bacterial features. These properties distinguish this method from the already proposed sensing techniques based on light diffraction/scattering of bacterial colonies. The reconstructed diffraction patterns have a similar spatial distribution as the recorded Fresnel patterns, previously applied for bacterial identification with over 98% accuracy, but they are characterized by both intensity and phase distributions. Our results using digital holography provide new optical discriminators of bacterial species revealed in one single step in form of new optical signatures of bacterial colonies: digital holograms, reconstructed amplitude and phase patterns, as well as diffraction patterns from all observation space, which exhibit species-dependent features. To the best of our knowledge, this is the first report on bacterial colony analysis via digital holography and our study represents an innovative approach

  9. Distribution of periodontopathic bacterial species in Japanese children with developmental disabilities

    Directory of Open Access Journals (Sweden)

    Nemoto Hirotoshi

    2009-09-01

    Full Text Available Abstract Background Recent developments in molecular biological techniques have enabled rapid detection of periodontopathic bacterial species in clinical specimens. Accumulated evidence suggests that detection of specific bacterial species enables identification of subjects at high risk for the onset of periodontitis. We investigated the distribution of 10 selected periodontopathic bacterial species in dental plaque specimens obtained from children with disabilities who were attending daycare centers. Methods A total of 187 children (136 boys, 51 girls aged 1-6 years old and diagnosed with such disabilities as mental retardation, cerebral palsy, and autism, participated in the study. Subgingival dental plaque specimens were collected from the buccal side of the maxillary left second primary molar after a clinical examination. Bacterial DNA was extracted from the specimens and PCR analyses were carried out to detect 10 selected periodontopathic species using specific primers for each. In addition, statistical analyses were performed to analyze the correlations among clinical parameters and the detected species. Results The most frequently detected species was Capnocytophaga sputigena (28.3%, followed by Aggregatibacter actinomycetemcomitans (20.9% and Campylobacter rectus (18.2%. Eikenella corrodens, Capnocytophaga ochracea, and Prevotella nigrescence were detected in approximately 10% of the specimens, whereas Treponema denticola, Tannerella forsythia, and Prevotella intermedia were rarely found, and Porphyromonas gingivalis was not detected in any of the subjects. The total numbers of detected species were positively correlated with the age of the subjects. There were 10 subjects with positive reactions for T. denticola and/or T. forsythia, in whom the total number of bacterial species was significantly higher as compared to the other subjects. Furthermore, subjects possessing C. rectus showed significantly greater values for periodontal pocket

  10. Application of microbial identification system (Sherlock MIS) for identification of forest litter bacterial strains - preliminary results

    Czech Academy of Sciences Publication Activity Database

    Jirout, Jiří; Petrásek, Jiří; Elhottová, Dana; Krištůfek, Václav; Nováková, Alena; Rusek, Josef

    České Budějovice : Institute of Soil Biology AS CR, 2004, s. 47-51. ISBN 80-86525-03-1. [Present methods for investigation of microbial community biodiversity in soils and substrates. Methodological workshop /9./. České Budějovice (CZ), 02.03.2004-03.03.2004] Institutional research plan: CEZ:AV0Z6066911 Keywords : Sherlock MIS * identification * forest litter bacterial strains Subject RIV: EH - Ecology, Behaviour

  11. Desulfovibrio bacterial species are increased in ulcerative colitis.

    LENUS (Irish Health Repository)

    Rowan, Fiachra

    2012-02-01

    BACKGROUND: Debate persists regarding the role of Desulfovibrio subspecies in ulcerative colitis. Combined microscopic and molecular techniques enable this issue to be investigated by allowing precise enumeration of specific bacterial species within the colonic mucous gel. The aim of this study was to combine laser capture microdissection and quantitative polymerase chain reaction to determine Desulfovibrio copy number in crypt-associated mucous gel in health and in acute and chronic ulcerative colitis. METHODS: Colonic mucosal biopsies were harvested from healthy controls (n = 19) and patients with acute (n = 10) or chronic (n = 10) ulcerative colitis. Crypt-associated mucous gel was obtained by laser capture microdissection throughout the colon. Pan-bacterial 16S rRNA and Desulfovibrio copy number\\/mm were obtained by polymerase chain reaction at each locus. Bacterial copy numbers were interrogated for correlation with location and disease activity. Data were evaluated using a combination of ordinary linear methods and linear mixed-effects models to cater for multiple interactions. RESULTS: Desulfovibrio positivity was significantly increased in acute and chronic ulcerative colitis at multiple levels within the colon, and after normalization with total bacterial signal, the relative Desulfovibrio load was increased in acute colitis compared with controls. Desulfovibrio counts did not significantly correlate with age, disease duration, or disease activity but interlevel correlations were found in adjacent colonic segments in the healthy control and chronic ulcerative colitis groups. CONCLUSION: The presence of Desulfovibrio subspecies is increased in ulcerative colitis and the data presented suggest that these bacteria represent an increased percentage of the colonic microbiome in acute ulcerative colitis.

  12. Benchmarking of methods for identification of antimicrobial resistance genes in bacterial whole genome data

    DEFF Research Database (Denmark)

    Clausen, Philip T. L. C.; Zankari, Ea; Aarestrup, Frank Møller;

    2016-01-01

    two different methods in current use for identification of antibiotic resistance genes in bacterial WGS data. A novel method, KmerResistance, which examines the co-occurrence of k-mers between the WGS data and a database of resistance genes, was developed. The performance of this method was compared...... with two previously described methods; ResFinder and SRST2, which use an assembly/BLAST method and BWA, respectively, using two datasets with a total of 339 isolates, covering five species, originating from the Oxford University Hospitals NHS Trust and Danish pig farms. The predicted resistance was...... compared with the observed phenotypes for all isolates. To challenge further the sensitivity of the in silico methods, the datasets were also down-sampled to 1% of the reads and reanalysed. The best results were obtained by identification of resistance genes by mapping directly against the raw reads. This...

  13. Recovery and identification of bacterial DNA from illicit drugs.

    Science.gov (United States)

    Cho, Kaymann T; Richardson, Michelle M; Kirkbride, K Paul; McNevin, Dennis; Nelson, Michelle; Pianca, Dennis; Roffey, Paul; Gahan, Michelle E

    2014-02-01

    Bacterial infections, including Bacillus anthracis (anthrax), are a common risk associated with illicit drug use, particularly among injecting drug users. There is, therefore, an urgent need to survey illicit drugs used for injection for the presence of bacteria and provide valuable information to health and forensic authorities. The objectives of this study were to develop a method for the extraction of bacterial DNA from illicit drugs and conduct a metagenomic survey of heroin and methamphetamine seized in the Australian Capital Territory during 2002-2011 for the presence of pathogens. Trends or patterns in drug contamination and their health implications for injecting drug users were also investigated. Methods based on the ChargeSwitch(®)gDNA mini kit (Invitrogen), QIAamp DNA extraction mini kit (QIAGEN) with and without bead-beating, and an organic phenol/chloroform extraction with ethanol precipitation were assessed for the recovery efficiency of both free and cellular bacterial DNA. Bacteria were identified using polymerase chain reaction and electrospray ionization-mass spectrometry (PCR/ESI-MS). An isopropanol pre-wash to remove traces of the drug and diluents, followed by a modified ChargeSwitch(®) method, was found to efficiently lyse cells and extract free and cellular DNA from Gram-positive and Gram-negative bacteria in heroin and methamphetamine which could then be identified by PCR/ESI-MS. Analysis of 12 heroin samples revealed the presence of DNA from species of Comamonas, Weissella, Bacillus, Streptococcus and Arthrobacter. No organisms were detected in the nine methamphetamine samples analysed. This study develops a method to extract and identify Gram-positive and Gram-negative bacteria from illicit drugs and demonstrates the presence of a range of bacterial pathogens in seized drug samples. These results will prove valuable for future work investigating trends or patterns in drug contamination and their health implications for injecting drug

  14. Optimized genotyping method for identification of bacterial contaminants in pharmaceutical industry

    Directory of Open Access Journals (Sweden)

    Stamatoski Borche

    2016-06-01

    Full Text Available Microbiological control is of crucial importance in the pharmaceutical industry regarding the possible bacterial contamination of the environment, water, raw materials and finished products. Molecular identification of bacterial contaminants based on DNA sequencing of the hypervariable 16SrRNA gene has been introduced recently. The aim of this study is to investigate the suitability of gene sequencing using our selection of PCR primers and conditions for rapid and accurate bacterial identification in pharmaceutical industry quality control.

  15. Clinical implications of species identification in monomicrobial Aeromonas bacteremia.

    Directory of Open Access Journals (Sweden)

    Chi-Jung Wu

    Full Text Available Advances in Aeromonas taxonomy have led to the reclassification of aeromonads. Hereon, we aimed to re-evaluate the characteristics of Aeromonas bacteremia, including those of a novel species, Aeromonas dhakensis.A retrospective study of monomicrobial Aeromonas bacteremia at a medical center in southern Taiwan from 2004-2011 was conducted. Species identification was based on rpoB sequencing. Of bacteremia of 153 eligible patients, A. veronii (50 isolates, 32.7%, A. dhakensis (48, 31.4%, A. caviae (43, 28.1%, and A. hydrophila (10, 6.5% were the principal causative species. A. dhakensis and A. veronii bacteremia were mainly community-acquired and presented as primary bacteremia, spontaneous bacterial peritonitis, or skin and soft-tissue infection, whereas A. caviae was associated with hospital-onset bacteremia. The distribution of the AmpC β-lactamase and metallo-β-lactamase genes was species-specific: bla(AQU-1, bla(MOX, or bla(CepH was present in A. dhakensis, A. caviae, or A. hydrophila, respectively, and bla(CphA was present in A. veronii, A. dhakensis, and A. hydrophila. The cefotaxime resistance rates of the A. caviae, A. dhakensis, and A. hydrophila isolates were higher than that of A. veronii (39.5%%, 25.0%, and 30% vs. 2%, respectively. A. dhakensis bacteremia was linked to the highest 14-day sepsis-related mortality rate, followed by A. hydrophila, A. veronii, and A. caviae bacteremia (25.5%, 22.2%, 14.0%, and 4.7%, respectively; P = 0.048. Multivariate analysis revealed that A. dhakensis bacteremia, active malignancies, and a Pitt bacteremia score ≥ 4 was an independent mortality risk factor.Characteristics of Aeromonas bacteremia vary between species. A. dhakensis prevalence and its associated poor outcomes suggest it an important human pathogen.

  16. Separation of the bacterial species, Escherichia coli, from mixed-species microbial communities for transcriptome analysis

    Directory of Open Access Journals (Sweden)

    Holder Diane

    2011-03-01

    Full Text Available Abstract Background The study of bacterial species interactions in a mixed-species community can be facilitated by transcriptome analysis of one species in the community using cDNA microarray technology. However, current applications of microarrays are mostly limited to single species studies. The purpose of this study is to develop a method to separate one species, Escherichia coli as an example, from mixed-species communities for transcriptome analysis. Results E. coli cells were separated from a dual-species (E. coli and Stenotrophomonas maltophilia community using immuno-magnetic separation (IMS. High recovery rates of E. coli were achieved. The purity of E. coli cells was as high as 95.0% separated from suspended mixtures consisting of 1.1 - 71.3% E. coli, and as high as 96.0% separated from biofilms with 8.1% E. coli cells. Biofilms were pre-dispersed into single-cell suspensions. The reagent RNAlater (Ambion, Austin, TX was used during biofilm dispersion and IMS to preserve the transcriptome of E. coli. A microarray study and quantitative PCR confirmed that very few E. coli genes (only about eight out of 4,289 ORFs exhibited a significant change in expression during dispersion and separation, indicating that transcriptional profiles of E. coli were well preserved. Conclusions A method based on immuno-magnetic separation (IMS and application of RNAlater was developed to separate a bacterial species, E. coli as an example, from mixed-species communities while preserving its transcriptome. The method combined with cDNA microarray analysis should be very useful to study species interactions in mixed-species communities.

  17. 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

  18. Stability of chloroquine phosphate tablets inoculated with bacterial species

    International Nuclear Information System (INIS)

    Five popular brands of chloroquine tablets available to the average Nigerian consumers were examined for the effects of Staphylococcus aureus and Bacillus cereus, on the dissolution, disintegration and hardness after six weeks of incubation. The maximum percent dissolution was 98.34% with bacillus subtilis while the minimum was 19.12% with staphylococcus aureus. The disintegration results showed a maximum of 69 min. 19 sec with Staphylococcus aureus while the least was 56 sec with Bacillus subtilis. The maximum hardness obtained was 12.75 kg and the least was 1.25 kg also with Staphylococcus aureus. The dissolution, disintegration and hardness also varied with the control. The metabolic activities of the bacterial species were believed to have caused the variations in the physical properties of the chloroquine phosphate tablets. The results from this investigation strongly advises adequate storage of chloroquine phosphate tablets, especially when it is the drug of choice for the of sub-Saharan Africa. (author)

  19. Bacterial communities and species-specific associations with the mucus of Brazilian coral species.

    Science.gov (United States)

    Carlos, Camila; Torres, Tatiana T; Ottoboni, Laura M M

    2013-01-01

    We investigated the existence of species-specific associations between Brazilian coral species and bacteria. Pyrosequencing of the V3 region of the 16S rDNA was used to analyze the taxonomic composition of bacterial communities associated with the mucus of four coral species (Madracis decactis, Mussismilia hispida, Palythoa caribaeorum, and Tubastraea coccinea) in two seasons (winter and summer), which were compared with the surrounding water and sediment. The microbial communities found in samples of mucus, water, and sediment differed according to the composition and relative frequency of OTUs. The coral mucus community seemed to be more stable and resistant to seasonal variations, compared to the water and sediment communities. There was no influence of geographic location on the composition of the communities. The sediment community was extremely diverse and might act as a "seed bank" for the entire environment. Species-specific OTUs were found in P. caribaeorum, T. coccinea, and M. hispida. PMID:23567936

  20. Identification of Indian crocodile species through DNA barcodes.

    Science.gov (United States)

    Meganathan, P R; Dubey, Bhawna; Jogayya, Kothakota Naga; Haque, Ikramul

    2013-07-01

    The biodiversity of India includes three crocodile species, Crocodylus palustris, Crocodylus porosus, and Gavialis gangeticus, whose status is threatened due to bushmeat crisis and illegal hunting. The crocodilian conservation management requires novel techniques to help forensic analysts to reveal species identity. DNA barcoding is a species identification technique, where a partial cytochrome c oxidase subunit 1 gene is used as a marker for species identification. Herein, the DNA barcoding technique is evaluated for three Indian crocodiles by analyzing an approximately 750-bp barcode region. The alignment result shows interspecific variations between sequences for discrimination of the three Indian crocodiles leading to species identification. The phylogenetic analyses also substantiate the established crocodilian relationships, which add further advantage to use this DNA barcoding approach for Indian crocodiles. This study provides preliminary evidences for the use of DNA barcoding technique in the identification of Indian crocodile species. PMID:23718785

  1. Rapid and reliable identification of waterborne Legionella species by MALDI-TOF mass spectrometry.

    Science.gov (United States)

    Dilger, Thorsten; Melzl, Holger; Gessner, André

    2016-08-01

    Detection and enumeration of Legionella bacteria in drinking water is regulated in Germany by ISO 11731-2. The mandatory method for species identification employs parallel subculturing of suspicious colonies on selective media requiring the handling of a large number of cultivation plates. After changes to the drinking water quality regulation in Germany in 2012 the demand for Legionella contamination testing increased drastically. A more reliable, faster and less laborious method for species identification is therefore desirable. Matrix-assisted laser desorption ionization followed by time of flight detection mass spectrometry (MALDI-TOF MS) promises an accelerated identification of bacteria with high reliability and reduced expenditure. Our study shows that MS-based species identification results are in full concordance with cultural and biochemical detection and differentiation and that valuable additional information can be gained, even though the ISO regulation demands an extended incubation period for primary bacterial cultures that is actually in contrast to the prerequisites of the MALDI Biotyper system. In addition, the established identification algorithm is very economical and improves time-to-result. Based on our findings, the amendment of MALID-TOF MS identification to ISO11731-2 as an alternative identification method should be taken into consideration. PMID:27260989

  2. Identification of Bombus species based on wing venation structure

    OpenAIRE

    Kozmus, Peter; Virant-Doberlet, Meta; Meglič, Vladimir; Dovč, Peter

    2011-01-01

    International audience About 250 bumblebee species in 15 subgenera are known in the world. Identification of some species is difficult due to small morphological differences. In this study, wing venation patterns were analysed to obtain characters for species identification. Four hundred and sixty-nine bumblebees from 121 localities in Slovenia and 61 imported individuals were included in the analyses. The coordinates of 19 vein junctions on the forewings were measured and used in the calc...

  3. Bacterial communities of two parthenogenetic aphid species cocolonizing two host plants across the Hawaiian Islands.

    Science.gov (United States)

    Jones, Ryan T; Bressan, Alberto; Greenwell, April M; Fierer, Noah

    2011-12-01

    Aphids (Hemiptera: Aphididae) have been the focus of several studies with respect to their interactions with inherited symbionts, but bacterial communities of most aphid species are still poorly characterized. In this research, we used bar-coded pyrosequencing to characterize bacterial communities in aphids. Specifically, we examined the diversity of bacteria in two obligately parthenogenetic aphid species (the melon aphid, Aphis gossypii, and the cardamom aphid, Pentalonia caladii) cocolonizing two plant species (taro, Colocasia esculenta, and ginger, Alpinia purpurata) across four Hawaiian Islands (Hawaii, Kauai, Maui, and Oahu). Results from this study revealed that heritable symbionts dominated the bacterial communities for both aphid species. The bacterial communities differed significantly between the two species, and A. gossypii harbored a more diverse bacterial community than P. caladii. The bacterial communities also differed across aphid populations sampled from the different islands; however, communities did not differ between aphids collected from the two host plants. PMID:21965398

  4. Biomimetic/Optical Sensors for Detecting Bacterial Species

    Science.gov (United States)

    Homer, Margie; Ksendzov, Alexander; Yen, Shiao-Pin; Ryan, Margaret; Lazazzera, Beth

    2006-01-01

    Biomimetic/optical sensors have been proposed as means of real-time detection of bacteria in liquid samples through real-time detection of compounds secreted by the bacteria. Bacterial species of interest would be identified through detection of signaling compounds unique to those species. The best-characterized examples of quorum-signaling compounds are acyl-homoserine lactones and peptides. Each compound, secreted by each bacterium of an affected species, serves as a signal to other bacteria of the same species to engage in a collective behavior when the population density of that species reaches a threshold level analogous to a quorum. A sensor according to the proposal would include a specially formulated biomimetic film, made of a molecularly imprinted polymer (MIP), that would respond optically to the signaling compound of interest. The MIP film would be integrated directly onto an opticalwaveguide- based ring resonator for optical readout. Optically, the sensor would resemble the one described in Chemical Sensors Based on Optical Ring Resonators (NPO-40601), NASA Tech Briefs, Vol. 29, No. 10 (October 2005), page 32. MIPs have been used before as molecular- recognition compounds, though not in the manner of the present proposal. Molecular imprinting is an approach to making molecularly selective cavities in a polymer matrix. These cavities function much as enzyme receptor sites: the chemical functionality and shape of a cavity in the polymer matrix cause the cavity to bind to specific molecules. An MIP matrix is made by polymerizing monomers in the presence of the compound of interest (template molecule). The polymer forms around the template. After the polymer solidifies, the template molecules are removed from the polymer matrix by decomplexing them from their binding sites and then dissolving them, leaving cavities that are matched to the template molecules in size, shape, and chemical functionality. The cavities thus become molecular-recognition sites

  5. Identification of campylobacteria isolated from Danish broilers by phenotypic tests and species-specific PCR assays

    DEFF Research Database (Denmark)

    Wainø, M; Bang, Dan; Lund, Marianne;

    2003-01-01

    To validate a phenotypic Campylobacter species identification method employed to identify campylobacters in broilers by comparison with campylobacterial species identification using various species-specific PCR analyses.......To validate a phenotypic Campylobacter species identification method employed to identify campylobacters in broilers by comparison with campylobacterial species identification using various species-specific PCR analyses....

  6. Computer-aided identification of polymorphism sets diagnostic for groups of bacterial and viral genetic variants

    Directory of Open Access Journals (Sweden)

    Huygens Flavia

    2007-08-01

    Full Text Available Abstract Background Single nucleotide polymorphisms (SNPs and genes that exhibit presence/absence variation have provided informative marker sets for bacterial and viral genotyping. Identification of marker sets optimised for these purposes has been based on maximal generalized discriminatory power as measured by Simpson's Index of Diversity, or on the ability to identify specific variants. Here we describe the Not-N algorithm, which is designed to identify small sets of genetic markers diagnostic for user-specified subsets of known genetic variants. The algorithm does not treat the user-specified subset and the remaining genetic variants equally. Rather Not-N analysis is designed to underpin assays that provide 0% false negatives, which is very important for e.g. diagnostic procedures for clinically significant subgroups within microbial species. Results The Not-N algorithm has been incorporated into the "Minimum SNPs" computer program and used to derive genetic markers diagnostic for multilocus sequence typing-defined clonal complexes, hepatitis C virus (HCV subtypes, and phylogenetic clades defined by comparative genome hybridization (CGH data for Campylobacter jejuni, Yersinia enterocolitica and Clostridium difficile. Conclusion Not-N analysis is effective for identifying small sets of genetic markers diagnostic for microbial sub-groups. The best results to date have been obtained with CGH data from several bacterial species, and HCV sequence data.

  7. Printed Identification Key or Web-Based Identification Guide: An Effective Tool for Species Identification?

    Directory of Open Access Journals (Sweden)

    Thomas Edison E. dela Cruz

    2012-09-01

    Full Text Available Species identification is often done with the aid of traditional dichotomous keys. This printed material is based on one’s decision between two alternatives, which is followed by another pair of alternatives until the final species name is reached. With the advent of internet technology, the use of an online database offers an updatable and accumulative approach to species identification. It can also be accessed anytime, and this is very useful for fast-changing groups of organisms. In this paper, we report the preference of sophomore Bachelor of Science (B.Sc. in Microbiology students to two identification guides as a tool in taxonomy. We wish to test our hypothesis that today’s students will prefer to use web-based ID guides over printed dichotomous keys. We also describe how these printed dichotomous key and web-based ID guides were used by the students as one of their laboratory activities in the course Biology of Algae and Fungi.  

  8. A Real-time Portable Bioacoustics Species Identification Design Concepts

    Directory of Open Access Journals (Sweden)

    Naufal Alee

    2015-04-01

    Full Text Available Recently there has been an increasing demand of an automated system for animal species identification, where it needs a perfect good knowledge, understanding of the nature under vision and proper efficient system design. Embedded systems nowadays are offering a brilliant solution. Based on nature of economic and feasibility of advanced, embedded technology is chosen. This paper proposes a design of real-time portable bioacoustics species identification system. It contains two major correlated modules apart, the identification module and the system control module. The identification module is to be implemented in FPGA hardware to achieve species identification process while the system control module will manage and control the entire system. The proposed system is a combination of hardware, software development and operating system customization. It is designed to be decentralize, therefore the need of any server is eliminated. It can be placed anywhere, can be viewed and accessed from anywhere through a web server built-in.

  9. AFSC/ABL: Juvenile rockfish DNA species identification

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Many pelagic juvenile rockfish (Sebastes) were collected in juvenile salmonid surveys in the Gulf of Alaska (GOA) from 1998 to 2002. Often species identification of...

  10. Interactions between Lactobacillus crispatus and bacterial vaginosis (BV)-Associated bacterial species in initial attachment and biofilm formation

    OpenAIRE

    Kimberly Kay Jefferson; Nuno Cerca; António Machado

    2013-01-01

    Certain anaerobic bacterial species tend to predominate the vaginal flora during bacterial vaginosis (BV), with Gardnerella vaginalis being the most common. However, the exact role of G. vaginalis in BV has not yet been determined. The main goal of this study was to test the hypothesis that G. vaginalis is an early colonizer, paving the way for intermediate (e.g., Fusobacterium nucleatum) and late colonizers (e.g., Prevotella bivia). Theoretically, in order to function as an early colonizer, ...

  11. Identification and characterization of a bacterial hydrosulphide ion channel

    Energy Technology Data Exchange (ETDEWEB)

    Czyzewski, Bryan K.; Wang, Da-Neng (NYUSM)

    2012-10-26

    The hydrosulphide ion (HS{sup -}) and its undissociated form, hydrogen sulphide (H{sub 2}S), which are believed to have been critical to the origin of life on Earth, remain important in physiology and cellular signalling. As a major metabolite in anaerobic bacterial growth, hydrogen sulphide is a product of both assimilatory and dissimilatory sulphate reduction. These pathways can reduce various oxidized sulphur compounds including sulphate, sulphite and thiosulphate. The dissimilatory sulphate reduction pathway uses this molecule as the terminal electron acceptor for anaerobic respiration, in which process it produces excess amounts of H{sub 2}S. The reduction of sulphite is a key intermediate step in all sulphate reduction pathways. In Clostridium and Salmonella, an inducible sulphite reductase is directly linked to the regeneration of NAD{sup +}, which has been suggested to have a role in energy production and growth, as well as in the detoxification of sulphite. Above a certain concentration threshold, both H{sub 2}S and HS{sup -} inhibit cell growth by binding the metal centres of enzymes and cytochrome oxidase, necessitating a release mechanism for the export of this toxic metabolite from the cell. Here we report the identification of a hydrosulphide ion channel in the pathogen Clostridium difficile through a combination of genetic, biochemical and functional approaches. The HS{sup -} channel is a member of the formate/nitrite transport family, in which about 50 hydrosulphide ion channels form a third subfamily alongside those for formate (FocA) and for nitrite (NirC). The hydrosulphide ion channel is permeable to formate and nitrite as well as to HS{sup -} ions. Such polyspecificity can be explained by the conserved ion selectivity filter observed in the channel's crystal structure. The channel has a low open probability and is tightly regulated, to avoid decoupling of the membrane proton gradient.

  12. Gut bacterial community structure of two Australian tropical fruit fly species (Diptera: Tephritidae)

    OpenAIRE

    Narit Thaochan; Richard A.I. Drew; Anuchit Chinajariyawong; Anurag Sunpapao; Chaninun Pornsuriya

    2015-01-01

    The community structure of the alimentary tract bacteria of two Australian fruit fly species, Bactrocera cacuminata (Hering) and Bactrocera tryoni (Froggatt), was studied using a molecular cloning method based on the 16S rRNA gene. Differences in the bacterial community structure were shown between the crops and midguts of the two species and sexes of each species. Proteobacteria was the dominant bacterial phylum in the flies, especially bacteria in the order Gammaproteobacteria w...

  13. Automated identification of animal species in camera trap images

    NARCIS (Netherlands)

    Yu, X.; Wang, J.; Kays, R.; Jansen, P.A.; Wang, T.; Huang, T.

    2013-01-01

    Image sensors are increasingly being used in biodiversity monitoring, with each study generating many thousands or millions of pictures. Efficiently identifying the species captured by each image is a critical challenge for the advancement of this field. Here, we present an automated species identif

  14. Identification and Antimicrobial Susceptibility of Salmonella species Isolated from Washing and Rinsed Water of Broilers in Pluck Shops

    OpenAIRE

    Tuhin-Al-Ferdous; S.M. Lutful Kabir; M. Mansurul Amin; K.M. Mahmud Hossain

    2013-01-01

    The study was designed with a view to isolate, identifies and characterizes Salmonella species from washing and rinsed water of broilers in pluck shops at Sreepur of Gazipur district in Bangladesh during the period from December 2011 to May 2012. A total of 30 samples collected from the different layers of drums of pluck shops’ were subjected to bacterial isolation and identification by using cultural and biochemical techniques. Furthermore, the isolated Salmonella species were characterized ...

  15. Pathogenic Leptospira species express surface-exposed proteins belonging to the bacterial immunoglobulin superfamily.

    Science.gov (United States)

    Matsunaga, James; Barocchi, Michele A; Croda, Julio; Young, Tracy A; Sanchez, Yolanda; Siqueira, Isadora; Bolin, Carole A; Reis, Mitermayer G; Riley, Lee W; Haake, David A; Ko, Albert I

    2003-08-01

    Proteins with bacterial immunoglobulin-like (Big) domains, such as the Yersinia pseudotuberculosis invasin and Escherichia coli intimin, are surface-expressed proteins that mediate host mammalian cell invasion or attachment. Here, we report the identification and characterization of a new family of Big domain proteins, referred to as Lig (leptospiral Ig-like) proteins, in pathogenic Leptospira. Screening of L. interrogans and L. kirschneri expression libraries with sera from leptospirosis patients identified 13 lambda phage clones that encode tandem repeats of the 90 amino acid Big domain. Two lig genes, designated ligA and ligB, and one pseudogene, ligC, were identified. The ligA and ligB genes encode amino-terminal lipoprotein signal peptides followed by 10 or 11 Big domain repeats and, in the case of ligB, a unique carboxy-terminal non-repeat domain. The organization of ligC is similar to that of ligB but contains mutations that disrupt the reading frame. The lig sequences are present in pathogenic but not saprophytic Leptospira species. LigA and LigB are expressed by a variety of virulent leptospiral strains. Loss of Lig protein and RNA transcript expression is correlated with the observed loss of virulence during culture attenuation of pathogenic strains. High-pressure freeze substitution followed by immunocytochemical electron microscopy confirmed that the Lig proteins were localized to the bacterial surface. Immunoblot studies with patient sera found that the Lig proteins are a major antigen recognized during the acute host infection. These observations demonstrate that the Lig proteins are a newly identified surface protein of pathogenic Leptospira, which by analogy to other bacterial immunoglobulin superfamily virulence factors, may play a role in host cell attachment and invasion during leptospiral pathogenesis. PMID:12890019

  16. Dealing with the identification of protein species in ancient amphorae.

    Science.gov (United States)

    Dallongeville, Sophie; Garnier, Nicolas; Casasola, Dario Bernal; Bonifay, Michel; Rolando, Christian; Tokarski, Caroline

    2011-03-01

    This manuscript deals with the identification of protein residues in amphorae, including particularly identification of protein species. The work described was performed on fishes, the anchovy (Engraulis encrasicolus) and bonito (Sarda sarda) species frequently found in the Mediterranean area. Based on proteomic techniques, the analytical strategy was adapted to analysis of protein residues from tiny ceramic fragments. The major difficulty was to extract proteins and limit their hydrolysis during the sample preparation; consequently, multiple soft extraction techniques were evaluated. The most valuable results were obtained using a solution containing high amounts of denaturing agents, urea and thiourea, reducing agent, dithiothreitol, and detergent, 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate. The analysis using nano liquid chromatography-nano electrospray ionization double quadrupole time-of-flight mass spectrometry resulted in the identification of up to 200 proteins for the anchovy and bonito species, among which 73 peptides were found to be fish-specific. Because bonito and anchovy species are not documented and fully sequenced in genomic databases, the preliminary protein identification was realized via sequence homology to other fish sequenced species. Amino acid substitutions of peptides were assigned on the basis of the interpretation of tandem mass spectrometry spectra using de novo sequencing; these peptides, not reported up to now in databases, constitute species-specific markers. The method developed was finally applied to an archaeological sample replica impregnated with a mixture of fish tissue from both species; this experiment successfully led to the identification of 17 fish proteins, including 33 fish-specific peptides. This work shows that the analytical method developed has great potential for the identification of protein species in complex archaeological samples. PMID:20890751

  17. Application of Routine Diagnostic Procedure, VITEK 2 Compact, MALDI-TOF MS, and PCR Assays in Identification Procedure of Bacterial Strain with Ambiguous Phenotype.

    Science.gov (United States)

    Książczyk, Marta; Kuczkowski, Maciej; Dudek, Bartłomiej; Korzekwa, Kamila; Tobiasz, Anna; Korzeniowska-Kowal, Agnieszka; Paluch, Emil; Wieliczko, Alina; Bugla-Płoskońska, Gabriela

    2016-05-01

    In diagnostic microbiology as well as in microbiological research, the identification of a microorganism is a crucial and decisive stage. A broad choice of methods is available, based on both phenotypic and molecular properties of microbes. The aim of this study was to compare the application of phenotypic and molecular tools in bacterial identification on the example of Gram-negative intestine rod with an ambiguous phenotype. Different methods of identification procedure, which based on various properties of bacteria, were applied, e.g., microscopic observation of single-bacterial cells, macroscopic observation of bacterial colonies morphology, the automated system of microorganism identification (biochemical tests), the mass spectrometry method (analysis of bacterial proteome), and genetic analysis with PCR reactions. The obtained results revealed discrepancies in the identification of the tested bacterial strain with an atypical phenotype: mucous morphology of colonies, not characteristic for either E. coli and Citrobacter spp., mass spectrometry analysis of proteome initially assigned the tested strain to Citrobacter genus (C. freundii) and biochemical profiles pointed to Escherichia coli. A decisive method in the current study was genetic analysis with PCR reactions which identified conserved genetic sequences highly specific to E. coli species in the genome of the tested strain. PMID:26804795

  18. Spatial Organization of Dual-Species Bacterial Aggregates on Leaf Surfaces

    OpenAIRE

    Monier, J.-M.; Lindow, S E

    2005-01-01

    The spatial organization of cells within bacterial aggregates on leaf surfaces was determined for pair-wise mixtures of three different bacterial species commonly found on leaves, Pseudomonas syringae, Pantoea agglomerans, and Pseudomonas fluorescens. Cells were coinoculated onto bean plants and allowed to grow under moist conditions, and the resulting aggregates were examined in situ by epifluorescence microscopy. Each bacterial strain could be localized because it expressed either the green...

  19. Identification of self-consistent modulons from bacterial microarray expression data with the help of structured regulon gene sets

    KAUST Repository

    Permina, Elizaveta A.

    2013-01-01

    Identification of bacterial modulons from series of gene expression measurements on microarrays is a principal problem, especially relevant for inadequately studied but practically important species. Usage of a priori information on regulatory interactions helps to evaluate parameters for regulatory subnetwork inference. We suggest a procedure for modulon construction where a seed regulon is iteratively updated with genes having expression patterns similar to those for regulon member genes. A set of genes essential for a regulon is used to control modulon updating. Essential genes for a regulon were selected as a subset of regulon genes highly related by different measures to each other. Using Escherichia coli as a model, we studied how modulon identification depends on the data, including the microarray experiments set, the adopted relevance measure and the regulon itself. We have found that results of modulon identification are highly dependent on all parameters studied and thus the resulting modulon varies substantially depending on the identification procedure. Yet, modulons that were identified correctly displayed higher stability during iterations, which allows developing a procedure for reliable modulon identification in the case of less studied species where the known regulatory interactions are sparse. Copyright © 2013 Taylor & Francis.

  20. Identification and Characterization of Inhibitors of Bacterial Enoyl-Acyl Carrier Protein Reductase

    OpenAIRE

    Ling, Losee L.; Xian, Jun; Ali, Syed; Geng, Bolin; Fan, Jun; Mills, Debra M.; Arvanites, Anthony C.; Orgueira, Hernan; Ashwell, Mark A.; Carmel, Gilles; Xiang, Yibin; Moir, Donald T.

    2004-01-01

    Bacterial enoyl-acyl carrier protein reductase (ENR) catalyzes an essential step in fatty acid biosynthesis. ENR is an attractive target for narrow-spectrum antibacterial drug discovery because of its essential role in metabolism and its sequence conservation across many bacterial species. In addition, the bacterial ENR sequence and structural organization are distinctly different from those of mammalian fatty acid biosynthesis enzymes. High-throughput screening to identify inhibitors of Esch...

  1. Amazonian dark Earth and plant species from the Amazon region contribute to shape rhizosphere bacterial communities.

    Science.gov (United States)

    Barbosa Lima, Amanda; Cannavan, Fabiana Souza; Navarrete, Acacio Aparecido; Teixeira, Wenceslau Geraldes; Kuramae, Eiko Eurya; Tsai, Siu Mui

    2015-05-01

    Amazonian Dark Earths (ADE) or Terra Preta de Índio formed in the past by pre-Columbian populations are highly sustained fertile soils supported by microbial communities that differ from those extant in adjacent soils. These soils are found in the Amazon region and are considered as a model soil when compared to the surrounding and background soils. The aim of this study was to assess the effects of ADE and its surrounding soil on the rhizosphere bacterial communities of two leguminous plant species that frequently occur in the Amazon region in forest sites (Mimosa debilis) and open areas (Senna alata). Bacterial community structure was evaluated using terminal restriction fragment length polymorphism (T-RFLP) and bacterial community composition by V4 16S rRNA gene region pyrosequencing. T-RFLP analysis showed effect of soil types and plant species on rhizosphere bacterial community structure. Differential abundance of bacterial phyla, such as Acidobacteria, Actinobacteria, Verrucomicrobia, and Firmicutes, revealed that soil type contributes to shape the bacterial communities. Furthermore, bacterial phyla such as Firmicutes and Nitrospira were mostly influenced by plant species. Plant roots influenced several soil chemical properties, especially when plants were grown in ADE. These results showed that differences observed in rhizosphere bacterial community structure and composition can be influenced by plant species and soil fertility due to variation in soil attributes. PMID:25103911

  2. Cryptococcus species identification by multiplex PCR.

    Science.gov (United States)

    Leal, Ana Lusia; Faganello, Josiane; Bassanesi, Maria Cristina; Vainstein, Marilene H

    2008-06-01

    Members of the Cryptococcus species complex are encapsulated basidiomycetous yeasts, which can affect the central nervous system (CNS) and if untreated may cause meningitis. Cryptococcus neoformans is an opportunistic pathogen causing infections mainly in immunocompromised individuals. Cryptococcus gattii is a primary pathogen responsible for a high incidence of cryptococcomas in the lung and brain and shows a delayed response to antifungal therapy. The differentiation between the two species is primarily based on their growth on and color change of canavanine - glycine-bromothymol blue agar (CGB). Since this test is not always reliable, a multiplex PCR to identify both Cryptococcus species using more than 130 samples was standardized and the results obtained compared to those with the CGB test, using the Crypto Check serotyping kit as the standard. The multiplex PCR was shown to be more specific than the CGB test, in that results obtained with it were in agreement with those from serotyping all the samples, while the data from the CGB test disagreed with 6 out of 131 samples. PMID:18415847

  3. Species identification of archaeological skin objects from Danish bogs

    DEFF Research Database (Denmark)

    Brandt, Luise Ørsted; Schmidt, Anne Lisbeth; Mannering, Ulla; Kelstrup, Christian D.; Olsen, Jesper V.; Cappellini, Enrico

    2014-01-01

    species used for the production of skin garments. Until recently, species identification of archaeological skin was primarily performed by light and scanning electron microscopy or the analysis of ancient DNA. However, the efficacy of these methods can be limited due to the harsh, mostly acidic...... MS-based methods, mostly relying on peptide fingerprinting, the shotgun sequencing approach we describe aims to identify the complete extracted ancient proteome, without preselected specific targets. As an example, we report the identification, in one of the samples, of two peptides uniquely assigned...

  4. Identification of bacterial taxa in archaeological waterlogged wood

    OpenAIRE

    Franco Palla; Giovanna Barresi; Enza Di Carlo

    2014-01-01

    The microscopic and molecular techniques described in this study are aimed at understanding the degradation processes of the anatomical structure of submerged archaeological wood, correlating it to the degradation induced by bacteria. The SEM micrographs showed alterations of the wooden structure due to bacterial colonization, as well as the presence of pyrite framboids. The difficulty of extracting bacterial DNA from wooden fragments belonging to submerged finds is well-known, due to the pre...

  5. Identification of Bacterial Small RNAs by RNA Sequencing

    DEFF Research Database (Denmark)

    Gómez Lozano, María; Marvig, Rasmus Lykke; Molin, Søren;

    2014-01-01

    Small regulatory RNAs (sRNAs) in bacteria are known to modulate gene expression and control a variety of processes including metabolic reactions, stress responses, and pathogenesis in response to environmental signals. A method to identify bacterial sRNAs on a genome-wide scale based on RNA seque...

  6. Identification of an emergent bacterial blight of garlic in Brazil

    Science.gov (United States)

    Outbreaks of a bacterial blight disease occurred on garlic (Allium sativum) cultivars Roxo Caxiense, Quiteria and Cacador in Southern Brazil, and threatened the main production regions of Rio Grande do Sul State. Symptoms were characterized by watersoaked reddish streaks along the leaf midrib, follo...

  7. DNA barcoding: complementing morphological identification of mosquito species in Singapore

    OpenAIRE

    Chan, Abigail; Chiang, Lee-Pei; Hapuarachchi, Hapuarachchige C; Tan, Cheong-Huat; Pang, Sook-Cheng; Lee, Ruth; Lee, Kim-Sung; Ng, Lee-Ching; Lam-Phua, Sai-Gek

    2014-01-01

    Background Taxonomy that utilizes morphological characteristics has been the gold standard method to identify mosquito species. However, morphological identification is challenging when the expertise is limited and external characters are damaged because of improper specimen handling. Therefore, we explored the applicability of mitochondrial cytochrome C oxidase subunit 1 (COI) gene-based DNA barcoding as an alternative tool to identify mosquito species. In the present study, we compared the ...

  8. Bacterial profiling of White Plague Disease in a comparative coral species framework.

    KAUST Repository

    Roder, Cornelia

    2014-01-01

    Coral reefs are threatened throughout the world. A major factor contributing to their decline is outbreaks and propagation of coral diseases. Due to the complexity of coral-associated microbe communities, little is understood in terms of disease agents, hosts and vectors. It is known that compromised health in corals is correlated with shifts in bacterial assemblages colonizing coral mucus and tissue. However, general disease patterns remain, to a large extent, ambiguous as comparative studies over species, regions, or diseases are scarce. Here, we compare bacterial assemblages of samples from healthy (HH) colonies and such displaying signs of White Plague Disease (WPD) of two different coral species (Pavona duerdeni and Porites lutea) from the same reef in Koh Tao, Thailand, using 16S rRNA gene microarrays. In line with other studies, we found an increase of bacterial diversity in diseased (DD) corals, and a higher abundance of taxa from the families that include known coral pathogens (Alteromonadaceae, Rhodobacteraceae, Vibrionaceae). In our comparative framework analysis, we found differences in microbial assemblages between coral species and coral health states. Notably, patterns of bacterial community structures from HH and DD corals were maintained over species boundaries. Moreover, microbes that differentiated the two coral species did not overlap with microbes that were indicative of HH and DD corals. This suggests that while corals harbor distinct species-specific microbial assemblages, disease-specific bacterial abundance patterns exist that are maintained over coral species boundaries.

  9. Bacterial profiling of White Plague Disease in a comparative coral species framework.

    Science.gov (United States)

    Roder, Cornelia; Arif, Chatchanit; Bayer, Till; Aranda, Manuel; Daniels, Camille; Shibl, Ahmed; Chavanich, Suchana; Voolstra, Christian R

    2014-01-01

    Coral reefs are threatened throughout the world. A major factor contributing to their decline is outbreaks and propagation of coral diseases. Due to the complexity of coral-associated microbe communities, little is understood in terms of disease agents, hosts and vectors. It is known that compromised health in corals is correlated with shifts in bacterial assemblages colonizing coral mucus and tissue. However, general disease patterns remain, to a large extent, ambiguous as comparative studies over species, regions, or diseases are scarce. Here, we compare bacterial assemblages of samples from healthy (HH) colonies and such displaying signs of White Plague Disease (WPD) of two different coral species (Pavona duerdeni and Porites lutea) from the same reef in Koh Tao, Thailand, using 16S rRNA gene microarrays. In line with other studies, we found an increase of bacterial diversity in diseased (DD) corals, and a higher abundance of taxa from the families that include known coral pathogens (Alteromonadaceae, Rhodobacteraceae, Vibrionaceae). In our comparative framework analysis, we found differences in microbial assemblages between coral species and coral health states. Notably, patterns of bacterial community structures from HH and DD corals were maintained over species boundaries. Moreover, microbes that differentiated the two coral species did not overlap with microbes that were indicative of HH and DD corals. This suggests that while corals harbor distinct species-specific microbial assemblages, disease-specific bacterial abundance patterns exist that are maintained over coral species boundaries. PMID:23924783

  10. Interactions between Lactobacillus crispatus and bacterial vaginosis (BV)-associated bacterial species in initial attachment and biofilm formation.

    Science.gov (United States)

    Machado, António; Jefferson, Kimberly Kay; Cerca, Nuno

    2013-01-01

    Certain anaerobic bacterial species tend to predominate the vaginal flora during bacterial vaginosis (BV), with Gardnerella vaginalis being the most common. However, the exact role of G. vaginalis in BV has not yet been determined. The main goal of this study was to test the hypothesis that G. vaginalis is an early colonizer, paving the way for intermediate (e.g., Fusobacterium nucleatum) and late colonizers (e.g., Prevotella bivia). Theoretically, in order to function as an early colonizer, species would need to be able to adhere to vaginal epithelium, even in the presence of vaginal lactobacilli. Therefore, we quantified adherence of G. vaginalis and other BV-associated bacteria to an inert surface pre-coated with Lactobacillus crispatus using a new Peptide Nucleic Acid (PNA) Fluorescence In Situ Hybridization (FISH) methodology. We found that G. vaginalis had the greatest capacity to adhere in the presence of L. crispatus. Theoretically, an early colonizer would contribute to the adherence and/or growth of additional species, so we next quantified the effect of G. vaginalis biofilms on the adherence and growth of other BV-associated species by quantitative Polymerase Chain Reaction (qPCR) technique. Interestingly, G. vaginalis derived a growth benefit from the addition of a second species, regardless of the species. Conversely, G. vaginalis biofilms enhanced the growth of P. bivia, and to a minor extent of F. nucleatum. These results contribute to our understanding of BV biofilm formation and the progression of the disorder. PMID:23739678

  11. Interactions between Lactobacillus crispatus and Bacterial Vaginosis (BV-Associated Bacterial Species in Initial Attachment and Biofilm Formation

    Directory of Open Access Journals (Sweden)

    Kimberly Kay Jefferson

    2013-06-01

    Full Text Available Certain anaerobic bacterial species tend to predominate the vaginal flora during bacterial vaginosis (BV, with Gardnerella vaginalis being the most common. However, the exact role of G. vaginalis in BV has not yet been determined. The main goal of this study was to test the hypothesis that G. vaginalis is an early colonizer, paving the way for intermediate (e.g., Fusobacterium nucleatum and late colonizers (e.g., Prevotella bivia. Theoretically, in order to function as an early colonizer, species would need to be able to adhere to vaginal epithelium, even in the presence of vaginal lactobacilli. Therefore, we quantified adherence of G. vaginalis and other BV-associated bacteria to an inert surface pre-coated with Lactobacillus crispatus using a new Peptide Nucleic Acid (PNA Fluorescence In Situ Hybridization (FISH methodology. We found that G. vaginalis had the greatest capacity to adhere in the presence of L. crispatus. Theoretically, an early colonizer would contribute to the adherence and/or growth of additional species, so we next quantified the effect of G. vaginalis biofilms on the adherence and growth of other BV-associated species by quantitative Polymerase Chain Reaction (qPCR technique. Interestingly, G. vaginalis derived a growth benefit from the addition of a second species, regardless of the species. Conversely, G. vaginalis biofilms enhanced the growth of P. bivia, and to a minor extent of F. nucleatum. These results contribute to our understanding of BV biofilm formation and the progression of the disorder.

  12. Direct identification of pure penicillium species using image analysis

    DEFF Research Database (Denmark)

    Dørge, Thorsten Carlheim; Carstensen, Jens Michael; Frisvad, Jens Christian

    2000-01-01

    This paper presents a method for direct identification of fungal species solely by means of digital image analysis of colonies as seen after growth on a standard medium. The method described is completely automated and hence objective once digital images of the reference fungi have been establish...

  13. Identification and characterization of a bacterial glutamic peptidase

    Directory of Open Access Journals (Sweden)

    Jensen Kenneth

    2010-12-01

    Full Text Available Abstract Background Glutamic peptidases, from the MEROPS family G1, are a distinct group of peptidases characterized by a catalytic dyad consisting of a glutamate and a glutamine residue, optimal activity at acidic pH and insensitivity towards the microbial derived protease inhibitor, pepstatin. Previously, only glutamic peptidases derived from filamentous fungi have been characterized. Results We report the first characterization of a bacterial glutamic peptidase (pepG1, derived from the thermoacidophilic bacteria Alicyclobacillus sp. DSM 15716. The amino acid sequence identity between pepG1 and known fungal glutamic peptidases is only 24-30% but homology modeling, the presence of the glutamate/glutamine catalytic dyad and a number of highly conserved motifs strongly support the inclusion of pepG1 as a glutamic peptidase. Phylogenetic analysis places pepG1 and other putative bacterial and archaeal glutamic peptidases in a cluster separate from the fungal glutamic peptidases, indicating a divergent and independent evolution of bacterial and fungal glutamic peptidases. Purification of pepG1, heterologously expressed in Bacillus subtilis, was performed using hydrophobic interaction chromatography and ion exchange chromatography. The purified peptidase was characterized with respect to its physical properties. Temperature and pH optimums were found to be 60°C and pH 3-4, in agreement with the values observed for the fungal members of family G1. In addition, pepG1 was found to be pepstatin-insensitive, a characteristic signature of glutamic peptidases. Conclusions Based on the obtained results, we suggest that pepG1 can be added to the MEROPS family G1 as the first characterized bacterial member.

  14. Identification of leptospiral isolates by bacterial restriction endonuclease analysis (Brenda

    Directory of Open Access Journals (Sweden)

    Venkatesha M

    2001-01-01

    Full Text Available DNA samples from 19 reference serovars belonging to 19 different serogroups of Leptospira interrogans and two serovars belonging to Leptospira biflexa were examined by bacterial restriction endonuclease analysis using EcoR I and Hae III enzymes. All the serovars gave unique restriction patterns that differed from each other. DNA from 10 local isolates digested with these enzymes produced patterns which on comparison with the standard patterns produced by reference strains could be identified to serovar level.

  15. Association between Lactobacillus species and bacterial vaginosis-related bacteria, and bacterial vaginosis scores in pregnant Japanese women

    Directory of Open Access Journals (Sweden)

    Yamada Hideto

    2007-11-01

    Full Text Available Abstract Background Bacterial vaginosis (BV, the etiology of which is still uncertain, increases the risk of preterm birth. Recent PCR-based studies suggested that BV is associated with complex vaginal bacterial communities, including many newly recognized bacterial species in non-pregnant women. Methods To examine whether these bacteria are also involved in BV in pregnant Japanese women, vaginal fluid samples were taken from 132 women, classified as normal (n = 98, intermediate (n = 21, or BV (n = 13 using the Nugent gram stain criteria, and studied. DNA extracted from these samples was analyzed for bacterial sequences of any Lactobacillus, four Lactobacillus species, and four BV-related bacteria by PCR with primers for 16S ribosomal DNA including a universal Lactobacillus primer, Lactobacillus species-specific primers for L. crispatus, L. jensenii, L. gasseri, and L. iners, and BV-related bacterium-specific primers for BVAB2, Megasphaera, Leptotrichia, and Eggerthella-like bacterium. Results The prevalences of L. crispatus, L. jensenii, and L. gasseri were significantly higher, while those of BVAB2, Megasphaera, Leptotrichia, and Eggerthella-like bacterium were significantly lower in the normal group than in the BV group. Unlike other Lactobacillus species, the prevalence of L. iners did not differ between the three groups and women with L. iners were significantly more likely to have BVAB2, Megasphaera, Leptotrichia, and Eggerthella-like bacterium. Linear regression analysis revealed associations of BVAB2 and Megasphaera with Nugent score, and multivariate regression analyses suggested a close relationship between Eggerthella-like bacterium and BV. Conclusion The BV-related bacteria, including BVAB2, Megasphaera, Leptotrichia, and Eggerthella-like bacterium, are common in the vagina of pregnant Japanese women with BV. The presence of L. iners may be correlated with vaginal colonization by these BV-related bacteria.

  16. Direct identification of pure penicillium species using image analysis

    DEFF Research Database (Denmark)

    Dørge, Thorsten Carlheim; Carstensen, Jens Michael; Frisvad, Jens Christian

    2000-01-01

    This paper presents a method for direct identification of fungal species solely by means of digital image analysis of colonies as seen after growth on a standard medium. The method described is completely automated and hence objective once digital images of the reference fungi have been established....... The method used to determine the position of the colonies will be covered as well as the feature selection. The texture measurements of colonies of the nine species were analyzed and a clustering of the data into the correct species was confirmed. This indicates that it is indeed possible to identify...

  17. Direct identification of clinically relevant bacterial and yeast microcolonies and macrocolonies on solid culture media by Raman spectroscopy.

    Science.gov (United States)

    Espagnon, Isabelle; Ostrovskii, Denis; Mathey, Raphaël; Dupoy, Mathieu; Joly, Pierre L; Novelli-Rousseau, Armelle; Pinston, Frédéric; Gal, Olivier; Mallard, Frédéric; Leroux, Denis F

    2014-02-01

    Decreasing turnaround time is a paramount objective in clinical diagnosis. We evaluated the discrimination power of Raman spectroscopy when analyzing colonies from 80 strains belonging to nine bacterial and one yeast species directly on solid culture medium after 24-h (macrocolonies) and 6-h (microcolonies) incubation. This approach, that minimizes sample preparation and culture time, would allow resuming culture after identification to perform downstream antibiotic susceptibility testing. Correct identification rates measured for macrocolonies and microcolonies reached 94.1% and 91.5%, respectively, in a leave-one-strain-out cross-validation mode without any correction for possible medium interference. Large spectral differences were observed between macrocolonies and microcolonies, that were attributed to true biological differences. Our results, conducted on a very diversified panel of species and strains, were obtained by using simple and robust sample preparation and preprocessing procedures, while still confirming published results obtained by using more complex elaborated protocols. Instrumentation is simplified by the use of 532-nm laser excitation yielding a Raman signal in the visible range. It is, to our knowledge, the first side-by-side full classification study of microorganisms in the exponential and stationary phases confirming the excellent performance of Raman spectroscopy for early species-level identification of microorganisms directly from an agar culture. PMID:24522809

  18. Identification of Burkholderia pseudomallei Near-Neighbor Species in the Northern Territory of Australia.

    Directory of Open Access Journals (Sweden)

    Jennifer L Ginther

    Full Text Available Identification and characterization of near-neighbor species are critical to the development of robust molecular diagnostic tools for biothreat agents. One such agent, Burkholderia pseudomallei, a soil bacterium and the causative agent of melioidosis, is lacking in this area because of its genomic diversity and widespread geographic distribution. The Burkholderia genus contains over 60 species and occupies a large range of environments including soil, plants, rhizospheres, water, animals and humans. The identification of novel species in new locations necessitates the need to identify the true global distribution of Burkholderia species, especially the members that are closely related to B. pseudomallei. In our current study, we used the Burkholderia-specific recA sequencing assay to analyze environmental samples from the Darwin region in the Northern Territory of Australia where melioidosis is endemic. Burkholderia recA PCR negative samples were further characterized using 16s rRNA sequencing for species identification. Phylogenetic analysis demonstrated that over 70% of the bacterial isolates were identified as B. ubonensis indicating that this species is common in the soil where B. pseudomallei is endemic. Bayesian phylogenetic analysis reveals many novel branches within the B. cepacia complex, one novel B. oklahomensis-like species, and one novel branch containing one isolate that is distinct from all other samples on the phylogenetic tree. During the analysis with recA sequencing, we discovered 2 single nucleotide polymorphisms in the reverse priming region of B. oklahomensis. A degenerate primer was developed and is proposed for future use. We conclude that the recA sequencing technique is an effective tool to classify Burkholderia and identify soil organisms in a melioidosis endemic area.

  19. AADNMR: A Simple Method for Rapid Identification of Bacterial/Mycobacterial Infections in Antibiotic Treated Peritoneal Dialysis Effluent Samples for Diagnosis of Infectious Peritonitis

    CERN Document Server

    Guleria, Anupam; Rawat, Atul; Khetrapal, C L; Prasad, Narayan; Kumar, Dinesh

    2014-01-01

    An efficient method is reported for rapid identification of bacterial or mycobacterial infection in a suspected clinical/biological sample. The method is based on the fact that the ring methylene protons of cyclic fatty acids (constituting the cell membrane of several species of bacteria and mycobacteria) resonate specifically between -0.40 and 0.68 ppm region of the 1H NMR spectrum. These cyclic fatty acids are rarely found in the eukaryotic cell membranes. Therefore, the signals from cyclic ring moiety of these fatty acids can be used as markers (a) for the identification of bacterial and mycobacterial infections and (b) for differential diagnosis of bacterial and fungal infections. However, these microbial fatty acids when present inside the membrane are not easily detectable by NMR owing to their fast T2 relaxation. Nonetheless, the problem can easily be circumvented if these fatty acids become suspended in solution. This has been achieved by abolishing the membrane integrity using broad spectrum antibiot...

  20. Chromosphores in cellulosics, XI: isoloation and identification of residual chromophores from bacterial cellulose

    Science.gov (United States)

    In the present work, bacterial cellulose (BC) was analyzed for its chromophore content with the chromophore release and identification (CRI) method. In aged BC, seven chromophores were unambiguously identified, despite their very low (ppb) presence. The compounds contain 2-hydroxy-[1,4]benzoquinone,...

  1. Species-specific mitochondrial gene rearrangements in biting midges and vector species identification.

    Science.gov (United States)

    Matsumoto, Y; Yanase, T; Tsuda, T; Noda, H

    2009-03-01

    Partial mitochondrial gene sequences of 16 Culicoides species were determined to elucidate phylogenetic relations among species and to develop a molecular identification method for important virus vector species. In addition, the analysis found mitochondrial gene rearrangement in several species. Sequences of the mitochondrial genome region, cox1-trnL2-cox2 (1940-3785 bp) of 16 Culicoides and additional sequences were determined in some species, including whole mitochondrial genome sequences of Culicoides arakawae. Nine species showed common organization in this region, with three genes cox1-trnL2-cox2 and a small or no intergenic region (0-30 bp) between them. The other seven species showed translocation of tRNA and protein-coding genes and/or insertion of AT-rich non-coding sequences (65-1846 bp) between the genes. The varied gene rearrangements among species within a genus is very rare for mitochondrial genome organization. Phylogenetic analyses based on the sequences of cox1+cox2 suggest a few clades among Japanese Culicoides species. No relationships between phylogenetic closeness and mitochondrial gene rearrangements were observed. Sequence data were used to establish a polymerase chain reaction tool to distinguish three important vector species from other Culicoides species, for which classification during larval stages is not advanced and identification is difficult. PMID:19239613

  2. The Identification of Haemonchus Species and Diagnosis of Haemonchosis.

    Science.gov (United States)

    Zarlenga, D S; Hoberg, E P; Tuo, W

    2016-01-01

    Diagnosis is often equated with identification or detection when discussing parasitic diseases. Unfortunately, these are not necessarily mutually exclusive activities; diseases and infections are generally diagnosed and organisms are identified. Diagnosis is commonly predicated upon some clinical signs; in an effort to determine the causative agent, identification of genera and species is subsequently performed. Both identification and diagnosis play critical roles in managing an infection, and involve the interplay of direct and indirect methods of detection, particularly in light of the complex and expanding problem of drug-resistance in parasites. Accurate and authoritative identification that is cost- and time-effective, based on structural and molecular attributes of specimens, provides a foundation for defining parasite diversity and changing patterns of geographical distribution, host association and emergence of disease. Most techniques developed thus far have been grounded in assumptions based on strict host associations between Haemonchus contortus and small ruminants, that is, sheep and goats, and between Haemonchus placei and bovids. Current research and increasing empirical evidence of natural infections in the field demonstrates that this assumption misrepresents the host associations for these species of Haemonchus. Furthermore, the capacity of H. contortus to utilize a considerably broad spectrum of ungulate hosts is reflected in our understanding of the role of anthropogenic forcing, the 'breakdown' of ecological isolation, global introduction and host switching as determinants of distribution. Nuanced insights about distribution, host association and epidemiology have emerged over the past 30years, coincidently with the development of increasingly robust means for parasite identification. In this review and for the sake of argument, we would like to delineate the diagnosis of haemonchosis from the identification of the specific pathogen. As a

  3. New Bacterial Species Isolated from Malaysian Sea Cucumbers with Optimized Secreted Antibacterial Activity

    Directory of Open Access Journals (Sweden)

    Abd E. Farouk

    2007-01-01

    Full Text Available In this study, several Malaysian sea cucumber species that have traditional medicine value were selected and from them, the native bacterial population was isolated. Optimization of growth was designed and all bacterial secretions were tested for antibacterial properties. 30 bacterial types were isolated and 7 types recorded moderate antibacterial activity against K. pneumoniae, S. marscens, P. aeruginosa and E. feacalis. Antibacterial plate screening was done, with various testing parameters. Turbidometry revealed a single dose of the 10x concentrated crude antibacterial extracts were effective in preventing pathogenic growth for up to 4 hrs. PCR and subsequent sequencing of the 16S rDNA showed that the bacterial species were from the halopholic Bacillus and Klebsiella genera.

  4. High-Throughput Identification and Quantification of Candida Species Using High Resolution Derivative Melt Analysis of Panfungal Amplicons

    OpenAIRE

    Mandviwala, Tasneem; Shinde, Rupali; Kalra, Apoorv; Jack D. Sobel; Akins, Robert A.

    2010-01-01

    Fungal infections pose unique challenges to molecular diagnostics; fungal molecular diagnostics consequently lags behind bacterial and viral counterparts. Nevertheless, fungal infections are often life-threatening, and early detection and identification of species is crucial to successful intervention. A high throughput PCR-based method is needed that is independent of culture, is sensitive to the level of one fungal cell per milliliter of blood or other tissue types, and is capable of detect...

  5. A peptide identification-free, genome sequence-independent shotgun proteomics workflow for strain-level bacterial differentiation

    OpenAIRE

    Wenguang Shao; Min Zhang; Henry Lam; Lau, Stanley C K

    2015-01-01

    Shotgun proteomics is an emerging tool for bacterial identification and differentiation. However, the identification of the mass spectra of peptides to genome-derived peptide sequences remains a key issue that limits the use of shotgun proteomics to bacteria with genome sequences available. In this proof-of-concept study, we report a novel bacterial fingerprinting method that enjoys the resolving power and accuracy of mass spectrometry without the burden of peptide identification (i.e. genome...

  6. Real-time bioacoustics monitoring and automated species identification

    Directory of Open Access Journals (Sweden)

    T. Mitchell Aide

    2013-07-01

    Full Text Available Traditionally, animal species diversity and abundance is assessed using a variety of methods that are generally costly, limited in space and time, and most importantly, they rarely include a permanent record. Given the urgency of climate change and the loss of habitat, it is vital that we use new technologies to improve and expand global biodiversity monitoring to thousands of sites around the world. In this article, we describe the acoustical component of the Automated Remote Biodiversity Monitoring Network (ARBIMON, a novel combination of hardware and software for automating data acquisition, data management, and species identification based on audio recordings. The major components of the cyberinfrastructure include: a solar powered remote monitoring station that sends 1-min recordings every 10 min to a base station, which relays the recordings in real-time to the project server, where the recordings are processed and uploaded to the project website (arbimon.net. Along with a module for viewing, listening, and annotating recordings, the website includes a species identification interface to help users create machine learning algorithms to automate species identification. To demonstrate the system we present data on the vocal activity patterns of birds, frogs, insects, and mammals from Puerto Rico and Costa Rica.

  7. Reactive oxygen species-mediated bacterial killing by B lymphocytes.

    Science.gov (United States)

    Kovács, István; Horváth, Magdolna; Lányi, Árpád; Petheő, Gábor L; Geiszt, Miklós

    2015-06-01

    Regulated production of ROS is mainly attributed to Nox family enzymes. In neutrophil granulocytes and macrophages, Nox2 has a crucial role in bacterial killing, and the absence of phagocytic ROS production leads to the development of CGD. Expression of Nox2 was also described in B lymphocytes, where the role of the enzyme is still poorly understood. Here, we show that peritoneal B cells, which were shown recently to possess phagocytic activity, have a high capacity to produce ROS in a Nox2-dependent manner. In phagocytosing B cells, intense intraphagosomal ROS production is detected. Finally, by studying 2 animal models of CGD, we demonstrate that phagocyte oxidase-deficient B cells have a reduced capacity to kill bacteria. Our observations extend the number of immune cell types that produce ROS to kill pathogens. PMID:25821233

  8. Inter- and intraspecies identification of Bartonella (Rochalimaea) species.

    Science.gov (United States)

    Roux, V; Raoult, D

    1995-06-01

    Species of the genus Rochalimaea, recently renamed Bartonella, are of a growing medical interest. Bartonella quintana was reported as the cause of trench fever, endocarditis, and bacillary angiomatosis. B. henselae has been implicated in symptoms and infections of human immunodeficiency virus-infected patients, such as fever, endocarditis, and bacillary angiomatosis, and is involved in the etiology of cat scratch disease. Such a wide spectrum of infections makes it necessary to obtain an intraspecies identification tool in order to perform epidemiological studies. B. vinsonii, B. elizabethae, seven isolates of B. quintana, and four isolates of B. henselae were studied by pulsed-field gel electrophoresis (PFGE) after restriction with the infrequently cutting endonucleases NotI, EagI, and SmaI. Specific profiles were obtained for each of the four Bartonella species. Comparison of genomic fingerprints of isolates of the same species showed polymorphism in DNA restriction patterns, and a specific profile was obtained for each isolate. A phylogenetic analysis of the B. quintana isolates was obtained by using the Dice coefficient, UPGMA (unweighted pair-group method of arithmetic averages), and Package Philip programming. Amplification by PCR and subsequent sequencing using an automated laser fluorescent DNA sequencer (Pharmacia) was performed on the intergenic spacer region (ITS) between the 16 and 23S rRNA genes. It was found that each B. henselae isolate had a specific sequence, while the B. quintana isolates fell into only two groups. When endonuclease restriction analysis of the ITS PCR product was done, three enzymes, TaqI, HindIII, and HaeIII, allowed species identification of Bartonella spp. Restriction fragment length polymorphism after PCR amplification of the 16S-23S rRNA gene ITS may be useful for rapid species identification, and PFGE could be an efficient method for isolate identification. PMID:7650189

  9. Identification of listeria species isolated in Tunisia by Microarray based assay : results of a preliminary study

    International Nuclear Information System (INIS)

    Microarray-based assay is a new molecular approach for genetic screening and identification of microorganisms. We have developed a rapid microarray-based assay for the reliable detection and discrimination of Listeria spp. in food and clinical isolates from Tunisia. The method used in the present study is based on the PCR amplification of a virulence factor gene (iap gene). the PCR mixture contained cyanine Cy5labeled dCTP. Therefore, The PCR products were fluorescently labeled. The presence of multiple species-specific sequences within the iap gene enabled us to design different oligoprobes per species. The species-specific sequences of the iap gene used in this study were obtained from genBank and then aligned for phylogenetic analysis in order to identify and retrieve the sequences of homologues of the amplified iap gene analysed. 20 probes were used for detection and identification of 22 food isolates and clinical isolates of Listeria spp (L. monocytogenes, L. ivanovi), L. welshimeri, L. seeligeri, and L. grayi). Each bacterial gene was identified by hybridization to oligoprobes specific for each Listeria species and immobilized on a glass surface. The microarray analysis showed that 5 clinical isolates and 2 food isolates were identified listeria monocytogenes. Concerning the remaining 15 food isolates; 13 were identified listeria innocua and 2 isolates could not be identified by microarray based assay. Further phylogenetic and molecular analysis are required to design more species-specific probes for the identification of Listeria spp. Microarray-based assay is a simple and rapid method used for Listeria species discrimination

  10. An algorithm and program for finding sequence specific oligo-nucleotide probes for species identification

    Directory of Open Access Journals (Sweden)

    Tautz Diethard

    2002-03-01

    Full Text Available Abstract Background The identification of species or species groups with specific oligo-nucleotides as molecular signatures is becoming increasingly popular for bacterial samples. However, it shows also great promise for other small organisms that are taxonomically difficult to tract. Results We have devised here an algorithm that aims to find the optimal probes for any given set of sequences. The program requires only a crude alignment of these sequences as input and is optimized for performance to deal also with very large datasets. The algorithm is designed such that the position of mismatches in the probes influences the selection and makes provision of single nucleotide outloops. Program implementations are available for Linux and Windows.

  11. METHODS FOR FISH SPECIES IDENTIFICATION IN FOOD PRODUCTS

    Directory of Open Access Journals (Sweden)

    Ľubica Mrázová

    2010-07-01

    Full Text Available The need for identification of fishery products in food is currently ongoing issue for both consumers and producers of food. Consumer interest is driven in one the healthy diet, which prefers fish products, as an indispensable ingredient food and on the other hand, is a potential allergen causing health problems in humans allergic to fish protein. Allergy is a phenomenon that significantly affects human health, as well as overall life expectancy of an individual. The large number of fish species are known to trigger allergic reactions directly food intake or inhalation of fumes only, depending on the sensitivity orgamizmu. Large quantity of fish allergens are proteins from the stock protein to enzymes. Methods used for species identifications of fish in food products are PCR sequencing, multiplex PCR, PCR-RFLP, PCR-SSCP, RAPD, real-time PCR. doi:10.5219/25

  12. Species identification of skins and development of sheep wool

    DEFF Research Database (Denmark)

    Brandt, Luise Ørsted

    at death for one of the animal skin samples - information not obtainable by DNA and with crucial implications for the interpretations of preferences of skins and animal husbandry. Online available protein databases used for comparison are still not complete. While the most common domesticated species...... are well described, the databases did not provide enough resolution of seals and birds to presently justify the species identification by PMF of ancient Greenlandic skin samples dating to the Saqqaq culture. Overall, the success of the analysis of ancient biomolecules is closely connected to the...

  13. Testing four barcoding markers for species identification of Potamogetonaceae

    Institute of Scientific and Technical Information of China (English)

    Zhi-Yuan DU; Alitong QIMIKE; Chun-Feng YANG; Jin-Ming CHEN; Qing-Feng WANG

    2011-01-01

    The pondweeds (Potamogetonaceae) are among the most important plant groups in the aquatic environment. Owing to their high morphological and ecological diversity, species identification of this aquatic family remains problematic. DNA barcoding involves sequencing a standard DNA region and has been shown to be a powerful tool for species identification. In the present study, we tested four barcoding markers (rbcL, matK, internal transcribed spacer (ITS), and trnH-psbA) in 15 Potamogeton species and two Stuckenia species, representing most species of the Potamogetonaceae in China. The results show that all four regions can distinguish and support the newly proposed genera of Stuckenia from Potamogeton. Using ITS and trnH-psbA, significant interspecific genetic variability was shown. However, intraspecific genetic variability of trnH-psbA is high and so it is not suitable for barcoding in Potamogetonaceae. The ITS and matK regions showed good discrimination. However, matK was not easy to sequence using universal primers. The best performing single locus was ITS, making it a potentially useful DNA barcode in Potamogetonaceae.

  14. Analysis of paint degradation by fungal and bacterial species

    International Nuclear Information System (INIS)

    Paint is a liquor blend, used as a decorative or protective coating. Paints are the main source of volatile organic compounds (VOCs), very harmful for the environment and human beings. In the present study, fungal and bacterial growth on paint flakes sandwiched between the mineral salt medium agar layers were subjected to various analysis. Dry cell mass quantification was carried out by shake flask experiment with fungal inoculum. The maximum growth of 0.7g observed on 28th day. Further evidence of paint film biodegradation was confirmed by scanning electron microscopy (SEM) and Fourier transform infrared spectroscopy (FTIR) studies. The loss in intensity of the bands at a wavelength of 1115.7 cm-1 and 1065.67 cm-1 for ester linkages indicated degradation of the paints through the breaking of the ester group. A loss in intensity of bands at a wavelength of 3286.87 cm-1 (corresponding alcoholic peak) due to breakage of alcoholic linkages. Scanning electron micrographs clearly showed the adherence and fungal growth on paint flakes and the distorted / ruptured surface was also observed in three months treated paint samples. The current research study represents the significant trends of paint biodegradation by isolated microorganism. (author)

  15. Genetic Identification and Risk Factor Analysis of Asymptomatic Bacterial Colonization on Cardiovascular Implantable Electronic Devices

    Science.gov (United States)

    Chu, Xian-Ming; An, Yi; Li, Xue-Bin; Guo, Ji-Hong

    2014-01-01

    Asymptomatic bacterial colonization of cardiovascular implantable electronic devices (CIEDs) is widespread and increases the risk of clinical CIED infection. The aim of the study was to evaluate the incidence of bacterial colonization of generator pockets in patients without signs of infection and to analyze the relationship with clinical infection and risk factors. From June 2011 to December 2012, 78 patients underwent CIED replacement or upgrade. Exclusion criteria included a clinical diagnosis of CIED infection, bacteremia, or infective endocarditis. All patients were examined for evidence of bacterial 16S rDNA on the device and in the surrounding tissues. Infection cases were recorded during follow-up. The bacterial-positive rate was 38.5% (30 cases); the coagulase-negative Staphylococcus detection rate was the highest (9 cases, 11.5%). Positive bacterial DNA results were obtained from pocket tissue in 23.1% of patients (18 cases), and bacterial DNA was detected on the device in 29.5% of patients (23 cases). During follow-up (median 24.6 months), two patients (6.7%, 2/30) became symptomatic with the same species of microorganism, S. aureus and S. epidermidis. Multivariable logistic regression analysis found that the history of bacterial infection, use of antibiotics, application of antiplatelet drugs, replacement frequency, and renal insufficiency were independent risk factors for asymptomatic bacterial colonization. PMID:25530969

  16. Genetic Identification and Risk Factor Analysis of Asymptomatic Bacterial Colonization on Cardiovascular Implantable Electronic Devices

    Directory of Open Access Journals (Sweden)

    Xian-Ming Chu

    2014-01-01

    Full Text Available Asymptomatic bacterial colonization of cardiovascular implantable electronic devices (CIEDs is widespread and increases the risk of clinical CIED infection. The aim of the study was to evaluate the incidence of bacterial colonization of generator pockets in patients without signs of infection and to analyze the relationship with clinical infection and risk factors. From June 2011 to December 2012, 78 patients underwent CIED replacement or upgrade. Exclusion criteria included a clinical diagnosis of CIED infection, bacteremia, or infective endocarditis. All patients were examined for evidence of bacterial 16S rDNA on the device and in the surrounding tissues. Infection cases were recorded during follow-up. The bacterial-positive rate was 38.5% (30 cases; the coagulase-negative Staphylococcus detection rate was the highest (9 cases, 11.5%. Positive bacterial DNA results were obtained from pocket tissue in 23.1% of patients (18 cases, and bacterial DNA was detected on the device in 29.5% of patients (23 cases. During follow-up (median 24.6 months, two patients (6.7%, 2/30 became symptomatic with the same species of microorganism, S. aureus and S. epidermidis. Multivariable logistic regression analysis found that the history of bacterial infection, use of antibiotics, application of antiplatelet drugs, replacement frequency, and renal insufficiency were independent risk factors for asymptomatic bacterial colonization.

  17. Gut bacterial community structure of two Australian tropical fruit fly species (Diptera: Tephritidae

    Directory of Open Access Journals (Sweden)

    Narit Thaochan

    2015-12-01

    Full Text Available The community structure of the alimentary tract bacteria of two Australian fruit fly species, Bactrocera cacuminata (Hering and Bactrocera tryoni (Froggatt, was studied using a molecular cloning method based on the 16S rRNA gene. Differences in the bacterial community structure were shown between the crops and midguts of the two species and sexes of each species. Proteobacteria was the dominant bacterial phylum in the flies, especially bacteria in the order Gammaproteobacteria which was prominent in all clones. The total bacterial community consisted of Proteobacteria (more than 75% of clones, except in the crop of B. cacuminata where more than 50% of clones belonged to Firmicutes. Firmicutes gave the number of the secondary community structure in the fly’s gut. Four orders, Alpha-, Beta-, Delta- and Gammaproteobacteria and the phyla Firmicutes and Actinobacteria were found in both fruit fly species, while the order Epsilonproteobacteria and the phylum Bacteroidetes were found only in B. tryoni. Two phyla, Actinobacteria and Bacteroidetes, were rare and less frequent in the flies. There was a greater diversity of bacteria in the crop of the two fruit fly species than in the midgut. The midgut of B. tryoni females and the midgut of B. cacuminata males had the lowest bacterial diversity.

  18. Bacterial community in sclerotia of Cenococcum species and soil in sub-alpine forest, central Japan

    Science.gov (United States)

    Nonoyama, Y.; Narisawa, K.; Ohta, H.; Watanabe, M.

    2009-04-01

    Species of Cenococcum, ectomycorrhizal fungi, may be particularly abundant in cold- or nutrient-stressed habitats. The fungus is easily recognized by its jet-black hyphae, and distinct compact masses of fungal mycelium called sclerotia. They are hard, black, comparatively smooth and mostly spherical. Sclerotia are formed in rhizosphere and can provide sufficient inoculums for several years. The purpose of this study is to investigate bacterial community inside sclerotia, with an interest on contribution of sclerotia to microbial diversity in rhizosphere. To investigate bacterial community inside of the fungal sclerotia by 16S rDNA gene clone library, several hundred of sclerotia (ca. 1g) were collected from sub-alpine forest soil in central Japan. Furthermore, three sclerotium grains were applied to investigate internal bacteria community by culture method. The isolated bacterial strains were then proceeded to determine their 16S rDNA partial sequences. The predominant group determined by clone library analysis of 16S ribosomal RNA genes with DNA from the sclerotia was Acidobacteria in both sclerotia and soil. Bacterial community of sclerotia showed higher diversity compared to soil. On the contrary, bacterial flora isolated from single sclerotium differed each other. Additionally, the bacterial community was composed by limited species of related genus.

  19. Comparison of the Quantum II Bacterial Identification System and the AutoMicrobic System for the identification of gram-negative bacilli.

    OpenAIRE

    Pfaller, M A; Bale, M J; Schulte, K R; Koontz, F P

    1986-01-01

    The Quantum II Bacterial Identification System (BID; Abbott Laboratories) is a microprocessor-based spectrophotometric system for identification within 4 to 5 h of both enteric and nonenteric gram-negative bacilli. We compared the BID with the AutoMicrobic System (AMS; Vitek Systems, Inc.), using the most recent gram-negative identification card and software (AMS-GNI), for the identification of 501 clinical isolates of gram-negative bacilli, including 382 belonging to the Enterobacteriaceae a...

  20. Microbiological method for radiation sterilization (I). General knowledge and handling technique for bacterial identification

    International Nuclear Information System (INIS)

    The part I in this title series describes the basic knowledge and technique for identification of bacteria in the radiation sterilization of medical devices, where the radiation dose can be decided from the number and radio-resistance of the bioburden (bacteria on the device). Four essential, actual technologies for identification are described: isolation and storage of bacteria; decision of bacterial natures, involving 3 Gram staining methods, morphology by microscopy and/or phase-contrast microscopy, spore-forming bacteria, and size measurement by micrometry; Other test items for identification of genus, involving motility, oxygen demand, catalase, oxidase, acid production from glucose, and OF (oxidation or fermentation for glucose degradation) test; and colony observation. Media, identification kits and record forms for these are presented. (N.I.)

  1. Improving Remote Species Identification through Efficient Training Data Collection

    Directory of Open Access Journals (Sweden)

    Claire A. Baldeck

    2014-03-01

    Full Text Available Plant species identification and mapping based on remotely-sensed spectral signatures is a challenging task with the potential to contribute enormously to ecological studies. Success in this task rests upon the appropriate collection and use of costly field-based training data, and researchers are in need of ways to improve collection efficiency based on quantitative evidence. Using imaging spectrometer data collected by the Carnegie Airborne Observatory for hundreds of field-identified tree crowns in Kruger National Park, South Africa, we developed woody plant species classification models and evaluated how classification accuracy increases with increasing numbers of training crowns. First, we show that classification accuracy must be estimated while respecting the crown as the basic unit of data; otherwise, accuracy will be overestimated and the amount of training data needed to perform successful classification will be underestimated. We found that classification accuracy and the number of training crowns needed to perform successful classification varied depending on the number and spectral separability of species in the model. We also used a modified Michaelis-Menten function to describe the empirical relationship between training crowns and model accuracy, and show how this function may be useful for predicting accuracy. This framework can assist researchers in designing field campaigns to maximize the efficiency of field data collection, and thus the amount of biodiversity information gained from remote species identification models.

  2. Identification of Dominant Immunogenic Bacteria and Bacterial Proteins in Periodontitis

    DEFF Research Database (Denmark)

    Agerbæk, Mette Rylev; Haubek, Dorte; Birkelund, Svend;

    Marginal periodontitis is considered an infectious disease that triggers host inflammatory responses resulting in destruction of the periodontium. A complex biofilm of bacteria is associated with periodontitis. Some species have been identified as putative pathogens such as Porphyromonas gingivalis...... (P.g) and Actinobacillus actinomycetemcomitans (A.a), but the identity of dominate immunogens of these bacteria is poorly elucidated. The aim of the study was to identify dominant immunogenic proteins of P.g and A.a in patients suffering from chronic and aggressive periodontitis by proteomic analysis...... will be able to identify immunodominant proteins and potentially important virulence factors of putative periodontal pathogens....

  3. The changing epitome of species identification - DNA barcoding.

    Science.gov (United States)

    Ajmal Ali, M; Gyulai, Gábor; Hidvégi, Norbert; Kerti, Balázs; Al Hemaid, Fahad M A; Pandey, Arun K; Lee, Joongku

    2014-07-01

    The discipline taxonomy (the science of naming and classifying organisms, the original bioinformatics and a basis for all biology) is fundamentally important in ensuring the quality of life of future human generation on the earth; yet over the past few decades, the teaching and research funding in taxonomy have declined because of its classical way of practice which lead the discipline many a times to a subject of opinion, and this ultimately gave birth to several problems and challenges, and therefore the taxonomist became an endangered race in the era of genomics. Now taxonomy suddenly became fashionable again due to revolutionary approaches in taxonomy called DNA barcoding (a novel technology to provide rapid, accurate, and automated species identifications using short orthologous DNA sequences). In DNA barcoding, complete data set can be obtained from a single specimen irrespective to morphological or life stage characters. The core idea of DNA barcoding is based on the fact that the highly conserved stretches of DNA, either coding or non coding regions, vary at very minor degree during the evolution within the species. Sequences suggested to be useful in DNA barcoding include cytoplasmic mitochondrial DNA (e.g. cox1) and chloroplast DNA (e.g. rbcL, trnL-F, matK, ndhF, and atpB rbcL), and nuclear DNA (ITS, and house keeping genes e.g. gapdh). The plant DNA barcoding is now transitioning the epitome of species identification; and thus, ultimately helping in the molecularization of taxonomy, a need of the hour. The 'DNA barcodes' show promise in providing a practical, standardized, species-level identification tool that can be used for biodiversity assessment, life history and ecological studies, forensic analysis, and many more. PMID:24955007

  4. Identification, Characterization and Antibiotic Resistance of Bacterial Isolates Obtained from Waterpipe Device Hoses

    Directory of Open Access Journals (Sweden)

    Majed M. Masadeh

    2015-05-01

    Full Text Available The general lack of knowledge about the health effects of waterpipe smoking is among the reasons for its global spread. In this study, bacterial contamination of waterpipe hoses was investigated. Twenty hoses were collected from waterpipe cafés and screened for bacterial pathogens using standard culture and isolation techniques. Additionally, resistance of isolated bacteria to common antibiotics was determined by identifying the minimum inhibitory concentration (MIC of each isolate. Forty eight bacterial isolates were detected. Isolates included both Gram-positive and Gram-negative pathogens from species that included Micrococcus (12, Corynebacterium (13 and Bacillus (9. In addition, some of the detected pathogens were found to be resistant to aztreonam (79%, cefixime (79%, norfloxacin, amoxicillin (47%, clarithromycin (46% and enrofloxacin (38%. In conclusion, the hose of the waterpipe device is a good environment for the growth of bacterial pathogens, which can then be transmitted to users.

  5. Identification, characterization and antibiotic resistance of bacterial isolates obtained from waterpipe device hoses.

    Science.gov (United States)

    Masadeh, Majed M; Hussein, Emad I; Alzoubi, Karem H; Khabour, Omar; Shakhatreh, Muhamad Ali K; Gharaibeh, Mahmoud

    2015-05-01

    The general lack of knowledge about the health effects of waterpipe smoking is among the reasons for its global spread. In this study, bacterial contamination of waterpipe hoses was investigated. Twenty hoses were collected from waterpipe cafés and screened for bacterial pathogens using standard culture and isolation techniques. Additionally, resistance of isolated bacteria to common antibiotics was determined by identifying the minimum inhibitory concentration (MIC) of each isolate. Forty eight bacterial isolates were detected. Isolates included both Gram-positive and Gram-negative pathogens from species that included Micrococcus (12), Corynebacterium (13) and Bacillus (9). In addition, some of the detected pathogens were found to be resistant to aztreonam (79%), cefixime (79%), norfloxacin, amoxicillin (47%), clarithromycin (46%) and enrofloxacin (38%). In conclusion, the hose of the waterpipe device is a good environment for the growth of bacterial pathogens, which can then be transmitted to users. PMID:25985311

  6. Identification of individual biofilm-forming bacterial cells using Raman tweezers

    Science.gov (United States)

    Samek, Ota; Bernatová, Silvie; Ježek, Jan; Šiler, Martin; Šerý, Mojmir; Krzyžánek, Vladislav; Hrubanová, Kamila; Zemánek, Pavel; Holá, Veronika; Růžička, Filip

    2015-05-01

    A method for in vitro identification of individual bacterial cells is presented. The method is based on a combination of optical tweezers for spatial trapping of individual bacterial cells and Raman microspectroscopy for acquisition of spectral "Raman fingerprints" obtained from the trapped cell. Here, Raman spectra were taken from the biofilm-forming cells without the influence of an extracellular matrix and were compared with biofilm-negative cells. Results of principal component analyses of Raman spectra enabled us to distinguish between the two strains of Staphylococcus epidermidis. Thus, we propose that Raman tweezers can become the technique of choice for a clearer understanding of the processes involved in bacterial biofilms which constitute a highly privileged way of life for bacteria, protected from the external environment.

  7. Identification of Genes Induced in Lolium multiflorum by Bacterial Wilt Infection

    DEFF Research Database (Denmark)

    Wichmann, Fabienne; Asp, Torben; Widmer, Franco; Kölliker, Roland

    Xanthomonas translucens pv. graminis(Xtg) causes bacterial wilt in many forage grasses including Italian ryegrass (Lolium multiflorum Lam), seriously reducing yield and quality. Breeding for resistance is currently the only practicable means of disease control. Molecular markers closely linked to...... resistance genes or QTL could complement and support phenotypic selection. We used comparative gene expression analysis of a partially resistant L. multiflorum genotype infected and not infected with Xtg to identify genes involved in the control of resistance to bacterial wilt. The genes differentially...... expressed upon infection will serve as the basis for the identification of key genes involved in bacterial wilt resistance and to develop molecular markers for marker assisted breeding. Fluorescently labelled cDNA prepared from plant leaves collected at four different time points after infection was...

  8. Expansion of space station diagnostic capability to include serological identification of viral and bacterial infections

    Science.gov (United States)

    Hejtmancik, Kelly E.

    1987-01-01

    It is necessary that an adequate microbiology capability be provided as part of the Health Maintenance Facility (HMF) to support expected microbial disease events during long periods of space flight. The applications of morphological and biochemical studies to confirm the presence of certain bacterial and fungal disease agents are currently available and under consideration. This confirmation would be greatly facilitated through employment of serological methods to aid in the identification for not only bacterial and fungal agents, but viruses as well. A number of serological approached were considered, particularly the use of Enzyme Linked Immunosorbent Assays (ELISAs), which could be utilized during space flight conditions. A solid phase, membrane supported ELISA for the detection of Bordetella pertussis was developed to show a potential model system that would meet the HMF requirements and specifications for the future space station. A second model system for the detection of Legionella pneumophilia, an expected bacterial disease agent, is currently under investigation.

  9. Degradation of lucerne stem cell walls by five rumen bacterial species

    NARCIS (Netherlands)

    Jung, H.G.; Engels, F.M.; Weimer, P.J.

    2004-01-01

    The rumen bacterial strains Butyrivibrio fibrisolvens H17c, Fibrobacter succinogenes S85, Lachnospira multiparus 40, Ruminococcus albus 7 and R. flavefaciens FD-1 were compared individually and as a five-species mixture with a rumen inoculum for their ability to degrade lucerne (Medicago sativa L.)

  10. Bacterial Diversity and Community Structure in Two Bornean Nepenthes Species with Differences in Nitrogen Acquisition Strategies.

    Science.gov (United States)

    Sickel, Wiebke; Grafe, T Ulmar; Meuche, Ivonne; Steffan-Dewenter, Ingolf; Keller, Alexander

    2016-05-01

    Carnivorous plants of the genus Nepenthes have been studied for over a century, but surprisingly little is known about associations with microorganisms. The two species Nepenthes rafflesiana and Nepenthes hemsleyana differ in their pitcher-mediated nutrient sources, sequestering nitrogen from arthropod prey and arthropods as well as bat faeces, respectively. We expected bacterial communities living in the pitchers to resemble this diet difference. Samples were taken from different parts of the pitchers (leaf, peristome, inside, outside, digestive fluid) of both species. Bacterial communities were determined using culture-independent high-throughput amplicon sequencing. Bacterial richness and community structure were similar in leaves, peristomes, inside and outside walls of both plant species. Regarding digestive fluids, bacterial richness was higher in N. hemsleyana than in N. rafflesiana. Additionally, digestive fluid communities were highly variable in structure, with strain-specific differences in community composition between replicates. Acidophilic taxa were mostly of low abundance, except the genus Acidocella, which strikingly reached extremely high levels in two N. rafflesiana fluids. In N. hemsleyana fluid, some taxa classified as vertebrate gut symbionts as well as saprophytes were enriched compared to N. rafflesiana, with saprophytes constituting potential competitors for nutrients. The high variation in community structure might be caused by a number of biotic and abiotic factors. Nitrogen-fixing bacteria were present in both study species, which might provide essential nutrients to the plant at times of low prey capture and/or rare encounters with bats. PMID:26790863

  11. Assessment of Bacterial Communities in Thirteen Species of Laboratory-Cultured Domestic Mites (Acari: Acaridida).

    Science.gov (United States)

    Hubert, Jan; Kopecky, Jan; Sagova-Mareckova, Marketa; Nesvorna, Marta; Zurek, Ludek; Erban, Tomas

    2016-08-01

    House dust mites (HDMs) and stored-product mites (SPMs) of various species inhabit human homes and stored agricultural products. These mites are carriers and hosts of microorganisms that enable their survival. The bacteriome from 13 species of SPMs and HDMs was analyzed and compared by 454 pyrosequencing of partial 16S rRNA gene amplicons. Altogether 128,052 sequences were obtained and assigned to 71 operational taxonomic units (OTUs) at the 97% identity level. The number of sequences in the OTUs between species of mites ranged from 6 to 31 in the individual mite species. We did not find any significant effect of diet or evolutionary origin of mites or their interaction on the composition of the mite bacteriome. In mite species with low bacterial diversity, the bacterial communities were dominated by potential symbiotic or parasitic bacteria, i.e., Cardinium in Dermatophagoides farinae (Hughes, 1961) and Aeroglyphus robustus (Banks 1906) and the enteric bacteria Erwinia in Blomia tropicalis Van Bronswijk, de Cock & Oshima, 1974 and Xenorhabdus in Tyroborus lini (Oudemans, 1924). Among the bacterial species identified, Staphylococcus, Bacillus, Kocuria, Brevibacterium, Corynebacterium, and Brachybacterium likely serve as food sources for the mites. The domestic acaridid mites carried high numbers of various bacteria that are potential threats to human health. These results contribute to the general understanding of the ecology of mite adaptation to human-made habitats. PMID:27122496

  12. IDENTIFICATION OF NICOTINAMIDE MONONUCLEOTIDE DEAMIDASE OF THE BACTERIAL PYRIDINE NUCLEOTIDE CYCLE REVEALS A NOVEL BROADLY CONSERVED AMIDOHYDROLASE FAMILY

    Energy Technology Data Exchange (ETDEWEB)

    Galeazzi, Luca; Bocci, Paolo; Amici, Adolfo; Brunetti, Lucia; Ruggieri, Silverio; Romine, Margaret F.; Reed, Samantha B.; Osterman, Andrei; Rodionov, Dmitry A.; Sorci, Leonardo; Raffaelli, Nadia

    2011-09-27

    The pyridine nucleotide cycle (PNC) is a network of salvage and recycling routes maintaining homeostasis of NAD(P) cofactor pool in the cell. Nicotinamide mononucleotide (NMN) deamidase (EC 3.5.1.42), one of the key enzymes of the bacterial PNC was originally described in Enterobacteria, but the corresponding gene eluded identification for over 30 years. A genomics-based reconstruction of NAD metabolism across hundreds bacterial species suggested that NMN deamidase reaction is the only possible way of nicotinamide salvage in the marine bacterium Shewanella oneidensis. This prediction was verified via purification of native NMN deamidase from S. oneidensis followed by the identification of the respective gene, termed pncC. Enzymatic characterization of the PncC protein, as well as phenotype analysis of deletion mutants, confirmed its proposed biochemical and physiological function in S. oneidensis. Of the three PncC homologs present in E. coli, NMN deamidase activity was confirmed only for the recombinant purified product of the ygaD gene. A comparative analysis at the level of sequence and three dimensional structure, which is available for one of the PncC family member, shows no homology with any previously described amidohydrolases. Multiple alignment analysis of functional and non functional PncC homologs, together with NMN docking experiments, allowed us to tentatively identify the active site area and conserved residues therein. An observed broad phylogenomic distribution of predicted functional PncCs in bacterial kingdom is consistent with a possible role in detoxification of NMN, resulting from NAD utilization by DNA ligase.

  13. Identification of different species of Bacillus isolated from Nisargruna Biogas Plant by FTIR, UV-Vis and NIR spectroscopy

    Science.gov (United States)

    Ghosh, S. B.; Bhattacharya, K.; Nayak, S.; Mukherjee, P.; Salaskar, D.; Kale, S. P.

    2015-09-01

    Definitive identification of microorganisms, including pathogenic and non-pathogenic bacteria, is extremely important for a wide variety of applications including food safety, environmental studies, bio-terrorism threats, microbial forensics, criminal investigations and above all disease diagnosis. Although extremely powerful techniques such as those based on PCR and microarrays exist, they require sophisticated laboratory facilities along with elaborate sample preparation by trained researchers. Among different spectroscopic techniques, FTIR was used in the 1980s and 90s for bacterial identification. In the present study five species of Bacillus were isolated from the aerobic predigester chamber of Nisargruna Biogas Plant (NBP) and were identified to the species level by biochemical and molecular biological (16S ribosomal DNA sequence) methods. Those organisms were further checked by solid state spectroscopic absorbance measurements using a wide range of electromagnetic radiation (wavelength 200 nm to 25,000 nm) encompassing UV, visible, near Infrared and Infrared regions. UV-Vis and NIR spectroscopy was performed on dried bacterial cell suspension on silicon wafer in specular mode while FTIR was performed on KBr pellets containing the bacterial cells. Consistent and reproducible species specific spectra were obtained and sensitivity up to a level of 1000 cells was observed in FTIR with a DTGS detector. This clearly shows the potential of solid state spectroscopic techniques for simple, easy to implement, reliable and sensitive detection of bacteria from environmental samples.

  14. Animal Species Identification by PCR – RFLP of Cytochrome b

    Directory of Open Access Journals (Sweden)

    Tomáš Minarovič

    2010-05-01

    Full Text Available An alternative DNA detection system is based on the polymerase chain reaction (PCR amplification of a segment of the mitochondrial cytochrome b gene. Subsequent cleavage by a restriction enzymes gives rise to a specie-specific pattern on an agarose gel. We used five animal species (Mustela vison, Mustela putorius furo, Sus scrofa domesticus, Oryctolagus cuninculus, Anser anser. Length of PCR product was 359 bp and we used universal primers. Restriction fragment length polymorphism was analyzed by using the restriction endonuclease AluI. Results of cleavage were visualized by using electrophoresis and UV transiluminator. Every animal specie has a unique combination of restriction fragments i.e. Mustela vison 81 bp, 109 bp and 169 bp, Mustela putorius furo 169 bp and 190 bp, Sus scrofa domesticus 115 bp and 244 bp, Oryctolagus cunninculus is not cleaved by AluI so it has whole 359 bp fragment on agarose gel, Anser anser 130 bp and 229 bp. The results suggest that the method of PCR - RFLP is rapid and simple method for identification of species. PCR – RFLP can reliably identify chosen species. Application of genetic methods is very useful for breeding of livestock and protection of biodiversity.

  15. Barcode of life: Advancing species identification and discovery

    Digital Repository Service at National Institute of Oceanography (India)

    Chandramohan, D.

    and (ii) possess greater range of phylogenetic signal than any other mitochondrial gene. The accumulated evidence now shows that these short DNA sequences can be a distinguishing feature from insects to birds. As a Linnaean binomial is an abbreviated... DNA as a model system. Gene 238, 195-210. 5. Simmons, R.B. and Weller,S.J. 2001. Utility and evolution of cytochrome b in insects.Mol. Phylogenet. Evol. 20, 196-210. Barcode of Life: Advancing Species Identification and Discovery ...

  16. Karyotype and identification of sex in two endangered crane species

    Science.gov (United States)

    Goodpasture, C.; Seluja, G.; Gee, G.

    1992-01-01

    A laboratory procedure for sex identification of monomorphic birds was developed using modern cytological methods of detecting chromosome abnormalities in human amniotic fluid samples. A pin feather is taken from a pre-fledging bird for tissue culture and karyotype analysis. Through this method, the sex was identified and the karyotype described of the whooping crane (Grus americana) and the Mississippi sandhill crane (G. canadensis pulla). Giemsa-stained karyotypes of these species showed an identical chromosome constitution with 2n = 78 + 2. However, differences in the amount of centromeric heterochromatin were observed in the Mississippi sandhill crane when compared to the whooping crane C-banded karyotype.

  17. Diazotrophic potential among bacterial communities associated with wild and cultivated Agave species.

    Science.gov (United States)

    Desgarennes, Damaris; Garrido, Etzel; Torres-Gomez, Miryam J; Peña-Cabriales, Juan J; Partida-Martinez, Laila P

    2014-12-01

    Agaves are major biotic resources in arid and semi-arid ecosystems. Despite their ecological, economical and cultural relevance, many aspects of the microbial communities associated with agaves are still unknown. Here, we investigated the bacterial communities associated with two Agave species by 16S rRNA- Denaturing gradient gel electrophoresis fingerprinting and sequencing. We also evaluated the effects of biotic and abiotic factors in the structure of the bacterial communities. In parallel, we isolated and characterized diazotrophic bacteria associated with agaves, as Agave soils are characterized by their low nitrogen content. Our results demonstrate that in Agave, the structure of prokaryotic assemblages was mostly influenced by the community group, where the soil, episphere, and endosphere were clearly distinct. Proteobacteria (γ and α), Actinobacteria, and Acidobacteria were the dominant phyla. Bacterial communities in the episphere of agaves were mainly influenced by the host species, whereas in the endosphere were affected by the season. Fifteen bacterial taxa were common and abundant in the endosphere of both Agave species during the dry season. Notably, some of the confirmed diazotrophic strains belonged to this group, suggesting a possible beneficial role in planta. PMID:25314594

  18. Pictorial identification key for species of Sarcophagidae (Diptera) of potential forensic importance in southern Brazil

    OpenAIRE

    Karine Pinto e Vairo; Cátia Antunes de Mello-Patiu; Claudio J.B. de Carvalho

    2011-01-01

    Pictorial identification key for species of Sarcophagidae (Diptera) of potential forensic importance in southern Brazil. Species of the subfamily Sarcophaginae are important to forensic entomology due to their necrophagous habits. This contribution presents a pictorial key for the identification of 22 Sarcophaginae species in 10 genera that are commonly found in southern Brazil. Photographs of the main structures used in species identification, mainly from the male terminalia, are provided.Ch...

  19. Pictorial identification key for species of Sarcophagidae (Diptera) of potential forensic importance in southern Brazil

    OpenAIRE

    Karine Pinto e Vairo; Cátia Antunes de Mello-Patiu; Claudio J. B. de Carvalho

    2011-01-01

    Pictorial identification key for species of Sarcophagidae (Diptera) of potential forensic importance in southern Brazil. Species of the subfamily Sarcophaginae are important to forensic entomology due to their necrophagous habits. This contribution presents a pictorial key for the identification of 22 Sarcophaginae species in 10 genera that are commonly found in southern Brazil. Photographs of the main structures used in species identification, mainly from the male terminalia, are provided.

  20. Pictorial identification key for species of Sarcophagidae (Diptera of potential forensic importance in southern Brazil

    Directory of Open Access Journals (Sweden)

    Karine Pinto e Vairo

    2011-09-01

    Full Text Available Pictorial identification key for species of Sarcophagidae (Diptera of potential forensic importance in southern Brazil. Species of the subfamily Sarcophaginae are important to forensic entomology due to their necrophagous habits. This contribution presents a pictorial key for the identification of 22 Sarcophaginae species in 10 genera that are commonly found in southern Brazil. Photographs of the main structures used in species identification, mainly from the male terminalia, are provided.

  1. Identification of weed species with hyperaccumulative characteristics of heavy metals

    Institute of Scientific and Technical Information of China (English)

    WEI Shuhe; ZHOU Qixing

    2004-01-01

    In order to promote the effective and economic remediation of soils contaminated with single Cd and Cd combined with Ph, Cu and Zn, a field-screening study on weed hyperaccumulators was carried out on the basis of field pot-culture experiments used to determine characteristics of weed plants enduring and accumulating heavy metals. In this study, 54 weed species belonging to 20 families from agricultural fields of the Shengyang suburbs were tested. The results showed that Taraxracum mongolicum, Solanum nigrum and Conyza canadensis could strongly tolerate single Cd and Cd-Pb-Cu-Zn combined pollution, had high Cd-accumulative ability, and generally possessed basic characteristics of hyperaccumulators. Because there are synergic and antagonistic effects among Cd, Pb, Cu and Zn, singlefactor pollution tests should be done as well as combined pollution tests during the identification of hyperaccumulators to ensure the efficiency of phytoremediation and the practical significance of hyperaccumulators identified. The field pot-culture experiment should be a new tentative method to screen out accumulative and tolerant species in view of its obvious advantages such as simple operation, low cost, and easy identification of investigated plants.

  2. DNA barcoding for species Identification in prepared fishery products

    Directory of Open Access Journals (Sweden)

    ANNA MOTTOLA

    2014-06-01

    Full Text Available Considering that seafood mislabeling has been widely reported throughout the world and that the authentication of food components is one of the key issues in food quality, the aim of this study was to use DNA barcoding to investigate the prevalence of mislabeling among fresh prepared fishery products from markets and supermarkets located in Apulia (SE Italy. The study reveals a high occurrence of species mislabeling (42% in the prepared fillet products, further evidence of the need for increased traceability and assessment of the authenticity of food products. Given the increasing demand for transparency in the food industry and the enforcement of proper labeling have provided a driving force for the development of suitable analytical methodologies for species identification. There is therefore a great need to develop fast and reliable methods to identify meat species and to quantify their levels in seafood products, in order to ensure product quality and thus to protect consumers. The study provides further evidence that molecular investigations based on DNA barcoding may be one of the most powerful tools for the assessment of species identity, food traceability, safety and fraud.

  3. Bacterial communities associated with the pitcher fluids of three Nepenthes (Nepenthaceae) pitcher plant species growing in the wild.

    Science.gov (United States)

    Chou, Lee Yiung; Clarke, Charles M; Dykes, Gary A

    2014-10-01

    Nepenthes pitcher plants produce modified jug-shaped leaves to attract, trap and digest insect prey. We used 16S rDNA cloning and sequencing to compare bacterial communities in pitcher fluids of each of three species, namely Nepenthes ampullaria, Nepenthes gracilis and Nepenthes mirabilis, growing in the wild. In contrast to previous greenhouse-based studies, we found that both opened and unopened pitchers harbored bacterial DNA. Pitchers of N. mirabilis had higher bacterial diversity as compared to other Nepenthes species. The composition of the bacterial communities could be different between pitcher types for N. mirabilis (ANOSIM: R = 0.340, p Nepenthes species had similar bacterial composition between pitcher types. SIMPER showed that more than 50 % of the bacterial taxa identified from the open pitchers of N. mirabilis were not found in other groups. Our study suggests that bacteria in N. mirabilis are divided into native and nonnative groups. PMID:25005571

  4. Coral-Associated Bacterial Diversity Is Conserved across Two Deep-Sea Anthothela Species.

    Science.gov (United States)

    Lawler, Stephanie N; Kellogg, Christina A; France, Scott C; Clostio, Rachel W; Brooke, Sandra D; Ross, Steve W

    2016-01-01

    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. PMID:27092120

  5. Detection of bacterial species involved in perimplantitis concerned with cultural and RT-PCR

    Directory of Open Access Journals (Sweden)

    Marcello Gatti

    2010-06-01

    Full Text Available Dental implants offer new treatment options for edentulous either partially or completely, now represent a viable alternative to conventional fixed protheses. Dental implants are colonized by a flora dominated by Gram-positive facultative aerobic, while in patients with bone loss and formation of pockets peri-implant diseases was found a significant difference in the composition of microflora, bacteria, Gram-negative anaerobes in particular Fusobacterium spp., Treponema denticola (Spirochetes, Tannerella forsythensis, Aggregatibacter actinomycetemcomitans, Prevotella intermedia as interim black-pigmented bacteria, Porphyromonas gingivalis, often in high concentrations. Aims. The purpose of this study was to identify those at risk of perimplantitis using 2 techniques: RT-PCR examination of trade and culture. The results were compared taking into consideration the advantages and disadvantages of both methods. Materials and methods.We studied 24 patients (14 women and 10 men, aged, women between 43 and 76 years, with an average of 63.8 + / - 10.9 years, men between 45 and 88 years with a average of 64.3 years + / - 12.5 years. Was performed a double levy of sub-gingival plaque at multiple sites that had an implant CAL (clinical attachment level> 4mm in order to assess the microbiological identification with the two techniques: Examining culture and Real-Time PCR of Commerce ( Gum-Sunstar that identifies 4 bacterial species: A. actinomycetemcomitans (A.a., P.gingivalis (P.g., T.forsythensis (T.f., and T.denticola (T.d.. Results. All patients studied were positive to both tests with charger high: the consideration of tenure, with CFU / ml > 105, was positive in 66.6% of samples by:T.f., and P.g., in 12.5% for A.a., while T.d. not been sought by examining culture, the RT-PCR was positive, with high loads, in 95.8% of samples for T.f., in 79.1% for P.g., in 12.5% for A.a. and 20.8% for T.d.The test crop showed the presence of even P.intermedia in 91

  6. Plant-associated bacterial populations on native and invasive plant species: comparisons between 2 freshwater environments.

    Science.gov (United States)

    Olapade, Ola A; Pung, Kayleigh

    2012-06-01

    Plant-microbial interactions have been well studied because of the ecological importance of such relationships in aquatic systems. However, general knowledge regarding the composition of these biofilm communities is still evolving, partly as a result of several confounding factors that are attributable to plant host properties and to hydrodynamic conditions in aquatic environments. In this study, the occurrences of various bacterial phylogenetic taxa on 2 native plants, i.e., mayapple (Podophyllum peltatum L.) and cow parsnip (Heracleum maximum Bartram), and on an invasive species, i.e., garlic mustard (Alliaria petiolata (M. Bieb.) Cavara & Grande), were quantitatively examined using nucleic acid staining and fluorescence in situ hybridization. The plants were incubated in triplicates for about a week within the Kalamazoo River and Pierce Cedar Creek as well as in microcosms. The bacterial groups targeted for enumeration are known to globally occur in relatively high abundance and are also ubiquitously distributed in freshwater environments. Fluorescence in situ hybridization analyses of the bacterioplankton assemblages revealed that the majority of bacterial cells that hybridized with the different probes were similar between the 2 sites. In contrast, the plant-associated populations while similar on the 3 plants incubated in Kalamazoo River, their representations were highest on the 2 native plants relative to the invasive species in Pierce Cedar Creek. Overall, our results further suggested that epiphytic bacterial assemblages are probably under the influences of and probably subsequently respond to multiple variables and conditions in aquatic milieus. PMID:22625420

  7. Bacterial-biota dynamics of eight bryophyte species from different ecosystems.

    Science.gov (United States)

    Koua, Faisal Hammad Mekky; Kimbara, Kazuhide; Tani, Akio

    2015-03-01

    Despite the importance of bryophyte-associated microorganisms in various ecological aspects including their crucial roles in the soil-enrichment of organic mass and N2 fixation, nonetheless, little is known about the microbial diversity of the bryophyte phyllospheres (epi-/endophytes). To get insights into bacterial community structures and their dynamics on the bryophyte habitats in different ecosystems and their potential biological roles, we utilized the 16S rRNA gene PCR-DGGE and subsequent phylogenetic analyses to investigate the bacterial community of eight bryophyte species collected from three distinct ecosystems from western Japan. Forty-two bacterial species belonging to γ-proteobacteria and Firmicutes with 71.4% and 28.6%, respectively, were identified among 90 DGGE gel band population. These DGGE-bands were assigned to 13 different genera with obvious predomination the genus Clostridium with 21.4% from the total bacterial community. These analyses provide new insights into bryophyte-associated bacteria and their relations to the ecosystems. PMID:25737654

  8. Chemically emulsified crude oil as substrate for bacterial oxidation : differences in species response

    International Nuclear Information System (INIS)

    The ability of bacterial species to oxidize alkanes in crude oil in water emulsions was studied. Alkanes in crude oil need specific physiological adaptations to the microorganisms. Synthesis of biosurfactants has been considered as a prerequisite for either specific adhesion mechanisms to large oil drops or emulsification of oil followed by uptake of submicron oil droplets. In this study four bacterial species were tested. Emulsions were prepared by nonionic sorbitan ester and polyoxyethylene ether surfactants. The oxidation rates were measured. Both positive and negative effects of surfactant amendments were observed. The same surfactant affected different bacteria in different ways. The response to the surfactant amendment depended on the physiological state of the bacteria. The results showed that surfactants resulted in decreased cell adhesion to the oil phase for all the bacteria. 19 refs., 3 tabs., 4 figs

  9. Modular riboswitch toolsets for synthetic genetic control in diverse bacterial species.

    Science.gov (United States)

    Robinson, Christopher J; Vincent, Helen A; Wu, Ming-Cheng; Lowe, Phillip T; Dunstan, Mark S; Leys, David; Micklefield, Jason

    2014-07-30

    Ligand-dependent control of gene expression is essential for gene functional analysis, target validation, protein production, and metabolic engineering. However, the expression tools currently available are difficult to transfer between species and exhibit limited mechanistic diversity. Here we demonstrate how the modular architecture of purine riboswitches can be exploited to develop orthogonal and chimeric switches that are transferable across diverse bacterial species, modulating either transcription or translation, to provide tunable activation or repression of target gene expression, in response to synthetic non-natural effector molecules. Our novel riboswitch-ligand pairings are shown to regulate physiologically important genes required for bacterial motility in Escherichia coli and cell morphology in Bacillus subtilis. These findings are relevant for future gene function studies and antimicrobial target validation, while providing new modular and orthogonal regulatory components for deployment in synthetic biology regimes. PMID:24971878

  10. System automation for a bacterial colony detection and identification instrument via forward scattering

    International Nuclear Information System (INIS)

    A system design and automation of a microbiological instrument that locates bacterial colonies and captures the forward-scattering signatures are presented. The proposed instrument integrates three major components: a colony locator, a forward scatterometer and a motion controller. The colony locator utilizes an off-axis light source to illuminate a Petri dish and an IEEE1394 camera to capture the diffusively scattered light to provide the number of bacterial colonies and two-dimensional coordinate information of the bacterial colonies with the help of a segmentation algorithm with region-growing. Then the Petri dish is automatically aligned with the respective centroid coordinate with a trajectory optimization method, such as the Traveling Salesman Algorithm. The forward scatterometer automatically computes the scattered laser beam from a monochromatic image sensor via quadrant intensity balancing and quantitatively determines the centeredness of the forward-scattering pattern. The final scattering signatures are stored to be analyzed to provide rapid identification and classification of the bacterial samples

  11. Co-operative inhibitory effects of hydrogen peroxide and iodine against bacterial and yeast species

    OpenAIRE

    Zubko, Elena I; Zubko, Mikhajlo K

    2013-01-01

    Background Hydrogen peroxide and iodine are powerful antimicrobials widely used as antiseptics and disinfectants. Their antimicrobial properties are known to be enhanced by combining them with other compounds. We studied co-operative inhibitory activities (synergism, additive effects and modes of growth inhibition) of hydrogen peroxide and iodine used concurrently against 3 bacterial and 16 yeast species. Results Synergistic or additive inhibitory effects were shown for hydrogen peroxide and ...

  12. Development of species-specific SCAR markers for identification of three medicinal species of Phyllanthus

    Institute of Scientific and Technical Information of China (English)

    Piyada THEERAKULPISUT; Nantawan KANAWAPEE; Duangkamol MAENSIRI; Sumontip BUNNAG; Pranom CHANTARANOTHAI

    2008-01-01

    Phyllanthus amarus Schum.& Thonn.has been widely used in traditional medicine in Thailand as an antipyretic.a diuretic.to treat liver diseases and viml infections.Two closely related species,P. debills L.and P.urinaria KIein ex Willd.,with different and less effective medicinal properties,are less commonly used.These three species are similar in morphology and often Occur in overlapping populations in nature.The latter two species can easily be mistaken for P.amarus and collected for medicinal uses, which can lead to undesirable results.DNA fingerprints of these species were obtained using RAPD-PCR techniques.RAPD markers specific for each species were identified.Primers for highly specific sequence-characterized-amplified-regions (SCAR) were then designed from nucleotide sequences of specific RAPD markers.These primers efficiently amplified SCAR markers of 408,501 and 319 bp unique to P.amarus,P.debilis and P.urinaria respectively.This method of plant identification Was rapid and highly specific when tested against DNA of several closely related species and was able to amplify specific markers from mixed DNA samples.

  13. Effects of viruses on bacterial functions under contrasting nutritional conditions for four species of bacteria isolated from Hong Kong waters

    Science.gov (United States)

    Liu, Hao; Yuan, Xiangcheng; Xu, Jie; Harrison, Paul J.; He, Lei; Yin, Kedong

    2015-09-01

    Free living viruses are ubiquitous in marine waters and concentrations are usually several times higher than the bacterial abundance. These viruses are capable of lysing host bacteria and therefore, play an important role in the microbial loop in oligotrophic waters. However, few studies have been conducted to compare the role of viruses in regulating bacterial abundance and heterotrophic activities between natural oligotrophic waters and anthropogenic influenced eutrophic waters. In this study, we examined viral effects on bacterial functions of four single bacterial species incubated with natural viral assemblages in seawater samples from eutrophic and oligotrophic waters. The viral-lysis of bacteria was significantly higher in eutrophic than oligotrophic waters. This suggests that viruses were capable of controlling bacterial abundance, respiration and production in the eutrophic waters. Cellular bacterial respiration and production was higher with viruses than without viruses, which was more evident in the oligotrophic waters. These results indicate that viruses can slow down bacterial consumption of oxygen and reduce bacteria-induced eutrophication effects in anthropogenic eutrophic waters, but switch to the role of sustaining the bacterial population when nutrients are limiting. There were bacterial species differences in resisting viral attack, which can influence the dominance and biodiversity of bacterial species in coastal waters.

  14. Pathogenicity of some bacterial species isolated from the bee digestive tract

    Directory of Open Access Journals (Sweden)

    Dugalić-Vrndić Nada

    2010-01-01

    Full Text Available The aim of this paper was to examine the pathogenicity of most commonly isolated bacteria from the digestive tract of bees. Bees from 150 colonies (n=3000 were examined and 19 bacterial species were isolated, which are either permanent or temporary inhabitants of the digestive tract. Pathogenic activity of the most commonly isolated species (Enterobacter aerogenes, Klebsiella ozaenae, Klebsiella pneumonie, Citrobacter freundii, Enterobacter cloacae and Enterobacter agglomerans was examined on seven-day-old chicken embryos and tissue of MDBK cells. Bacterial inoculation of the examined bacteria was conducted in the alantoic cavity of chicken embryos in the quantity of 0.5 mL. Control noninoculated and inoculated embryos were incubated at 38oC with about 60% relative humidity. All six bacterial species manifested pathogenic activity on chicken embryos and caused their death within 2-4 days and changes such as lagging in embryo development, bleeding and unpleasant smell. The bacteria examined in MDBK cell lines of bovine kidney tissue did not manifest cytopathogenic effect and the structure of control tissue was normal.

  15. Intestine Bacterial Composition of the Chromosomal forms of genus Nannospalax and Comparison of Some Rodent Species

    OpenAIRE

    Coşkun, Yüksel; El-Namee, Ausama; KAYA, Alaettin

    2013-01-01

    In this study, five selected different rodent species, Meriones tristrami (karyotype 2n=72 from Mardin/Turkey), Nannospalax ehrenbergi (karyotype 2n=52 from Diyarbakır/Turkey and Mosul/Iraq), Nannospalax nehringi (karyotype 2n = 60 from Sivas/Turkey), Rattus rattus (karyotype 2n=42 from Diyarbakır/Turkey), Sciurus anomalus (karyotype 2n=40 from Bingöl/Turkey) were studied in respect to bacterial species.The results showed the presence of two types of bacteria Pantoea agglomerans and Serratia ...

  16. Automated species and strain identification of bacteria in complex matrices using FTIR spectroscopy

    Science.gov (United States)

    Puzey, K. A.; Gardner, P. J.; Petrova, V. K.; Donnelly, C. W.; Petrucci, G. A.

    2008-04-01

    Fourier Transform Infrared (FTIR) spectroscopy provides a highly selective and reproducible means for the chemically-based discrimination of intact microbial cells which make the method valuable for large-scale screening of foods. The goals of the present study were to assess the effect of chemical interferents, such as food matrices, different sanitizing compounds and growth media, on the ability of the method to accurately identify and classify L. innocua, L. welshimeri, E. coli, S. cholerasuis, S. subterranea, E. sakazakii, and E. aerogenes. Moreover, the potential of FTIR spectroscopy for discrimination of L. innocua and L. welshimeri of different genotypes and the effect of growth phase on identification accuracy of L. innocua and L. welshimeri were tested. FTIR spectra were collected using two different sample presentation techniques - transmission and attenuated total reflection (ATR), and then analyzed using multivariate discriminant analysis based on the first derivative of the FTIR spectra with the unknown spectra assigned to the species group with the shortest Mahalanobis distance. The results of the study demonstrated 100% correct identification and differentiation of all bacterial strains used in this study in the presence of chemical interferents or food matrices, better than 99% identification rate in presence of media matrices, and 100% correct detection for specific bacteria in mixed flora species. Additionally, FTIR spectroscopy proved to be 100% accurate when differentiating between genotypes of L. innocua and L. welshimeri, with the classification accuracy unaffected by the growth stage. These results suggest that FTIR spectroscopy can be used as a valuable tool for identifying pathogenic bacteria in food and environmental samples.

  17. Nordic-Baltic Student Teachers' Identification of and Interest in Plant and Animal Species: The Importance of Species Identification and Biodiversity for Sustainable Development

    Science.gov (United States)

    Palmberg, Irmeli; Berg, Ida; Jeronen, Eila; Kärkkäinen, Sirpa; Norrgård-Sillanpää, Pia; Persson, Christel; Vilkonis, Rytis; Yli-Panula, Eija

    2015-01-01

    Knowledge of species, interest in nature, and nature experiences are the factors that best promote interest in and understanding of environmental issues, biodiversity and sustainable life. The aim of this study is to investigate how well student teachers identify common local species, their interest in and ideas about species identification, and…

  18. Lytic Characteristics and Identification of Two Alga-lysing Bacterial Strains

    Institute of Scientific and Technical Information of China (English)

    PEI Haiyan; HU Wenrong

    2006-01-01

    All previously reported bacterial species which are capable of lysing harmful algae have been isolated from coastal environments in which harmful algae blooms have occurred. Due to the low concentration of alga-lysing bacteria in an algal bloom, it is difficult to isolate the alga-lysing bacteria by existing methods. In this paper, two algae-lysing bacterial strains,P01 and P03, have been isolated from a biosystem immobilized on a sponge that was highly effective in removing algae and microcystins. Their lysing modes and effects on Microcystis aeruginosa have been studied. The results show that the degradation processes of these two strains for M. aeruginosa accorded with a first-order reaction model when the chlorophylla concentration was in the range from 0 to 1000 μg L-1. The degradation rate constants were 0.106 7, 0.127 4 and 0.279 2 for P01and0.0683, 0.0744 and 0.02897 for P03, when the bacterial densities were 8.6 × 105, 8.6 × 106 and 8.6 × 107cells mL 1, respectively. Moreover, the two bacterial strains had favourable lytic effects not only on M. aeruginosa, but also on Chlorella and Scene-desmus. Their lytic effect on M. aeruginosa did not require physical cell to cell contact, but proceeded by the production of an extracellular product. The bacterial strains were identified as Bacillus species by PCR amplification of the 16S rRNA gene, BLAST analysis, and comparison with sequences in the GenBank nucleotide database.

  19. The Generalist Inside the Specialist: Gut Bacterial Communities of Two Insect Species Feeding on Toxic Plants Are Dominated by Enterococcus sp.

    Science.gov (United States)

    Vilanova, Cristina; Baixeras, Joaquín; Latorre, Amparo; Porcar, Manuel

    2016-01-01

    Some specialist insects feed on plants rich in secondary compounds, which pose a major selective pressure on both the phytophagous and the gut microbiota. However, microbial communities of toxic plant feeders are still poorly characterized. Here, we show the bacterial communities of the gut of two specialized Lepidoptera, Hyles euphorbiae and Brithys crini, which exclusively feed on latex-rich Euphorbia sp. and alkaloid-rich Pancratium maritimum, respectively. A metagenomic analysis based on high-throughput sequencing of the 16S rRNA gene revealed that the gut microbiota of both insects is dominated by the phylum Firmicutes, and especially by the common gut inhabitant Enterococcus sp. Staphylococcus sp. are also found in H. euphorbiae though to a lesser extent. By scanning electron microscopy, we found a dense ring-shaped bacterial biofilm in the hindgut of H. euphorbiae, and identified the most prominent bacterium in the biofilm as Enterococcus casseliflavus through molecular techniques. Interestingly, this species has previously been reported to contribute to the immobilization of latex-like molecules in the larvae of Spodoptera litura, a highly polyphagous lepidopteran. The E. casseliflavus strain was isolated from the gut and its ability to tolerate natural latex was tested under laboratory conditions. This fact, along with the identification of less frequent bacterial species able to degrade alkaloids and/or latex, suggest a putative role of bacterial communities in the tolerance of specialized insects to their toxic diet. PMID:27446044

  20. Bacterial colonization and extinction on marine aggregates: stochastic model of species presence and abundance

    Science.gov (United States)

    Kramer, Andrew M; Lyons, M Maille; Dobbs, Fred C; Drake, John M

    2013-01-01

    Organic aggregates provide a favorable habitat for aquatic microbes, are efficiently filtered by shellfish, and may play a major role in the dynamics of aquatic pathogens. Quantifying this role requires understanding how pathogen abundance in the water and aggregate size interact to determine the presence and abundance of pathogen cells on individual aggregates. We build upon current understanding of the dynamics of bacteria and bacterial grazers on aggregates to develop a model for the dynamics of a bacterial pathogen species. The model accounts for the importance of stochasticity and the balance between colonization and extinction. Simulation results suggest that while colonization increases linearly with background density and aggregate size, extinction rates are expected to be nonlinear on small aggregates in a low background density of the pathogen. Under these conditions, we predict lower probabilities of pathogen presence and reduced abundance on aggregates compared with predictions based solely on colonization. These results suggest that the importance of aggregates to the dynamics of aquatic bacterial pathogens may be dependent on the interaction between aggregate size and background pathogen density, and that these interactions are strongly influenced by ecological interactions and pathogen traits. The model provides testable predictions and can be a useful tool for exploring how species-specific differences in pathogen traits may alter the effect of aggregates on disease transmission. PMID:24340173

  1. What Makes a Bacterial Species Pathogenic?:Comparative Genomic Analysis of the Genus Leptospira.

    Directory of Open Access Journals (Sweden)

    Derrick E Fouts

    2016-02-01

    Full Text Available Leptospirosis, caused by spirochetes of the genus Leptospira, is a globally widespread, neglected and emerging zoonotic disease. While whole genome analysis of individual pathogenic, intermediately pathogenic and saprophytic Leptospira species has been reported, comprehensive cross-species genomic comparison of all known species of infectious and non-infectious Leptospira, with the goal of identifying genes related to pathogenesis and mammalian host adaptation, remains a key gap in the field. Infectious Leptospira, comprised of pathogenic and intermediately pathogenic Leptospira, evolutionarily diverged from non-infectious, saprophytic Leptospira, as demonstrated by the following computational biology analyses: 1 the definitive taxonomy and evolutionary relatedness among all known Leptospira species; 2 genomically-predicted metabolic reconstructions that indicate novel adaptation of infectious Leptospira to mammals, including sialic acid biosynthesis, pathogen-specific porphyrin metabolism and the first-time demonstration of cobalamin (B12 autotrophy as a bacterial virulence factor; 3 CRISPR/Cas systems demonstrated only to be present in pathogenic Leptospira, suggesting a potential mechanism for this clade's refractoriness to gene targeting; 4 finding Leptospira pathogen-specific specialized protein secretion systems; 5 novel virulence-related genes/gene families such as the Virulence Modifying (VM (PF07598 paralogs proteins and pathogen-specific adhesins; 6 discovery of novel, pathogen-specific protein modification and secretion mechanisms including unique lipoprotein signal peptide motifs, Sec-independent twin arginine protein secretion motifs, and the absence of certain canonical signal recognition particle proteins from all Leptospira; and 7 and demonstration of infectious Leptospira-specific signal-responsive gene expression, motility and chemotaxis systems. By identifying large scale changes in infectious (pathogenic and intermediately

  2. What Makes a Bacterial Species Pathogenic?:Comparative Genomic Analysis of the Genus Leptospira.

    Science.gov (United States)

    Fouts, Derrick E; Matthias, Michael A; Adhikarla, Haritha; Adler, Ben; Amorim-Santos, Luciane; Berg, Douglas E; Bulach, Dieter; Buschiazzo, Alejandro; Chang, Yung-Fu; Galloway, Renee L; Haake, David A; Haft, Daniel H; Hartskeerl, Rudy; Ko, Albert I; Levett, Paul N; Matsunaga, James; Mechaly, Ariel E; Monk, Jonathan M; Nascimento, Ana L T; Nelson, Karen E; Palsson, Bernhard; Peacock, Sharon J; Picardeau, Mathieu; Ricaldi, Jessica N; Thaipandungpanit, Janjira; Wunder, Elsio A; Yang, X Frank; Zhang, Jun-Jie; Vinetz, Joseph M

    2016-02-01

    Leptospirosis, caused by spirochetes of the genus Leptospira, is a globally widespread, neglected and emerging zoonotic disease. While whole genome analysis of individual pathogenic, intermediately pathogenic and saprophytic Leptospira species has been reported, comprehensive cross-species genomic comparison of all known species of infectious and non-infectious Leptospira, with the goal of identifying genes related to pathogenesis and mammalian host adaptation, remains a key gap in the field. Infectious Leptospira, comprised of pathogenic and intermediately pathogenic Leptospira, evolutionarily diverged from non-infectious, saprophytic Leptospira, as demonstrated by the following computational biology analyses: 1) the definitive taxonomy and evolutionary relatedness among all known Leptospira species; 2) genomically-predicted metabolic reconstructions that indicate novel adaptation of infectious Leptospira to mammals, including sialic acid biosynthesis, pathogen-specific porphyrin metabolism and the first-time demonstration of cobalamin (B12) autotrophy as a bacterial virulence factor; 3) CRISPR/Cas systems demonstrated only to be present in pathogenic Leptospira, suggesting a potential mechanism for this clade's refractoriness to gene targeting; 4) finding Leptospira pathogen-specific specialized protein secretion systems; 5) novel virulence-related genes/gene families such as the Virulence Modifying (VM) (PF07598 paralogs) proteins and pathogen-specific adhesins; 6) discovery of novel, pathogen-specific protein modification and secretion mechanisms including unique lipoprotein signal peptide motifs, Sec-independent twin arginine protein secretion motifs, and the absence of certain canonical signal recognition particle proteins from all Leptospira; and 7) and demonstration of infectious Leptospira-specific signal-responsive gene expression, motility and chemotaxis systems. By identifying large scale changes in infectious (pathogenic and intermediately pathogenic

  3. Salivary bacterial fingerprints of established oral disease revealed by the Human Oral Microbe Identification using Next Generation Sequencing (HOMINGS) technique

    DEFF Research Database (Denmark)

    Belstrøm, Daniel; Paster, Bruce J; Fiehn, Nils-Erik; Jensen, Allan Bardow; Holmstrup, Palle

    2016-01-01

    Identification using Next Generation Sequencing) for comparison of the salivary microbiota in patients with periodontitis, patients with dental caries, and orally healthy individuals. The hypothesis was that this method could add on to the existing knowledge on salivary bacterial profiles in oral health and...... HOMINGS analysis showed that different salivary bacterial profiles were associated with oral health and disease. Future large-scale prospective studies are needed to evaluate if saliva-based screening for disease-associated oral bacterial profiles may be used for identification of patients at risk of...... caries (mean 221, range 165-353) as compared to orally healthy individuals (mean 174, range 120-260) (p=0.04 and p=0.04). Nine probe targets were identified with a different relative abundance between groups (p<0.05). CONCLUSIONS: Cross-sectional comparison of salivary bacterial profiles by means of...

  4. Nucleoside analogues are activated by bacterial deoxyribonucleoside kinases in a species-specific manner

    DEFF Research Database (Denmark)

    Sandrini, Michael; Clausen, Anders; On, Stephen L. W.;

    2007-01-01

    bactericidal activity against several clinical bacterial isolates and type strains. We identified and subcloned the genes coding for putative deoxyribonucleoside kinases in Escherichia coli, Pasteurella multocida, Salmonella enterica, Yersinia enterocolitica, Bacillus cereus, Clostridium perfringens and....... The tested Gram-negative bacteria were susceptible to 3"-azido-3"-deoxythymidine (AZT) in the concentration range 0.032-31.6 µM except for a single E. coli isolate and two Pseudomonas aeruginosa isolates which were resistant to the tested AZT concentrations. Purified recombinant S. enterica thymidine...... deoxyadenosine kinase had a Km for gemcitabine of 33.5 µM and kcat/Km of 5.1 × 10^3 s-1 M-1 and activates gemcitabine in vivo. S. enterica and B. cereus are now amongst the first bacteria with a completely characterized set of dNK enzymes. Bacterial dNKs efficiently activate nucleoside analogues in a species...

  5. Host and Environmental Specificity in Bacterial Communities Associated to Two Highly Invasive Marine Species (Genus Asparagopsis)

    Science.gov (United States)

    Aires, Tânia; Serrão, Ester A.; Engelen, Aschwin H.

    2016-01-01

    As habitats change due to global and local pressures, population resilience, and adaptive processes depend not only on their gene pools but also on their associated bacteria communities. The hologenome can play a determinant role in adaptive evolution of higher organisms that rely on their bacterial associates for vital processes. In this study, we focus on the associated bacteria of the two most invasive seaweeds in southwest Iberia (coastal mainland) and nearby offshore Atlantic islands, Asparagopsis taxiformis and Asparagopsis armata. Bacterial communities were characterized using 16S rRNA barcoding through 454 next generation sequencing and exploratory shotgun metagenomics to provide functional insights and a backbone for future functional studies. The bacterial community composition was clearly different between the two species A. taxiformis and A. armata and between continental and island habitats. The latter was mainly due to higher abundances of Acidimicrobiales, Sphingomonadales, Xanthomonadales, Myxococcales, and Alteromonadales on the continent. Metabolic assignments for these groups contained a higher number of reads in functions related to oxidative stress and resistance to toxic compounds, more precisely heavy metals. These results are in agreement with their usual association with hydrocarbon degradation and heavy-metals detoxification. In contrast, A. taxiformis from islands contained more bacteria related to oligotrophic environments which might putatively play a role in mineralization of dissolved organic matter. The higher number of functional assignments found in the metagenomes of A. taxiformis collected from Cape Verde Islands suggest a higher contribution of bacteria to compensate nutrient limitation in oligotrophic environments. Our results show that Asparagopsis-associated bacterial communities have host-specificity and are modulated by environmental conditions. Whether this environmental effect reflects the host's selective requirements or

  6. Host and Environmental Specificity in Bacterial Communities Associated to Two Highly Invasive Marine Species (Genus Asparagopsis).

    Science.gov (United States)

    Aires, Tânia; Serrão, Ester A; Engelen, Aschwin H

    2016-01-01

    As habitats change due to global and local pressures, population resilience, and adaptive processes depend not only on their gene pools but also on their associated bacteria communities. The hologenome can play a determinant role in adaptive evolution of higher organisms that rely on their bacterial associates for vital processes. In this study, we focus on the associated bacteria of the two most invasive seaweeds in southwest Iberia (coastal mainland) and nearby offshore Atlantic islands, Asparagopsis taxiformis and Asparagopsis armata. Bacterial communities were characterized using 16S rRNA barcoding through 454 next generation sequencing and exploratory shotgun metagenomics to provide functional insights and a backbone for future functional studies. The bacterial community composition was clearly different between the two species A. taxiformis and A. armata and between continental and island habitats. The latter was mainly due to higher abundances of Acidimicrobiales, Sphingomonadales, Xanthomonadales, Myxococcales, and Alteromonadales on the continent. Metabolic assignments for these groups contained a higher number of reads in functions related to oxidative stress and resistance to toxic compounds, more precisely heavy metals. These results are in agreement with their usual association with hydrocarbon degradation and heavy-metals detoxification. In contrast, A. taxiformis from islands contained more bacteria related to oligotrophic environments which might putatively play a role in mineralization of dissolved organic matter. The higher number of functional assignments found in the metagenomes of A. taxiformis collected from Cape Verde Islands suggest a higher contribution of bacteria to compensate nutrient limitation in oligotrophic environments. Our results show that Asparagopsis-associated bacterial communities have host-specificity and are modulated by environmental conditions. Whether this environmental effect reflects the host's selective requirements or

  7. Bacterial and fungal endophthalmitis in Upper Egypt:related species and risk factors

    Institute of Scientific and Technical Information of China (English)

    AA Gharamah; AM Moharram; MA Ismail; AK AL-Hussaini

    2012-01-01

    Objective: To study risk factors, contributing factors of bacterial and fungal endophthalmitis in Upper Egypt, test the isolated species sensitive to some therapeutic agents, and to investigate the air-borne bacteria and fungi in opthalmology operating rooms. Methods: Thirty one cases of endophthalmitis were clinically diagnosed and microbiologically studied. Indoor air-borne bacteria and fungi inside four air-conditioned operating rooms in the Ophthalmology Department at Assiut University Hospitals were also investigated. The isolated microbes from endophthalmitis cases were tested for their ability to produce some extracellular enzymes including protease, lipase, urease, phosphatase and catalase. Also the ability of 5 fungal isolates from endophthalmitis origin to produce mycotoxins and their sensitivity to some therapeutic agents were studied. Results: Results showed that bacteria and fungi were responsihle for infection in 10 and 6 cases of endophthalmitis, respectively and only 2 cases produced a mixture of bacteria and fungi. Trauma was the most prevalent risk factor of endophthalmitis where 58.1% of the 31 cases were due to trauma. In ophthalmology operating rooms, different bacterial and fungal species were isolated. 8 bacterial and 5 fungal isolates showed their ability to produce enzymes while only 3 fungal isolates were able to produce mycotoxins. Terbinafine showed the highest effect against most isolates in vitro. Conclusions: The ability of bacterial and fungal isolates to produce extracellular enzymes and mycotoxins may be aid in the invasion and destruction of eye tissues. Microbial contamination of operating rooms with air-borne bacteria and fungi in the present work may be a source of postoperative endophthalmitis.

  8. Molecular Identification of Fusarium Species in Gibberella fujikuroi Species Complex from Rice, Sugarcane and Maize from Peninsular Malaysia

    OpenAIRE

    Heng Mei Hsuan; Latiffah Zakaria; Baharuddin Salleh

    2011-01-01

    The objective of this study was to identify Fusarium species in the Gibberella fujikuroi species complex from rice, sugarcane and maize as most of the Fusarium species in the species complex are found on the three crops. Isolates used were collected from the field and obtained from culture collection. The Fusarium isolates were initially sorted based on morphology and identifications confirmed based on the DNA sequence of the translation elongation factor 1-α (TEF-1α) gene. Based on the close...

  9. Direct Image-Based Correlative Microscopy Technique for Coupling Identification and Structural Investigation of Bacterial Symbionts Associated with Metazoans

    OpenAIRE

    Halary, S.; Duperron, S.; Boudier, T

    2011-01-01

    Coupling prokaryote identification with ultrastructural investigation of bacterial communities has proven difficult in environmental samples. Prokaryotes can be identified by using specific probes and fluorescence in situ hybridization (FISH), but resolution achieved by light microscopes does not allow ultrastructural investigation. In the case of symbioses involving bacteria associated with metazoan tissues, FISH-based studies often indicate the co-occurrence of several bacterial types withi...

  10. Teaching Species Identification--A Prerequisite for Learning Biodiversity and Understanding Ecology

    Science.gov (United States)

    Randler, Christoph

    2008-01-01

    Animal and plant species identification is often emphasized as a basic prerequisite for an understanding of ecology and training identification skills seems a worthwhile task in biology education. Such identification tasks could be embedded into hands-on, group-based and self-determined learning: a) Teaching and learning should make use of a small…

  11. Isolation and identification of bacterial causes of clinical mastitis in cattle in Sulaimania region

    Directory of Open Access Journals (Sweden)

    S. A. Hussein

    2008-01-01

    Full Text Available A total of 51 cases of bovine clinical mastitis in Sulaimani district were investigated for their bacteriological causative agents; 76 milk samples were cultured on primary and selective media and the isolated bacteria were tested for their susceptibility to antimicrobial agents used in commercial intramammary infusion products. Eighty two bacterial isolates were obtained and further identified using biochemical tests. Escherichia coli was the most common bacteria followed by Staphylococcus aureus, Streptococcus agalactia and coagulase–negative staphylococci. Two other bacterial species (Pseudomonas aeruginosa and Streptococcucs uberis were also isolated but in a lower proportion. Antibacterial susceptibility testing showed that the use of florfenicol, cephalexin and gentamicin may be useful for the treatment of clinical mastitis cases in cows.

  12. Direct identification and susceptibility testing of gram-negative bacilli from BACTEC bottles by use of the MS-2 system with updated bacterial identification software.

    OpenAIRE

    Dipersio, J R; Ficorilli, S M; Varga, F J

    1984-01-01

    The Abbott MS-2 system (Abbott Laboratories, Diagnostic Division, Irving, Tex.), equipped with updated bacterial identification software (version 03.02), was used to perform both direct identification and susceptibility tests on gram-negative bacilli from positive BACTEC blood culture bottles. Ninety-eight of 101 Enterobacteriaceae strains, one strain of Acinetobacter calcoaceticus, and two strains of Pseudomonas aeruginosa were correctly identified by following a direct inoculation procedure...

  13. Nordic-Baltic Student Teachers' Identification of and Interest in Plant and Animal Species: The Importance of Species Identification and Biodiversity for Sustainable Development

    Science.gov (United States)

    Palmberg, Irmeli; Berg, Ida; Jeronen, Eila; Kärkkäinen, Sirpa; Norrgård-Sillanpää, Pia; Persson, Christel; Vilkonis, Rytis; Yli-Panula, Eija

    2015-10-01

    Knowledge of species, interest in nature, and nature experiences are the factors that best promote interest in and understanding of environmental issues, biodiversity and sustainable life. The aim of this study is to investigate how well student teachers identify common local species, their interest in and ideas about species identification, and their perceptions of the importance of species identification and biodiversity for sustainable development. Totally 456 student teachers for primary schools were tested using an identification test and a questionnaire consisting of fixed and open questions. A combination of quantitative and qualitative methods was used to get a more holistic view of students' level of knowledge and their preferred learning methods. The student teachers' ability to identify very common species was low, and only 3 % were able to identify most of the tested species. Experiential learning outdoors was suggested by the majority of students as the most efficient learning method, followed by experiential learning indoors, project work and experimental learning. They looked upon the identification of plants and animals as `important' or `very important' for citizens today and for sustainable development. Likewise, they looked upon biodiversity as `important' or `very important' for sustainable development. Our conclusion is that teaching and learning methods for identification and knowledge of species and for education of biodiversity and sustainable development should always include experiential and project-based methods in authentic environments.

  14. Photoinactivation of Eight Health-Relevant Bacterial Species: Determining the Importance of the Exogenous Indirect Mechanism.

    Science.gov (United States)

    Maraccini, Peter A; Wenk, Jannis; Boehm, Alexandria B

    2016-05-17

    It is presently unknown to what extent the endogenous direct, endogenous indirect, and exogenous indirect mechanisms contribute to bacterial photoinactivation in natural surface waters. In this study, we investigated the importance of the exogenous indirect mechanism by conducting photoinactivation experiments with eight health-relevant bacterial species (Bacteroides thetaiotaomicron, Campylobacter jejuni, Enterococcus faecalis, Escherichia coli K12, E. coli O157:H7, Salmonella enterica serovar Typhimurium LT2, Staphylococcus aureus, and Streptococcus bovis). We used three synthetic photosensitizers (methylene blue, rose bengal, and nitrite) and two model natural photosensitizers (Suwannee River natural organic matter and dissolved organic matter isolated from a wastewater treatment wetland) that generated singlet oxygen and hydroxyl radical. B. thetaiotaomicron had larger first order rate constants than all other organisms under all conditions tested. The presence of the synthetic photosensitizers generally enhanced photoinactivation of Gram-positive facultative anaerobes (Ent. faecalis, Staph. aureus, and Strep. bovis). Among Gram-negative bacteria, only methylene blue with E. coli K12 and rose bengal with C. jejuni showed an enhancing effect. The presence of model natural photosensitizers either reduced or did not affect photoinactivation rate constants. Our findings highlight the importance of the cellular membrane and photosensitizer properties in modulating the contribution of the exogenous indirect mechanism to the overall bacterial photoinactivation. PMID:27121126

  15. Individual growth detection of bacterial species in an in vitro oral polymicrobial biofilm model.

    Science.gov (United States)

    Tabenski, L; Maisch, T; Santarelli, F; Hiller, K-A; Schmalz, G

    2014-11-01

    Most in vitro studies on the antibacterial effects of antiseptics have used planktonic bacteria in monocultures. However, this study design does not reflect the in vivo situation in oral cavities harboring different bacterial species that live in symbiotic relationships in biofilms. The aim of this study was to establish a simple in vitro polymicrobial model consisting of only three bacterial strains of different phases of oral biofilm formation to simulate in vivo oral conditions. Therefore, we studied the biofilm formation of Actinomyces naeslundii (An), Fusobacterium nucleatum (Fn), and Enterococcus faecalis (Ef) on 96-well tissue culture plates under static anaerobic conditions using artificial saliva according to the method established by Pratten et al. that was supplemented with 1 g l(-1) sucrose. Growth was separately determined for each bacterial strain after incubation periods of up to 72 h by means of quantitative real-time polymerase chain reaction and live/dead staining. Presence of an extracellular polymeric substance (EPS) was visualized by Concanavalin A staining. Increasing incubation times of up to 72 h showed adhesion and propagation of the bacterial strains with artificial saliva formulation. An and Ef had significantly higher growth rates than Fn. Live/dead staining showed a median of 49.9 % (range 46.0-53.0 %) of living bacteria after 72 h of incubation, and 3D fluorescence microscopy showed a three-dimensional structure containing EPS. An in vitro oral polymicrobial biofilm model was established to better simulate oral conditions and had the advantage of providing the well-controlled experimental conditions of in vitro testing. PMID:25119373

  16. Identification and elimination of bacterial contamination during in vitro propagation of Guadua angustifolia Kunth

    Directory of Open Access Journals (Sweden)

    Harleen Kaur Nadha

    2012-01-01

    Full Text Available Background: Guadua angustifolia Kunth is a very important bamboo species with significant utility in pharmaceutical, paper, charcoal, and construction industries. Microbial contamination is a major problem encountered during establishment of in vitro cultures of Guadua. Objective: This study has been designed to analyze the identity of contaminating bacteria and to develop the strategy to eliminate them during micropropagation of Guadua. Materials and Methods: We isolated and consequently analyzed partial sequence analysis of the 16S rRNA gene to identify two contaminating bacteria as (1 Pantoea agglomerans and (2 Pantoea ananatis. In addition, we also- performed antibiotic sensitivity testing on these bacterial isolates. Results: We identified kanamycin and streptomycin sulfate as potentially useful antibiotics in eliminating the contaminating bacteria. We grew shoots on multiplication medium containing BAP (2 mg/l and adenine sulfate (10 mg/l supplemented with kanamycin (10 μg/ml for 10 days and transferred them to fresh medium without antibiotics and found that bacterial growth was inhibited. Moreover, we observed intensive formation of high-quality shoots. Streptomycin sulfate also inhibited bacterial growth but at higher concentration. We also demonstrated that shoots grown in streptomycin sulfate tended to be shorter and had yellow leaves. Conclusion: Thus, we have developed a novel strategy to identify and inhibit intriguing microbial contaminations of (1 Pantoea agglomerans and (2 Pantoea ananatis during establishment of in vitro cultures of Guadua. This would improve in vitro establishment of an important bamboo, Guadua angustifolia Kunth for large scale propagation.

  17. Evaluation of chromogenic media and seminested PCR in the identification of Candida species

    OpenAIRE

    Enas Daef; Ahmed Moharram; Salwa Seif Eldin; Nahla Elsherbiny; Mona Mohammed

    2014-01-01

    Identification of Candida cultured from various clinical specimens to the species level is increasingly necessary for clinical laboratories. Although sn PCR identifies the species within hours but its cost-effectiveness is to be considered. So there is always a need for media which help in the isolation and identification at the species level. The study aimed to evaluate the performance of different chromogenic media and to compare the effectiveness of the traditional phenotypic methods vs. s...

  18. Comparing Multiple Criteria for Species Identification in Two Recently Diverged Seabirds

    OpenAIRE

    Teresa Militão; Elena Gómez-Díaz; Antigoni Kaliontzopoulou; Jacob González-Solís

    2014-01-01

    Correct species identification is a crucial issue in systematics with key implications for prioritising conservation effort. However, it can be particularly challenging in recently diverged species due to their strong similarity and relatedness. In such cases, species identification requires multiple and integrative approaches. In this study we used multiple criteria, namely plumage colouration, biometric measurements, geometric morphometrics, stable isotopes analysis (SIA) and genetics (mtDN...

  19. Identification and dynamic modeling of biomarkers for bacterial uptake and effect of sulfonamide antimicrobials

    International Nuclear Information System (INIS)

    The effects of sulfathiazole (STA) on Escherichia coli with glucose as a growth substrate was investigated to elucidate the effect-based reaction of sulfonamides in bacteria and to identify biomarkers for bacterial uptake and effect. The predominant metabolite was identified as pterine-sulfathiazole by LC-high resolution mass spectrometry. The formation of pterine-sulfathiazole per cell was constant and independent of the extracellular STA concentrations, as they exceeded the modeled half-saturation concentration KMS of 0.011 μmol L−1. The concentration of the dihydrofolic acid precursor para-aminobenzoic acid (pABA) increased with growth and with concentrations of the competitor STA. This increase was counteracted for higher STA concentrations by growth inhibition as verified by model simulation of pABA dynamics. The EC value for the inhibition of pABA increase was 6.9 ± 0.7 μmol L−1 STA, which is similar to that calculated from optical density dynamics indicating that pABA is a direct biomarker for the SA effect. - Highlights: ► Elucidation of the effect-based reaction of sulfonamides in bacteria. ► Identification of a biomarker for uptake and effect-based reaction of sulfonamides. ► Investigation of a biomarker for the bacterial growth inhibition by sulfonamides. ► Quantitative mechanistic modeling of biomarker dynamics using enzyme kinetics. ► Mechanistic quantitative linking of sulfonamide concentrations and effects. - Identification of specific biomarkers for the uptake and effect-based reaction of sulfonamides in bacteria and resulting growth inhibition.

  20. Comparative genomics of non-pseudomonal bacterial species colonising paediatric cystic fibrosis patients.

    Science.gov (United States)

    Ormerod, Kate L; George, Narelle M; Fraser, James A; Wainwright, Claire; Hugenholtz, Philip

    2015-01-01

    The genetic disorder cystic fibrosis is a life-limiting condition affecting ∼70,000 people worldwide. Targeted, early, treatment of the dominant infecting species, Pseudomonas aeruginosa, has improved patient outcomes; however, there is concern that other species are now stepping in to take its place. In addition, the necessarily long-term antibiotic therapy received by these patients may be providing a suitable environment for the emergence of antibiotic resistance. To investigate these issues, we employed whole-genome sequencing of 28 non-Pseudomonas bacterial strains isolated from three paediatric patients. We did not find any trend of increasing antibiotic resistance (either by mutation or lateral gene transfer) in these isolates in comparison with other examples of the same species. In addition, each isolate contained a virulence gene repertoire that was similar to other examples of the relevant species. These results support the impaired clearance of the CF lung not demanding extensive virulence for survival in this habitat. By analysing serial isolates of the same species we uncovered several examples of strain persistence. The same strain of Staphylococcus aureus persisted for nearly a year, despite administration of antibiotics to which it was shown to be sensitive. This is consistent with previous studies showing antibiotic therapy to be inadequate in cystic fibrosis patients, which may also explain the lack of increasing antibiotic resistance over time. Serial isolates of two naturally multi-drug resistant organisms, Achromobacter xylosoxidans and Stenotrophomonas maltophilia, revealed that while all S. maltophilia strains were unique, A. xylosoxidans persisted for nearly five years, making this a species of particular concern. The data generated by this study will assist in developing an understanding of the non-Pseudomonas species associated with cystic fibrosis. PMID:26401445

  1. Acinetobacter species identification by using tRNA spacer fingerprinting.

    OpenAIRE

    Ehrenstein, B; Bernards, A T; Dijkshoorn, L.; Gerner-Smidt, P; Towner, K. J.; Bouvet, P J; Daschner, F D; Grundmann, H

    1996-01-01

    Identification of Acinetobacter spp. to the DNA group level by phenotypic techniques is problematic, and there is a need for an alternative identification method for routine use. The present study validated the suitability of a rapid identification technique based on tRNA spacer (tDNA) fingerprinting in comparison with that of a commercially available assay involving carbon source utilization tests (Biolog MicroStation System) for identifying the 21 DNA-DNA hybridization groups belonging to t...

  2. Spatial and Species Variations in Bacterial Communities Associated with Corals from the Red Sea as Revealed by Pyrosequencing

    KAUST Repository

    Lee, O. O.

    2012-08-03

    Microbial associations with corals are common and are most likely symbiotic, although their diversity and relationships with environmental factors and host species remain unclear. In this study, we adopted a 16S rRNA gene tag-pyrosequencing technique to investigate the bacterial communities associated with three stony Scleractinea and two soft Octocorallia corals from three locations in the Red Sea. Our results revealed highly diverse bacterial communities in the Red Sea corals, with more than 600 ribotypes detected and up to 1,000 species estimated from a single coral species. Altogether, 21 bacterial phyla were recovered from the corals, of which Gammaproteobacteria was the most dominant group, and Chloroflexi, Chlamydiae, and the candidate phylum WS3 were reported in corals for the first time. The associated bacterial communities varied greatly with location, where environmental conditions differed significantly. Corals from disturbed areas appeared to share more similar bacterial communities, but larger variations in community structures were observed between different coral species from pristine waters. Ordination methods identified salinity and depth as the most influential parameters affecting the abundance of Vibrio, Pseudoalteromonas, Serratia, Stenotrophomonas, Pseudomonas, and Achromobacter in the corals. On the other hand, bacteria such as Chloracidobacterium and Endozoicomonas were more sensitive to the coral species, suggesting that the host species type may be influential in the associated bacterial community, as well. The combined influences of the coral host and environmental factors on the associated microbial communities are discussed. This study represents the first comparative study using tag-pyrosequencing technology to investigate the bacterial communities in Red Sea corals.

  3. Spatial Organization of Dual-Species Bacterial Aggregates on Leaf Surfaces

    Science.gov (United States)

    Monier, J.-M.; Lindow, S. E.

    2005-01-01

    The spatial organization of cells within bacterial aggregates on leaf surfaces was determined for pair-wise mixtures of three different bacterial species commonly found on leaves, Pseudomonas syringae, Pantoea agglomerans, and Pseudomonas fluorescens. Cells were coinoculated onto bean plants and allowed to grow under moist conditions, and the resulting aggregates were examined in situ by epifluorescence microscopy. Each bacterial strain could be localized because it expressed either the green or the cyan fluorescent protein constitutively, and the viability of individual cells was assessed by propidium iodide staining. Each pair of bacterial strains that was coinoculated onto leaves formed mixed aggregates. The degree of segregation of cells in mixed aggregates differed between the different coinoculated pairs of strains and was higher in mixtures of P. fluorescens A506 and P. agglomerans 299R and mixtures of P. syringae B728a and P. agglomerans 299R than in mixtures of two isogenic strains of P. agglomerans 299R. The fractions of the total cell population that were dead in mixed and monospecific aggregates of a gfp-marked strain of P. agglomerans 299R and a cfp-marked strain of P. agglomerans 299R, or of P. fluorescens A506 and P. agglomerans 299R, were similar. However, the proportion of dead cells in mixed aggregates of P. syringae B728a and P. agglomerans 299R was significantly higher (13.2% ± 8.2%) than that in monospecific aggregates of these two strains (1.6% ± 0.7%), and it increased over time. While dead cells in such mixed aggregates were preferentially found at the interface between clusters of cells of these strains, cells of these two strains located at the interface did not exhibit equal probabilities of mortality. After 9 days of incubation, about 77% of the P. agglomerans 299R cells located at the interface were dead, while only about 24% of the P. syringae B728a cells were dead. The relevance of our results to understanding bacterial interactions

  4. Epidemiology of urinary tract infections, bacterial species and resistances in primary care in France.

    Science.gov (United States)

    Malmartel, A; Ghasarossian, C

    2016-03-01

    General practitioners often have to manage urinary tract infections (UTI) with probabilistic treatments, although bacterial resistances are increasing. Therefore, the French Society of Infectious Diseases published new guidelines in 2014. The aim of this study was to investigate the bacterial epidemiology of UTI in the general population in primary care and analyse risk factors for Escherichia coli resistance to antibiotics. A cross-sectional study was conducted in 12 ambulatory laboratories. Patients over 18 years of age coming for urinalysis were included. Risk factors for UTI were collected using a questionnaire and the laboratory records. Bacteria meeting criteria for UTI were analysed. A positive urinalysis was found in 1119 patients, corresponding to 1125 bacterial isolates. The bacterial species were: E. coli (73 %), Enterococcus spp. (7 %), Klebsiella spp. (6 %), Proteus spp. (4 %), Staphylococcus spp. (3 %) and Pseudomonas spp. (2 %). Regardless of the bacteria, the most common resistance was that to co-trimoxazole: 27 % (95 % confidence interval [CI] = [0.24; 0.30]), followed by ofloxacin resistance: 16 % [0.14; 0.18]. Escherichia coli resistances to co-trimoxazole, ofloxacin, cefixime, nitrofurantoin and fosfomycin were, respectively, 25.5 % [0.23; 0.28], 17 % [0.14; 0.20], 5.6 % [0.04; 0.07], 2.2 % [0.01; 0.03] and 1.2 % [0.005; 0.02]. Independent risk factors for E. coli resistance to ofloxacin were age over 85 years (odds ratio [OR] = 3.08; [1.61; 5.87]) and a history of UTI in the last 6 months (OR = 2.34; [1.54; 3.52]). Our findings support the guidelines recommending fluoroquinolone sparing. The scarcity of E. coli resistance to fosfomycin justifies its use as a first-line treatment in acute cystitis. These results should be reassessed in a few years to identify changes in the bacterial epidemiology of UTI. PMID:26740324

  5. Helicobacter species and common gut bacterial DNA in gallbladder with cholecystitis

    Institute of Scientific and Technical Information of China (English)

    Peren; H; Karagin; Unne; Stenram; Torkel; Wadstrm; sa; Ljungh

    2010-01-01

    AIM:To analyze the association between Helicobacter spp. and some common gut bacteria in patients with cholecystitis. METHODS:A nested-polymerase chain reaction (PCR), specif ic to 16S rRNA of Helicobacter spp. was performed on paraff in-embedded gallbladder samples of 100 cholecystitis and 102 control cases. The samples were also analyzed for some common gut bacteria by PCR. Positive samples were sequenced for species identif ication. RESULTS: Helicobacter DNA was found in seven out of 100 cases of acute a...

  6. Molecular Identification of Fusarium Species in Gibberella fujikuroi Species Complex from Rice, Sugarcane and Maize from Peninsular Malaysia

    Directory of Open Access Journals (Sweden)

    Heng Mei Hsuan

    2011-10-01

    Full Text Available The objective of this study was to identify Fusarium species in the Gibberella fujikuroi species complex from rice, sugarcane and maize as most of the Fusarium species in the species complex are found on the three crops. Isolates used were collected from the field and obtained from culture collection. The Fusarium isolates were initially sorted based on morphology and identifications confirmed based on the DNA sequence of the translation elongation factor 1-α (TEF-1α gene. Based on the closest match of BLAST analysis, five species were recovered, namely, F. sacchari, F. fujikuroi, F. proliferatum, F. andiyazi and F. verticillioides. This is the first report regarding F. andiyazi from rice in Malaysia and Southeast Asia. The phylogenetic tree generated by using the neighbor joining method showed that isolates from the same species were grouped in the same clade. The present study indicated that Fusarium species in the G. fujikuroi species complex are widespread in rice, sugarcane and maize in Peninsular Malaysia. The findings also suggest that the use of morphological characters for identification of Fusarium species in the G. fujikuroi species complex from the three crops will lead to incorrect species designation.

  7. Anti-bacterial effect of Mentha spicata L. essential oil on eight standard species of gastrointestinal pathogens

    OpenAIRE

    Majid Zare Bidaki; Mina Arab; Mohtarame Khazaei; Ehsan Afkar

    2014-01-01

    Background and Aim: Nowadays resistance to antibiotics and their side effects has emerged as a worldwide problem. As a result, tend to use anti-bacterial compounds of plant origin has been increased. Mint plant scientifically called Mentha spicata L. is one of the plants which has many medicinal uses and its antibacterial effects is a matter of debate. We aimed to study antibacterial effects of Mentha spicata L essential oil on 8 standard bacterial species including Escherichia coli, Bacillus...

  8. Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer

    Directory of Open Access Journals (Sweden)

    Kaul Rajinder

    2009-11-01

    Full Text Available Abstract Background Phylogeographic reconstruction of some bacterial populations is hindered by low diversity coupled with high levels of lateral gene transfer. A comparison of recombination levels and diversity at seven housekeeping genes for eleven bacterial species, most of which are commonly cited as having high levels of lateral gene transfer shows that the relative contributions of homologous recombination versus mutation for Burkholderia pseudomallei is over two times higher than for Streptococcus pneumoniae and is thus the highest value yet reported in bacteria. Despite the potential for homologous recombination to increase diversity, B. pseudomallei exhibits a relative lack of diversity at these loci. In these situations, whole genome genotyping of orthologous shared single nucleotide polymorphism loci, discovered using next generation sequencing technologies, can provide very large data sets capable of estimating core phylogenetic relationships. We compared and searched 43 whole genome sequences of B. pseudomallei and its closest relatives for single nucleotide polymorphisms in orthologous shared regions to use in phylogenetic reconstruction. Results Bayesian phylogenetic analyses of >14,000 single nucleotide polymorphisms yielded completely resolved trees for these 43 strains with high levels of statistical support. These results enable a better understanding of a separate analysis of population differentiation among >1,700 B. pseudomallei isolates as defined by sequence data from seven housekeeping genes. We analyzed this larger data set for population structure and allele sharing that can be attributed to lateral gene transfer. Our results suggest that despite an almost panmictic population, we can detect two distinct populations of B. pseudomallei that conform to biogeographic patterns found in many plant and animal species. That is, separation along Wallace's Line, a biogeographic boundary between Southeast Asia and Australia

  9. Detection and identification of bacterial pathogens of fish in kidney tissue using terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA genes.

    Science.gov (United States)

    Nilsson, William B; Strom, Mark S

    2002-04-01

    We report the application of a nucleic acid-based assay that enables direct detection and identification of bacterial pathogens in fish kidney tissue without the need for bacterial culture. The technique, known as terminal restriction fragment length polymorphism (T-RFLP), employs the polymerase chain reaction (PCR) using a primer pair that targets 2 highly conserved regions of the gene that encodes for the 16S small subunit of the bacterial ribosome. Each primer is 5' labeled with a different fluorescent dye, which results in each terminus of the resulting amplicon having a distinguishable fluorescent tag. The amplicon is then digested with a series of 6 restriction endonucleases, followed by size determination of the 2 labeled terminal fragments by capillary electrophoresis with laser-induced fluorescence detection. Comparison of the lengths of the full set of 12 terminal fragments with those predicted based on analyses of GenBank submissions of 16S sequences leads to presumptive identification of the pathogen to at least the genus, but more typically the species level. Results of T-RFLP analyses of genomic DNA from multiple strains of a number of fish bacterial pathogens are presented. The assay is further demonstrated on fish kidney tissue spiked with a known number of cells of Flavobacterium psychrophilum where a detection limit of ca. 30 CFU mg(-1) of tissue was estimated. A similar detection limit was observed for several other gram-negative pathogens. This procedure was also used to detect Aeromonas salmonicida and Renibacterium salmoninarum in the kidney tissue of 2 naturally infected salmonids. PMID:12033704

  10. Life history correlates of fecal bacterial species richness in a wild population of the blue tit Cyanistes caeruleus.

    Science.gov (United States)

    Benskin, Clare McW H; Rhodes, Glenn; Pickup, Roger W; Mainwaring, Mark C; Wilson, Kenneth; Hartley, Ian R

    2015-02-01

    Very little is known about the normal gastrointestinal flora of wild birds, or how it might affect or reflect the host's life-history traits. The aim of this study was to survey the species richness of bacteria in the feces of a wild population of blue tits Cyanistes caeruleus and to explore the relationships between bacterial species richness and various life-history traits, such as age, sex, and reproductive success. Using PCR-TGGE, 55 operational taxonomic units (OTUs) were identified in blue tit feces. DNA sequencing revealed that the 16S rRNA gene was amplified from a diverse range of bacteria, including those that shared closest homology with Bacillus licheniformis, Campylobacter lari, Pseudomonas spp., and Salmonella spp. For adults, there was a significant negative relationship between bacterial species richness and the likelihood of being detected alive the following breeding season; bacterial richness was consistent across years but declined through the breeding season; and breeding pairs had significantly more similar bacterial richness than expected by chance alone. Reduced adult survival was correlated with the presence of an OTU most closely resembling C. lari; enhanced adult survival was associated with an OTU most similar to Arthrobacter spp. For nestlings, there was no significant change in bacterial species richness between the first and second week after hatching, and nestlings sharing the same nest had significantly more similar bacterial richness. Collectively, these results provide compelling evidence that bacterial species richness was associated with several aspects of the life history of their hosts. PMID:25750710

  11. Efficacy of two sperm preparation techniques in reducing non-specific bacterial species from human semen

    Directory of Open Access Journals (Sweden)

    Prabath K Abeysundara

    2013-01-01

    Full Text Available Context: Artificial reproductive techniques using seminal preparations with bacteria may cause pelvic inflammatory disease and its sequalae. Aims: To assess efficacy of two sperm preparation techniques to clear bacteria and the effect of bacteriospermia on sperm recovery rates. Settings and Design: A descriptive cross-sectional study was carried out among males of subfertile couples. Subjects and Methods: Semen samples were randomly allocated into swim-up method (group S, n = 68 and density gradient method (group D, n = 50 for sperm preparation. Seminal fluid analysis and bacterial cultures were performed in each sample before and after sperm preparation. Statistical Analysis: McNemar′s chi-squared test and independent samples t-test in SPSS version 16.0 were used. Results: Organisms were found in 86 (72.88% out of 118 samples, before sperm preparation; Streptococcus species (n = 40, 46.51% of which 14 were Group D Streptococcus species, Coagulase negative Staphylococcus species (n = 17, 19.76%, Staphylococcus aureus (n = 13, 15.11%, Coliform species (n = 11, 12.79% of which 09 were Escherichia coli and Corynebacterium species (n = 5, 5.81%. There was a statistically significant reduction of culture positive samples in raw vs. processed samples; in group S, 49 (72.05% vs. 16 (23.52% and in group D, 37 (74% vs. 18 (36%. In group S and D, mean (SD recovery rates of culture positive vs. culture negative samples were 39.44% (SD-14.02 vs. 44.22% (SD-22.38, P = 0.39 and 52.50% (SD-37.16 vs. 49.58% (SD-40.32, P = 0.82 respectively. Conclusions: Both sperm preparation methods significantly reduced bacteria in semen, but total clearance was not achieved. Sperm recovery rate was not affected by bacteriospermia.

  12. Chromosome Painting In Silico in a Bacterial Species Reveals Fine Population Structure

    Science.gov (United States)

    Yahara, Koji; Furuta, Yoshikazu; Oshima, Kenshiro; Yoshida, Masaru; Azuma, Takeshi; Hattori, Masahira; Uchiyama, Ikuo; Kobayashi, Ichizo

    2013-01-01

    Identifying population structure forms an important basis for genetic and evolutionary studies. Most current methods to identify population structure have limitations in analyzing haplotypes and recombination across the genome. Recently, a method of chromosome painting in silico has been developed to overcome these shortcomings and has been applied to multiple human genome sequences. This method detects the genome-wide transfer of DNA sequence chunks through homologous recombination. Here, we apply it to the frequently recombining bacterial species Helicobacter pylori that has infected Homo sapiens since their birth in Africa and shows wide phylogeographic divergence. Multiple complete genome sequences were analyzed including sequences from Okinawa, Japan, that we recently sequenced. The newer method revealed a finer population structure than revealed by a previous method that examines only MLST housekeeping genes or a phylogenetic network analysis of the core genome. Novel subgroups were found in Europe, Amerind, and East Asia groups. Examination of genetic flux showed some singleton strains to be hybrids of subgroups and revealed evident signs of population admixture in Africa, Europe, and parts of Asia. We expect this approach to further our understanding of intraspecific bacterial evolution by revealing population structure at a finer scale. PMID:23505045

  13. Long-term maintenance of species-specific bacterial microbiota in the basal metazoan Hydra

    Science.gov (United States)

    Fraune, Sebastian; Bosch, Thomas C. G.

    2007-01-01

    Epithelia in animals are colonized by complex communities of microbes. Although a topic of long-standing interest, understanding the evolution of the microbial communities and their role in triggering innate immune responses has resisted analysis. Cnidaria are among the simplest animals at the tissue grade of organization. To obtain a better understanding of the microbiota associated with phylogenetically ancient epithelia, we have identified the epibiotic and endosymbiotic bacteria of two species of the cnidarian Hydra on the basis of rRNA comparisons. We analyzed individuals of Hydra oligactis and Hydra vulgaris from both laboratory cultures and the wild. We discovered that individuals from both species differ greatly in their bacterial microbiota. Although H. vulgaris polyps have a quite diverse microbiota, H. oligactis appears to be associated with only a limited number of microbes; some of them were found, unexpectedly, to be endosymbionts. Surprisingly, the microfauna showed similar characteristics in individuals of cultures maintained in the laboratory for >30 years and polyps directly isolated from the wild. The significant differences in the microbial communities between the two species and the maintenance of specific microbial communities over long periods of time strongly indicate distinct selective pressures imposed on and within the epithelium. Our analysis suggests that the Hydra epithelium actively selects and shapes its microbial community. PMID:17664430

  14. Surviving chytridiomycosis: differential anti-Batrachochytrium dendrobatidis activity in bacterial isolates from three lowland species of Atelopus.

    Directory of Open Access Journals (Sweden)

    Sandra V Flechas

    Full Text Available In the Neotropics, almost every species of the stream-dwelling harlequin toads (genus Atelopus have experienced catastrophic declines. The persistence of lowland species of Atelopus could be explained by the lower growth rate of Batrachochytrium dendrobatidis (Bd at temperatures above 25 °C. We tested the complementary hypothesis that the toads' skin bacterial microbiota acts as a protective barrier against the pathogen, perhaps delaying or impeding the symptomatic phase of chytridiomycosis. We isolated 148 cultivable bacterial strains from three lowland Atelopus species and quantified the anti-Bd activity through antagonism assays. Twenty-six percent (38 strains representing 12 species of the bacteria inhibited Bd growth and just two of them were shared among the toad species sampled in different localities. Interestingly, the strongest anti-Bd activity was measured in bacteria isolated from A. elegans, the only species that tested positive for the pathogen. The cutaneous bacterial microbiota is thus likely a fitness-enhancing trait that may (adaptation or not (exaptation have appeared because of natural selection mediated by chytridiomycosis. Our findings reveal bacterial strains for development of local probiotic treatments against chytridiomycosis and also shed light on the mechanisms behind the frog-bacteria-pathogen interaction.

  15. Surviving chytridiomycosis: differential anti-Batrachochytrium dendrobatidis activity in bacterial isolates from three lowland species of Atelopus.

    Science.gov (United States)

    Flechas, Sandra V; Sarmiento, Carolina; Cárdenas, Martha E; Medina, Edgar M; Restrepo, Silvia; Amézquita, Adolfo

    2012-01-01

    In the Neotropics, almost every species of the stream-dwelling harlequin toads (genus Atelopus) have experienced catastrophic declines. The persistence of lowland species of Atelopus could be explained by the lower growth rate of Batrachochytrium dendrobatidis (Bd) at temperatures above 25 °C. We tested the complementary hypothesis that the toads' skin bacterial microbiota acts as a protective barrier against the pathogen, perhaps delaying or impeding the symptomatic phase of chytridiomycosis. We isolated 148 cultivable bacterial strains from three lowland Atelopus species and quantified the anti-Bd activity through antagonism assays. Twenty-six percent (38 strains representing 12 species) of the bacteria inhibited Bd growth and just two of them were shared among the toad species sampled in different localities. Interestingly, the strongest anti-Bd activity was measured in bacteria isolated from A. elegans, the only species that tested positive for the pathogen. The cutaneous bacterial microbiota is thus likely a fitness-enhancing trait that may (adaptation) or not (exaptation) have appeared because of natural selection mediated by chytridiomycosis. Our findings reveal bacterial strains for development of local probiotic treatments against chytridiomycosis and also shed light on the mechanisms behind the frog-bacteria-pathogen interaction. PMID:22970314

  16. Biosorption of some ions on different bacterial species from aqueous and radioactive waste solutions

    International Nuclear Information System (INIS)

    The uptake of metal ions, cerium, Ce(III); cobalt, Co(II); thorium, Th(IV); and uranium U(VI) by Bacillus pumilus-LRW1, Bacillus cereus-LRW2 and Micrococcus lylae-LRW3 from aqueous solution was examined as a function of metal ion concentration, pH, temperature, and the presence of some foreign ions. The bacterial species exhibited high affinity to accumulate metal ions from their solutions at pH 4-5.0 ± 0.5. The amount of each ion (in mg) accumulated by one gram dry weight of each bacteria was calculated. The uptake by the Bacillus cereus-LRW2 from aqueous solutions and simulated radioactive wastes were also investigated. Electron microscopic investigations showed that the ions were accumulated around the cell wall. (author)

  17. Coevolution between Stop Codon Usage and Release Factors in Bacterial Species.

    Science.gov (United States)

    Wei, Yulong; Wang, Juan; Xia, Xuhua

    2016-09-01

    Three stop codons in bacteria represent different translation termination signals, and their usage is expected to depend on their differences in translation termination efficiency, mutation bias, and relative abundance of release factors (RF1 decoding UAA and UAG, and RF2 decoding UAA and UGA). In 14 bacterial species (covering Proteobacteria, Firmicutes, Cyanobacteria, Actinobacteria and Spirochetes) with cellular RF1 and RF2 quantified, UAA is consistently over-represented in highly expressed genes (HEGs) relative to lowly expressed genes (LEGs), whereas UGA usage is the opposite even in species where RF2 is far more abundant than RF1. UGA usage relative to UAG increases significantly with PRF2 [=RF2/(RF1 + RF2)] as expected from adaptation between stop codons and their decoders. PRF2 is > 0.5 over a wide range of AT content (measured by PAT3 as the proportion of AT at third codon sites), but decreases rapidly toward zero at the high range of PAT3 This explains why bacterial lineages with high PAT3 often have UGA reassigned because of low RF2. There is no indication that UAG is a minor stop codon in bacteria as claimed in a recent publication. The claim is invalid because of the failure to apply the two key criteria in identifying a minor codon: (1) it is least preferred by HEGs (or most preferred by LEGs) and (2) it corresponds to the least abundant decoder. Our results suggest a more plausible explanation for why UAA usage increases, and UGA usage decreases, with PAT3, but UAG usage remains low over the entire PAT3 range. PMID:27297468

  18. DNA barcoding for the identification of sand fly species (Diptera, Psychodidae, Phlebotominae in Colombia.

    Directory of Open Access Journals (Sweden)

    María Angélica Contreras Gutiérrez

    Full Text Available Sand flies include a group of insects that are of medical importance and that vary in geographic distribution, ecology, and pathogen transmission. Approximately 163 species of sand flies have been reported in Colombia. Surveillance of the presence of sand fly species and the actualization of species distribution are important for predicting risks for and monitoring the expansion of diseases which sand flies can transmit. Currently, the identification of phlebotomine sand flies is based on morphological characters. However, morphological identification requires considerable skills and taxonomic expertise. In addition, significant morphological similarity between some species, especially among females, may cause difficulties during the identification process. DNA-based approaches have become increasingly useful and promising tools for estimating sand fly diversity and for ensuring the rapid and accurate identification of species. A partial sequence of the mitochondrial cytochrome oxidase gene subunit I (COI is currently being used to differentiate species in different animal taxa, including insects, and it is referred as a barcoding sequence. The present study explored the utility of the DNA barcode approach for the identification of phlebotomine sand flies in Colombia. We sequenced 700 bp of the COI gene from 36 species collected from different geographic localities. The COI barcode sequence divergence within a single species was <2% in most cases, whereas this divergence ranged from 9% to 26.6% among different species. These results indicated that the barcoding gene correctly discriminated among the previously morphologically identified species with an efficacy of nearly 100%. Analyses of the generated sequences indicated that the observed species groupings were consistent with the morphological identifications. In conclusion, the barcoding gene was useful for species discrimination in sand flies from Colombia.

  19. Rapid species identification of fresh and processed scallops by multiplex PCR

    OpenAIRE

    Marín, Alan; Fujimoto, Takafumi; Arai, Katsutoshi

    2013-01-01

    Food control policies regarding to seafood label authenticity have become a global issue due to increased incidence of species substitution or mislabelling. Proper species-level identification in processed scallop products is hindered by the lack of morphological characters such as their valves. In order to identify four commercially important scallop species (Argopecten purpuratus, A. irradians, Mizuhopecten yessoensis, Pecten albicans) a species-specific multiplex PCR reaction is described ...

  20. Influences of Plant Species, Season and Location on Leaf Endophytic Bacterial Communities of Non-Cultivated Plants

    Science.gov (United States)

    Ding, Tao; Melcher, Ulrich

    2016-01-01

    Bacteria are known to be associated endophytically with plants. Research on endophytic bacteria has identified their importance in food safety, agricultural production and phytoremediation. However, the diversity of endophytic bacterial communities and the forces that shape their compositions in non-cultivated plants are largely uncharacterized. In this study, we explored the diversity, community structure, and dynamics of endophytic bacteria in different plant species in the Tallgrass Prairie Preserve of northern Oklahoma, USA. High throughput sequencing of amplified segments of bacterial rDNA from 81 samples collected at four sampling times from five plant species at four locations identified 335 distinct OTUs at 97% sequence similarity, representing 16 phyla. Proteobacteria was the dominant phylum in the communities, followed by the phyla Bacteriodetes and Actinobacteria. Bacteria from four classes of Proteobacteria were detected with Alphaproteobacteria as the dominant class. Analysis of molecular variance revealed that host plant species and collecting date had significant influences on the compositions of the leaf endophytic bacterial communities. The proportion of Alphaproteobacteria was much higher in the communities from Asclepias viridis than from other plant species and differed from month to month. The most dominant bacterial groups identified in LDA Effect Size analysis showed host-specific patterns, indicating mutual selection between host plants and endophytic bacteria and that leaf endophytic bacterial compositions were dynamic, varying with the host plant’s growing season in three distinct patterns. In summary, next generation sequencing has revealed variations in the taxonomic compositions of leaf endophytic bacterial communities dependent primarily on the nature of the plant host species. PMID:26974817

  1. The pneumococcal serine-rich repeat protein is an intra-species bacterial adhesin that promotes bacterial aggregation in vivo and in biofilms.

    Directory of Open Access Journals (Sweden)

    Carlos J Sanchez

    Full Text Available The Pneumococcal serine-rich repeat protein (PsrP is a pathogenicity island encoded adhesin that has been positively correlated with the ability of Streptococcus pneumoniae to cause invasive disease. Previous studies have shown that PsrP mediates bacterial attachment to Keratin 10 (K10 on the surface of lung cells through amino acids 273-341 located in the Basic Region (BR domain. In this study we determined that the BR domain of PsrP also mediates an intra-species interaction that promotes the formation of large bacterial aggregates in the nasopharynx and lungs of infected mice as well as in continuous flow-through models of mature biofilms. Using numerous methods, including complementation of mutants with BR domain deficient constructs, fluorescent microscopy with Cy3-labeled recombinant (rBR, Far Western blotting of bacterial lysates, co-immunoprecipitation with rBR, and growth of biofilms in the presence of antibodies and competitive peptides, we determined that the BR domain, in particular amino acids 122-166 of PsrP, promoted bacterial aggregation and that antibodies against the BR domain were neutralizing. Using similar methodologies, we also determined that SraP and GspB, the Serine-rich repeat proteins (SRRPs of Staphylococcus aureus and Streptococcus gordonii, respectively, also promoted bacterial aggregation and that their Non-repeat domains bound to their respective SRRPs. This is the first report to show the presence of biofilm-like structures in the lungs of animals infected with S. pneumoniae and show that SRRPs have dual roles as host and bacterial adhesins. These studies suggest that recombinant Non-repeat domains of SRRPs (i.e. BR for S. pneumoniae may be useful as vaccine antigens to protect against Gram-positive bacteria that cause infection.

  2. Unveiling cryptic species diversity of flowering plants: successful biological species identification of Asian Mitella using nuclear ribosomal DNA sequences

    Directory of Open Access Journals (Sweden)

    Okuyama Yudai

    2009-05-01

    Full Text Available Abstract Background Although DNA sequence analysis is becoming a powerful tool for identifying species, it is not easy to assess whether the observed genetic disparity corresponds to reproductive isolation. Here, we compared the efficiency of biological species identification between nuclear ribosomal and chloroplast DNA sequences, focusing on an Asian endemic perennial lineage of Mitella (Asimitellaria; Saxifragaceae. We performed artificial cross experiments for 43 pairs of ten taxonomic species, and examined their F1 hybrid pollen fertility in vitro as a quantitative measure of postzygotic reproductive isolation. Results A nonlinear, multiple regression analysis indicated that the nuclear ribosomal DNA distances are sufficient to explain the observed pattern of F1 hybrid pollen fertility, and supplementation with chloroplast DNA distance data does not improve the explanatory power. Overall, with the exception of a recently diverged species complex with more than three biological species, nuclear ribosomal DNA sequences successfully circumscribed ten distinct biological species, of which two have not been described (and an additional one has not been regarded as a distinct taxonomic species to date. Conclusion We propose that nuclear ribosomal DNA sequences contribute to reliable identification of reproductively isolated and cryptic species of Mitella. More comparable studies for other plant groups are needed to generalize our findings to flowering plants.

  3. MASS SPECTROMETRIC ANALYSIS FOR THE IDENTIFICATION OF THUNNUS GENUS FOUR SPECIES

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    T. Pepe

    2011-01-01

    Full Text Available An accurate identification of similar fish species is necessary to prevent illegal substitution and is imposed by labeling regulations in UE countries (1. The genus Thunnus comprises many species of different quality and commercial value. The increasing trade of fish preparations of the species included in this genus and the consequent loss of the external anatomical and morphological features enables fraudulent substitutions. This study reports data relating to the proteomic analysis of four tuna species (T. thynnus, T. alalunga, T. albacares, T. obesus. Sarcoplasmic proteins were studied by mono and two dimensional electrophoresis. The most significant proteins for the characterization of the species were analyzed by mass spectrometric techniques. As reported in a previous study (2, an accurate identification of the species seems possible, owing to the polymorphism displayed by the species of the Thunnus genus.

  4. Identification of Bacterial Community Composition in Freshwater Aquaculture System Farming of Litopenaeus vannamei Reveals Distinct Temperature-Driven Patterns

    Directory of Open Access Journals (Sweden)

    Yuyi Tang

    2014-08-01

    Full Text Available Change in temperature is often a major environmental factor in triggering waterborne disease outbreaks. Previous research has revealed temporal and spatial patterns of bacterial population in several aquatic ecosystems. To date, very little information is available on aquaculture environment. Here, we assessed environmental temperature effects on bacterial community composition in freshwater aquaculture system farming of Litopenaeus vannamei (FASFL. Water samples were collected over a one-year period, and aquatic bacteria were characterized by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE and 16S rDNA pyrosequencing. Resulting DGGE fingerprints revealed a specific and dynamic bacterial population structure with considerable variation over the seasonal change, suggesting that environmental temperature was a key driver of bacterial population in the FASFL. Pyrosequencing data further demonstrated substantial difference in bacterial community composition between the water at higher (WHT and at lower (WLT temperatures in the FASFL. Actinobacteria, Proteobacteria and Bacteroidetes were the highest abundant phyla in the FASFL, however, a large number of unclassified bacteria contributed the most to the observed variation in phylogenetic diversity. The WHT harbored remarkably higher diversity and richness in bacterial composition at genus and species levels when compared to the WLT. Some potential pathogenenic species were identified in both WHT and WLT, providing data in support of aquatic animal health management in the aquaculture industry.

  5. Chlamydia pneumoniae and atherosclerosis. Identification of bacterial DNA in the arterial wall

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    Coutinho Mário Sérgio Soares de Azeredo

    2000-01-01

    Full Text Available OBJECTIVE: The intracellular Gram-negative bacterium Chlamydia pneumoniae has been associated with atherosclerosis. The presence of Chlamydia pneumoniae has been investigated in fragments of the arterial wall with a technique for DNA identification. METHODS: Arterial fragments obtained from vascular surgical procedures in 58 patients were analyzed. From these patients, 39 were males and the mean age was 65±6 years. The polymerase chain reaction was used to identify the bacterial DNA with a pair of primers that codify the major outer membrane protein (MOMP of Chlamydia pneumoniae. The amplified product was visualized by electrophoresis in the 2% agarose gel stained with ethidium bromide, and it was considered positive when migrating in the band of molecular weight of the positive controls. RESULTS: Seven (12% out of the 58 patients showed positive results for Chlamydia pneumoniae. CONCLUSION: DNA from Chlamydia pneumoniae was identified in the arterial wall of a substantial number of patients with atherosclerosis. This association, which has already been described in other countries, corroborates the evidence favoring a role played by Chlamydia pneumoniae in atherogenesis.

  6. Viral and bacterial pathogens identification in children hospitalised for severe pneumonia and parapneumonic empyema

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    Jean-Noël Telles

    2012-05-01

    Full Text Available Pneumonia is caused by respiratory bacteria and/or viruses. Little is known if co-infections are an aggravating factor in hospitalised children with severe pneumonia. We studied the impact of respiratory pathogens on the severity of pneumonia. Between 2007 and 2009, 52 children hospitalised with a well-documented diagnosis of communityacquired pneumonia (CAP, with or without parapneumonic empyema (PPE, were enrolled in the study. The patients were classified into 2 groups: CAP + PPE (n = 28 and CAP (n = 24. The identification of respiratory viruses and bacteria in nasopharyngeal aspirates and pleural effusion samples were performed using conventional bacterial techniques and molecular assays. Using real-time multiplex PCR and antigen detection, Streptococcus pneumoniae was the main agent identified in 76% of the cases by molecular tests and BinaxNOW® in pleural fluid. A total of 8% of pleural fluid samples remained undiagnosed. In nasopharyngeal aspirates, rhinovirus, parainfluenza viruses, human metapneumovirus, and respiratory syncytial virus were detected in both CAP and CAP + PPE populations; however, the percentage of viral co-detection was significantly higher in nasopharyngeal aspirates from CAP + PPE patients (35% compared with CAP patients (5%. In conclusion, viral co-detection was observed mainly in patients with more severe pneumonia. Molecular biology assays improved the pathogens detection in pneumonia and confirmed the S. pneumoniae detection by BinaxNOW® in pleural effusion samples. Interestingly, the main S. pneumoniae serotypes found in PPE are not the ones targeted by the heptavalent pneumococcal conjugate vaccine.

  7. Evaluation of chromogenic media and seminested PCR in the identification of Candida species

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    Enas Daef

    2014-01-01

    Full Text Available Identification of Candida cultured from various clinical specimens to the species level is increasingly necessary for clinical laboratories. Although sn PCR identifies the species within hours but its cost-effectiveness is to be considered. So there is always a need for media which help in the isolation and identification at the species level. The study aimed to evaluate the performance of different chromogenic media and to compare the effectiveness of the traditional phenotypic methods vs. seminested polymerase chain reaction (sn PCR for identification of Candida species. One hundred and twenty seven Candida strains isolated from various clinical specimens were identified by conventional methods, four different chromogenic media and sn PCR. HiCrome Candida Differential and CHROMagar Candida media showed comparably high sensitivities and specificities in the identification of C. albicans, C. tropicalis, C. glabrata and C. krusei. CHROMagar Candida had an extra advantage of identifying all C. parapsilosis isolates. CHROMagar-Pal's medium identified C. albicans, C. tropicalis and C. krusei with high sensitivities and specificities, but couldn't identify C. glabrata or C. parapsilosis. It was the only medium that identified C. dubliniensis with a sensitivity and specificity of 100%. Biggy agar showed the least sensitivities and specificities. The overall concordance of the snPCR compared to the conventional tests including CHROMAgar Candida in the identification of Candida species was 97.5%. The use of CHROMAgar Candida medium is an easy and accurate method for presumptive identification of the most commonly encountered Candida spp.

  8. Genome- and transcriptome-assisted development of nuclear insertion/deletion markers for Calanus species (Copepoda: Calanoida) identification

    DEFF Research Database (Denmark)

    Smolina, I.; Kollias, S.; Poortvliet, M.;

    2014-01-01

    Copepods of the genus Calanus are key zooplankton species in temperate to arctic marine ecosystems. Despite their ecological importance, species identification remains challenging. Furthermore, the recent report of hybrids among Calanus species highlights the need for diagnostic nuclear markers t...

  9. Surviving Chytridiomycosis: Differential Anti-Batrachochytrium dendrobatidis Activity in Bacterial Isolates from Three Lowland Species of Atelopus

    OpenAIRE

    Flechas, Sandra V.; Sarmiento, Carolina; Martha E Cárdenas; Edgar M Medina; Restrepo, Silvia; Amézquita, Adolfo

    2012-01-01

    In the Neotropics, almost every species of the stream-dwelling harlequin toads (genus Atelopus) have experienced catastrophic declines. The persistence of lowland species of Atelopus could be explained by the lower growth rate of Batrachochytrium dendrobatidis (Bd) at temperatures above 25°C. We tested the complementary hypothesis that the toads' skin bacterial microbiota acts as a protective barrier against the pathogen, perhaps delaying or impeding the symptomatic phase of chytridiomycosis....

  10. Wing pattern morphology of three closely related Melitaea (Lepidoptera, Nymphalidae species reveals highly inaccurate external morphology-based species identification

    Directory of Open Access Journals (Sweden)

    Jure Jugovic

    2014-06-01

    Full Text Available Wing morphology of the three closely related species of Melitaea – M. athalia (Rottemburg, 1775, M. aurelia (Nickerl, 1850 and M. britomartis Assmann, 1847 – co-occurring in the Balkans (SE Europe was investigated in detail through visual inspection, morphometric analysis and multivariate statistical analysis. Results are compared to recent phylogenetic studies, searching for concordant patterns and discrepancies between the two approaches. The morphology of the genitalic structures is also compared with the results of the other two approaches. The main conclusions are as follows: (1 small albeit significant differences in wing morphology exist among the three species and (2 while the structure of male genitalia and phylogenetic position of the three species are concordant, they are (3 in discordance with the wing morphology. The present study represents another example where identification based on external morphology would lead to highly unreliable determinations, hence identification based on phylogenetic studies and/or genitalia is strongly recommended not only for the three studied species but also more broadly within the genus. Furthermore, we show that some of the characters generally used in the identification of these three Melitaea species should be avoided in future.

  11. Comparison of Phenotypical and Molecular Methods for the Identification of Bacterial Strains Isolated from a Deep Subsurface Environment

    OpenAIRE

    Boivin-Jahns, V.; Bianchi, A.; Ruimy, R; Garcin, J.; Daumas, S.; Christen, R

    1995-01-01

    Seventy-four bacterial strains were freshly isolated from a mine gallery. Using these bacteria, we have investigated how a molecular identification based on the analysis of small subunit rDNA sequences would compare in terms of precision and reliability to a more classical comparison of phenotypical descriptions (100 morphological and physiological traits). Our data clearly showed that a phylogenetic analysis of small subunit rDNA sequences is more efficient than classical phenotypic methods ...

  12. Identification of multiple physicochemical and structural properties associated with soluble expression of eukaryotic proteins in cell-free bacterial extracts

    OpenAIRE

    AlexanderA.Tokmakov

    2014-01-01

    Bacterial extracts are widely used to synthesize recombinant proteins. Vast data volumes have been accumulated in cell-free expression databases, covering a whole range of existing proteins. It makes possible comprehensive bioinformatics analysis and identification of multiple features associated with protein solubility and aggregation. In the present paper, an approach to identify the multiple physicochemical and structural properties of amino acid sequences associated with soluble expressio...

  13. Host species and environmental effects on bacterial communities associated with Drosophila in the laboratory and in the natural environment.

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    Fabian Staubach

    Full Text Available The fruit fly Drosophila is a classic model organism to study adaptation as well as the relationship between genetic variation and phenotypes. Although associated bacterial communities might be important for many aspects of Drosophila biology, knowledge about their diversity, composition, and factors shaping them is limited. We used 454-based sequencing of a variable region of the bacterial 16S ribosomal RNA gene to characterize the bacterial communities associated with wild and laboratory Drosophila isolates. In order to specifically investigate effects of food source and host species on bacterial communities, we analyzed samples from wild Drosophila melanogaster and D. simulans collected from a variety of natural substrates, as well as from adults and larvae of nine laboratory-reared Drosophila species. We find no evidence for host species effects in lab-reared flies; instead, lab of origin and stochastic effects, which could influence studies of Drosophila phenotypes, are pronounced. In contrast, the natural Drosophila-associated microbiota appears to be predominantly shaped by food substrate with an additional but smaller effect of host species identity. We identify a core member of this natural microbiota that belongs to the genus Gluconobacter and is common to all wild-caught flies in this study, but absent from the laboratory. This makes it a strong candidate for being part of what could be a natural D. melanogaster and D. simulans core microbiome. Furthermore, we were able to identify candidate pathogens in natural fly isolates.

  14. Widespread Transfer of Resistance Genes between Bacterial Species in an Intensive Care Unit: Implications for Hospital Epidemiology

    OpenAIRE

    Naiemi, N.A.; Duim, B.; Savelkoul, P. H. M.; Spanjaard, L.; de Jonge,; Bart, A.; Vandenbroucke-Grauls, C. M. J. E.; Jong, de, M.C.M.

    2005-01-01

    A transferable plasmid encoding SHV-12 extended-spectrum β-lactamase, TEM-116, and aminoglycoside resistance was responsible for two sequential clonal outbreaks of Enterobacter cloacae and Acinetobacter baumannii bacteria. A similar plasmid was present among isolates of four different bacterial species. Recognition of plasmid transfer is crucial for control of outbreaks of multidrug-resistant nosocomial pathogens.

  15. Development of aptamers for use as radiopharmaceuticals in the bacterial infection identification

    International Nuclear Information System (INIS)

    The difficulty in early detection of specific foci caused by bacteria in the bacterial infection has raised the need to search for new techniques for this purpose, since these foci require prolonged treatment with antibiotics and in some cases even drainage or, if applicable, removal of prostheses or grafts. Detection of bacterial infections by scintigraphy had the advantage that a whole body image could be obtained, since specific tracers were available. This study aims to obtain aptamers specific for bacteria identification for future use as radiopharmaceutical. The SELEX (Systematic Evolution of Ligands by Exponential Enrichment) methodology can generate oligonucleotides (aptamers) that are able to bind with high affinity and specificity to a specific target, from small molecules to complex proteins, by using rounds of enrichment and amplification. Aptamers can be labeled with different radionucleotides such as 99mTc, 18F and 32P. In this study, aptamers anti-peptidoglycan, the main component of the bacterial outer cell wall, were obtained through SELEX. Whole cells of Staphylococcus aureus were also used to perform the SELEX to cells (cell-SELEX). The selection of aptamers was performed by two different procedures (A and B). The A process has been accomplished by 15 SELEX rounds in which the separation of the oligonucleotides bound to the peptidoglycan of unbound ones was performed by filtration. In the B process 15 SELEX rounds were performed using the centrifugation for this separation, followed by 5 rounds cell-SELEX. The SELEX started with a pool of ssDNA (single stranded DNA). For A process, initially a library of ssDNA was incubated with peptidoglycan and the amplification of oligonucleotides that were able to bind to peptidoglycan was performed by PCR (Polymerase Chain Reation). The amplified oligonucleotides were again incubated with peptidoglycan, amplified and purified. At the end of 15 selection rounds the selected oligonucleotides were cloned. The

  16. Neural network-based species identification in venom-interacted cases in India

    Directory of Open Access Journals (Sweden)

    R. Maheshwari

    2007-01-01

    Full Text Available India is home to a number of venomous species. Every year in harvesting season, a large number of productive citizens are envenomed by such species. For efficient medical management of the victims, identification of the aggressor species as well as assessment of the envenomation degree is necessary. Species identification is generally based on the visual description by the victim or a witness and is therefore quite likely to be erroneous. Symptomatic identification remains the only available method. In a previous published work, the authors proposed a classification table for snake species based on manifested symptoms applicable in Indian subcontinent. The classification table serves the purpose to a great deal but as a manual method it demands human expertise. The current paper presents a neural network-based symptomatic species identification system. A symptom vector is fed as input to the neural network and the system yields the most probable species as well as the envenomation severity as the output. The severity status can be very helpful in calculating the antivenom dosage and in deciding the species-specific prognostic measures for efficient medical management.

  17. Species and hybrid identification of sturgeon caviar: a new molecular approach to detect illegal trade.

    Science.gov (United States)

    Boscari, E; Barmintseva, A; Pujolar, J M; Doukakis, P; Mugue, N; Congiu, L

    2014-05-01

    Overexploitation of wild populations due to the high economic value of caviar has driven sturgeons to near extinction. The high prices commanded by caviar on world markets have made it a magnet for illegal and fraudulent caviar trade, often involving low-value farmed caviar being sold as top-quality caviar. We present a new molecular approach for the identification of pure sturgeon species and hybrids that are among the most commercialized species in Europe and North America. Our test is based on the discovery of species-specific single nucleotide polymorphisms (SNPs) in the ribosomal protein S7, supplemented with the Vimentin gene and the mitochondrial D-loop. Test validations performed in 702 specimens of target and nontarget sturgeon species demonstrated a 100% identification success for Acipenser naccarii, A. fulvescens, A. stellatus, A. sinensis and A. transmontanus. In addition to species identification, our approach allows the identification of Bester and AL hybrids, two of the most economically important hybrids in the world, with 80% and 100% success, respectively. Moreover, the approach has the potential to identify many other existing sturgeon hybrids. The development of a standardized sturgeon identification tool will directly benefit trade law enforcement, providing the tools to monitor and regulate the legal trade of caviar and protect sturgeon stocks from illicit producers and traders, hence contributing to safeguarding this group of heavily threatened species. PMID:24219811

  18. Wildlife DNA Forensic in Curbing Illegal Wildlife Trade: Specie Identification from Seizures

    OpenAIRE

    Ved P Kumar; Dhyanendra Kumar; Goyal, Surendra P.

    2014-01-01

    Species identification in wildlife forensics is the one of the major concern to enforce law and curbing illegal wildlife trade. Among all the available analytical teqniques DNA based species identification is the most robust and acceptable evidence in the court of law. We analysed cytochrome b and 12S rRNA mtDNA fragments to identify species from three different seizures. DNA based analysis of Cyt b and 12S rRNA has identified three seizures as Hog deer, Chital and Swamp deer.

  19. Molecular Identification of Gemella Species from Three Patients with Endocarditis

    OpenAIRE

    La Scola, Bernard; Raoult, Didier

    1998-01-01

    Gemella morbillorum and Gemella haemolysans are opportunistic pathogens which cause endocarditis and other severe infections. We report on three patients with endocarditis, one with endocarditis caused by G. haemolysans and two with endocarditis caused by G. morbillorum. The paucity of reports concerning these bacteria is probably related to the difficulties associated with their identification. For example, one of the strains reported in this study was originally sent to our laboratory with ...

  20. Tualatin River - Invasive Species Identification, Control and Monitoring 2007

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Project goals were to train volunteers to conduct invasive species mapping using GPS and GIS technology. Volunteers were able to map 450 acres on the Atflati Unit...

  1. Molecular and Morphological Identification of Colletotrichum Species of Clinical Interest

    OpenAIRE

    Cano, Josep; Guarro, Josep; Gené, Josepa

    2004-01-01

    Colletotrichum species have caused human infections in recent years. Because of the difficulties in recognizing them in vitro, we have designed a quick and unambiguous molecular test, based on the amplification of a specific fragment of the internal transcribed spacer 1 region, to distinguish any Colletotrichum isolate from other fungi, including the common pathogenic species. Analysis of the sequences of the ribosomal DNA (rDNA) fragment showed sufficient variability to clearly separate the ...

  2. Helicobacter species and gut bacterial DNA in Meckel's diverticulum and the appendix

    Institute of Scientific and Technical Information of China (English)

    Peren H Karagin; Unne Stenram; Torkel Wadstr(o)m; (A)sa Ljungh

    2011-01-01

    AIM: To analyse the possible association of various Helicobacter species and certain common gut bacteria in patients with Meckel's diverticulum and appendicitis. METHODS: A nested-polymerase chain reaction (PCR), specific to 16S rRNA of the Helicobacter genus, was performed on paraffin embedded samples, 50 with acute appendicitis, 50 normal appendixes, and 33 Meckel's diverticulum with gastric heterotopia and/or ulcer. Helicobacter genus positive samples were sequenced for species identification. All samples were also analysed for certain gut bacteria by PCR. RESULTS: Helicobacter pullorum DNA was found in one out of 33 cases and Enterobacteria in two cases of Meckel's diverticulum. Helicobacter pylori (H. pylori ) was found in three, Enterobacter in 18, and Bacteroides in 19 out of 100 appendix samples by PCR. Enterococcus was not found in any MD or appendix samples. All H. pylori positive cases were from normal appendixes. CONCLUSION: Helicobacter is not an etiological agent in the pathogenesis of symptomatic Meckel's diverticulum or in acute appendicitis.

  3. Environmental monitoring using next generation sequencing: rapid identification of macroinvertebrate bioindicator species

    OpenAIRE

    Carew, Melissa E.; Pettigrove, Vincent J; Metzeling, Leon; Hoffmann, Ary A.

    2013-01-01

    Introduction Invertebrate communities are central to many environmental monitoring programs. In freshwater ecosystems, aquatic macroinvertebrates are collected, identified and then used to infer ecosystem condition. Yet the key step of species identification is often not taken, as it requires a high level of taxonomic expertise, which is lacking in most organizations, or species cannot be identified as they are morphologically cryptic or represent little known groups. Identifying species usin...

  4. DNA barcoding and microsatellites help species delimitation and hybrid identification in endangered galaxiid fishes

    OpenAIRE

    Vanhaecke, D.; García de Leániz, C.; G. Gajardo; Young, K.; Sanzana, J.; Orellana, G.; Fowler, D.; Howes, P.; Monzon-Arguello, C.; Consuegra, S.

    2012-01-01

    The conservation of data deficient species is often hampered by inaccurate species delimitation. The galaxiid fishes Aplochiton zebra and Aplochiton taeniatus are endemic to Patagonia (and for A. zebra the Falkland Islands), where they are threatened by invasive salmonids. Conservation of Aplochiton is complicated because species identification is hampered by the presence of resident as well as migratory ecotypes that may confound morphological discrimination. We used DNA barcoding (COI, cyto...

  5. A near-infrared spectroscopy routine for unambiguous identification of cryptic ant species.

    Science.gov (United States)

    Kinzner, Martin-Carl; Wagner, Herbert C; Peskoller, Andrea; Moder, Karl; Dowell, Floyd E; Arthofer, Wolfgang; Schlick-Steiner, Birgit C; Steiner, Florian M

    2015-01-01

    Species identification-of importance for most biological disciplines-is not always straightforward as cryptic species hamper traditional identification. Fibre-optic near-infrared spectroscopy (NIRS) is a rapid and inexpensive method of use in various applications, including the identification of species. Despite its efficiency, NIRS has never been tested on a group of more than two cryptic species, and a working routine is still missing. Hence, we tested if the four morphologically highly similar, but genetically distinct ant species Tetramorium alpestre, T. caespitum, T. impurum, and T. sp. B, all four co-occurring above 1,300 m above sea level in the Alps, can be identified unambiguously using NIRS. Furthermore, we evaluated which of our implementations of the three analysis approaches, partial least squares regression (PLS), artificial neural networks (ANN), and random forests (RF), is most efficient in species identification with our data set. We opted for a 100% classification certainty, i.e., a residual risk of misidentification of zero within the available data, at the cost of excluding specimens from identification. Additionally, we examined which strategy among our implementations, one-vs-all, i.e., one species compared with the pooled set of the remaining species, or binary-decision strategies, worked best with our data to reduce a multi-class system to a two-class system, as is necessary for PLS. Our NIRS identification routine, based on a 100% identification certainty, was successful with up to 66.7% of unambiguously identified specimens of a species. In detail, PLS scored best over all species (36.7% of specimens), while RF was much less effective (10.0%) and ANN failed completely (0.0%) with our data and our implementations of the analyses. Moreover, we showed that the one-vs-all strategy is the only acceptable option to reduce multi-class systems because of a minimum expenditure of time. We emphasise our classification routine using fibre-optic NIRS

  6. Advances in DNA metabarcoding for food and wildlife forensic species identification.

    Science.gov (United States)

    Staats, Martijn; Arulandhu, Alfred J; Gravendeel, Barbara; Holst-Jensen, Arne; Scholtens, Ingrid; Peelen, Tamara; Prins, Theo W; Kok, Esther

    2016-07-01

    Species identification using DNA barcodes has been widely adopted by forensic scientists as an effective molecular tool for tracking adulterations in food and for analysing samples from alleged wildlife crime incidents. DNA barcoding is an approach that involves sequencing of short DNA sequences from standardized regions and comparison to a reference database as a molecular diagnostic tool in species identification. In recent years, remarkable progress has been made towards developing DNA metabarcoding strategies, which involves next-generation sequencing of DNA barcodes for the simultaneous detection of multiple species in complex samples. Metabarcoding strategies can be used in processed materials containing highly degraded DNA e.g. for the identification of endangered and hazardous species in traditional medicine. This review aims to provide insight into advances of plant and animal DNA barcoding and highlights current practices and recent developments for DNA metabarcoding of food and wildlife forensic samples from a practical point of view. Special emphasis is placed on new developments for identifying species listed in the Convention on International Trade of Endangered Species (CITES) appendices for which reliable methods for species identification may signal and/or prevent illegal trade. Current technological developments and challenges of DNA metabarcoding for forensic scientists will be assessed in the light of stakeholders' needs. PMID:27178552

  7. Red and infrared laser therapy inhibits in vitro growth of major bacterial species that commonly colonize skin ulcers.

    Science.gov (United States)

    de Sousa, Natanael Teixeira Alves; Gomes, Rosana Caetano; Santos, Marcos Ferracioli; Brandino, Hugo Evangelista; Martinez, Roberto; de Jesus Guirro, Rinaldo Roberto

    2016-04-01

    Low-level laser therapy (LLLT) is used in chronic wounds due to its healing effects. However, bacterial species may colonize these wounds and the optimal parameters for effective bacterial inhibition are not clear. The aim of this study was to analyze the effect of LLLT on bacterial growth in vitro. Bacterial strains including Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa were suspended in saline solution at a concentration of 10(3) cells/ml and exposed to laser irradiation at wavelengths of 660, 830, and 904 nm at fluences of 0 (control), 3, 6, 12, 18, and 24 J/cm(2). An aliquot of the irradiated suspension was spread on the surface of petri plates and incubated at 37 °C for quantification of colony-forming unit after 24, 48, and 72 h. Laser irradiation inhibited the growth of S. aureus at all wavelengths and fluences higher than 12 J/cm(2), showing a strong correlation between increase in fluence and bacterial inhibition. However, for P. aeruginosa, LLLT inhibited growth at all wavelengths only at a fluence of 24 J/cm(2). E. coli had similar growth inhibition at a wavelength of 830 nm at fluences of 3, 6, 12, and 24 J/cm(2). At wavelengths of 660 and 904 nm, growth inhibition was only observed at fluences of 12 and 18 J/cm(2), respectively. LLLT inhibited bacterial growth at all wavelengths, for a maximum of 72 h after irradiation, indicating a correlation between bacterial species, fluence, and wavelength. PMID:26886585

  8. DNA barcoding in Atlantic Forest plants: what is the best marker for Sapotaceae species identification?

    Directory of Open Access Journals (Sweden)

    Caio Vinicius Vivas

    2014-12-01

    Full Text Available The Atlantic Forest is a phytogeographic domain with a high rate of endemism and large species diversity. The Sapotaceae is a botanical family for which species identification in the Atlantic Forest is difficult. An approach that facilitates species identification in the Sapotaceae is urgently needed because this family includes threatened species and valuable timber species. In this context, DNA barcoding could provide an important tool for identifying species in the Atlantic Forest. In this work, we evaluated four plant barcode markers (matK, rbcL, trnH-psbA and the nuclear ribosomal internal transcribed spacer region -ITS in 80 samples from 26 species of Sapotaceae that occur in the Atlantic Forest. ITS yielded the highest average interspecific distance (0.122, followed by trnH-psbA (0.019, matK (0.008 and rbcL (0.002. For species discrimination, ITS provided the best results, followed by matK, trnH-psbA and rbcL. Furthermore, the combined analysis of two, three or four markers did not result in higher rates of discrimination than obtained with ITS alone. These results indicate that the ITS region is the best option for molecular identification of Sapotaceae species from the Atlantic Forest.

  9. Use of species-specific PCR for the identification of 10 sea cucumber species

    Science.gov (United States)

    Wen, Jing; Zeng, Ling

    2014-11-01

    We developed a species-specific PCR method to identify species among dehydrated products of 10 sea cucumber species. Ten reverse species-specific primers designed from the 16S rRNA gene, in combination with one forward universal primer, generated PCR fragments of ca. 270 bp length for each species. The specificity of the PCR assay was tested with DNA of samples of 21 sea cucumber species. Amplification was observed in specific species only. The species-specific PCR method we developed was successfully applied to authenticate species of commercial products of dehydrated sea cucumber, and was proven to be a useful, rapid, and low-cost technique to identify the origin of the sea cucumber product.

  10. MALDI-TOF mass spectrometry - a rapid method for the identification of dermatophyte species.

    Science.gov (United States)

    Nenoff, Pietro; Erhard, Marcel; Simon, Jan C; Muylowa, Grace K; Herrmann, Jürgen; Rataj, Waldemar; Gräser, Yvonne

    2013-01-01

    Altogether 285 dermatophyte isolates of 21 different species - including both Trichophyton rubrum and T. interdigitale, but also eight additional Trichophyton species, Microsporum canis and seven other Microsporum species, as well as Epidermophyton floccosum and Arthroderma spp. - were analyzed using Matrix Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) and the AnagnosTec 'SARAMIS' (Spectral Archiving and Microbial Identification System) software. In addition, sequence analysis of the internal transcribed spacer (ITS) of the ribosomal DNA was performed for a high number of the tested strains. Sufficient agreement was found between the results obtained with standard identification methods and those with the MALDI-TOF MS for species identification of dermatophytes. A mass spectra database was constructed which contained the species identifications of all 285 isolates. The results were confirmed for 164 of the isolates by sequence analysis of the internal transcribed spacer (ITS) of the ribosomal DNA. Statistical analysis of all 285 dermatophyte strains showed that conventional identification matched the results of MALDI-TOF MS for 78.2% of the isolates tested. In the case of the 164 isolates for which the identifications were confirmed by PCR, the results of their conventional diagnosis and MALDI-TOF MS were in agreement for only 68.9 % (113 of 164 strains) of the test isolates. In contrast, there was agreement of 99.3 % or 98.8 % in the identifications obtained with PCR and MALDI-TOF MS techniques (283/285 or 162/164). The two exceptions were isolates that proved to be T. violaceum which could not be identified by the MALDI-TOF MS technique. In conclusion, the MALDI-TOF mass spectroscopy represents a fast and very specific method for species differentiation of dermatophytes grown in culture. PMID:22574631

  11. Ecological drift and local exposures drive enteric bacterial community differences within species of Galápagos iguanas.

    Science.gov (United States)

    Lankau, Emily W; Hong, Pei-Ying; Mackie, Roderick I

    2012-04-01

    Diet strongly influences the intestinal microbial communities through species sorting. Alternatively, these communicates may differ because of chance variation in local microbial exposures or species losses among allopatric host populations (i.e. ecological drift). We investigated how these forces shape enteric communities of Galápagos marine and land iguanas. Geographically proximate populations shared more similar communities within a host ecotype, suggesting a role for ecological drift during host colonization of the islands. Additionally, evidence of taxa sharing between proximate heterospecific host populations suggests that contemporary local exposures also influence the gut community assembly. While selective forces such as host-bacterial interactions or dietary differences are dominant drivers of intestinal community differences among hosts, historical and contemporary processes of ecological drift may lead to differences in bacterial composition within a host species. Whether such differences in community structure translate into geographic variation in benefits derived from these intimate microbial communities remains to be explored. PMID:22369350

  12. Antibiofilm Activity, Compound Characterization, and Acute Toxicity of Extract from a Novel Bacterial Species of Paenibacillus

    Directory of Open Access Journals (Sweden)

    Saad Musbah Alasil

    2014-01-01

    Full Text Available The effectiveness of many antimicrobial agents is currently decreasing; therefore, it is important to search for alternative therapeutics. Our study was carried out to assess the in vitro antibiofilm activity using microtiter plate assay, to characterize the bioactive compounds using Ultra Performance Liquid Chromatography-Diode Array Detection and Liquid Chromatography-Mass Spectrometry and to test the oral acute toxicity on Sprague Dawley rats of extract derived from a novel bacterial species of Paenibacillus strain 139SI. Our results indicate that the crude extract and its three identified compounds exhibit strong antibiofilm activity against a broad range of clinically important pathogens. Three potential compounds were identified including an amino acid antibiotic C8H20N3O4P (MW 253.237, phospholipase A2 inhibitor C21H36O5 (MW 368.512, and an antibacterial agent C14H11N3O2 (MW 253.260. The acute toxicity test indicates that the mortality rate among all rats was low and that the biochemical parameters, hematological profile, and histopathology examination of liver and kidneys showed no significant differences between experimental groups P>0.05. Overall, our findings suggest that the extract and its purified compounds derived from novel Paenibacillus sp. are nontoxic exhibiting strong antibiofilm activity against Gram-positive and Gram-negative pathogens that can be useful towards new therapeutic management of biofilm-associated infections.

  13. Composition of the Cutaneous Bacterial Community in Japanese Amphibians: Effects of Captivity, Host Species, and Body Region.

    Science.gov (United States)

    Sabino-Pinto, Joana; Bletz, Molly Catherine; Islam, Mohammed Mafizul; Shimizu, Norio; Bhuju, Sabin; Geffers, Robert; Jarek, Michael; Kurabayashi, Atsushi; Vences, Miguel

    2016-08-01

    The cutaneous microbiota plays a significant role in the biology of their vertebrate hosts, and its composition is known to be influenced both by host and environment, with captive conditions often altering alpha diversity. Here, we compare the cutaneous bacterial communities of 61 amphibians (both wild and captive) from Hiroshima, Japan, using high-throughput amplicon sequencing of a segment of the 16S rRNA gene. The majority of these samples came from a captive breeding facility at Hiroshima University where specimens from six species are maintained under highly standardized conditions for several generations. This allowed to identify host effects on the bacterial communities under near identical environmental conditions in captivity. We found the structure of the cutaneous bacterial community significantly differing between wild and captive individuals of newts, Cynops pyrrhogaster, with a higher alpha diversity found in the wild individuals. Community structure also showed distinct patterns when comparing different species of amphibians kept under highly similar conditions, revealing an intrinsic host effect. Bacterial communities of dorsal vs. ventral skin surfaces did not significantly differ in most species, but a trend of higher alpha diversity on the ventral surface was found in Oriental fire-bellied toads, Bombina orientalis. This study confirms the cutaneous microbiota of amphibians as a highly dynamic system influenced by a complex interplay of numerous factors. PMID:27278778

  14. Testing four proposed barcoding markers for the identification of species within Ligustrum L.(Oleaceae)

    Institute of Scientific and Technical Information of China (English)

    Jing GU; Jun-Xia SU; Ruo-Zhu LIN; Rui-Qi LI; Pei-Gen XIAO

    2011-01-01

    DNA barcoding is a biological technique that uses short and standardized genes or DNA regions to facilitate species identification. DNA barcoding has been used successfully in several animal and plant groups. Ligustrum (Oleaceae) species occur widely throughout the world and are used as medicinal plants in China. Therefore, the accurate identification of species in this genus is necessary. Four potential DNA barcodes, namely the nuclear ribosomal internal transcribed spacer (ITS) and three chloroplast (cp) DNA regions (rbcL, marK, and trnH-psbA),were used to differentiate species within Ligustrum. BLAST, character-based method, tree-based methods and TAXONDNA analysis were used to investigate the molecular identification capabilities of the chosen markers for discriminating 92 samples representing 20 species of this genus. The results showed that the ITS sequences have the most variable information, followed by trnH-psbA, matK, and rbcL. All sequences of the four regions correctly identified the species at the genus level using BLAST alignment. At the species level, the discriminating power of rbcL, matK, trnH-psbA and ITS based on neighbor-joining (NJ) trees was 36.8%, 38.9%, 77.8%, and 80%,respectively. Using character-based and maximum parsimony (MP) tree methods together, the discriminating ability of trnH-psbA increased to 88.9%. All species could be differentiated using ITS when combining the NJ tree method with character-based or MP tree methods. Overall, the results indicate that DNA barcoding is an effective molecular identification method for Ligustrum species. We propose the nuclear ribosomal ITS as a plant barcode for plant identification and trnH-psbA as a candidate barcode sequence.

  15. METHODS FOR FISH SPECIES IDENTIFICATION IN FOOD PRODUCTS

    OpenAIRE

    Ľubica Mrázová; Matúš Ondrejka; Ľubomír Belej; Jozef Čapla; Jozef Golian; Radoslav Židek; Lenka Maršálková; Pavol Bajzík

    2010-01-01

    The need for identification of fishery products in food is currently ongoing issue for both consumers and producers of food. Consumer interest is driven in one the healthy diet, which prefers fish products, as an indispensable ingredient food and on the other hand, is a potential allergen causing health problems in humans allergic to fish protein. Allergy is a phenomenon that significantly affects human health, as well as overall life expectancy of an individual. The large...

  16. Identification of Meat Species by Polymerase Chain Reaction (PCR) Technique

    OpenAIRE

    İLHAK, O. İrfan; Arslan, Ali

    2007-01-01

    The origin of horse, dog, cat, bovine, sheep, porcine, and goat meat was determined by the polymerase chain reaction (PCR) technique, using species-specific primers. Test mixtures of meat were prepared by adding 5%, 2.5%, 1%, 0.5%, and 0.1% levels of pork, horse, cat, or dog meat to beef, sheep, and goat meat. Samples taken from those combinations were analyzed by PCR for species determination. Mitochondrial DNA (mt DNA) fragments of 439, 322, 274, 271, 225, 212, and 157 bp for horse, dog, ca...

  17. Gardnerella vaginalis outcompetes 29 other bacterial species isolated from patients with bacterial vaginosis, using in an in vitro biofilm formation model.

    Science.gov (United States)

    Alves, Patrícia; Castro, Joana; Sousa, Cármen; Cereija, Tatiana B; Cerca, Nuno

    2014-08-15

    Despite the worldwide prevalence of bacterial vaginosis (BV), its etiology is still unknown. Although BV has been associated with the presence of biofilm, the ability of BV-associated bacteria to form biofilms is still largely unknown. Here, we isolated 30 BV-associated species and characterized their virulence, using an in vitro biofilm formation model. Our data suggests that Gardnerella vaginalis had the highest virulence potential, as defined by higher initial adhesion and cytotoxicity of epithelial cells, as well as the greater propensity to form a biofilm. Interestingly, we also demonstrated that most of the BV-associated bacteria had a tendency to grow as biofilms. PMID:24596283

  18. The current status of species recognition and identification in Aspergillus

    Science.gov (United States)

    The genus Aspergillus is a large economically important genus of fungi. In agriculture, some of the 250 species in this genus cause disease in plants and animals and some also produce poisons (mycotoxins) in foods and feeds. Aspergillus is a major killer of immunosuppressed people, such as diabeti...

  19. Identification of sympatric bat species by the echolocation calls

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    One hundred and thirty-eight echolocation calls of 63 free-flying individuals of five bat species (Rhinolophus ferrumequinum,Myotis formosus,Myotis ikonnikovi,Myotis daubentoni and Murina leucogaster)were recorded (by ultrasonic bat detector (D980)) in Zhi'an village of Jilin Province,China.According to the frequency-time spectra,these calls were categorized into two types:FM/CF (constant frequency) / FM (R.ferrumequinum) and FM (frequency modulated)(M.formosus,M.ikonnikovi,M.daubentoni and M.leucogaster).Sonograms of the calls of R.ferrumequinum could easily be distinguished from those of the other four species.For the calls of the remaining four species,six echolocation call parameters,including starting frequency,ending frequency,peak frequency duration,longest inter-pulse interval and shortest inter-pulse interval,were examined by stepwise discriminant analysis.The results show that 84.1% of calls were correctly classified,which indicates that these parameters of echolocation calls play an important role in identifying bat species.These parameters can be used to test the accuracy of general predictions based on bats' morphology in the same forest and can provide essential information for assessing patterns of bat habitat use.

  20. Identification of campylobacteria isolated from Danish broilers by phenotypic tests and species-specific PCR assays

    DEFF Research Database (Denmark)

    Wainø, M.; Bang, Dang Duong; Lund, Marianne;

    2003-01-01

    Aims: To validate a phenotypic Campylobacter species identification method employed to identify campylobacters in broilers by comparison with campylobacterial species identification using various species-specific PCR analyses. Methods and Results: From a collection of 2733 phenotypically identified...... campylobacterial cultures, 108 Campylobacter jejuni cultures and 351 campylobacterial cultures other than Camp. jejuni were subjected to various species-specific PCR assays. On the basis of the genotypic tests, it was demonstrated that Camp. jejuni and Camp. coli constituted approx. 99% of all cultures, while...... other species identified were Helicobacter pullorum, Camp. lari and Camp. upsaliensis. However, 29% of the 309 Camp. coli cultures identified by phenotypic tests were hippurate-variable or negative Camp. jejuni cultures, whereas some Camp. lari cultures and unspeciated campylobacter cultures belonged to...

  1. Mitochondrial 16S ribosomal RNA gene for forensic identification of crocodile species.

    Science.gov (United States)

    Naga Jogayya, K; Meganathan, P R; Dubey, Bhawna; Haque, I

    2013-05-01

    All crocodilians are under various threats due to over exploitation and these species have been listed in Appendix I or II of CITES. Lack of molecular techniques for the forensic identification of confiscated samples makes it difficult to enforce the law. Therefore, we herein present a molecular method developed on the basis on 16S rRNA gene of mitochondrial DNA for identification of crocodile species. We have developed a set of 16S rRNA primers for PCR based identification of crocodilian species. These novel primers amplify partial 16S rRNA sequences of six crocodile species which can be later combined to obtain a larger region (1290 bp) of 16S rRNA gene. This 16S rRNA gene could be used as an effective tool for forensic authentication of crocodiles. The described primers hold great promise in forensic identification of crocodile species, which can aid in the effective enforcement of law and conservation of these species. PMID:23622485

  2. DNA Barcoding of Malagasy Rosewoods: Towards a Molecular Identification of CITES-Listed Dalbergia Species

    Science.gov (United States)

    Lowry, Porter P.; Bauert, Martin R.; Razafintsalama, Annick; Ramamonjisoa, Lolona; Widmer, Alex

    2016-01-01

    Illegal selective logging of tropical timber is of increasing concern worldwide. Madagascar is a biodiversity hotspot and home to some of the world’s most sought after tropical timber species. Malagasy rosewoods belong to the genus Dalbergia (Fabaceae), which is highly diverse and has a pantropical distribution, but these timber species are among the most threatened as a consequence of intensive illegal selective logging and deforestation. Reliable identification of Dalbergia species from Madagascar is important for law enforcement but is almost impossible without fertile plant material, which is often unavailable during forest inventories or when attempting to identify logged trees of cut wood. DNA barcoding has been promoted as a promising tool for species identification in such cases. In this study we tested whether DNA barcoding with partial sequences of three plastid markers (matK, rbcL and trnL (UAA)) can distinguish between Dalbergia from Madagascar and from other areas of its distributional range, and whether Malagasy species can be distinguished from one another. Phylogenetic analyses revealed that the Malagasy Dalbergia species studied form two monophyletic groups, each containing two subgroups, only one of which corresponds to a single species. We characterized diagnostic polymorphisms in the three DNA barcoding markers that allow rapid discrimination between Dalbergia from Madagascar and from other areas of its distribution range. Species identification success based on individual barcoding markers or combinations was poor, whereas subgroup identification success was much higher (up to 98%), revealing both the value and limitations of a DNA barcoding approach for the identification of closely related Malagasy rosewoods. PMID:27362258

  3. DNA Barcoding of Malagasy Rosewoods: Towards a Molecular Identification of CITES-Listed Dalbergia Species.

    Science.gov (United States)

    Hassold, Sonja; Lowry, Porter P; Bauert, Martin R; Razafintsalama, Annick; Ramamonjisoa, Lolona; Widmer, Alex

    2016-01-01

    Illegal selective logging of tropical timber is of increasing concern worldwide. Madagascar is a biodiversity hotspot and home to some of the world's most sought after tropical timber species. Malagasy rosewoods belong to the genus Dalbergia (Fabaceae), which is highly diverse and has a pantropical distribution, but these timber species are among the most threatened as a consequence of intensive illegal selective logging and deforestation. Reliable identification of Dalbergia species from Madagascar is important for law enforcement but is almost impossible without fertile plant material, which is often unavailable during forest inventories or when attempting to identify logged trees of cut wood. DNA barcoding has been promoted as a promising tool for species identification in such cases. In this study we tested whether DNA barcoding with partial sequences of three plastid markers (matK, rbcL and trnL (UAA)) can distinguish between Dalbergia from Madagascar and from other areas of its distributional range, and whether Malagasy species can be distinguished from one another. Phylogenetic analyses revealed that the Malagasy Dalbergia species studied form two monophyletic groups, each containing two subgroups, only one of which corresponds to a single species. We characterized diagnostic polymorphisms in the three DNA barcoding markers that allow rapid discrimination between Dalbergia from Madagascar and from other areas of its distribution range. Species identification success based on individual barcoding markers or combinations was poor, whereas subgroup identification success was much higher (up to 98%), revealing both the value and limitations of a DNA barcoding approach for the identification of closely related Malagasy rosewoods. PMID:27362258

  4. Species-Specific Detection and Identification of Fusarium Species Complex, the Causal Agent of Sugarcane Pokkah Boeng in China

    OpenAIRE

    Zhenyue Lin; Shiqiang Xu; Youxiong Que; Jihua Wang; Comstock, Jack C.; Jinjin Wei; McCord, Per H.; Baoshan Chen; Rukai Chen; Muqing Zhang

    2014-01-01

    BACKGROUND: Pokkah boeng disease caused by the Fusarium species complex results in significant yield losses in sugarcane. Thus, the rapid and accurate detection and identification of the pathogen is urgently required to manage and prevent the spreading of sugarcane pokkah boeng. METHODS: A total of 101 isolates were recovered from the pokkah boeng samples collected from five major sugarcane production areas in China throughout 2012 and 2013. The causal pathogen was identified by morphological...

  5. Susceptibility of different bacterial species isolated from food animals to copper sulphate, zinc chloride and antimicrobial substances used for disinfection

    DEFF Research Database (Denmark)

    Aarestrup, Frank Møller; Hasman, Henrik

    2004-01-01

    showed that Danish bacterial isolates from livestock so far have not or have only to a limited degree developed resistance to antimicrobial compounds commonly used for disinfection. Acquired copper resistance was only found in enterococci. There were large differences in the intrinsic susceptibility of...... susceptibilities to the different antimicrobial agents. Large variations were observed in the susceptibility of the different bacterial species to the different compounds. Staphylococci were in general very susceptible to all antimicrobial compounds tested. The Salmonella isolates were in general less susceptible......A total of 569 different bacterial isolates (156 Salmonella, 202 E. coli, 43 S. aureus, 38 S. hyicus, 52 E. faecalis, 78 E faecium) were tested for susceptibility to copper sulphate, benzalkonium chloride, hydrogen peroxide and chlorhexidine using MIC determinations. A total of 442 isolates were...

  6. Identification and Antimicrobial Susceptibility of Salmonella species Isolated from Washing and Rinsed Water of Broilers in Pluck Shops

    Directory of Open Access Journals (Sweden)

    Tuhin-Al-Ferdous

    2013-02-01

    Full Text Available The study was designed with a view to isolate, identifies and characterizes Salmonella species from washing and rinsed water of broilers in pluck shops at Sreepur of Gazipur district in Bangladesh during the period from December 2011 to May 2012. A total of 30 samples collected from the different layers of drums of pluck shops’ were subjected to bacterial isolation and identification by using cultural and biochemical techniques. Furthermore, the isolated Salmonella species were characterized by antimicrobial susceptibility testing. Among the 27 positiveSalmonella isolates 11.11% (n = 3 were Salmonella pullorum, 29.83% isolates (n = 8 were Salmonella gallinarum and the rest 59.26% isolates (n = 16 were Salmonella typhimurium. In case of motility test performed by MIU media and hanging drop slide method, 40.74% isolates were non-motile and 59.26% isolates were motile. Salmonella spp. were resistant to doxycyclin and erythromycin. However, most of the Salmonella spp. were susceptible to sulfamethoxazole-trimethoprim and gentamicin. Out of 27 Salmonella isolates, 75% Salmonella typhimurium, 100% Salmonella gallinarum and 100% Salmonella pullorum were detected as multidrug resistant. The findings of the study revealed the presence of multidrug resistant Salmonella species in washing and rinsed water of broilers in Pluck shops at Sreepur of Gazipur district in Bangladesh.

  7. Microbe-ID: an open source toolbox for microbial genotyping and species identification.

    Science.gov (United States)

    Tabima, Javier F; Everhart, Sydney E; Larsen, Meredith M; Weisberg, Alexandra J; Kamvar, Zhian N; Tancos, Matthew A; Smart, Christine D; Chang, Jeff H; Grünwald, Niklaus J

    2016-01-01

    Development of tools to identify species, genotypes, or novel strains of invasive organisms is critical for monitoring emergence and implementing rapid response measures. Molecular markers, although critical to identifying species or genotypes, require bioinformatic tools for analysis. However, user-friendly analytical tools for fast identification are not readily available. To address this need, we created a web-based set of applications called Microbe-ID that allow for customizing a toolbox for rapid species identification and strain genotyping using any genetic markers of choice. Two components of Microbe-ID, named Sequence-ID and Genotype-ID, implement species and genotype identification, respectively. Sequence-ID allows identification of species by using BLAST to query sequences for any locus of interest against a custom reference sequence database. Genotype-ID allows placement of an unknown multilocus marker in either a minimum spanning network or dendrogram with bootstrap support from a user-created reference database. Microbe-ID can be used for identification of any organism based on nucleotide sequences or any molecular marker type and several examples are provided. We created a public website for demonstration purposes called Microbe-ID (microbe-id.org) and provided a working implementation for the genus Phytophthora (phytophthora-id.org). In Phytophthora-ID, the Sequence-ID application allows identification based on ITS or cox spacer sequences. Genotype-ID groups individuals into clonal lineages based on simple sequence repeat (SSR) markers for the two invasive plant pathogen species P. infestans and P. ramorum. All code is open source and available on github and CRAN. Instructions for installation and use are provided at https://github.com/grunwaldlab/Microbe-ID. PMID:27602267

  8. Half of the European fruit fly species barcoded (Diptera, Tephritidae; a feasibility test for molecular identification

    Directory of Open Access Journals (Sweden)

    John Smit

    2013-12-01

    Full Text Available A feasibility test of molecular identification of European fruit flies (Diptera: Tephritidae based on COI barcode sequences has been executed. A dataset containing 555 sequences of 135 ingroup species from three subfamilies and 42 genera and one single outgroup species has been analysed. 73.3% of all included species could be identified based on their COI barcode gene, based on similarity and distances. The low success rate is caused by singletons as well as some problematic groups: several species groups within the genus Terellia and especially the genus Urophora. With slightly more than 100 sequences - almost 20% of the total - this genus alone constitutes the larger part of the failure for molecular identification for this dataset. Deleting the singletons and Urophora results in a success-rate of 87.1% of all queries and 93.23% of the not discarded queries as correctly identified. Urophora is of special interest due to its economic importance as beneficial species for weed control, therefore it is desirable to have alternative markers for molecular identification.We demonstrate that the success of DNA barcoding for identification purposes strongly depends on the contents of the database used to blast against. Especially the necessity of including multiple specimens per species of geographically distinct populations and different ecologies for the understanding of the intra- versus interspecific variation is demonstrated. Furthermore thresholds and the distinction between true and false positives and negatives should not only be used to increase the reliability of the success of molecular identification but also to point out problematic groups, which should then be flagged in the reference database suggesting alternative methods for identification.

  9. Identification of Tilletia species using rep-PCR fingerprinting technique

    Directory of Open Access Journals (Sweden)

    Župunski Vesna

    2011-01-01

    Full Text Available Analyzing 167 non-processed seed samples of wheat, it was found that 145 samples (86.8 % were contaminated with Tilletia species, while 22 (13.2 % samples were not contaminated. By using rep-PCR fingerprinting technique, it was found that DNA isolates of T. tritici originated from Serbian wheat samples had 80 % similarity with positive control for T. tritici. One isolate shared similarity of 60% with T. tritici, T. controversa and T. laevis. It was supposed that this isolate belongs to T. bromi. Isolate of T. laevis shared a similarity of 70 % with isolates of T. tritici and T. controversa, while T. walkeri was more than 10 % similar with T. tritici, T. controversa and T. laevis. Although T. controversa and T. tritici had high percent of genetic similarity, they were clustered separately. Our results suggest that rep-PCR fingerprinting could be a useful tool for monitoring presence of morphologically similar Tilletia species in wheat production areas.

  10. Rapid identification by specific PCR of coagulase-negative staphylococcal species important in hospital infection.

    Science.gov (United States)

    Gribaldo, S; Cookson, B; Saunders, N; Marples, R; Stanley, J

    1997-01-01

    Polymerase chain reaction (PCR) identification assays were designed for eight major species of coagulase-negative staphylococci (CNS) on the basis of three variable regions found in the 16S rRNA gene. The PCR assays were tested with 41 staphylococcal strains representing the diversity of staphylococci defined by classical biotyping schemes. Each PCR result was compared with species-specific polymorphism in and around the 16S rRNA gene (i.e., 16S ribotype) and the phenotypic identification of the strain in a miniaturised biochemical test gallery (bioMerieux ATB 32 Staph). Twenty-six of the 41 strains were identified by PCR as belonging to one of the eight species for which primers had been designed and none of the remaining strains was misidentified. For 22 of the 26 strains there was complete agreement between the PCR identification, 16S ribotype and ATB identification. For the remaining four strains there was agreement between PCR identification and 16S ribotype. Two National Collection of Type Culture strains were re-assigned to different species and 10 previously unassigned strains were formally speciated for the first time. These PCR assays are suitable for rapid and definitive speciation of CNS. PMID:9003745

  11. Species identification of invasive yeasts including Candida in Pakistan: limitations of phenotypic methods

    Science.gov (United States)

    Farooqi, Joveria; Jabeen, Kauser; Saeed, Noureen; Zafar, Afia; Brandt, Mary Eleanor; Hasan, Rumina

    2015-01-01

    Objective To compare phenotypic and genotypic methods of yeast identification. Methods The in-vitro cross-sectional study was conducted from January 2006 to May 2009. Invasive yeasts isolated at the clinical microbiology laboratory at the Aga Khan University (AKU), Karachi, Pakistan, were identified. Speciation by phenotypic and molecular methods was compared. All yeasts isolated during the study period from blood and other invasive sites were identified using standard methods. Isolates were shipped to Mycotic Diseases Branch, Centres for Disease Control and Prevention, Atlanta, Georgia, USA, for identification by Luminex flow cytometric multianalyte profiling (xMAP) system. Ribosomal ITS2 DNA sequencing was performed on isolates not identified by Luminex. Result Of the 214 invasive yeasts evaluated, Candida species were 209 (97.7%) while the frequency of non-Candida species was 5 (2.3%). Overall agreement between phenotypic and molecular identification was 81.3%, 90.3% amongst the more common Candida species, and only 38.8% amongst the uncommon yeasts. Conclusion Phenotypic methods of identification proved adequate for common Candida species, but were deficient in recognising rare Candida and non-Candida yeasts, highlighting the importance of molecular methods for identification. PMID:23866432

  12. Identification of lectin-binding proteins in Chlamydia species.

    OpenAIRE

    Swanson, A F; Kuo, C. C.

    1990-01-01

    Lectin-binding proteins of chlamydiae were detected by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and immunoblotting. All three Chlamydia species tested expressed two proteins when whole-elementary-body lysates were reacted with the biotinylated lectin Dolichos biflorus agglutinin. The protein with a molecular mass of 18 kilodaltons (kDa) responded strongly compared with a higher-molecular-mass protein that varied from 27 to 32 kDa with each chlamydia strain tested. Among six l...

  13. Identification of the Trichinella species by PCR method

    OpenAIRE

    Vasilev Saša; Cvetković Jelena; Radović Ivana; Sofronić-Milosavljević Ljiljana

    2012-01-01

    Serbia is country with a high prevalence of Trichinella infection in pigs, which continues to be a serious human health problem. In Serbia, only a few isolates of Trichinella found in pork have been genetically specified to date, and all were proven as T. spiralis. New data shows that in the sylvatic cycle in Serbia, at least in the Belgrade district, more than one Trichinella species co-exist (T. spiralis and T. britovi). Increased awareness of the possibl...

  14. DNA barcoding for species Identification in prepared fishery products

    OpenAIRE

    ANNA MOTTOLA; PATRIZIA MARCHETTI; MARILISA BOTTARO; ANGELA DI PINTO

    2014-01-01

    Considering that seafood mislabeling has been widely reported throughout the world and that the authentication of food components is one of the key issues in food quality, the aim of this study was to use DNA barcoding to investigate the prevalence of mislabeling among fresh prepared fishery products from markets and supermarkets located in Apulia (SE Italy). The study reveals a high occurrence of species mislabeling (42%) in the prepared fillet products, further evidence of the need for incr...

  15. Identification of five highly priced tuna species by quantitative real-time polymerase chain reaction.

    Science.gov (United States)

    Liu, Shasha; Xu, Kunhua; Wu, Zhigang; Xie, Xiao; Feng, Junli

    2016-09-01

    Tunas are economically important fishery worldwide, and are often used for commercial processed production. For effective fishery management and protection of consumers' rights, it is important to develop a molecular method to identify species in canned tuna products rapidly and reliably. Here, we have developed a duplex quantitative real-time PCR (qPCR) for identification of five highly priced tuna species (Thunnus maccoyii, Thunnus obesus, Thunnus albacares, Thunnus alalunga and Katsuwonus pelamis) from processed as well as fresh fish. After amplification and sequencing of seven genetic markers commonly used for species identification, 16S rDNA and control region (CR) of mitochondrial DNA were selected as the reference gene markers for genus Thunnus and tuna species identification, respectively. Subsequently, a 73 bp fragment of 16S rDNA and 85-99 bp fragment of CR were simultaneously amplified from each target species by qPCR. The qPCR efficiency of each reaction was calculated according to the standard curves, and the method was validated by amplification DNA extracted from single or mixed tuna specimen. The developed duplex qPCR system was applied to authenticate species of 14 commercial tuna products successfully, which demonstrated it was really a useful and academic technique to identify highly priced tuna species. PMID:25714139

  16. Molecular Identification of Nosema species in East Azerbaijan province, Iran

    Directory of Open Access Journals (Sweden)

    Razmaraii, N.

    2013-05-01

    Full Text Available Nosema is a genus of microsporidia, which have significant negative impacts on honeybees. The aim of thisstudy is the epidemiological evaluation and molecular characterization of Nosema spices in various countiesof East-Azerbaijan province (Northwest of Iran. 387 samples were collected from colonies maintained invarious counties of East-Azerbaijan province. Samples after preparation were examined by a lightmicroscope for presence of Nosema spores. PCR method (SSUrRNA gene was used to differentiatebetween Nosema apis (N. apis and N. ceranae. Descriptive statistics were used for data analysis. Totalinfection prevalence of the microscopic evaluation and PCR tests were 225 (58.1% and 260 (67.1%respectively, total validity of PCR test against the microscopic test was computed equal to 1.1 in this case.Disease distribution in various counties of study area was variable and N. ceranae was the only Nosema species found to infect honeybees. The one species presence and different distribution of Nosema positive samples in various counties of East-Azerbaijan province may be due to multiple reasons. Furthermore,epidemiological information helps us to improve disease management practices in the studied area, apply new hygiene policy and reduce extra costs of production.

  17. Comparative proteome analysis of psychrophilic versus mesophilic bacterial species: Insights into the molecular basis of cold adaptation of proteins

    OpenAIRE

    Metpally, Raghu Prasad Rao; Reddy, Boojala Vijay B.

    2009-01-01

    Background Cold adapted or psychrophilic organisms grow at low temperatures, where most of other organisms cannot grow. This adaptation requires a vast array of sequence, structural and physiological adjustments. To understand the molecular basis of cold adaptation of proteins, we analyzed proteomes of psychrophilic and mesophilic bacterial species and compared the differences in amino acid composition and substitution patterns to investigate their likely association with growth temperatures....

  18. Gardnerella vaginalis outcompetes 29 other bacterial species isolated from BV patients in an in vitro biofilm formation model

    OpenAIRE

    Alves, P.; Castro, J.; Sousa, Cármen; Cereija, Tatiana Barros Reis; Cerca, Nuno

    2014-01-01

    Despite the worldwide prevalence of bacterial vaginosis (BV), its etiology is still unknown. Although BV has been associated with the presence of biofilm, the ability of BV-associated bacteria to form biofilms is still largely unknown. Here, we isolated 30 BV-associated species and characterized their virulence, using an in vitro biofilm formation model. Our data suggests that Gardnerella vaginalis had the highest virulence potential, as defined by higher initial adhesion and cytotoxicity of ...

  19. Detection and Identification of Bursaphelenchus Species with DNA Fingerprinting and Polymerase Chain Reaction

    OpenAIRE

    Harmey, Judith H.; Harmey, Matthew A.

    1993-01-01

    We have evaluated the potential of DNA-based methods to identify and differentiate Bursaphelenchus spp. and isolates. The isolation of a DNA probe, designated X14, and development of a DNA fingerprinting method for the identification and differentiation of Bursaphelenchus species and strains is described. Polymerase chain reaction (PCR) amplification of DNA isolated from Bursaphelenchus species using two primers derived from the sequence of the cloned repetitive DNA fragment X14 resulted in m...

  20. Ontology-based Malaria Parasite Stage and Species Identification from Peripheral Blood Smear Images

    OpenAIRE

    Makkapati, V.; Rao, R

    2011-01-01

    The diagnosis and treatment of malaria infection requires detectingthe presence of malaria parasite in the patient as well as identification of the parasite species. We present an image processing-basedapproach to detect parasites in microscope images of blood smear andan ontology-based classification of the stage of the parasite for identifying the species of infection. This approach is patterned after the diagnosis approach adopted by a pathologist for visual examination and hence is expect...

  1. Egg forensics: an appraisal of DNA sequencing to assist in species identification of illegally smuggled eggs.

    Science.gov (United States)

    Coghlan, Megan L; White, Nicole E; Parkinson, Liza; Haile, James; Spencer, Peter B S; Bunce, Michael

    2012-03-01

    Psittaciformes (parrots and cockatoos) are charismatic birds, their plumage and capacity for learning make them highly sought after pets. The illegal trade in parrots and cockatoos poses a serious threat to the viability of native populations; in addition, species transported to non-endemic areas may potentially vector disease and genetically 'pollute' local native avifauna. To reduce the logistical difficulties associated with trafficking live birds, smugglers often transport eggs. This creates a problem for authorities in elucidating accurate species identification without the laborious task of incubation and hand rearing until a morphological identification can be made. Here, we use 99 avian eggs seized from carriers coming into and within Australia, as a result of suspected illegal trade. We investigate and evaluate the use of mitochondrial DNA (mtDNA) to accurately identify eggs to family, genus or species level. However, Identification of a species based on percentage mtDNA similarities is difficult without good representations of the inter- and intra-levels of species variation. Based on the available reference database, we were able to identify 52% of the eggs to species level. Of those, 10 species from eight genera were detected, all of which belong to the parrot (Psittacidae) and cockatoo (Cacatuidae) families. Of the remaining 48%, a further 36% of eggs were identified to genus level, and 12% identified to family level using our assignment criteria. Clearly the lack of validated DNA reference sequences is hindering our ability to accurately assign a species identity, and accordingly, we advocate that more attention needs to be paid to establishing validated, multi locus mtDNA reference databases for exotic birds that can both assist in genetic identifications and withstand legal scrutiny. PMID:21741338

  2. Application of thermal desorption for the identification of mercury species in solids derived from coal utilization

    OpenAIRE

    Rumayor Villamil, Marta; Díaz Somoano, Mercedes; López Antón, María Antonia; Martínez Tarazona, María Rosa

    2014-01-01

    The speciation of mercury is currently attracting widespread interest because the emission, transport, deposition and behaviour of toxic mercury species depend on its chemical form. The identification of these species in low concentrations is no easy task and it is even more complex in coal combustion products due to the fact that these products contain organic and mineral matter that give rise to broad peaks and make it difficult to carry out qualitative and quantitative analysis. In this wo...

  3. Molecular and morphological identification of mealybug species (Hemiptera: Pseudococcidae in Brazilian vineyards.

    Directory of Open Access Journals (Sweden)

    Vitor C Pacheco da Silva

    Full Text Available Mealybugs (Hemiptera: Pseudococcidae are pests constraining the international trade of Brazilian table grapes. They damage grapes by transmitting viruses and toxins, causing defoliation, chlorosis, and vigor losses and favoring the development of sooty mold. Difficulties in mealybug identification remain an obstacle to the adequate management of these pests. In this study, our primary aim was to identify the principal mealybug species infesting the major table grape-producing regions in Brazil, by morphological and molecular characterization. Our secondary aim was to develop a rapid identification kit based on species-specific Polymerase Chain Reactions, to facilitate the routine identification of the most common pest species. We surveyed 40 sites infested with mealybugs and identified 17 species: Dysmicoccus brevipes (Cockerell, Dysmicoccus sylvarum Williams and Granara de Willink, Dysmicoccus texensis (Tinsley, Ferrisia cristinae Kaydan and Gullan, Ferrisia meridionalis Williams, Ferrisia terani Williams and Granara de Willink, Phenacoccus baccharidis Williams, Phenacoccus parvus Morrison, Phenacoccus solenopsis Tinsley, Planococcus citri (Risso, Pseudococcus viburni (Signoret, Pseudococcus cryptus Hempel, four taxa closely related each of to Pseudococcus viburni, Pseudococcus sociabilis Hambleton, Pseudococcus maritimus (Ehrhorn and Pseudococcus meridionalis Prado, and one specimen from the genus Pseudococcus Westwood. The PCR method developed effectively identified five mealybug species of economic interest on grape in Brazil: D. brevipes, Pl. citri, Ps. viburni, Ph. solenopsis and Planococcus ficus (Signoret. Nevertheless, it is not possible to assure that this procedure is reliable for taxa that have not been sampled already and might be very closely related to the target species.

  4. Molecular and morphological identification of mealybug species (Hemiptera: Pseudococcidae) in Brazilian vineyards.

    Science.gov (United States)

    Pacheco da Silva, Vitor C; Bertin, Aline; Blin, Aurélie; Germain, Jean-François; Bernardi, Daniel; Rignol, Guylène; Botton, Marcos; Malausa, Thibaut

    2014-01-01

    Mealybugs (Hemiptera: Pseudococcidae) are pests constraining the international trade of Brazilian table grapes. They damage grapes by transmitting viruses and toxins, causing defoliation, chlorosis, and vigor losses and favoring the development of sooty mold. Difficulties in mealybug identification remain an obstacle to the adequate management of these pests. In this study, our primary aim was to identify the principal mealybug species infesting the major table grape-producing regions in Brazil, by morphological and molecular characterization. Our secondary aim was to develop a rapid identification kit based on species-specific Polymerase Chain Reactions, to facilitate the routine identification of the most common pest species. We surveyed 40 sites infested with mealybugs and identified 17 species: Dysmicoccus brevipes (Cockerell), Dysmicoccus sylvarum Williams and Granara de Willink, Dysmicoccus texensis (Tinsley), Ferrisia cristinae Kaydan and Gullan, Ferrisia meridionalis Williams, Ferrisia terani Williams and Granara de Willink, Phenacoccus baccharidis Williams, Phenacoccus parvus Morrison, Phenacoccus solenopsis Tinsley, Planococcus citri (Risso), Pseudococcus viburni (Signoret), Pseudococcus cryptus Hempel, four taxa closely related each of to Pseudococcus viburni, Pseudococcus sociabilis Hambleton, Pseudococcus maritimus (Ehrhorn) and Pseudococcus meridionalis Prado, and one specimen from the genus Pseudococcus Westwood. The PCR method developed effectively identified five mealybug species of economic interest on grape in Brazil: D. brevipes, Pl. citri, Ps. viburni, Ph. solenopsis and Planococcus ficus (Signoret). Nevertheless, it is not possible to assure that this procedure is reliable for taxa that have not been sampled already and might be very closely related to the target species. PMID:25062012

  5. Identification and characterization of pathogenic Pestalotiopsis species to pecan tree in Brazil

    Directory of Open Access Journals (Sweden)

    Marília Lazarotto

    2014-06-01

    Full Text Available The objective of this work was to characterize and cluster isolates of Pestalotiopsis species and to identify those that are pathogenic to pecan, based on morphological and molecular characters. Pestalotiopsis spp. isolates were identified by sequencing the internal transcribed spacer (ITS and β?tubulin regions. Identification methods were compared to indicate the key morphological characters for species characterization. Thirteen isolates were used for the pathogenicity tests. Morphological characterization was performed using the following variables: mycelial growth rate, sporulation, colony pigmentation, and conidial length and width. Ten pathogenic isolates were identified, three as -tubulin regions. Identification methods were compared to indicate the key morphological characters for species characterization. Thirteen isolates were used for the pathogenicity tests. Morphological characterization was performed using the following variables: mycelial growth rate, sporulation, colony pigmentation, and conidial length and width. Ten pathogenic isolates were identified, three as Pestalotiopsis clavispora and three as P. cocculi. The other isolates remained as an undefined species. The morphological characters were efficient for an initial separation of the isolates, which were grouped according to differences at species level, mainly colony diameter, which was identified as an important morphological describer. Beta-tubulin gene sequencing was less informative than the ITS region sequencing for species identification.

  6. Blood species identification using Near-Infrared diffuse transmitted spectra and PLS-DA method

    Science.gov (United States)

    Zhang, Linna; Zhang, Shengzhao; Sun, Meixiu; Wang, Zhennan; Li, Hongxiao; Li, Yingxin; Li, Gang; Lin, Ling

    2016-05-01

    Blood species identification is of great significance for blood supervision and wildlife investigations. The current methods used to identify the blood species are destructive. Near-Infrared spectroscopy method is known for its non-invasive properties. In this research, we combined Near-Infrared diffuse transmitted spectra and Partial Least Square Discrimination Analysis (PLS-DA) to identify three blood species, including macaque, human and mouse. Blind test and external test were used to assess the PLS-DA model. The model performed 100% accuracy in its identification between three blood species. This approach does not require a specific knowledge of biochemical features for each individual class but relies on a spectroscopic statistical differentiation of the whole components. This is the first time to demonstrate Near-Infrared diffuse transmitted spectra have the ability to identify the species of origin of blood samples. The results also support a good potential of absorption and scattering spectroscopy for species identification in practical applications for real-time detection.

  7. Identification of veterinary pathogens by use of commercial identification systems and new trends in antimicrobial susceptibility testing of veterinary pathogens.

    OpenAIRE

    Watts, J. L.; Yancey, R J

    1994-01-01

    Veterinary diagnostic microbiology is a unique specialty within microbiology. Although isolation and identification techniques are similar to those used for human pathogens, many veterinary pathogens require unique cultivation or identification procedures. Commercial identification systems provide rapid, accurate identification of human pathogens. However, the accuracy of these systems with veterinary pathogens varies widely depending on the bacterial species and the host animal from which it...

  8. Raman and surface-enhanced Raman spectroscopy of amino acids and nucleotide bases for target bacterial vibrational mode identification

    Science.gov (United States)

    Guicheteau, Jason; Argue, Leanne; Hyre, Aaron; Jacobson, Michele; Christesen, Steven D.

    2006-05-01

    Raman and surface-enhanced Raman spectroscopy (SERS) studies of bacteria have reported a wide range of vibrational mode assignments associated with biological material. We present Raman and SER spectra of the amino acids phenylalanine, tyrosine, tryptophan, glutamine, cysteine, alanine, proline, methionine, asparagine, threonine, valine, glycine, serine, leucine, isoleucine, aspartic acid and glutamic acid and the nucleic acid bases adenosine, guanosine, thymidine, and uridine to better characterize biological vibrational mode assignments for bacterial target identification. We also report spectra of the bacteria Bacillus globigii, Pantoea agglomerans, and Yersinia rhodei along with band assignments determined from the reference spectra obtained.

  9. DNA barcode identification of lichen-forming fungal species in the Rhizoplaca melanophthalma species-complex (Lecanorales, Lecanoraceae, including five new species

    Directory of Open Access Journals (Sweden)

    Steven Leavitt

    2013-05-01

    Full Text Available Recent studies using sequence data from multiple loci and coalescent-based species delimitation have revealed several species-level lineages within the phenotypically circumscribed taxon Rhizoplaca melanophthalma sensu lato. Here, we formally describe five new species within this group, R. occulta, R. parilis, R. polymorpha, R. porterii, and R. shushanii, using support from the coalescent-based species delimitation method implemented in the program Bayesian Phylogenetics and Phylogeography (BPP as the diagnostic feature distinguishing new species. We provide a reference DNA sequence database using the ITS marker as a DNA barcode for identifying species within this complex. We also assessed intraspecific genetic distances within the six R. melanophthalma sensu lato species. While intraspecific genetic distances within the five new species were less than or equal to the lowest interspecific pairwise comparison values, an overlap in genetic distances within the R. melanophthalma sensu stricto clade suggests the potential for additional phenotypically cryptic lineages within this broadly distributed lineage. Overall, our results demonstrate the potential for accurately identifying species within the R. melanophthalma group by using molecular-based identification methods.

  10. Use of MALDI-TOF MS for Identification of Nontuberculous Mycobacterium Species Isolated from Clinical Specimens

    Directory of Open Access Journals (Sweden)

    María Concepción Mediavilla-Gradolph

    2015-01-01

    Full Text Available The aim of this study was to compare the results obtained for identification by MALDI-TOF of nontuberculous mycobacteria (NTM isolated in clinical samples with those obtained by GenoType Mycobacterium CM/AS (common mycobacteria/additional species. A total of 66 Mycobacterium isolates from various clinical specimens (mainly respiratory were tested in this study. They were identified using MALDI-TOF Bruker from strains isolated in Lowenstein, following the recommended protocol of heat inactivation and extraction, and were simultaneously analyzed through hybridization by GenoType Mycobacterium from liquid culture MGIT. Our results showed that identification by MALDI-TOF was correct in 98.4% (65/66 of NTM isolated in our clinical practice (M. avium, M. intracellulare, M. abscessus, M. chelonae, M. fortuitum, M. mucogenicum, M. kansasii, and M. scrofulaceum. MALDI-TOF was found to be an accurate, rapid, and cost-effective system for identification of mycobacteria species.

  11. Bacterial Communities of different Mediterranean Sponge Species - Basic investigations for biotechnological sponge cultivation

    OpenAIRE

    Gerce, Berna

    2011-01-01

    The aim to use sponges and their associated microorganisms for the supply of natural compounds for their investigation in clinical trials for subsequent development of drugs was the motivation for the investigation of bacterial communities of sponges. The investigation revealed surface- and tissue-associated bacterial communities of free-living sponges were different from each other and microbial communities and secondary metabolites of sponges remain stable during biotechnological cultivation.

  12. Laser-excited fluorescence spectra of eastern SPF wood species. An optical technique for identification and separation of wood species?

    International Nuclear Information System (INIS)

    Use of UV-laser excitation to produce fluorescence spectra for heartwood and sapwood from jack pine (Pinus banksiana), white spruce (Picea glauca) and balsam fir (Abies balsamea) was examined. Spectra were fairly broad without sharp spectral features and overlap of spectra between species was common. Sample to sample and in-sample variation of the recorded fluorescence spectra was observed. The fluorescence spectra obtained from heartwood samples of jack pine showed evidence of photochemical bleaching as a result of the multiple laser pulses needed to produce a complete spectrum. Bleaching may have obscured differences between species. For the mix of species examined no sapwood nor heartwood samples were distinguishable by this technique with the detector used. Use of an optical multichannel analyzer (OMA) could reduce the number of laser pulses needed to obtain an entire spectrum. Under these conditions it would be possible to determine whether the minor differences in spectral features observed for the different species are more pronounced in the first few laser pulses and if they are characteristic of species. Certain aspects of the data suggest that with improved analytical equipment UV-fluorescence might prove to be a useful technique for the identification of certain species

  13. Identification of Dermatophyte Species after Implementation of the In-House MALDI-TOF MS Database

    Directory of Open Access Journals (Sweden)

    Adriana Calderaro

    2014-09-01

    Full Text Available Despite that matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF mass spectrometry (MS has become a powerful tool in the clinical microbiology setting, few studies have till now focused on MALDI-TOF MS-based identification of dermatophytes. In this study, we analyze dermatophytes strains isolated from clinical samples by MALDI-TOF MS to supplement the reference database available in our laboratory. Twenty four dermatophytes (13 reference strains and 11 field isolated strains, identified by both conventional and molecular standard procedures, were analyzed by MALDI-TOF MS, and the spectra obtained were used to supplement the available database, limited to a few species. To verify the robustness of the implemented database, 64 clinical isolates other than those used for the implementation were identified by MALDI-TOF MS. The implementation allowed the identification of the species not included in the original database, reinforced the identification of the species already present and correctly identified those within the Trichophyton mentagrophytes complex previously classified as Trichophyton. tonsurans by MALDI-TOF MS. The dendrogram obtained by analyzing the proteic profiles of the different species of dermatophytes reflected their taxonomy, showing moreover, in some cases, a different clusterization between the spectra already present in the database and those newly added. In this study, MALDI-TOF MS proved to be a useful tool suitable for the identification of dermatophytes for diagnostic purpose.

  14. Forensic botany: species identification of botanical trace evidence using a multigene barcoding approach.

    Science.gov (United States)

    Ferri, Gianmarco; Alù, Milena; Corradini, Beatrice; Beduschi, Giovanni

    2009-09-01

    Forensic botany can provide significant supporting evidence during criminal investigations. However, it is still an underutilized field of investigation with its most common application limited to identifying specific as well as suspected illegal plants. The ubiquitous presence of plant species can be useful in forensics, but the absence of an accurate identification system remains the major obstacle to the present inability to routinely and correctly identify trace botanical evidence. Many plant materials cannot be identified and differentiated to the species level by traditional morphological characteristics when botanical specimens are degraded and lack physical features. By taking advantage of a universal barcode system, DNA sequencing, and other biomolecular techniques used routinely in forensic investigations, two chloroplast DNA regions were evaluated for their use as "barcoding" markers for plant identification in the field of forensics. We therefore investigated the forensic use of two non-coding plastid regions, psbA-trnH and trnL-trnF, to create a multimarker system for species identification that could be useful throughout the plant kingdom. The sequences from 63 plants belonging to our local flora were submitted and registered on the GenBank database. Sequence comparison to set up the level of identification (species, genus, or family) through Blast algorithms allowed us to assess the suitability of this method. The results confirmed the effectiveness of our botanic universal multimarker assay in forensic investigations. PMID:19504263

  15. Molecular species identification of cryptic apple and snowberry maggots (Diptera: Tephritidae) in Western and Central Washington

    Science.gov (United States)

    In Washington state, identification of the quarantine apple pest Rhagoletis pomonella (Walsh) is complicated by the presence of the cryptic species R. zephyria Snow (Diptera: Tephritidae). Distinguishing the two flies is important because there is a zero tolerance policy for R. pomonella in apple p...

  16. Ontology-based Malaria Parasite Stage and Species Identification from Peripheral Blood Smear Images

    NARCIS (Netherlands)

    Makkapati, V.; Rao, R.

    2011-01-01

    The diagnosis and treatment of malaria infection requires detectingthe presence of malaria parasite in the patient as well as identification of the parasite species. We present an image processing-basedapproach to detect parasites in microscope images of blood smear andan ontology-based classificati

  17. Collaborative Processes in Species Identification Using an Internet-Based Taxonomic Resource

    Science.gov (United States)

    Kontkanen, Jani; Kärkkäinen, Sirpa; Dillon, Patrick; Hartikainen-Ahia, Anu; Åhlberg, Mauri

    2016-01-01

    Visual databases are increasingly important resources through which individuals and groups can undertake species identification. This paper reports research on the collaborative processes undertaken by pre-service teacher students when working in small groups to identify birds using an Internet-based taxonomic resource. The student groups are…

  18. Multiple-genome comparison reveals new loci for Mycobacterium species identification.

    Science.gov (United States)

    Dai, Jianli; Chen, Yuansha; Dean, Susan; Morris, J Glenn; Salfinger, Max; Johnson, Judith A

    2011-01-01

    To identify loci useful for species identification and to enhance our understanding of the population structure and genetic variability of the genus Mycobacterium, we conducted a multiple-genome comparison of a total of 27 sequenced genomes in the suborder of Corynebacterineae (18 from the Mycobacterium genus, 7 from the Corynebacterium genus, 1 each from the Nocardia and Rhodococcus genera). Our study revealed 26 informative loci for species identification in Mycobacterium. The sequences from these loci were used in a phylogenetic analysis to infer the evolutionary relations of the 18 mycobacterial genomes. Among the loci that we identified, rpoBC, dnaK, and hsp65 were amplified from 29 ATCC reference strains and 17 clinical isolates and sequenced. The phylogenetic trees generated from these loci show similar topologies. The newly identified dnaK locus is more discriminatory and more robust than the widely used hsp65 locus. The length-variable rpoBC locus is the first intergenic locus between two protein-encoding genes being used for mycobacterial species identification. A multilocus sequence analysis system including the rpoBC, dnaK, and hsp65 loci is a robust tool for accurate identification of Mycobacterium species. PMID:21048007

  19. Effects of antibiotic on the bacterial microflora in two commercially important catfish species, Clarias batrachus and Heteropneustes fossilis in Bangladesh

    Directory of Open Access Journals (Sweden)

    Md. Shahdat Hossain

    2014-11-01

    Full Text Available Objective: To assess the effects of a widely used antibiotic, oxytetracycline (OTC on the bacterial microflora in two catfish species under artificial culture conditions in the laboratory. Methods: The experiment was conducted in the Faculty of Fisheries, Bangladesh Agricultural University, Mymensingh-2202. The fish were reared in six aquaria (size 37 cm×30 cm×60 cm where three aquaria served as replicates of the antibiotic treatment groups and the remaining three aquaria served as an untreated control group. Each aquarium was stocked with 25 fish on an average body weight 15 g. OTC was administered to the fish in the treatment groups at the rate of 2 g/kg in-feed twice daily upto ad libitum, whereas fish in the untreated control groups were given the same feed without antibiotics for 20 d. During the experiment, bacterial loads were estimated as colony forming unit (CFU/g by every alternate day in the aquarium water, gills, skin and intestine of fish. Results: The administration of OTC in feed resulted in gradual decrease of bacterial loads in the gills, intestine and skin of the two catfish species tested. In contrast, the bacterial loads remain unchanged or slightly increased in the control groups not fed with OTC. Water quality parameters such as dissolved oxygen, pH and total hardness were found to be within suitable range in the test aquaria but not in control aquarium throughout the experimental period. Conclusions: The results of this experiment showed that in-feed antibiotic OTC for a period of 20 d reduced the bacterial loads in the gills, intestines and skin of treated fish.

  20. Effects of antibiotic on the bacterial microflora in two commercially important catfish species, Clarias batrachus and Heteropneustes fossilis in Bangladesh

    Institute of Scientific and Technical Information of China (English)

    Md Shahdat Hossain; Md Rajib Sharker; Syed Ariful Haque; Md Shaheed Reza; Md Anwar Hossain Mondal

    2014-01-01

    Objective: To assess the effects of a widely used antibiotic, oxytetracycline (OTC) on the bacterial microflora in two catfish species under artificial culture conditions in the laboratory. Methods:The experiment was conducted in the Faculty of Fisheries, Bangladesh Agricultural University, Mymensingh-2202. The fish were reared in six aquaria (size 37 cmí30 cmí60 cm) where three aquaria served as replicates of the antibiotic treatment groups and the remaining three aquaria served as an untreated control group. Each aquarium was stocked with 25 fish on an average body weight 15 g. OTC was administered to the fish in the treatment groups at the rate of 2 g/kg in-feed twice daily upto ad libitum, whereas fish in the untreated control groups were given the same feed without antibiotics for 20 d. During the experiment, bacterial loads were estimated as colony forming unit (CFU/g) by every alternate day in the aquarium water, gills, skin and intestine of fish. Results:The administration of OTC in feed resulted in gradual decrease of bacterial loads in the gills, intestine and skin of the two catfish species tested. In contrast, the bacterial loads remain unchanged or slightly increased in the control groups not fed with OTC. Water quality parameters such as dissolved oxygen, pH and total hardness were found to be within suitable range in the test aquaria but not in control aquarium throughout the experimental period. Conclusions:The results of this experiment showed that in-feed antibiotic OTC for a period of 20d reduced the bacterial loads in the gills, intestines and skin of treated fish.

  1. Low temperature storage test phase 2 : identification of problem species

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2009-12-15

    The use of renewable fuels such as biodiesel, in motor vehicle fuels is expected to grow rapidly in North America as a result of governmental mandates. Biodiesel is a fuel component made from plant and animal feedstocks via a transesterification process. The fatty acid methyl esters (FAME) of biodiesel have cloud points that range from 5 degrees C to -15 degrees C. The poor low temperature performance of blends containing FAME must be understood in order to avoid operability issues. This paper presented the results of several testing programs conducted by researchers to investigate filter plugging in biodiesel fuels caused by high levels of saturated monoglycerides. The low temperature storage stability of 57 biodiesel fuels comprised of B5 and B20 made with canola methyl ester (CME), soybean methyl ester (SME), tallow methyl ester (TME) and palm methyl ester (PME) was investigated. Filter blocking tests were conducted to assess storage stability. Deposits from the blends were analyzed using gas chromatography and mass spectrometry (GC-MS) in order to identify the problem species. Results of the study confirmed the deleterious impact of saturated mono-glycerides in FAME on the low temperature operability of filters in fuel handling systems. 11 refs., 7 tabs., 5 figs. 9 appendices.

  2. Comparison of API 50 CH Strips to Whole-Chromosomal DNA Probes for Identification of Lactobacillus Species

    OpenAIRE

    Boyd, Melinda A.; Antonio, May A. D.; Hillier, Sharon L.

    2005-01-01

    The API 50 CH identification system was evaluated for the identification of 97 strains of commensal lactobacilli. This system agreed with the species-level identifications for none of the 7 reference strains and only 4 of 90 vaginal isolates identified using whole-chromosomal DNA probes.

  3. Detection and identification of bacterial DNA in serum from patients with acute pancreatitis

    OpenAIRE

    E. de Madaria; Martínez, J.; Lozano, B; L. Sempere; S. Benlloch; J. Such; Uceda, F; Francés, R; Pérez-Mateo, M

    2005-01-01

    Background and aims: Bacterial infections are common complications in patients with acute pancreatitis, and translocation of bacteria from the intestinal lumen is probably the first step in the pathogenesis of these infections. As blood cultures in afebrile patients are usually negative, more sensitive methods to investigate this hypothesis in patients are needed. Our group has recently developed a method to detect the presence of bacterial DNA in biological fluids, and we aimed to detect bac...

  4. Rapid identification of oral Actinomyces species cultivated from subgingival biofilm by MALDI-TOF-MS

    Directory of Open Access Journals (Sweden)

    Catalina S. Stingu

    2015-01-01

    Full Text Available Background: Actinomyces are a common part of the residential flora of the human intestinal tract, genitourinary system and skin. Isolation and identification of Actinomyces by conventional methods is often difficult and time consuming. In recent years, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS has become a rapid and simple method to identify bacteria. Objective: The present study evaluated a new in-house algorithm using MALDI-TOF-MS for rapid identification of different species of oral Actinomyces cultivated from subgingival biofilm. Design: Eleven reference strains and 674 clinical strains were used in this study. All the strains were preliminarily identified using biochemical methods and then subjected to MALDI-TOF-MS analysis using both similarity-based analysis and classification methods (support vector machine [SVM]. The genotype of the reference strains and of 232 clinical strains was identified by sequence analysis of the 16S ribosomal RNA (rRNA. Results: The sequence analysis of the 16S rRNA gene of all references strains confirmed their previous identification. The MALDI-TOF-MS spectra obtained from the reference strains and the other clinical strains undoubtedly identified as Actinomyces by 16S rRNA sequencing were used to create the mass spectra reference database. Already a visual inspection of the mass spectra of different species reveals both similarities and differences. However, the differences between them are not large enough to allow a reliable differentiation by similarity analysis. Therefore, classification methods were applied as an alternative approach for differentiation and identification of Actinomyces at the species level. A cross-validation of the reference database representing 14 Actinomyces species yielded correct results for all species which were represented by more than two strains in the database. Conclusions: Our results suggest that a combination of MALDI

  5. Multiplex PCR assay for immediate identification of the infecting species in patients with mycobacterial disease.

    Science.gov (United States)

    Kox, L F; Jansen, H M; Kuijper, S; Kolk, A H

    1997-01-01

    Rapid identification of infecting mycobacterial species enables appropriate medical care decisions to be made. Our aim was to demonstrate the clinical usefulness of the multiplex PCR assay, a test based on PCR, which permits direct identification of 12 mycobacterial species in clinical specimens. A total of 259 specimens from 177 patients who had clinical symptoms of mycobacterial disease but for whom there were difficulties in diagnosis were tested. Specimens were analyzed within 48 h of receipt of the sample. Mycobacteria were identified in 102 specimens; 66 specimens contained nontuberculous mycobacteria, and 36 specimens contained Mycobacterium tuberculosis complex mycobacteria. The PCR assay identified the mycobacterial species in 43 (97.7%) of 44 microscopy- and culture-positive specimens and in 15 (93.8%) of 16 culture-positive, microscopy-negative specimens. It also permitted species identification in infections caused by more than one mycobacterial species. For 56 (96.5%) of the 58 specimens from patients with infections caused by opportunistic mycobacteria, the organisms were identified with the PCR assay. The test was useful also for the identification of fastidious mycobacteria, e.g., M. genavense, and those that cannot be cultured, e.g., M. leprae. After resolution of discrepant results, the sensitivity of the PCR assay was 97.9%, the specificity was 96.9%, the positive predictive value was 95.0%, and the negative predictive value was 98.7%. For culture these values were 60.8, 100, 100, and 81.0%, respectively. Thus, the multiplex PCR assay enables prompt diagnosis when rapid identification of infecting mycobacteria is necessary. PMID:9163468

  6. Species identification and profiling of complex microbial communities using shotgun Illumina sequencing of 16S rRNA amplicon sequences.

    Directory of Open Access Journals (Sweden)

    Swee Hoe Ong

    Full Text Available The high throughput and cost-effectiveness afforded by short-read sequencing technologies, in principle, enable researchers to perform 16S rRNA profiling of complex microbial communities at unprecedented depth and resolution. Existing Illumina sequencing protocols are, however, limited by the fraction of the 16S rRNA gene that is interrogated and therefore limit the resolution and quality of the profiling. To address this, we present the design of a novel protocol for shotgun Illumina sequencing of the bacterial 16S rRNA gene, optimized to amplify more than 90% of sequences in the Greengenes database and with the ability to distinguish nearly twice as many species-level OTUs compared to existing protocols. Using several in silico and experimental datasets, we demonstrate that despite the presence of multiple variable and conserved regions, the resulting shotgun sequences can be used to accurately quantify the constituents of complex microbial communities. The reconstruction of a significant fraction of the 16S rRNA gene also enabled high precision (>90% in species-level identification thereby opening up potential application of this approach for clinical microbial characterization.

  7. Molecular identification of scallop planktonic larvae using species-specific microsatellites

    Institute of Scientific and Technical Information of China (English)

    ZHAN Aibin; HU Xiaoli; BAO Lisui; LU Wei; PENG Wei; WANG Mingling; HU Jingjie

    2008-01-01

    The identification of scallop larvae is essential to understand the population structure and community dynamics and to assess the potential environmental impacts caused by scallop larvae released or escaped. However, the larvae identification by morphological characteristics is notoriously difficult, mainly due to the small size (usually being less than 150 μm) and vague morphological characteristics among different scallop species. A simple and accurate molecular method was developed to identify four economically farmed scallop species, the Zhikong scallop Chlamys farreri, the noble scallop C. nobilis, the bay scallop Argopecten irradians and the Yesso scallop Mizuhopecten yessoensis. The tests used the high degree of species-specific micresatellite markers, which was specified by transferability analyses, assessed by reference individuals and evaluated by BLAST searches. The sensitivity test indicated that the species-specific micresatellites were sensitive enough for the detection of 1%~2% larvae in mixed plankton samples, larvae collected from scallop hatcheries and their effluents and from the artificially controlled crosses were well identified to the species/hybrid level. The results demonstrated that the one-step PCR-based assay was technically simple, inexpensive and robust in identification analyses, and also less sensitive to initial quality of template DNA extracted from the ethanol-preserved samples for several years.

  8. Sex identification of four penguin species using locus-specific PCR.

    Science.gov (United States)

    Zhang, Peijun; Han, Jiabo; Liu, Quansheng; Zhang, Junxin; Zhang, Xianfeng

    2013-01-01

    Traditional methods for sex identification are not applicable to sexually monomorphic species, leading to difficulties in the management of their breeding programs. To identify sex in sexually monomorphic birds, molecular methods have been established. Two established primer pairs (2550F/2718R and p8/p2) amplify the CHD1 gene region from both the Z and W chromosomes. Here, we evaluated the use of these primers for sex identification in four sexually monomorphic penguin species: king penguins (Aptenodytes patagonicus), rockhopper penguins (Eudyptes chrysocome), gentoo penguins (Pygoscelis papua), and Magellanic penguins (Spheniscus magellanicus). For all species except rockhopper penguins, primer pair 2550F/2718R resulted in two distinct CHD1Z and CHD1W PCR bands, allowing for sex identification. For rockhopper penguins, only primer pair p8/p2 yielded different CHD1Z and CHD1W bands, which were faint and similar in size making them difficult to distinguish. As a result, we designed a new primer pair (PL/PR) that efficiently determined the gender of individuals from all four penguin species. Sequencing of the PCR products confirmed that they were from the CHD1 gene region. Primer pair PL/PR can be evaluated for use in sexing other penguin species, which will be crucial for the management of new penguin breeding programs. PMID:22383375

  9. Species identification and authentication of tissues of animal origin using mitochondrial and nuclear markers.

    Science.gov (United States)

    Rastogi, Gurdeep; Dharne, Mahesh S; Walujkar, Sandeep; Kumar, Ashutosh; Patole, Milind S; Shouche, Yogesh S

    2007-08-01

    We evaluated and compared the utility of mitochondrial markers viz. 16S rDNA and NADH dehydrogenase subunit 4 (ND4) and a nuclear marker viz. the actin gene to identify the specimens of animal origin for forensic identification, food regulatory control and to prevent illegal trading, poaching and conservation of endangered species. We also tested PCR fingerprinting methods like RAPD and actin barcoding to generate species-specific "fingerprints". Our results suggested that mitochondrial markers are more efficient than nuclear markers for the purpose of species identification and authentication. Among PCR fingerprinting approaches, RAPD was proved to be more discriminatory, accurate and efficient than actin fingerprinting. Considering the present scenario in trading of vertebrate animal tissues like buffalo, cow, pig, goat, chicken, frogs, fishes and snakes etc., mitogenomics based technology proved to be efficient and reliable in resolving problems like meat adulteration and smuggling across countries. PMID:22061243

  10. Next-generation sequencing for rodent barcoding: species identification from fresh, degraded and environmental samples.

    Directory of Open Access Journals (Sweden)

    Maxime Galan

    Full Text Available Rodentia is the most diverse order among mammals, with more than 2,000 species currently described. Most of the time, species assignation is so difficult based on morphological data solely that identifying rodents at the specific level corresponds to a real challenge. In this study, we compared the applicability of 100 bp mini-barcodes from cytochrome b and cytochrome c oxidase 1 genes to enable rodent species identification. Based on GenBank sequence datasets of 115 rodent species, a 136 bp fragment of cytochrome b was selected as the most discriminatory mini-barcode, and rodent universal primers surrounding this fragment were designed. The efficacy of this new molecular tool was assessed on 946 samples including rodent tissues, feces, museum samples and feces/pellets from predators known to ingest rodents. Utilizing next-generation sequencing technologies able to sequence mixes of DNA, 1,140 amplicons were tagged, multiplexed and sequenced together in one single 454 GS-FLX run. Our method was initially validated on a reference sample set including 265 clearly identified rodent tissues, corresponding to 103 different species. Following validation, 85.6% of 555 rodent samples from Europe, Asia and Africa whose species identity was unknown were able to be identified using the BLASTN program and GenBank reference sequences. In addition, our method proved effective even on degraded rodent DNA samples: 91.8% and 75.9% of samples from feces and museum specimens respectively were correctly identified. Finally, we succeeded in determining the diet of 66.7% of the investigated carnivores from their feces and 81.8% of owls from their pellets. Non-rodent species were also identified, suggesting that our method is sensitive enough to investigate complete predator diets. This study demonstrates how this molecular identification method combined with high-throughput sequencing can open new realms of possibilities in achieving fast, accurate and inexpensive

  11. Forensic species identification of large macaws using DNA barcodes and microsatellite profiles.

    Science.gov (United States)

    Abe, Hideaki; Hayano, Azusa; Inoue-Murayama, Miho

    2012-01-01

    Using mitochondrial and nuclear markers species identification was conducted in the case of seized feathers. Earlier, we had sequenced cytochrome c oxidase subunit I (COI) both from 10 seized specimens and 43 validation specimens from captive macaws belonging to 4 Ara species (A. macao, A. chloropterus, A. ararauna, and A. ambiguus) and identified 19 haplotypes based on COI sequences. Species-level identification using Barcode of Life Data Systems showed that seized feathers shared the highest similarity with scarlet macaws (A. macao), and this result was supported by the tree-base identification with high bootstrap values. Moreover, microsatellite profiles in AgGT17 locus showed that patterns of allelic distribution in the seized feathers were apparently distinct from those of red-and-green macaw (A. chloropterus), but were overlapped with those of A. macao, suggesting that all of seized feathers were derived from several individuals of A. macao. We also determined the parentage of hybrid macaws by the combination of COI barcodes and microsatellite profiles. The technique presented here will contribute to forensic identification and future conservation of large macaws that have been lost due to deforestation. PMID:21625864

  12. Phylogenetic identification of bacterial MazF toxin protein motifs among probiotic strains and foodborne pathogens and potential implications of engineered probiotic intervention in food

    Science.gov (United States)

    The most common mechanism involved in bacterial programmed cell death or apoptosis is through toxin-antitoxin (TA) modules, which exist in many bacterial species. An experimental procedure or method that provides novel insights into the molecular basis for the development of engineered/synthetic pr...

  13. The morphological identification ofProtoperidinium (Peridiniales, Dinophyceae) species on the coasts of China

    Institute of Scientific and Technical Information of China (English)

    LI Ruixiang; PAN Yulong; SUN Huiying; LI Yan; MA Xin; WANG Yan

    2016-01-01

    The classification and identification forProtoperidinium species are the most difficult work during its taxonomic study. In this research, taxonomic status ofProtoperidinium was clarified by tracing its taxonomic history, 23 species belong to genusProtoperidinium on the coasts of China were preliminarily identified, and morphological description and plate patterns were given for each species. The key differences of similar species were also discussed in this study, we believe thatP. oceanicum andP. murry,P. tumidum andP. fatulipes,P. globules andP. majus are separate species;P. diabolum should be treated as the valid name instead of the reported names Peridinium globosum orPeridinium longipes; the taxonomic relationship betweenP. punctulatum andP. subinerme requires further study.

  14. Analysis and exploitation of bacterial population from natural uranium-rich soils: selection of a model specie

    International Nuclear Information System (INIS)

    It is well known that soils play a key role in controlling the mobility of toxic metals and this property is greatly influenced by indigenous bacterial communities. This study has been conducted on radioactive and controls soils, collected in natural uraniferous areas (Limousin). A physico-chemical and mineralogical analysis of soils samples was carried out.The structure of bacterial communities was estimated by Denaturing Gradient Gel Electrophoresis (DGGE). The community structure is remarkably more stable in the uranium-rich soils than in the control ones, indicating that uranium exerts a high selection from the soils was constructed and screened for uranium resistance in order to study bacteria-uranium interactions. Scanning electron microscopy revealed that a phylo-genetically diverse set of uranium-resistant species ware able to chelate uranium at the cell surface. (author)

  15. Responses of Ammonia-Oxidising Bacterial Communities to Nitrogen, Lime, and Plant Species in Upland Grassland Soil

    Directory of Open Access Journals (Sweden)

    Deirdre C. Rooney

    2010-01-01

    Full Text Available Agricultural improvement of seminatural grasslands has been shown to result in changes to plant and microbial diversity, with consequences for ecosystem functioning. A microcosm approach was used to elucidate the effects of two key components of agricultural improvement (nitrogen addition and liming on ammonia-oxidising bacterial (AOB communities in an upland grassland soil. Plant species characteristic of unimproved and improved pastures (A. capillaris and L. perenne were planted in microcosms, and lime, nitrogen (NH4NO3, or lime plus nitrogen added. The AOB community was profiled using terminal restriction fragment length polymorphism (TRFLP of the amoA gene. AOB community structure was largely altered by NH4NO3 addition, rather than liming, although interactions between nitrogen addition and plant species were also evident. Results indicate that nitrogen addition drives shifts in the structure of key microbial communities in upland grassland soils, and that plant species may play a significant role in determining AOB community structure.

  16. Responses of Ammonia-Oxidising Bacterial Communities to Nitrogen, Lime, and Plant Species in Upland Grassland Soil

    International Nuclear Information System (INIS)

    Agricultural improvement of semi natural grasslands has been shown to result in changes to plant and microbial diversity, with consequences for ecosystem functioning. A microcosm approach was used to elucidate the effects of two key components of agricultural improvement (nitrogen addition and liming) on ammonia-oxidising bacterial (AOB) communities in an upland grassland soil. Plant species characteristic of unimproved and improved pastures (A. capillaries and L. perenne) were planted in microcosms, and lime, nitrogen (NH4NO3), or lime plus nitrogen added. The AOB community was profiled using terminal restriction fragment length polymorphism (TRFLP) of the amoA gene. AOB community structure was largely altered by NH4NO3 addition, rather than liming, although interactions between nitrogen addition and plant species were also evident. Results indicate that nitrogen addition drives shifts in the structure of key microbial communities in upland grassland soils, and that plant species may play a significant role in determining AOB community structure

  17. Independent studies using deep sequencing resolve the same set of core bacterial species dominating gut communities of honey bees.

    Science.gov (United States)

    Sabree, Zakee L; Hansen, Allison K; Moran, Nancy A

    2012-01-01

    Starting in 2003, numerous studies using culture-independent methodologies to characterize the gut microbiota of honey bees have retrieved a consistent and distinctive set of eight bacterial species, based on near identity of the 16S rRNA gene sequences. A recent study [Mattila HR, Rios D, Walker-Sperling VE, Roeselers G, Newton ILG (2012) Characterization of the active microbiotas associated with honey bees reveals healthier and broader communities when colonies are genetically diverse. PLoS ONE 7(3): e32962], using pyrosequencing of the V1-V2 hypervariable region of the 16S rRNA gene, reported finding entirely novel bacterial species in honey bee guts, and used taxonomic assignments from these reads to predict metabolic activities based on known metabolisms of cultivable species. To better understand this discrepancy, we analyzed the Mattila et al. pyrotag dataset. In contrast to the conclusions of Mattila et al., we found that the large majority of pyrotag sequences belonged to clusters for which representative sequences were identical to sequences from previously identified core species of the bee microbiota. On average, they represent 95% of the bacteria in each worker bee in the Mattila et al. dataset, a slightly lower value than that found in other studies. Some colonies contain small proportions of other bacteria, mostly species of Enterobacteriaceae. Reanalysis of the Mattila et al. dataset also did not support a relationship between abundances of Bifidobacterium and of putative pathogens or a significant difference in gut communities between colonies from queens that were singly or multiply mated. Additionally, consistent with previous studies, the dataset supports the occurrence of considerable strain variation within core species, even within single colonies. The roles of these bacteria within bees, or the implications of the strain variation, are not yet clear. PMID:22829932

  18. Independent studies using deep sequencing resolve the same set of core bacterial species dominating gut communities of honey bees.

    Directory of Open Access Journals (Sweden)

    Zakee L Sabree

    Full Text Available Starting in 2003, numerous studies using culture-independent methodologies to characterize the gut microbiota of honey bees have retrieved a consistent and distinctive set of eight bacterial species, based on near identity of the 16S rRNA gene sequences. A recent study [Mattila HR, Rios D, Walker-Sperling VE, Roeselers G, Newton ILG (2012 Characterization of the active microbiotas associated with honey bees reveals healthier and broader communities when colonies are genetically diverse. PLoS ONE 7(3: e32962], using pyrosequencing of the V1-V2 hypervariable region of the 16S rRNA gene, reported finding entirely novel bacterial species in honey bee guts, and used taxonomic assignments from these reads to predict metabolic activities based on known metabolisms of cultivable species. To better understand this discrepancy, we analyzed the Mattila et al. pyrotag dataset. In contrast to the conclusions of Mattila et al., we found that the large majority of pyrotag sequences belonged to clusters for which representative sequences were identical to sequences from previously identified core species of the bee microbiota. On average, they represent 95% of the bacteria in each worker bee in the Mattila et al. dataset, a slightly lower value than that found in other studies. Some colonies contain small proportions of other bacteria, mostly species of Enterobacteriaceae. Reanalysis of the Mattila et al. dataset also did not support a relationship between abundances of Bifidobacterium and of putative pathogens or a significant difference in gut communities between colonies from queens that were singly or multiply mated. Additionally, consistent with previous studies, the dataset supports the occurrence of considerable strain variation within core species, even within single colonies. The roles of these bacteria within bees, or the implications of the strain variation, are not yet clear.

  19. Differences in a ribosomal DNA sequence of Strongylus species allows identification of single eggs.

    Science.gov (United States)

    Campbell, A J; Gasser, R B; Chilton, N B

    1995-03-01

    In the current study, molecular techniques were evaluated for the species identification of individual strongyle eggs. Adult worms of Strongylus edentatus, S. equinus and S. vulgaris were collected at necropsy from horses from Australia and the U.S.A. Genomic DNA was isolated and a ribosomal transcribed spacer (ITS-2) amplified and sequenced using polymerase chain reaction (PCR) techniques. The length of the ITS-2 sequence of S. edentatus, S. equinus and S. vulgaris ranged between 217 and 235 nucleotides. Extensive sequence analysis demonstrated a low degree (0-0.9%) of intraspecific variation in the ITS-2 for the Strongylus species examined, whereas the levels of interspecific differences (13-29%) were significantly greater. Interspecific differences in the ITS-2 sequences allowed unequivocal species identification of single worms and eggs using PCR-linked restriction fragment length polymorphism. These results demonstrate the potential of the ribosomal spacers as genetic markers for species identification of single strongyle eggs from horse faeces. PMID:7601594

  20. Identification of five sea cucumber species through PCR-RFLP analysis

    Science.gov (United States)

    Lv, Yingchun; Zheng, Rong; Zuo, Tao; Wang, Yuming; Li, Zhaojie; Xue, Yong; Xue, Changhu; Tang, Qingjuan

    2014-10-01

    Sea cucumbers are traditional marine food and Chinese medicine in Asia. The rapid expansion of sea cucumber market has resulted in various problems, such as commercial fraud and mislabeling. Conventionally, sea cucumber species could be distinguished by their morphological and anatomical characteristics; however, their identification becomes difficult when they are processed. The aim of this study was to develop a new convenient method of identifying and distinguishing sea cucumber species. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis of mitochondrial cytochrome oxidase I gene ( COI) was used to identifing five sea cucumber species ( Apostichopus japonicus, Cucumaria frondosa, Thelenota ananas, Parastichopus californicus and Actinopyga lecanora). A 692 bp fragment of COI was searched for BamHI, KpnI, PstI, XbaI and Eco31I restriction sites with DNAMAN 6.0, which were then used to PCR-RFLP analysis. These five sea cucumber species can be discriminated from mixed sea cucumbers. The developed PCR-RFLP assay will facilitate the identification of sea cucumbers, making their source tracing and quality controlling feasible.

  1. Pictorial identification key for species of Sarcophagidae (Diptera of potential forensic importance in southern Brazil

    Directory of Open Access Journals (Sweden)

    Karine Pinto e Vairo

    2011-09-01

    Full Text Available Pictorial identification key for species of Sarcophagidae (Diptera of potential forensic importance in southern Brazil. Species of the subfamily Sarcophaginae are important to forensic entomology due to their necrophagous habits. This contribution presents a pictorial key for the identification of 22 Sarcophaginae species in 10 genera that are commonly found in southern Brazil. Photographs of the main structures used in species identification, mainly from the male terminalia, are provided.Chave pictórica para a identificação das espécies de Sarcophagidae (Diptera de potencial importância forense do sul do Brasil. Espécies da subfamília Sarcophaginae são importantes para a entomologia forense devido ao seu hábito necrófago. Este trabalho apresenta uma chave pictórica para a identificação de 22 espécies de Sarcophaginae de 10 gêneros encontradas na região sul do Brasil. São fornecidas fotografias dos principais estruturas das espécies, principalmente da terminália masculina.

  2. Identification of the serotypes of bacterial meningitis agents; implication for vaccine usage.

    Directory of Open Access Journals (Sweden)

    Mohammad Mehdi Attarpour-Yazdi

    2014-08-01

    Full Text Available Bacterial meningitis is one of the most serious infections and should be treated as emergency. As it has significant morbidity and mortality throughout the world, every country should have precise information regarding the etiological agents of disease and populations at risk to design public health prevention strategy. In the present study in addition of evaluation of common etiological agents (Haemophilus influenzae, Neisseria meningitidis, and Streptococcus pneumoniae in bacterial meningitis cases, we sero-grouped or serotyped the obtained agents in order to predict the usefulness of existing vaccines against bacterial meningitis.Cerebrospinal fluid of 182 suspected meningitis patients were collected, from which 114 cases were approved by biochemical, microbiological and molecular tests as bacterial meningitis. The isolated bacteria were serogrouped or serotyped to determine the dominant serotypes.Streptococcus pneumoniae accounted for 36%, Haemophilus influenza for 26% and Neisseria meningitidis for 14% of cases. From 13 serogroups of N. meningitides the most frequent serogroups, were meningococcus group B (51%, C(24% A (18%, Z(2%, W135 (1% and 3% was not identified. In H. influenzae group only serotype b (100% have been identified and in pneumococcal meningitis the most common serotype among our cases were 18C (44% followed by14 (17%, 19A (13%, 6A (9%, 7F (4%, 4(3%, 3 (3%, 9V (2%, 8 (2%, 23f (2%, 5 (1%.Since there is no nationwide mass immunization program for common agents of bacterial meningitis in Iran, the result of this study can be used to improve the existing vaccines to cover the detected serotypes and consequently reduce the incidence of bacterial meningitis.

  3. Molecular identification and classification of Trichophyton mentagrophytes complex strains isolated from humans and selected animal species.

    Science.gov (United States)

    Ziółkowska, Grażyna; Nowakiewicz, Aneta; Gnat, Sebastian; Trościańczyk, Aleksandra; Zięba, Przemysław; Dziedzic, Barbara Majer

    2015-03-01

    Species differentiation within Trichophyton mentagrophytes complex group currently poses a major diagnostic challenge, with molecular methods increasingly supplementing classical identification based on the morphological and physiological properties of the fungi. Diagnostic and epidemiological research aimed at determining the source and means of transmission of dermatophytoses in both humans and animals requires not only species differentiation of isolates but also differentiation within species. The study was conducted on 24 isolates originating in humans and various animal species with clinical symptoms of dermatophytosis. The analysis included phenotypical identification methods and molecular methods: internal transcribed spacer sequencing and ITS-restriction fragment length polymorphism (RFLP) with multi-enzyme restriction. ITS sequence analysis identified the isolates to species - Trichophyton interdigitale, Arthroderma benhamiae and A. vanbreuseghemii, and ITS-RFLP detected six different genotypes. Genotypes I, II and III characterised strains belonging to A. benhamiae, genotype IV characterised the A. vanbreuseghemii strain, and genotypes V and VI occurred only within the species T. interdigitale. Strains isolated from guinea pigs were dominant within genotype I, while genotype II was found mainly in strains from foxes. Multi-enzyme restriction analysis of this region enables intraspecific differentiation, which may be useful in epidemiological research, particularly in determining the source of infections. PMID:25643744

  4. Development of SCAR markers for species identification of the genus Nepenthes (Nepenthaceae).

    Science.gov (United States)

    Anuniwat, A; Chaveerach, A; Tanee, T; Sudmoon, R

    2009-11-15

    Nepenthes species in Thailand, namely N. mirabilis Druce, N. gracilis Korth., N. smilesii Hemsl., N. ampullaria Jack and N. kampotiana Lecomte, were collected for development of Sequence Characterized Amplified Region (SCAR) marker, a genotype identification tool. Forty Random Amplified Polymorphic DNA (RAPD) primers were screened and three successful primers produced different banding patterns including five candidate species-specific markers. The candidate markers were cloned and sequenced. The marker sequences are 602, 379, 420, 473 and 1017 bp for N. mirabilis, N. gracilis, N. smilesii, N. ampullaria and N. kampotiana, respectively. Then the sequences were used to design primers for development of a species-specific band being a SCAR marker, including Mir 1, Mir 2 and Mir 3 for N. mirabilis; Gra 1 and Gra 2 for N. gracilis; Smi 1, Smi 2 and Smi 3 for N. smilesii; Amp 1 and Amp 2 for N. ampullaria and Kam 1 and Kam 2 of N. kampotiana. The primers were evaluated with each other Nepenthes species. Finally, species-specific SCAR markers were successfully developed for N. gracilis, N. ampullaria and N. kampotiana. Application of these markers is feasible for identification of Nepenthes species in Thailand. PMID:20180319

  5. Identification of Yersinia enterocolitica at the Species and Subspecies Levels by Fourier Transform Infrared Spectroscopy ▿

    Science.gov (United States)

    Kuhm, Andrea Elisabeth; Suter, Daniel; Felleisen, Richard; Rau, Jörg

    2009-01-01

    Yersinia enterocolitica and other Yersinia species, such as Y. pseudotuberculosis, Y. bercovieri, and Y. intermedia, were differentiated using Fourier transform infrared spectroscopy (FT-IR) combined with artificial neural network analysis. A set of well defined Yersinia strains from Switzerland and Germany was used to create a method for FT-IR-based differentiation of Yersinia isolates at the species level. The isolates of Y. enterocolitica were also differentiated by FT-IR into the main biotypes (biotypes 1A, 2, and 4) and serotypes (serotypes O:3, O:5, O:9, and “non-O:3, O:5, and O:9”). For external validation of the constructed methods, independently obtained isolates of different Yersinia species were used. A total of 79.9% of Y. enterocolitica sensu stricto isolates were identified correctly at the species level. The FT-IR analysis allowed the separation of all Y. bercovieri, Y. intermedia, and Y. rohdei strains from Y. enterocolitica, which could not be differentiated by the API 20E test system. The probability for correct biotype identification of Y. enterocolitica isolates was 98.3% (41 externally validated strains). For correct serotype identification, the probability was 92.5% (42 externally validated strains). In addition, the presence or absence of the ail gene, one of the main pathogenicity markers, was demonstrated using FT-IR. The probability for correct identification of isolates concerning the ail gene was 98.5% (51 externally validated strains). This indicates that it is possible to obtain information about genus, species, and in the case of Y. enterocolitica also subspecies type with a single measurement. Furthermore, this is the first example of the identification of specific pathogenicity using FT-IR. PMID:19617388

  6. Molecular assessment of bacterial vaginosis by Lactobacillus abundance and species diversity

    NARCIS (Netherlands)

    J.A.M. Dols; D. Molenaar; J.J. van der Helm; M.P.M. Caspers; A. de Kat Angelino-Bart; F.H.J. Schuren; A.G.C.L. Speksnijder; H.V. Westerhoff; J.H. Richardus; M.E. Boon; G. Reid; H.J.C. de Vries; R. Kort

    2016-01-01

    BACKGROUND: To date, women are most often diagnosed with bacterial vaginosis (BV) using microscopy based Nugent scoring or Amsel criteria. However, the accuracy is less than optimal. The aim of the present study was to confirm the identity of known BV-associated composition profiles and evaluate ind

  7. Reactive oxygen species mediated bacterial biofilm inhibition via zinc oxide nanoparticles and their statistical determination.

    Directory of Open Access Journals (Sweden)

    Sourabh Dwivedi

    Full Text Available The formation of bacterial biofilm is a major challenge in clinical applications. The main aim of this study is to describe the synthesis, characterization and biocidal potential of zinc oxide nanoparticles (NPs against bacterial strain Pseudomonas aeruginosa. These nanoparticles were synthesized via soft chemical solution process in a very short time and their structural properties have been investigated in detail by using X-ray diffraction and transmission electron microscopy measurements. In this work, the potential of synthesized ZnO-NPs (∼ 10-15 nm has been assessed in-vitro inhibition of bacteria and the formation of their biofilms was observed using the tissue culture plate assays. The crystal violet staining on biofilm formation and its optical density revealed the effect on biofilm inhibition. The NPs at a concentration of 100 µg/mL significantly inhibited the growth of bacteria and biofilm formation. The biofilm inhibition by ZnO-NPs was also confirmed via bio-transmission electron microscopy (Bio-TEM. The Bio-TEM analysis of ZnO-NPs treated bacteria confirmed the deformation and damage of cells. The bacterial growth in presence of NPs concluded the bactericidal ability of NPs in a concentration dependent manner. It has been speculated that the antibacterial activity of NPs as a surface coating material, could be a feasible approach for controlling the pathogens. Additionally, the obtained bacterial solution data is also in agreement with the results from statistical analytical methods.

  8. Effect of holothurian and zoanthid extracts on growth of some bacterial and diatom species

    Digital Repository Service at National Institute of Oceanography (India)

    Gonsalves, C.

    The antifouling properties of the extracts from two zoanthids, viz. Zoanthus sp, Protopalythoa sp and one holothurian species, viz. Holothuria leucospilota occurring in the coastal waters off Goa were tested against 5 bacteria and 2 diatom species...

  9. Identification of fine-leaved species of genus Festuca by molecular methods

    International Nuclear Information System (INIS)

    Festuca (L.) is a taxonomically complex genus of family Poaceae. The fine-leaved species of fescue are well adapted to grow in sandy and dry habitats, therefore, they can be used for establishment of lawns of minimal maintenance as well as recultivations of damaged soils. Breeding for the new varieties to meet these purposes requires reliable methods for identification of the species. The discrimination of fine-leaved fescue species based on morphological features is rather difficult, therefore reliable molecular marker would greatly facilitate it and eliminate the need to wait till floral organs are fully formed. Seven fine-leaved species of genus Festuca collected in Lithuania, namely, F. ovina, F. trachyphylla, F. polesica, F. psammophila, F. sabulosa, F. pseudovina and F. wolgensis were investigated at the Institute of Agriculture, Lithuanian Research Centre for Agriculture and Forestry. The ISSR markers, seed storage proteins and isozymes were tested for their ability to distinguish between the fine-leaved species of the genus Festuca. Seed storage protein and ISSR fingerprint profiles could be used to distinguish between fine-leaved species of Festuca, except for closely related F. sabulosa and F. polesica species. Isozyme fingerprints did not contain sufficient number of species specific bands and were not feasible to discriminate between species. (author)

  10. A validated methodology for genetic identification of tuna species (genus Thunnus.

    Directory of Open Access Journals (Sweden)

    Jordi Viñas

    Full Text Available BACKGROUND: Tuna species of the genus Thunnus, such as the bluefin tunas, are some of the most important and yet most endangered trade fish in the world. Identification of these species in traded forms, however, may be difficult depending on the presentation of the products, which may hamper conservation efforts on trade control. In this paper, we validated a genetic methodology that can fully distinguish between the eight Thunnus species from any kind of processed tissue. METHODOLOGY: After testing several genetic markers, a complete discrimination of the eight tuna species was achieved using Forensically Informative Nucleotide Sequencing based primarily on the sequence variability of the hypervariable genetic marker mitochondrial DNA control region (mtDNA CR, followed, in some specific cases, by a second validation by a nuclear marker rDNA first internal transcribed spacer (ITS1. This methodology was able to distinguish all tuna species, including those belonging to the subgenus Neothunnus that are very closely related, and in consequence can not be differentiated with other genetic markers of lower variability. This methodology also took into consideration the presence of introgression that has been reported in past studies between T. thynnus, T. orientalis and T. alalunga. Finally, we applied the methodology to cross-check the species identity of 26 processed tuna samples. CONCLUSIONS: Using the combination of two genetic markers, one mitochondrial and another nuclear, allows a full discrimination between all eight tuna species. Unexpectedly, the genetic marker traditionally used for DNA barcoding, cytochrome oxidase 1, could not differentiate all species, thus its use as a genetic marker for tuna species identification is questioned.

  11. Development of a real-time PCR for identification of brachyspira species in human colonic biopsies.

    Directory of Open Access Journals (Sweden)

    Laurens J Westerman

    Full Text Available BACKGROUND: Brachyspira species are fastidious anaerobic microorganisms, that infect the colon of various animals. The genus contains both important pathogens of livestock as well as commensals. Two species are known to infect humans: B. aalborgi and B. pilosicoli. There is some evidence suggesting that the veterinary pathogenic B. pilosicoli is a potential zoonotic agent, however, since diagnosis in humans is based on histopathology of colon biopsies, species identification is not routinely performed in human materials. METHODS: The study population comprised 57 patients with microscopic evidence of Brachyspira infection and 26 patients with no histopathological evidence of Brachyspira infection. Concomitant faecal samples were available from three infected patients. Based on publically available 16S rDNA gene sequences of all Brachyspira species, species-specific primer sets were designed. DNA was extracted and tested by real-time PCR and 16S rDNA was sequenced. RESULTS: Sensitivity and specificity for identification of Brachyspira species in colon biopsies was 100% and 87.7% respectively. Sequencing revealed B. pilosicoli in 15.4% of patients, B. aalborgi in 76.9% and a third species, tentatively named "Brachyspira hominis", in 26.2%. Ten patients (12.3% had a double and two (3.1% a triple infection. The presence of Brachyspira pilosicoli was significantly associated with inflammatory changes in the colon-biopsy (p=0.028. CONCLUSIONS: This newly designed PCR allows for sub-differentiation of Brachyspira species in patient material and thus allows large-scaled surveillance studies to elucidate the pathogenicity of human Brachyspira infections. One-third of affected patients appeared to be infected with a novel species.

  12. Species-specific detection and identification of fusarium species complex, the causal agent of sugarcane pokkah boeng in China.

    Directory of Open Access Journals (Sweden)

    Zhenyue Lin

    Full Text Available BACKGROUND: Pokkah boeng disease caused by the Fusarium species complex results in significant yield losses in sugarcane. Thus, the rapid and accurate detection and identification of the pathogen is urgently required to manage and prevent the spreading of sugarcane pokkah boeng. METHODS: A total of 101 isolates were recovered from the pokkah boeng samples collected from five major sugarcane production areas in China throughout 2012 and 2013. The causal pathogen was identified by morphological observation, pathogenicity test, and phylogenetic analysis based on the fungus-conserved rDNA-ITS. Species-specific TaqMan real-time PCR and conventional PCR methods were developed for rapid and accurate detection of the causal agent of sugarcane pokkah boeng. The specificity and sensitivity of PCR assay were also evaluated on a total of 84 isolates of Fusarium from China and several isolates from other fungal pathogens of Sporisorium scitamineum and Phoma sp. and sugarcane endophyte of Acremonium sp. RESULT: Two Fusarium species (F. verticillioides and F. proliferatum that caused sugarcane pokahh boeng were identified by morphological observation, pathogenicity test, and phylogenetic analysis. Species-specific TaqMan PCR and conventional PCR were designed and optimized to target their rDNA-ITS regions. The sensitivity of the TaqMan PCR was approximately 10 pg of fungal DNA input, which was 1,000-fold over conventional PCR, and successfully detected pokkah boeng in the field-grown sugarcane. CONCLUSIONS/SIGNIFICANCE: This study was the first to identify two species, F. verticillioides and F. proliferatum, that were causal pathogens of sugarcane pokkah boeng in China. It also described the development of a species-specific PCR assay to detect and confirm these pathogens in sugarcane plants from mainland China. This method will be very useful for a broad range of research endeavors as well as the regulatory response and management of sugarcane pokkah boeng.

  13. Identification of markers associated with bacterial blight resistance loci in cowpea (Vigna unguiculata (L.) Walp.)

    NARCIS (Netherlands)

    Agbicodo, A.C.M.E.; Fatokun, C.A.; Bandyopadhyay, R.; Wydra, K.; Diop, N.N.; Muchero, W.; Ehlers, J.D.; Roberts, P.A.; Close, T.J.; Visser, R.G.F.; Linden, van der C.G.

    2010-01-01

    Cowpea bacterial blight (CoBB), caused by Xanthomonas axonopodis pv. vignicola (Xav), is a worldwide major disease of cowpea [Vigna unguiculata (L.) Walp.]. Among different strategies to control the disease including cultural practices, intercropping, application of chemicals, and sowing pathogen-fr

  14. Invasive alien species – framework for the identification of invasive alien species of EU concern

    OpenAIRE

    Roy, Helen; Schonrogge, Karsten; Dean, Hannah; Peyton, Jodey; Branquart, Etienne; Vanderhoeven, Sonia; Copp, Gordon; Stebbing, Paul; KENIS Marc; Rabitsch, Wolfgang; Essl, Franz; Schindler, Stefan; Brunel, Sarah; Kettunen, Marianne; Mazza, Leonardo

    2014-01-01

    Invasive alien species (IAS) are considered to be one of the greatest threats to biodiversity, particularly through their interactions with other drivers of change (MEA 2005, GBO 2011). In recent years the European Commission (EC) has intensified their commitment to provide a comprehensive, problem-oriented, well-balanced and manageable solution to IAS in Europe. The text of a European Union (EU) Regulation is expected to be adopted soon. A core component of the Regulation is a list of “IAS o...

  15. Regulatory RNAs in the Less Studied Streptococcal Species: From Nomenclature to Identification

    Science.gov (United States)

    Zorgani, Mohamed A.; Quentin, Roland; Lartigue, Marie-Frédérique

    2016-01-01

    Streptococcal species are Gram-positive bacteria involved in severe and invasive diseases in humans and animals. Although, this group includes different pathogenic species involved in life-threatening infections for humans, it also includes beneficial species, such as Streptococcus thermophilus, which is used in yogurt production. In bacteria virulence factors are controlled by various regulatory networks including regulatory RNAs. For clearness and to develop logical thinking, we start this review with a revision of regulatory RNAs nomenclature. Previous reviews are mostly dealing with Streptococcus pyogenes and Streptococcus pneumoniae regulatory RNAs. We especially focused our analysis on regulatory RNAs in Streptococcus agalactiae, Streptococcus mutans, Streptococcus thermophilus and other less studied Streptococcus species. Although, S. agalactiae RNome remains largely unknown, sRNAs (small RNAs) are supposed to mediate regulation during environmental adaptation and host infection. In the case of S. mutans, sRNAs are suggested to be involved in competence regulation, carbohydrate metabolism, and Toxin–Antitoxin systems. A new category of miRNA-size small RNAs (msRNAs) was also identified for the first time in this species. The analysis of S. thermophilus sRNome shows that many sRNAs are associated to the bacterial immune system known as CRISPR-Cas system. Only few of the other different Streptococcus species have been the subject of studies pointed toward the characterization of regulatory RNAs. Finally, understanding bacterial sRNome can constitute one step forward to the elaboration of new strategies in therapy such as substitution of antibiotics in the management of S. agalactiae neonatal infections, prevention of S. mutans dental caries or use of S. thermophilus CRISPR-Cas system in genome editing applications. PMID:27507970

  16. DNA barcoding of Arctic Ocean holozooplankton for species identification and recognition

    Science.gov (United States)

    Bucklin, Ann; Hopcroft, Russell R.; Kosobokova, Ksenia N.; Nigro, Lisa M.; Ortman, Brian D.; Jennings, Robert M.; Sweetman, Christopher J.

    2010-01-01

    Zooplankton species diversity and distribution are important measures of environmental change in the Arctic Ocean, and may serve as 'rapid-responders' of climate-induced changes in this fragile ecosystem. The scarcity of taxonomists hampers detailed and up-to-date monitoring of these patterns for the rarer and more problematic species. DNA barcodes (short DNA sequences for species recognition and discovery) provide an alternative approach to accurate identification of known species, and can speed routine analysis of zooplankton samples. During 2004-2008, zooplankton samples were collected during cruises to the central Arctic Ocean and Chukchi Sea. A ˜700 base-pair region of the mitochondrial cytochrome oxidase I (mtCOI) gene was amplified and sequenced for 82 identified specimens of 41 species, including cnidarians (six hydrozoans, one scyphozoan), arthropod crustaceans (five amphipods, 24 copepods, one decapod, and one euphausiid); two chaetognaths; and one nemertean. Phylogenetic analysis used the Neighbor-Joining algorithm with Kimura-2-Parameter (K-2-P) distances, with 1000-fold bootstrapping. K-2-P genetic distances between individuals of the same species ranged from 0.0 to 0.2; genetic distances between species ranged widely from 0.1 to 0.7. The mtCOI gene tree showed monophyly (at 100% bootstrap value) for each of the 26 species for which more than one individual was analyzed. Of seven genera for which more than one species was analyzed, four were shown to be monophyletic; three genera were not resolved. At higher taxonomic levels, only the crustacean order Copepoda was resolved, with bootstrap value of 83%. The mtCOI barcodes accurately discriminated and identified known species of 10 taxonomic groups of Arctic Ocean holozooplankton. A comprehensive DNA barcode database for the estimated 300 described species of Arctic holozooplankton will allow rapid assessment of species diversity and distribution in this climate-vulnerable ocean ecosystem.

  17. Evaluation of 11 PCR assays for species-level identification of Campylobacter jejuni and Campylobacter coli

    DEFF Research Database (Denmark)

    On, Stephen L.W.; Jordan, Penelope J.

    2003-01-01

    We examined the sensitivity and specificity of 11 PCR assays described for the species identification of Campylobacter jejuni and Campylobacter coli by using 111 type, reference, and field strains of C. jejuni, C. coli, and Campylobacter lari. For six assays, an additional 21 type strains...... representing related Campylobacter, Arcobacter, and Helicobacter species were also included. PCR tests were initially established in the laboratory by optimizing conditions with respect to five type and reference strains of C. jejuni, C. coli, and C. lari. One PCR test for C. coli failed to give appropriate...

  18. The SPECIES and ORGANISMS Resources for Fast and Accurate Identification of Taxonomic Names in Text

    DEFF Research Database (Denmark)

    Pafilis, Evangelos; Pletscher-Frankild, Sune; Fanini, Lucia;

    2013-01-01

    The exponential growth of the biomedical literature is making the need for efficient, accurate text-mining tools increasingly clear. The identification of named biological entities in text is a central and difficult task. We have developed an efficient algorithm and implementation of a dictionary......-based approach to named entity recognition, which we here use to identify names of species and other taxa in text. The tool, SPECIES, is more than an order of magnitude faster and as accurate as existing tools. The precision and recall was assessed both on an existing gold-standard corpus and on a new corpus of...

  19. Identification of conserved drought-adaptive genes using a cross-species meta-analysis approach

    OpenAIRE

    Shaar-Moshe, Lidor; Hübner, Sariel; Peleg, Zvi

    2015-01-01

    Background Drought is the major environmental stress threatening crop-plant productivity worldwide. Identification of new genes and metabolic pathways involved in plant adaptation to progressive drought stress at the reproductive stage is of great interest for agricultural research. Results We developed a novel Cross-Species meta-Analysis of progressive Drought stress at the reproductive stage (CSA:Drought) to identify key drought adaptive genes and mechanisms and to test their evolutionary c...

  20. Molecular and morphological identification of mealybug species (Hemiptera: Pseudococcidae) in brazilian vineyards

    OpenAIRE

    Pacheco da Silva, Vitor Cezar; Bertin, Aline; Blin, Aurélie; Germain, Jean-Francois; Bernardi, Daniel; Rignol, Guylène; Botton, Marcos

    2014-01-01

    Mealybugs (Hemiptera: Pseudococcidae) are pests constraining the international trade of Brazilian table grapes. They damage grapes by transmitting viruses and toxins, causing defoliation, chlorosis, and vigor losses and favoring the development of sooty mold. Difficulties in mealybug identification remain an obstacle to the adequate management of these pests. In this study, our primary aim was to identify the principal mealybug species infesting the major table grape-producing regions in Braz...

  1. Identification of Staphylococcus species with the API STAPH-IDENT system.

    OpenAIRE

    1982-01-01

    The API STAPH-IDENT system was compared with conventional methods for the identification of 14 Staphylococcus species. Conventional methods included the Kloos and Schleifer simplified scheme and DNA-DNA hybridization. The API STAPH-IDENT strip utilizes a battery of 10 miniaturized biochemical tests, including alkaline phosphatase, urease, beta-glucosidase, beta-glucuronidase, and beta-galactosidase activity, aerobic acid formation from D-(+)-mannose, D-mannitol, D-(+)-trehalose, and salicin, ...

  2. MORPHOLOGICAL AND MOLECULAR IDENTIFICATION OF Fusarium SPECIES AND THEIR PATHOGENICITY FOR WHEAT

    OpenAIRE

    Jelena Poštić

    2012-01-01

    From the root and lower stem parts of weeds andplant debris of maize, wheat, oat and sunflower weisolated 300 isolates of Fusarium spp. and performedmorphological and molecular identification. With molecularidentification using AFLP method we determined14 Fusarium species: F. acuminatum, F. avenaceum, F.concolor, F. crookwellense, F. equiseti, F. graminearum,F. oxysporum, F. proliferatum, F. semitectum, F. solani,F. sporotrichioides, F. subglutinans, F. venenatum and F.verticillioides.By comp...

  3. Rapid Identification of Emerging Human-Pathogenic Sporothrix Species with Rolling Circle Amplification.

    Science.gov (United States)

    Rodrigues, Anderson M; Najafzadeh, Mohammad J; de Hoog, G Sybren; de Camargo, Zoilo P

    2015-01-01

    Sporothrix infections are emerging as an important human and animal threat among otherwise healthy patients, especially in Brazil and China. Correct identification of sporotrichosis agents is beneficial for epidemiological surveillance, enabling implementation of adequate public-health policies and guiding antifungal therapy. In areas of limited resources where sporotrichosis is endemic, high-throughput detection methods that are specific and sensitive are preferred over phenotypic methods that usually result in misidentification of closely related Sporothrix species. We sought to establish rolling circle amplification (RCA) as a low-cost screening tool for species-specific identification of human-pathogenic Sporothrix. We developed six species-specific padlock probes targeting polymorphisms in the gene encoding calmodulin. BLAST-searches revealed candidate probes that were conserved intraspecifically; no significant homology with sequences from humans, mice, plants or microorganisms outside members of Sporothrix were found. The accuracy of our RCA-based assay was demonstrated through the specificity of probe-template binding to 25 S. brasiliensis, 58 S. schenckii, 5 S. globosa, 1 S. luriei, 4 S. mexicana, and 3 S. pallida samples. No cross reactivity between closely related species was evident in vitro, and padlock probes yielded 100% specificity and sensitivity down to 3 × 10(6) copies of the target sequence. RCA-based speciation matched identifications via phylogenetic analysis of the gene encoding calmodulin and the rDNA operon (kappa 1.0; 95% confidence interval 1.0-1.0), supporting its use as a reliable alternative to DNA sequencing. This method is a powerful tool for rapid identification and specific detection of medically relevant Sporothrix, and due to its robustness has potential for ecological studies. PMID:26696992

  4. Rapid identification of emerging human-pathogenic Sporothrix species with rolling circle amplification

    Directory of Open Access Journals (Sweden)

    Anderson Messias Rodrigues

    2015-12-01

    Full Text Available Sporothrix infections are emerging as an important human and animal threat among otherwise healthy patients, especially in Brazil and China. Correct identification of sporotrichosis agents is beneficial for epidemiological surveillance, enabling implementation of adequate public-health policies and guiding antifungal therapy. In areas of limited resources where sporotrichosis is endemic, high-throughput detection methods that are specific and sensitive are preferred over phenotypic methods that usually result in misidentification of closely related Sporothrix species. We sought to establish rolling circle amplification (RCA as a low-cost screening tool for species-specific identification of human-pathogenic Sporothrix. We developed six species-specific padlock probes targeting polymorphisms in the gene encoding calmodulin. BLAST-searches revealed candidate probes that were conserved intraspecifically; no significant homology with sequences from humans, mice, plants or microorganisms outside members of Sporothrix were found. The accuracy of our RCA-based assay was demonstrated through the specificity of probe-template binding to 25 S. brasiliensis, 58 S. schenckii, 5 S. globosa, 1 S. luriei, 4 S. mexicana, and 3 S. pallida samples. No cross reactivity between closely related species was evident in vitro, and padlock probes yielded 100% specificity and sensitivity down to 3 x 10 6 copies of the target sequence. RCA-based speciation matched identifications via phylogenetic analysis of the gene encoding calmodulin and the rDNA operon (kappa 1.0; 95% confidence interval 1.0-1.0, supporting its use as a reliable alternative to DNA sequencing. This method is a powerful tool for rapid identification and specific detection of medically relevant Sporothrix, and due to its robustness has potential for ecological studies.

  5. Oral Actinomyces Species in Health and Disease: Identification, Occurence and Importance of Early Colonization

    OpenAIRE

    Sarkonen, Nanna

    2007-01-01

    The genus Actinomyces consists of a heterogeneous group of gram-positive, mainly facultatively anaerobic or microaerobic rods showing various degrees of branching. In the oral cavity, streptococci and Actinomyces form a fundamental component of the indigenous microbiota, being among initial colonizers in polymicrobial biofilms. The significance of the genus Actinomyces is based on the capability of species to adhere to surfaces such as on teeth and to co-aggregate with other bacteria. Identif...

  6. The degradation of different Schypozoan jellyfish species by the ambient bacterial community

    OpenAIRE

    TURK Valentina

    2015-01-01

    The chemical composition and degradation of dead jellyfish tissue of Aurelia sp., pelagia noctiluca and Rhizostoma pulmo by the ambient bacterial communitywas studied in laboratory experiment using samples from the Gulf of Trieste (northern Adriatic). Preliminary results showed rapid hydrolyzes of proteins in the presence of the natural microbial community and significant release of disolved and anorganic nutrients, which can significantly alter thecarbon and nitrogen cycles and ohygen dynami...

  7. Synergistic interactions between Labiatae species and antibiotics on gram positive and gram negative bacterial strains

    OpenAIRE

    Adham, Aveen Nozad

    2015-01-01

    Objective and methods: This study was aimed to evaluate antibacterial activity; type of interaction between chloroform leaves extract of Mentha piperita, Mentha longifolia and Ocimum basilicum together and with antibiotics by agar well diffusion method on isolated bacterial strain and to determine active constituents responsible on antibacterial activity by agar overlay bioautographic method.Results: Mentha piperita exhibited more pronounced inhibition zone (20mm) against Staphylococcus aureu...

  8. Bacterial-biota dynamics of eight bryophyte species from different ecosystems

    OpenAIRE

    Koua, Faisal Hammad Mekky; Kimbara, Kazuhide; Tani, Akio

    2014-01-01

    Despite the importance of bryophyte-associated microorganisms in various ecological aspects including their crucial roles in the soil-enrichment of organic mass and N2 fixation, nonetheless, little is known about the microbial diversity of the bryophyte phyllospheres (epi-/endophytes). To get insights into bacterial community structures and their dynamics on the bryophyte habitats in different ecosystems and their potential biological roles, we utilized the 16S rRNA gene PCR-DGGE and subseque...

  9. Bacterial profiling of White Plague Disease in a comparative coral species framework

    OpenAIRE

    Roder, Cornelia; Arif, Chatchanit; Bayer, Till; Aranda, Manuel; Daniels, Camille; Shibl, Ahmed; Chavanich, Suchana; VOOLSTRA, CHRISTIAN R.

    2013-01-01

    Coral reefs are threatened throughout the world. A major factor contributing to their decline is outbreaks and propagation of coral diseases. Due to the complexity of coral-associated microbe communities, little is understood in terms of disease agents, hosts and vectors. It is known that compromised health in corals is correlated with shifts in bacterial assemblages colonizing coral mucus and tissue. However, general disease patterns remain, to a large extent, ambiguous as comparative studie...

  10. Bacterial Tethering Analysis Reveals a “Run-Reverse-Turn” Mechanism for Pseudomonas Species Motility

    OpenAIRE

    Qian, Chen; Wong, Chui Ching; SWARUP, SANJAY; Chiam, Keng-Hwee

    2013-01-01

    We have developed a program that can accurately analyze the dynamic properties of tethered bacterial cells. The program works especially well with cells that tend to give rise to unstable rotations, such as polar-flagellated bacteria. The program has two novel components. The first dynamically adjusts the center of the cell's rotational trajectories. The second applies piecewise linear approximation to the accumulated rotation curve to reduce noise and separate the motion of bacteria into pha...

  11. Species identification using genetic tools: the value of nuclear and mitochondrial gene sequences in whale conservation.

    Science.gov (United States)

    Palumbi, S R; Cipriano, F

    1998-01-01

    DNA sequence analysis is a powerful tool for identifying the source of samples thought to be derived from threatened or endangered species. Analysis of mitochondrial DNA (mtDNA) from retail whale meat markets has shown consistently that the expected baleen whale in these markets, the minke whale, makes up only about half the products analyzed. The other products are either unregulated small toothed whales like dolphins or are protected baleen whales such as humpback, Bryde's, fin, or blue whales. Independent verification of such mtDNA identifications requires analysis of nuclear genetic loci, but this is technically more difficult than standard mtDNA sequencing. In addition, evolution of species-specific sequences (i.e., fixation of sequence differences to produce reciprocally monophyletic gene trees) is slower in nuclear than in mitochondrial genes primarily because genetic drift is slower at nuclear loci. When will use of nuclear sequences allow forensic DNA identification? Comparison of neutral theories of coalescence of mitochondrial and nuclear loci suggests a simple rule of thumb. The "three-times rule" suggests that phylogenetic sorting at nuclear loci is likely to produce species-specific sequences when mitochondrial alleles are reciprocally monophyletic and the branches leading to the mtDNA sequences of a species are three times longer than the average difference observed within species. A preliminary test of the three-times rule, which depends on many assumptions about the species and genes involved, suggests that blue and fin whales should have species-specific sequences at most neutral nuclear loci, whereas humpback and fin whales should show species-specific sequences at fewer nuclear loci. Partial sequences of actin introns from these species confirm the predictions of the three-times rule and show that blue and fin whales are reciprocally monophyletic at this locus. These intron sequences are thus good tools for the identification of these species

  12. Potential of Some Fungal and Bacterial Species in Bioremediation of Heavy Metals

    Directory of Open Access Journals (Sweden)

    Raman Kumar

    2014-02-01

    Full Text Available Microorganisms including fungi and bacteria have been reported to extract heavy metals from wastewater through bioaccumulation and biosorption. An attempt was, therefore, made to isolate bacteria and fungi from sites contaminated with heavy metals for higher tolerance and removal from wastewater. Bacterial and fungal isolates were obtained from the samples collected from Karnal, Ambala and Yamunanagar districts of Haryana using enrichment culture technique. Bacterial and fungal isolates with tolerant up to 100 ppm concentration of heavy metals (Pb, Cd, Cr were tested for their removal from liquid media containing 50 ppm concentration of Pb, Cd and Cr each. Five fungi (Penicillium chrysogenum, Aspegillus nidulans, Aspergillus flavus, Rhizopus arrhizus, Trichoderma viride were also included in this study. Fungi Aspergillus nidulans, Rhizopus arrhizus and Trichoderma viride showed maximum uptake capacity of 25.67 mg/g for Pb, 13.15 mg/g for Cd and 2.55 mg/g of Cr, respectively. The maximum uptake capacity of tolerant bacterial isolates - BPb12 and BPb16, BCd5 and BCr14 were observed to be ~ 45 mg/g for Pb, 2.12 mg/g for Cd and 3.29 mg/g for Cr, respectively. This indicated the potential of these identified fungi and bacteria as biosorbent for removal of high concentration metals from wastewater and industrial effluents.

  13. Identification of mealybug pest species (Hemiptera: Pseudococcidae) in Egypt and France, using a DNA barcoding approach.

    Science.gov (United States)

    Abd-Rabou, S; Shalaby, H; Germain, J-F; Ris, N; Kreiter, P; Malausa, T

    2012-10-01

    Pseudococcidae (mealybugs) is a large taxonomic group, including a number of agronomic pests. Taxonomic identification of mealybug species is a recurrent problem and represents a major barrier to the establishment of adequate pest management strategies. We combined molecular analysis of three DNA markers (28S-D2, cytochrome oxidase I and internal transcribed spacer 2) with morphological examination, for the identification of 176 specimens collected from 40 mealybug populations infesting various crops and ornamental plants in Egypt and France. This combination of DNA and morphological analyses led to the identification of 17 species: seven in Egypt (Planococcus citri (Risso), Planococcus ficus (Signoret), Maconellicoccus hirsutus (Green), Ferrisia virgata (Cockerell), Phenacoccus solenopsis Tinsley, Phenacoccus parvus Morrison and Saccharicoccus sacchari (Cockerell)) and 11 in France (Planococcus citri, Pseudococcus viburni Signoret, Pseudococcus longispinus (Targioni-Tozzetti), Pseudococcus comstocki (Kuwana), Rhizoecus amorphophalli Betrem, Trionymus bambusae (Green), Balanococcus diminutus (Leonardi), Phenacoccus madeirensis Green, Planococcus vovae (Nasonov), Dysmicoccus brevipes (Cockerell) and Phenacoccus aceris Signoret), Pl. citri being found in both countries. We also found genetic variation between populations considered to belong to the same species, justifying further investigation of the possible occurrence of complexes of cryptic taxa. PMID:22360997

  14. Rapid plant identification using species- and group-specific primers targeting chloroplast DNA.

    Directory of Open Access Journals (Sweden)

    Corinna Wallinger

    Full Text Available Plant identification is challenging when no morphologically assignable parts are available. There is a lack of broadly applicable methods for identifying plants in this situation, for example when roots grow in mixture and for decayed or semi-digested plant material. These difficulties have also impeded the progress made in ecological disciplines such as soil- and trophic ecology. Here, a PCR-based approach is presented which allows identifying a variety of plant taxa commonly occurring in Central European agricultural land. Based on the trnT-F cpDNA region, PCR assays were developed to identify two plant families (Poaceae and Apiaceae, the genera Trifolium and Plantago, and nine plant species: Achillea millefolium, Fagopyrum esculentum, Lolium perenne, Lupinus angustifolius, Phaseolus coccineus, Sinapis alba, Taraxacum officinale, Triticum aestivum, and Zea mays. These assays allowed identification of plants based on size-specific amplicons ranging from 116 bp to 381 bp. Their specificity and sensitivity was consistently high, enabling the detection of small amounts of plant DNA, for example, in decaying plant material and in the intestine or faeces of herbivores. To increase the efficacy of identifying plant species from large number of samples, specific primers were combined in multiplex PCRs, allowing screening for multiple species within a single reaction. The molecular assays outlined here will be applicable manifold, such as for root- and leaf litter identification, botanical trace evidence, and the analysis of herbivory.

  15. [Flower species identification and coverage estimation based on hyperspectral remote sensing data in Hulunbeier grassland].

    Science.gov (United States)

    Gai, Ying-Ying; Fan, Wen-Jie; Xu, Xi-Ru; Yan, Bin-Yan; Wang, Huan-Jiong; Liu, Yuan

    2011-10-01

    Monitoring grassland species and area real-timely and accurately is of great significance in species diversity research, as well as in sustainable development of ecosystem. Flowers have their own unique spectral characteristics. Compared with the nutrient stage, species are more easily identified by florescence. So, florescence is a critical period for identification. In the present paper, spectral differences among such flowers as Galium verum Linn., Hemerocallis citrina Baroni, Serratula centauroides Linn., Clematis hexapetala Pall., Lilium concolor var. pulchellum, Lilium pumilum and Artemisia frigida Willd. Sp. Pl. were found, along with identification methods, by analyzing canopies spectra and parametrizing characteristics. Verification results showed that when the coverage of flowers was greater than 10%, the accuracy of identification methods would be higher than 90%. On this basis, linear unmixing model was adopted to calculate the area of flowers in quadrates. Results showed that linear unmixing model was an effective method for estimating the coverage of flowers in grassland because the accuracy was about 4%. PMID:22250555

  16. Multiplex-PCR for Identification of Two Species in Genus Hishimonus (Hemiptera: Cicadellidae) in Jujube Orchards.

    Science.gov (United States)

    Hao, Shaodong; Wang, He; Tao, Wanqiang; Wang, Jinzhong; Zhang, Zhiyong; Zhang, Qiuling; Zhang, Minzhao; Guo, Li; Shi, Xiaoyu

    2015-10-01

    The insect family Cicadellidae includes economically important vectors of plant pathogens. Hishimonus sellatus (Uhler) transmits jujube witches'-broom (JWB). Currently, H. sellatus and Hishimonus lamellatus Cai et Kuoh are observed to co-occur at the same locality on jujube. H. lamellatus is now suspected to be a JWB vector. As such, correct identification of Hishimonus species present in vineyards is essential for epidemiological surveys. However, traditional identification of Hishimonus by morphology is limited to the adult male. We provide a comprehensive description of morphological and molecular tools for discriminating between H. sellatus and H. lamellatus, for use in identification and monitoring of the two Hishimonus species and studies of their plant hosts. A rapid and inexpensive method is introduced to identify H. sellatus and H. lamellatus occurring in jujube orchards. This method is based on amplification of mitochondrial cytochrome oxidase I (COI) gene, using PCR with multiplexed, species-specific primers. The reliability of this new method has been tested on different populations from different sites in Beijing region of China. PMID:26453733

  17. What Makes a Bacterial Species Pathogenic?:Comparative Genomic Analysis of the Genus Leptospira

    OpenAIRE

    Fouts, Derrick E.; Matthias, Michael A.; Adhikarla, Haritha; Adler, Ben; Amorim-Santos, Luciane; Berg, Douglas E.; Bulach, Dieter; Buschiazzo, Alejandro; Chang, Yung-Fu; Galloway, Renee L.; Haake, David A.; Haft, Daniel H.; Hartskeerl, Rudy; Ko, Albert I.; Levett, Paul N

    2016-01-01

    Leptospirosis, caused by spirochetes of the genus Leptospira, is a globally widespread, neglected and emerging zoonotic disease. While whole genome analysis of individual pathogenic, intermediately pathogenic and saprophytic Leptospira species has been reported, comprehensive cross-species genomic comparison of all known species of infectious and non-infectious Leptospira, with the goal of identifying genes related to pathogenesis and mammalian host adaptation, remains a key gap in the field....

  18. Rice bacterial endophytes: isolation of a collection, identification of beneficial strains and microbiome analysis.

    Science.gov (United States)

    Bertani, Iris; Abbruscato, Pamela; Piffanelli, Pietro; Subramoni, Sujatha; Venturi, Vittorio

    2016-06-01

    Endophytes are harmless or beneficial microorganisms that live inside plants between cells. The relationship they develop with the plant as well as their potential role in plant health is at large unexplored and it is believed that the opportunity to find new and interesting endophytes among the large variety of plants is great. Here, we present the isolation and analysis of a large collection of endophytes from one cultivar of rice grown in Italy. A total 1318 putative endophytes were isolated from roots, leaves and stems from rice grown in submerged and dry conditions and a working collection of 229 isolates was created. Among these, several isolates were confirmed to be endophytes and a few displayed the trait of plant growth promotion. A cultivation independent analysis via 16S rDNA amplicons of the bacterial community of the endosphere was also performed providing information on bacterial diversity in the rice endopshere. PMID:27038229

  19. In vitro inhibitory potentials of crude plant extracts on multidrug resistant bacterial species from infected human wounds

    Directory of Open Access Journals (Sweden)

    Yetunde A Ekanola

    2013-01-01

    Full Text Available Background: Scientific data on usage of plants to promote wound healing is exclusively scare in Nigeria. AIM: The aim of this study was to determine in vitro inhibitory potentials of crude extracts of garlic (Allium sativum and ginger (Zingiber officinale on multiple antibiotic resistant bacteria isolated from deep and superficial human wounds. Materials and Methods: Using agar disc- and modified agar well-diffusion methods, 87 wound-borne bacterial strains, Staphylococcus aureus, Proteus mirabilis and Pseudomonas aeruginosa were screened for in vitro susceptibility to 15 commonly-available antibiotic discs, 18 antibiotic drugs and three plant extracts. Results: Staph. aureus strains exhibited 52.5-97.4% resistance to antibiotic (discs, with multiple antibiotic resistance (MAR of 25.0 -100%. Between 39.1 and 95.7% of Proteus mirabilis strains resisted the antibiotics (discs, while MAR was 37.5-100%. Resistance rates displayed by Ps. aeruginosa strains were 61.5-100% with MAR of 50.0-100%. Overall antibiotic resistance patterns of respective bacterial species recorded for the antibiotic drugs were Staph. aureus (11.1-83.3%, Pr. mirabilis (16.7-77.8% and Ps. aeruginosa (16.7-50.0% and the most-resisted antibiotic drugs were axacef (55.3-82.6%, septrin (84.2-92.3%, primpex (78.3-84.6%, mediphenicol (63.2-73.1% and augmentin 1 (43.2-76.9%. All the multidrug resistant wound-borne bacterial strains exhibited minimal to moderate susceptibility towards crude extracts of garlic (17.4-34.6% and ginger (57.7-60.8%. Conclusion: Human wound-borne bacterial strains, which were multi-resistant to commonly available antibiotics (discs/drugs were minimally or moderately susceptible to crude extracts of garlic (Allium sativum and ginger (Zingiber officinale, which can be of clinical importance as herbal therapy in wound dressings or other forms of wound treatments.

  20. Fluorescent Amplified Fragment Length Polymorphism Probabilistic Database for Identification of Bacterial Isolates from Urinary Tract Infections

    OpenAIRE

    Kassama, Yankuba; Rooney, Paul J.; Goodacre, Royston

    2002-01-01

    The ability of the fluorescent amplified fragment length polymorphism (FAFLP) technique to identify bacterial isolates from urinary tract infections (UTIs) was investigated. FAFLP was carried out using the single primer combination MseI plus CT and EcoRI plus 0, and information-rich FAFLP profiles were generated from all 69 UTI isolates studied, which comprised both gram-negative and gram-positive bacteria encompassing eight genera. The genetic relatedness of these 69 bacteria was determined ...

  1. Isolation and identification of bacterial causes of clinical mastitis in cattle in Sulaimania region

    OpenAIRE

    S. A. Hussein

    2008-01-01

    A total of 51 cases of bovine clinical mastitis in Sulaimani district were investigated for their bacteriological causative agents; 76 milk samples were cultured on primary and selective media and the isolated bacteria were tested for their susceptibility to antimicrobial agents used in commercial intramammary infusion products. Eighty two bacterial isolates were obtained and further identified using biochemical tests. Escherichia coli was the most common bacteria followed by Staphylococcus a...

  2. BACTERIAL MICROORGANISMS ASSOCIATED WITH THE PLANT TISSUE CULTURE: IDENTIFICATION AND POSSIBLE ROLE (review)

    OpenAIRE

    S.E. DUNAEVA; Yu, S.

    2015-01-01

    Effective sterilization of plant explants and antiseptics rules compliance do not exclude the presence of so-called covert (endophytic) bacteria in in vitro cultures. But the role of these bacteria in tissues cultures has been not enough studied whereas it was related to the explants regeneration capacity and the possibility of animal and human cells transformation under in vitro cultivation. Bacterial strains pathogenic to humans can be stably maintained in cultivated tissues and ex vitro pl...

  3. Forensic timber identification: a case study of a CITES listed species, Gonystylus bancanus (Thymelaeaceae).

    Science.gov (United States)

    Ng, Kevin Kit Siong; Lee, Soon Leong; Tnah, Lee Hong; Nurul-Farhanah, Zakaria; Ng, Chin Hong; Lee, Chai Ting; Tani, Naoki; Diway, Bibian; Lai, Pei Sing; Khoo, Eyen

    2016-07-01

    Illegal logging and smuggling of Gonystylus bancanus (Thymelaeaceae) poses a serious threat to this fragile valuable peat swamp timber species. Using G. bancanus as a case study, DNA markers were used to develop identification databases at the species, population and individual level. The species level database for Gonystylus comprised of an rDNA (ITS2) and two cpDNA (trnH-psbA and trnL) markers based on a 20 Gonystylus species database. When concatenated, taxonomic species recognition was achieved with a resolution of 90% (18 out of the 20 species). In addition, based on 17 natural populations of G. bancanus throughout West (Peninsular Malaysia) and East (Sabah and Sarawak) Malaysia, population and individual identification databases were developed using cpDNA and STR markers respectively. A haplotype distribution map for Malaysia was generated using six cpDNA markers, resulting in 12 unique multilocus haplotypes, from 24 informative intraspecific variable sites. These unique haplotypes suggest a clear genetic structuring of West and East regions. A simulation procedure based on the composition of the samples was used to test whether a suspected sample conformed to a given regional origin. Overall, the observed type I and II errors of the databases showed good concordance with the predicted 5% threshold which indicates that the databases were useful in revealing provenance and establishing conformity of samples from West and East Malaysia. Sixteen STRs were used to develop the DNA profiling databases for individual identification. Bayesian clustering analyses divided the 17 populations into two main genetic clusters, corresponding to the regions of West and East Malaysia. Population substructuring (K=2) was observed within each region. After removal of bias resulting from sampling effects and population subdivision, conservativeness tests showed that the West and East Malaysia databases were conservative. This suggests that both databases can be used independently

  4. Identification and characterization of humic substances-degrading bacterial isolates from an estuarine environment.

    Science.gov (United States)

    Esham; Ye; Moran

    2000-12-01

    Bacterial isolates were obtained from enrichment cultures containing humic substances extracted from estuarine water using an XAD-8 resin. Eighteen isolates were chosen for phylogenetic and physiological characterization based on numerical importance in serial dilutions of the enrichment culture and unique colony morphology. Partial sequences of the 16S rRNA genes indicated that six of the isolates were associated with the alpha subclass of Proteobacteria, three with the gamma-Proteobacteria, and nine with the Gram-positive bacteria. Ten isolates degraded at least one (and up to six) selected aromatic single-ring compounds. Six isolates showed ability to degrade [(14)C]humic substances derived from the dominant salt marsh grass in the estuary from which they were isolated (Spartina alterniflora), mineralizing 0.4-1.1% of the humic substances over 4 weeks. A mixture of all 18 isolates did not degrade humic substances significantly faster than any of the individual strains, however, and no isolate degraded humic substances to the same extent as the natural marine bacterial community (3.0%). Similar studies with a radiolabeled synthetic lignin ([beta-(14)C]dehydropolymerisate) showed measurable levels of degradation by all 18 bacteria (3.0-8.8% in 4 weeks), but mineralization levels were again lower than that observed for the natural marine bacterial community (28.2%). Metabolic capabilities of the 18 isolates were highly variable and generally did not map to phylogenetic affiliation. PMID:11102687

  5. DNA-based Simultaneous Identification of Three Terminalia Species Targeting Adulteration

    Science.gov (United States)

    Sharma, Sonal; Shrivastava, Neeta

    2016-01-01

    Background: Various parts of three Terminalia species, namely, Terminalia arjuna (stem bark), Terminalia bellirica (fruit), and Terminalia chebula (fruit) are widely known for their therapeutic principles and other commercial values. However, stem bark of T. bellirica and T. chebula along with Terminalia tomentosa are reported as adulterants of T. arjuna. Correct botanical identification is very critical for safe and effective herbal drugs. DNA-based identification approaches are advancing the conventional methods and sometime proved more beneficial. Objective: The purpose of the study was to develop polymerase chain reaction (PCR) method using internal transcribed spacer (ITS) region to ascertain the identity of T. arjuna herbal material as well as detection of mixing of other three Terminalia species. Materials and Methods: DNA from stem barks samples were isolated and subjected to ITS region amplification and sequencing. Sequences were compared for polymorphic nucleotides determination to develop species-specific primers. Final primers were selected on the basis of in silico analysis and experimentally validated. PCR assays for botanical identification of Terminalia species were developed. Sensitivity testing and assay validation were also performed. Results: The PCR assays developed for Terminalia species were resulted in definite amplicons of the corresponding species. No cross-reactivity of the primers was detected. Sensitivity was found enough to amplify as low as 2 ng of DNA. Mixing of DNA in various concentrations for validation also proved the sensitivity of assay to detect original botanicals in the mixture. The developed methods proved very specific and sensitive to authenticate Arjuna bark to develop evidence-based herbal medicines. SUMMARY Internal transcribed spacer-based species-specific polymerase chain reaction.(PCR) assays were developed to authenticate Terminalia arjuna stem bark and to identify substitution/adulteration of Terminalia bellirica

  6. Christensenella timonensis, a new bacterial species isolated from the human gut.

    Science.gov (United States)

    Ndongo, S; Dubourg, G; Khelaifia, S; Fournier, P-E; Raoult, D

    2016-09-01

    We propose a new species, Christensenella timonensis, strain Marseille-P2437(T) (CSUR P2437(T)), which was isolated from gut microbiota of a 66-year-old patient as a part of culturomics study. C. timonensis represents the second species isolated within the Christensenella genus. PMID:27408737

  7. Species identification of enterococci by biochemical test and molecular-genetic methods

    Directory of Open Access Journals (Sweden)

    Monika Lavová

    2014-02-01

    Full Text Available The aim of this study was comparison different methods of species identification of enterococci. One hundred and fifty three suspected colonies were isolated from milk and dairy products (cheeses from cow´s, ewe´s and goat´s milk. On the bases of their growth on BEA agar, microscopic characteristic, results of Gram staining, catalase test and PYRAtest was thirty four isolates assigned to the genus Enterococcus. These isolates were identified by commercial biochemical test EN-COCCUS. 52.9% of them were included in species E. faecalis, 29.4% in E. faecium, 14.7% in E. durans and 2.9% in E. group III. This group includes 3 species: E. durans, E. hirae, E. faecalis asaccharolytic var. Then 16S rRNA sequencing nucleotide of all isolates was realized. Results of sequencing were compared with NCBI database. Only 14.7% of isolates were in 100% accordance. One from them was species E. durans and others were designated as E. faecium. For 20.6% of detected isolates was in accordance with more reference strains. Other isolates were identical with reference strain on 99%. For verification of all results species-specific PCR was used and 52.9% isolates were identified as species E. faecalis, 32.4% as E. faecium and 14.7% as E. durans. Strains belonging to the species E. faecalis were identified the most reliable by all used methods.

  8. A tool for real-time acoustic species identification of delphinid whistles.

    Science.gov (United States)

    Oswald, Julie N; Rankin, Shannon; Barlow, Jay; Lammers, Marc O

    2007-07-01

    The ability to identify delphinid vocalizations to species in real-time would be an asset during shipboard surveys. An automated system, Real-time Odontocete Call Classification Algorithm (ROCCA), is being developed to allow real-time acoustic species identification in the field. This Matlab-based tool automatically extracts ten variables (beginning, end, minimum and maximum frequencies, duration, slope of the beginning and end sweep, number of inflection points, number of steps, and presence/absence of harmonics) from whistles selected from a real-time scrolling spectrograph (ISHMAEL). It uses classification and regression tree analysis (CART) and discriminant function analysis (DFA) to identify whistles to species. Schools are classified based on running tallies of individual whistle classifications. Overall, 46% of schools were correctly classified for seven species and one genus (Tursiops truncatus, Stenella attenuata, S. longirostris, S. coeruleoalba, Steno bredanensis, Delphinus species, Pseudorca crassidens, and Globicephala macrorhynchus), with correct classification as high as 80% for some species. If classification success can be increased, this tool will provide a method for identifying schools that are difficult to approach and observe, will allow species distribution data to be collected when visual efforts are compromised, and will reduce the time necessary for post-cruise data analysis. PMID:17614515

  9. DNA Barcoding and Microsatellites Help Species Delimitation and Hybrid Identification in Endangered Galaxiid Fishes

    Science.gov (United States)

    Vanhaecke, Delphine; Garcia de Leaniz, Carlos; Gajardo, Gonzalo; Young, Kyle; Sanzana, Jose; Orellana, Gabriel; Fowler, Daniel; Howes, Paul; Monzon-Arguello, Catalina; Consuegra, Sofia

    2012-01-01

    The conservation of data deficient species is often hampered by inaccurate species delimitation. The galaxiid fishes Aplochiton zebra and Aplochiton taeniatus are endemic to Patagonia (and for A. zebra the Falkland Islands), where they are threatened by invasive salmonids. Conservation of Aplochiton is complicated because species identification is hampered by the presence of resident as well as migratory ecotypes that may confound morphological discrimination. We used DNA barcoding (COI, cytochrome b) and a new developed set of microsatellite markers to investigate the relationships between A. zebra and A. taeniatus and to assess their distributions and relative abundances in Chilean Patagonia and the Falkland Islands. Results from both DNA markers were 100% congruent and revealed that phenotypic misidentification was widespread, size-dependent, and highly asymmetric. While all the genetically classified A. zebra were correctly identified as such, 74% of A. taeniatus were incorrectly identified as A. zebra, the former species being more widespread than previously thought. Our results reveal, for the first time, the presence in sympatry of both species, not only in Chilean Patagonia, but also in the Falkland Islands, where A. taeniatus had not been previously described. We also found evidence of asymmetric hybridisation between female A. taeniatus and male A. zebra in areas where invasive salmonids have become widespread. Given the potential consequences that species misidentification and hybridisation can have for the conservation of these endangered species, we advocate the use of molecular markers in order to reduce epistemic uncertainty. PMID:22412956

  10. DNA barcoding and microsatellites help species delimitation and hybrid identification in endangered galaxiid fishes.

    Directory of Open Access Journals (Sweden)

    Delphine Vanhaecke

    Full Text Available The conservation of data deficient species is often hampered by inaccurate species delimitation. The galaxiid fishes Aplochiton zebra and Aplochiton taeniatus are endemic to Patagonia (and for A. zebra the Falkland Islands, where they are threatened by invasive salmonids. Conservation of Aplochiton is complicated because species identification is hampered by the presence of resident as well as migratory ecotypes that may confound morphological discrimination. We used DNA barcoding (COI, cytochrome b and a new developed set of microsatellite markers to investigate the relationships between A. zebra and A. taeniatus and to assess their distributions and relative abundances in Chilean Patagonia and the Falkland Islands. Results from both DNA markers were 100% congruent and revealed that phenotypic misidentification was widespread, size-dependent, and highly asymmetric. While all the genetically classified A. zebra were correctly identified as such, 74% of A. taeniatus were incorrectly identified as A. zebra, the former species being more widespread than previously thought. Our results reveal, for the first time, the presence in sympatry of both species, not only in Chilean Patagonia, but also in the Falkland Islands, where A. taeniatus had not been previously described. We also found evidence of asymmetric hybridisation between female A. taeniatus and male A. zebra in areas where invasive salmonids have become widespread. Given the potential consequences that species misidentification and hybridisation can have for the conservation of these endangered species, we advocate the use of molecular markers in order to reduce epistemic uncertainty.

  11. A multiphasic approach for the identification of endophytic bacterial in strawberry fruit and their potential for plant growth promotion.

    Science.gov (United States)

    de Melo Pereira, Gilberto Vinícius; Magalhães, Karina Teixeira; Lorenzetii, Emi Rainildes; Souza, Thiago Pereira; Schwan, Rosane Freitas

    2012-02-01

    This study used a multiphasic approach, characterized by the simultaneous use of culture-dependent and culture-independent methods, to investigate endophytic bacterial communities in strawberry (Fragaria ananassa) fruit. A total of 92 bacterial endophytes were isolated and initially grouped by their repetitive extragenic palindromic (rep)-PCR banding pattern and biochemical features. Phylogenetic analysis of the 16S rRNA gene sequences of 45 representatives showed that the isolates belonged to the species Bacillus subtilis (eight isolates), Bacillus sp. (seven isolates), Enterobacter sp. (seven isolates), Enterobacter ludwigii (six isolates), Lactobacillus plantarum (six isolates), Pseudomonas sp. (five isolates), Pantoea punctata (three isolates), and Curtobacterium citreum (three isolates). Nucleic acids were extracted from the strawberry fruit and subjected to 16S rRNA gene directed polymerase chain reaction denaturing gradient gel electrophoresis (16S rRNA PCR-DGGE). The species B. subtilis, Enterobacter sp., and Pseudomonas sp. were detected both by isolation and DGGE. The DGGE fingerprints of total bacterial DNA did not exhibit bands corresponding to several of the representative species isolated in the extinction dilution (L. plantarum, C. citreum, and P. punctata). In contrast, bands in the DGGE profile that were identified as relatives of Arthrobacter sp. and one uncultivable Erythrobacter sp. were not recovered by cultivation techniques. After isolation, the nitrogen fixation ability and the in vitro production of indole-3-acetic acid (IAA) equivalents and siderophores were evaluated. A high percentage of isolates were found to possess the ability to produce siderophores and IAA equivalents; however, only a few isolates belonging to the genera Pseudomonas and Enterobacter showed the ability to fix nitrogen. Plant growth promotion was evaluated under greenhouse conditions and revealed the ability of the Bacillus strains to enhance the number of leaves

  12. Identification of four squid species by quantitative real-time polymerase chain reaction.

    Science.gov (United States)

    Ye, Jian; Feng, Junli; Liu, Shasha; Zhang, Yanping; Jiang, Xiaona; Dai, Zhiyuan

    2016-02-01

    Squids are distributed worldwide, including many species of commercial importance, and they are often made into varieties of flavor foods. The rapid identification methods for squid species especially their processed products, however, have not been well developed. In this study, quantitative real-time PCR (qPCR) systems based on specific primers and TaqMan probes have been established for rapid and accurate identification of four common squid species (Ommastrephes bartramii, Dosidicus gigas, Illex argentinus, Todarodes pacificus) in Chinese domestic market. After analyzing mitochondrial genes reported in GenBank, the mitochondrial cytochrome b (Cytb) gene was selected for O. bartramii detection, cytochrome c oxidase subunit I (COI) gene for D. gigas and T. Pacificus detection, ATPase subunit 6 (ATPase 6) gene for I. Argentinus detection, and 12S ribosomal RNA (12S rDNA) gene for designing Ommastrephidae-specific primers and probe. As a result, all the TaqMan systems are of good performance, and efficiency of each reaction was calculated by making standard curves. This method could detect target species either in single or mixed squid specimen, and it was applied to identify 12 squid processed products successfully. Thus, it would play an important role in fulfilling labeling regulations and squid fishery control. PMID:26772407

  13. Computational identification of 18 micrornas and their targets in three species of rose

    International Nuclear Information System (INIS)

    MicroRNAs (miRNAs) are non-protein coding, small endogenous RNAs. Their length ranges from 18-26 nucleotides (nt). The miRNAs convergence property becomes a rational approach for the hunt of novel miRNAs in other organisms by homology search. As presently very little miRNAs are reported for rose species, so this study deals with the identification of miRNAs in different species of rose. Consequently 18 miRNA belonging to 17 miRNA families were identified in 3 species of rose (Rosa hybrid, Rosa chinensis and Rosa virginiana). All of the identified miRNA families (miR156, 160, 164, 166, 398, 482, 831, 837, 838, 841, 847, 3436, 3627, 6135, 6285, 6287 and 6288) are being reported for the first time in rose. Precursors of the identified miRNAs form stable minimum free energy (MFE) stem-loop structures and the mature miRNAs are found in the stem portions of their corresponding precursors. 11 putative targets of the miRNAs have also been identified. The identified targets are various proteins including transcription factors. Identification of 18 miRNAs will be supportive to explore the gene regulation phenomenon in various species of roses and it will be a good contribution for understanding the post transcriptional gene regulation in various stages of the life cycles of roses. (author)

  14. Morphological and molecular identification of species of the Obsoletus group (Diptera: Ceratopogonidae) in Scandinavia

    DEFF Research Database (Denmark)

    Nielsen, Søren Achim; Kristensen, Michael

    2011-01-01

    After the introduction of bluetongue in northern Europe in 2006, populations of Culicoides have been monitored in many European countries. Large quantities of Culicoides specimens shall be determined to species, and it is thus important to find reliable morphological characters that are visualized...... the females of the four species by morphological characters has frequently been questioned, and in many cases, female specimens are grouped as an entity in veterinary and ecological studies. We show how it is possible using a stereomicroscope to separate the females of the four species by combining...... the shape of the third segment of the maxillary palp and the number and location of hairs on the first abdominal tergit. Validation of the quick stereomicroscope identification method was achieved by morphometric measurements and a molecular marker. In all cases, both methods verified the quick...

  15. Identification of the Species of Origin for Meat Products by Rapid Evaporative Ionization Mass Spectrometry.

    Science.gov (United States)

    Balog, Julia; Perenyi, Dora; Guallar-Hoyas, Cristina; Egri, Attila; Pringle, Steven D; Stead, Sara; Chevallier, Olivier P; Elliott, Chris T; Takats, Zoltan

    2016-06-15

    Increasingly abundant food fraud cases have brought food authenticity and safety into major focus. This study presents a fast and effective way to identify meat products using rapid evaporative ionization mass spectrometry (REIMS). The experimental setup was demonstrated to be able to record a mass spectrometric profile of meat specimens in a time frame of <5 s. A multivariate statistical algorithm was developed and successfully tested for the identification of animal tissue with different anatomical origin, breed, and species with 100% accuracy at species and 97% accuracy at breed level. Detection of the presence of meat originating from a different species (horse, cattle, and venison) has also been demonstrated with high accuracy using mixed patties with a 5% detection limit. REIMS technology was found to be a promising tool in food safety applications providing a reliable and simple method for the rapid characterization of food products. PMID:27167240

  16. RT-PCR–DGGE Analysis to Elucidate the Dominant Bacterial Species of Industrial Spanish-Style Green Table Olive Fermentations

    Science.gov (United States)

    Benítez-Cabello, Antonio; Bautista-Gallego, Joaquín; Garrido-Fernández, Antonio; Rantsiou, Kalliopi; Cocolin, Luca; Jiménez-Díaz, Rufino; Arroyo-López, Francisco N.

    2016-01-01

    This paper describes the dominant bacterial species metabolically active through the industrial production of Spanish-style Manzanilla and Gordal olives. For this purpose, samples (brines and fruits) obtained at 0, 15, and 90 fermentation days were analyzed by a culture-independent approach to determine viable cells by reverse transcription of RNA and further PCR-DGGE analysis, detecting at least 7 different species. Vibrio vulnificus, Lactobacillus plantarum group, and Lactobacillus parafarraginis were present in samples from both cultivars; Lactobacillus sanfranciscensis and Halolactobacillus halophilus were detected only in Gordal samples, while Staphylococcus sp. was exclusively found at the onset of Manzanilla fermentations. Physicochemical data showed a typical fermentation profile while scanning electron microscopy confirmed the in situ biofilm formation on the olive epidermis. Different Bacillus, Staphylococcus, and Enterococcus species, not detected during the fermentation process, were also found in the solid marine salt used by the industry for preparation of brines. Elucidation of these non-lactic acid bacteria species role during fermentation is then an appealingly challenge, particularly regarding safety issues. PMID:27582739

  17. RT-PCR-DGGE Analysis to Elucidate the Dominant Bacterial Species of Industrial Spanish-Style Green Table Olive Fermentations.

    Science.gov (United States)

    Benítez-Cabello, Antonio; Bautista-Gallego, Joaquín; Garrido-Fernández, Antonio; Rantsiou, Kalliopi; Cocolin, Luca; Jiménez-Díaz, Rufino; Arroyo-López, Francisco N

    2016-01-01

    This paper describes the dominant bacterial species metabolically active through the industrial production of Spanish-style Manzanilla and Gordal olives. For this purpose, samples (brines and fruits) obtained at 0, 15, and 90 fermentation days were analyzed by a culture-independent approach to determine viable cells by reverse transcription of RNA and further PCR-DGGE analysis, detecting at least 7 different species. Vibrio vulnificus, Lactobacillus plantarum group, and Lactobacillus parafarraginis were present in samples from both cultivars; Lactobacillus sanfranciscensis and Halolactobacillus halophilus were detected only in Gordal samples, while Staphylococcus sp. was exclusively found at the onset of Manzanilla fermentations. Physicochemical data showed a typical fermentation profile while scanning electron microscopy confirmed the in situ biofilm formation on the olive epidermis. Different Bacillus, Staphylococcus, and Enterococcus species, not detected during the fermentation process, were also found in the solid marine salt used by the industry for preparation of brines. Elucidation of these non-lactic acid bacteria species role during fermentation is then an appealingly challenge, particularly regarding safety issues. PMID:27582739

  18. Clustering of Antimicrobial Resistance Outbreaks Across Bacterial Species in the Intensive Care Unit

    OpenAIRE

    Vlek, AL; Cooper, BS; Kypraios, T.; Cox, A.; Edgeworth, JD; Auguet, OT

    2013-01-01

    BACKGROUND There are frequent reports of intensive care unit (ICU) outbreaks due to transmission of particular antibiotic-resistant bacteria. Less is known about the burden of outbreaks of resistance due to horizontal transfer of mobile genetic elements between species. Moreover, the potential of existing statistical software as a preliminary means for detecting such events has never been assessed. This study uses a software package to determine the burden of species and resistance outbreaks ...

  19. Identification of novel bacterial histidine biosynthesis inhibitors using docking, ensemble rescoring, and whole-cell assays

    DEFF Research Database (Denmark)

    Henriksen, Signe Teuber; Liu, J.; Estiu, G.;

    2010-01-01

    . aureus histidine biosynthesis pathway, which is predicted to be essential for bacterial biomass productions. Virtual screening of a library of similar to 10(6) compounds identified 49 potential inhibitors of three enzymes of this pathway. Eighteen representative compounds were directly tested on three S....... aureus-and two Escherichia coli strains in standard disk inhibition assays. Thirteen compounds are inhibitors of some or all of the S. aureus strains, while 14 compounds weakly inhibit growth in one or both E. coli strains. The high hit rate obtained from a fast virtual screen demonstrates the...

  20. Occlusal pattern of cheek teeth in extant Spermophilus: A new approach to the identification of species.

    Science.gov (United States)

    Popova, Lilia

    2016-06-01

    Discrete characters of the occlusal surface (additional cusps) have been studied to elaborate a new approach to the identification of the Ground Squirrel species Spermophilus odessanus, S. suslicus, S. pygmaeus, S. citellus, and S. xanthoprymnus. Data on the presence/absence of the additional cusps have been represented as star plots and, in addition, have been studied using discriminant function analysis. The species-specific sets of the characters (patterns of bunodonty) have been revealed and are of high diagnostic value. The Citellus-set is defined by the presence of mesostyles and the rareness of the metastylids, paraconules and metaconules, hypostyles and protostyles. The Pygmaeus-set is characterized by the presence of additional cusps in the lower cheek teeth. The Odessanus-oriented set is found in the Spermophilus pygmaeus, S. odessanus, and S. suslicus. The relatively high frequency of additional cusps of the metaloph and the paraloph is characteristic for this set. The Plesiomorphic-set (characters shared by all the studied species and for this reason regarded herein as ancestral) is found in S. xanthoprymnus. The patterns of bunodonty serve as diagnostic criteria only as a whole: the shape of a star plot (relations among the character frequencies), rather than certain character values, is indicative. An optimal level of identification of species is possible based on the combination of the discrete characters mentioned and on the size parameters of the third upper molar. The occlusal sets are intended to remain stable during the time of species existence and seem to correspond to trends in specialization. The functional meaning of the sets can be explained by the dependence between the presence/absence of the discrete characters and the shape of the crown and its main lophs. Each pattern is likely to correspond to a trophic niche, and this niche corresponds to the species. J. Morphol. 277:814-825, 2016. © 2016 Wiley Periodicals, Inc. PMID:27018323

  1. Rapid detection and identification of viral and bacterial fish pathogens using a DNA array‐based multiplex assay

    DEFF Research Database (Denmark)

    Lievens, B.; Frans, I.; Heusdens, C.;

    2011-01-01

    Fish diseases can be caused by a variety of diverse organisms, including bacteria, fungi, viruses and protozoa, and pose a universal threat to the ornamental fish industry and aquaculture. The lack of rapid, accurate and reliable means by which fish pathogens can be detected and identified has been...... one of the main limitations in fish pathogen diagnosis and fish disease management and has consequently stimulated the search for alternative diagnostic techniques. Here, we describe a method based on multiplex and broad‐range PCR amplification combined with DNA array hybridization...... for the simultaneous detection and identification of all cyprinid herpesviruses (CyHV‐1, CyHV‐2 and CyHV‐3) and some of the most important fish pathogenic Flavobacterium species, including F. branchiophilum, F. columnare and F. psychrophilum. For virus identification, the DNA polymerase and helicase genes were...

  2. Clinical Identification of Common Species of Dermatophytes by PCR and PCR-RFLP

    Institute of Scientific and Technical Information of China (English)

    丁娟; 李家文; 刘志香; 谭志建

    2004-01-01

    To find a fast and efficient way of identifying seven common dermatophytes in clinical practice, we used the techniques of polymerase chain reaction (PCR) and PCR-restriction fragment length polymorphism (RFLP) targeting Topoisomerase Ⅱ gene. The DNA of 7 dermatophytes, along with Candida albicans, Aspergillus terreus and Aspergillus flavus were amplified by consensus primer dPsD1. They were then subjected to a second PCR with primers dPsD2 and species-specific primers PsT and PsME separately. 6 of the products generated by dPsD2 were digested with restriction enzyme Hinc Ⅱ. DNA fragments of 3390 bp and 2380 bp was amplified by using consensus primer dPsD1 and dPsD2 from the genomic DNA of each dermatophyte species separately. By combining the results of the two species-specific primer sets (PsT and PsME), all species of dermatophyte yielded unique sizes-set of PCR products expect for T. mentagrophytes and T. tonsurans.From the restriction profiles of Hinc Ⅱ , 6 of the 7 dermatophytoses were diagnosed to species level including T. mentagrophytes and T. tonsurans. By combining the results of the PCR and PCRRFLP, the 7 common dermatophytes can be identified to species level. It is conclude that the multiplex PCR and PCR-RFLP identification targeting the DNA topoisomerase Ⅱ gene is rapid and efficient.

  3. Assessing DNA barcoding as a tool for species identification and data quality control.

    Directory of Open Access Journals (Sweden)

    Yong-Yi Shen

    Full Text Available In recent years, the number of sequences of diverse species submitted to GenBank has grown explosively and not infrequently the data contain errors. This problem is extensively recognized but not for invalid or incorrectly identified species, sample mixed-up, and contamination. DNA barcoding is a powerful tool for identifying and confirming species and one very important application involves forensics. In this study, we use DNA barcoding to detect erroneous sequences in GenBank by evaluating deep intraspecific and shallow interspecific divergences to discover possible taxonomic problems and other sources of error. We use the mitochondrial DNA gene encoding cytochrome b (Cytb from turtles to test the utility of barcoding for pinpointing potential errors. This gene is widely used in phylogenetic studies of the speciose group. Intraspecific variation is usually less than 2.0% and in most cases it is less than 1.0%. In comparison, most species differ by more than 10.0% in our dataset. Overlapping intra- and interspecific percentages of variation mainly involve problematic identifications of species and outdated taxonomies. Further, we detect identical problems in Cytb from Insectivora and Chiroptera. Upon applying this strategy to 47,524 mammalian CoxI sequences, we resolve a suite of potentially problematic sequences. Our study reveals that erroneous sequences are not rare in GenBank and that the DNA barcoding can serve to confirm sequencing accuracy and discover problems such as misidentified species, inaccurate taxonomies, contamination, and potential errors in sequencing.

  4. Species identification of small pelagic fish schools by means of hydroacoustics in the Eastern Mediterranean Sea

    Directory of Open Access Journals (Sweden)

    K. TSAGARAKIS

    2015-01-01

    Full Text Available   Reliable biomass estimates by means of hydroacoustics largely depend on the correct identification of acoustic targets. Data collected during five summer acoustic surveys (2004-2008 in the North Aegean Sea (Greece were analyzed to explore effective discrimination of small pelagic fish schools according to the species they belong. Discriminant Function Analyses (DFA using bathymetric, energetic and morphometric school descriptors as explanatory variables were applied per research cruise as well as to pooled data from all surveys. Results revealed that the schools can be successfully classified into the five species considered (anchovy Engraulis encrasicolus, sardine Sardina pilchardus, round sardinella Sardinella aurita, blue whiting Micromessistius poutassou, and Atlantic mackerel Scomber scombrus. The percentage of correct classifications in terms of number of schools was higher in the analyses of the annual cruises (75.6%-95.36% than in the analysis of pooled data (≈72%. This is because of (i the lower number of species, as well as (ii the reduced intraspecific variability, occurring in each separate cruise. Significant differences were detected among school descriptors for the different species, revealing discrete aspects of schooling behaviour for each species. The benefit of the specific approach is that the classification functions of the DFAs can be used to classify a larger set of schools, which has not been possible to assign to specific species. Overall the approach constitutes an objective, more automated and less time consuming procedure for the analysis of acoustic data and can contribute to the improvement of biomass estimates in the area.

  5. The effect of recording and analysis bandwidth on acoustic identification of delphinid species

    Science.gov (United States)

    Oswald, Julie N.; Rankin, Shannon; Barlow, Jay

    2004-11-01

    Because many cetacean species produce characteristic calls that propagate well under water, acoustic techniques can be used to detect and identify them. The ability to identify cetaceans to species using acoustic methods varies and may be affected by recording and analysis bandwidth. To examine the effect of bandwidth on species identification, whistles were recorded from four delphinid species (Delphinus delphis, Stenella attenuata, S. coeruleoalba, and S. longirostris) in the eastern tropical Pacific ocean. Four spectrograms, each with a different upper frequency limit (20, 24, 30, and 40 kHz), were created for each whistle (n=484). Eight variables (beginning, ending, minimum, and maximum frequency; duration; number of inflection points; number of steps; and presence/absence of harmonics) were measured from the fundamental frequency of each whistle. The whistle repertoires of all four species contained fundamental frequencies extending above 20 kHz. Overall correct classification using discriminant function analysis ranged from 30% for the 20-kHz upper frequency limit data to 37% for the 40-kHz upper frequency limit data. For the four species included in this study, an upper bandwidth limit of at least 24 kHz is required for an accurate representation of fundamental whistle contours..

  6. Assessing DNA Barcodes for Species Identification in North American Reptiles and Amphibians in Natural History Collections

    Science.gov (United States)

    Chambers, E. Anne; Hebert, Paul D. N.

    2016-01-01

    Background High rates of species discovery and loss have led to the urgent need for more rapid assessment of species diversity in the herpetofauna. DNA barcoding allows for the preliminary identification of species based on sequence divergence. Prior DNA barcoding work on reptiles and amphibians has revealed higher biodiversity counts than previously estimated due to cases of cryptic and undiscovered species. Past studies have provided DNA barcodes for just 14% of the North American herpetofauna, revealing the need for expanded coverage. Methodology/Principal Findings This study extends the DNA barcode reference library for North American herpetofauna, assesses the utility of this approach in aiding species delimitation, and examines the correspondence between current species boundaries and sequence clusters designated by the BIN system. Sequences were obtained from 730 specimens, representing 274 species (43%) from the North American herpetofauna. Mean intraspecific divergences were 1% and 3%, while average congeneric sequence divergences were 16% and 14% in amphibians and reptiles, respectively. BIN assignments corresponded with current species boundaries in 79% of amphibians, 100% of turtles, and 60% of squamates. Deep divergences (>2%) were noted in 35% of squamate and 16% of amphibian species, and low divergences (<2%) occurred in 12% of reptiles and 23% of amphibians, patterns reflected in BIN assignments. Sequence recovery declined with specimen age, and variation in recovery success was noted among collections. Within collections, barcodes effectively flagged seven mislabeled tissues, and barcode fragments were recovered from five formalin-fixed specimens. Conclusions/Significance This study demonstrates that DNA barcodes can effectively flag errors in museum collections, while BIN splits and merges reveal taxa belonging to deeply diverged or hybridizing lineages. This study is the first effort to compile a reference library of DNA barcodes for herpetofauna

  7. Identification of the Bacterial Microflora in Dairy Products by Temporal Temperature Gradient Gel Electrophoresis

    OpenAIRE

    Ogier, Jean-Claude; Son, Olivier; Gruss, Alexandra; Tailliez, Patrick; Delacroix-Buchet, Agnes

    2002-01-01

    Numerous microorganisms, including bacteria, yeasts, and molds, are present in cheeses, forming a complex ecosystem. Among these organisms, bacteria are responsible for most of the physicochemical and aromatic transformations that are intrinsic to the cheesemaking process. Identification of the bacteria that constitute the cheese ecosystem is essential for understanding their individual contributions to cheese production. We used temporal temperature gradient gel electrophoresis (TTGE) to ide...

  8. Rapid Bacterial Identification, Resistance, Virulence and Type Profiling using Selected Reaction Monitoring Mass Spectrometry

    OpenAIRE

    Yannick Charretier; Olivier Dauwalder; Christine Franceschi; Elodie Degout-Charmette; Gilles Zambardi; Tiphaine Cecchini; Chloe Bardet; Xavier Lacoux; Philippe Dufour; Laurent Veron; Hervé Rostaing; Veronique Lanet; Tanguy Fortin; Corinne Beaulieu; Nadine Perrot

    2015-01-01

    Mass spectrometry (MS) in Selected Reaction Monitoring (SRM) mode is proposed for in-depth characterisation of microorganisms in a multiplexed analysis. Within 60–80 minutes, the SRM method performs microbial identification (I), antibiotic-resistance detection (R), virulence assessment (V) and it provides epidemiological typing information (T). This SRM application is illustrated by the analysis of the human pathogen Staphylococcus aureus, demonstrating its promise for rapid characterisation ...

  9. Identification of Bacterial Cell Wall Lyases via Pseudo Amino Acid Composition.

    Science.gov (United States)

    Chen, Xin-Xin; Tang, Hua; Li, Wen-Chao; Wu, Hao; Chen, Wei; Ding, Hui; Lin, Hao

    2016-01-01

    Owing to the abuse of antibiotics, drug resistance of pathogenic bacteria becomes more and more serious. Therefore, it is interesting to develop a more reasonable way to solve this issue. Because they can destroy the bacterial cell structure and then kill the infectious bacterium, the bacterial cell wall lyases are suitable candidates of antibacteria sources. Thus, it is urgent to develop an accurate and efficient computational method to predict the lyases. Based on the consideration, in this paper, a set of objective and rigorous data was collected by searching through the Universal Protein Resource (the UniProt database), whereafter a feature selection technique based on the analysis of variance (ANOVA) was used to acquire optimal feature subset. Finally, the support vector machine (SVM) was used to perform prediction. The jackknife cross-validated results showed that the optimal average accuracy of 84.82% was achieved with the sensitivity of 76.47% and the specificity of 93.16%. For the convenience of other scholars, we built a free online server called Lypred. We believe that Lypred will become a practical tool for the research of cell wall lyases and development of antimicrobial agents. PMID:27437396

  10. OpWise: Operons aid the identification of differentially expressedgenes in bacterial microarray experiments

    Energy Technology Data Exchange (ETDEWEB)

    Price, Morgan N.; Arkin, Adam P.; Alm, Eric J.

    2005-11-23

    Differentially expressed genes are typically identified by analyzing the variation between replicate measurements. These procedures implicitly assume that there are no systematic errors in the data even though several sources of systematic error are known. Results-OpWise estimates the amount of systematic error in bacterial microarray data by assuming that genes in the same operon have matching expression patterns. OpWise then performs a Bayesian analysis of a linear model to estimate significance. In simulations, OpWise corrects for systematic error and is robust to deviations from its assumptions. In several bacterial data sets, significant amounts of systematic error are present, and replicate-based approaches overstate the confidence of the changers dramatically, while OpWise does not. Finally, OpWise can identify additional changers by assigning genes higher confidence if they are consistent with other genes in the same operon. Although microarray data can contain large amounts of systematic error, operons provide an external standard and allow for reasonable estimates of significance. OpWise is available at http://microbesonline.org/OpWise.

  11. OpWise: Operons aid the identification of differentially expressed genes in bacterial microarray experiments

    Directory of Open Access Journals (Sweden)

    Arkin Adam P

    2006-01-01

    Full Text Available Abstract Background Differentially expressed genes are typically identified by analyzing the variation between replicate measurements. These procedures implicitly assume that there are no systematic errors in the data even though several sources of systematic error are known. Results OpWise estimates the amount of systematic error in bacterial microarray data by assuming that genes in the same operon have matching expression patterns. OpWise then performs a Bayesian analysis of a linear model to estimate significance. In simulations, OpWise corrects for systematic error and is robust to deviations from its assumptions. In several bacterial data sets, significant amounts of systematic error are present, and replicate-based approaches overstate the confidence of the changers dramatically, while OpWise does not. Finally, OpWise can identify additional changers by assigning genes higher confidence if they are consistent with other genes in the same operon. Conclusion Although microarray data can contain large amounts of systematic error, operons provide an external standard and allow for reasonable estimates of significance. OpWise is available at http://microbesonline.org/OpWise.

  12. Identification of Bacterial Cell Wall Lyases via Pseudo Amino Acid Composition

    Science.gov (United States)

    Tang, Hua; Li, Wen-Chao; Wu, Hao; Ding, Hui

    2016-01-01

    Owing to the abuse of antibiotics, drug resistance of pathogenic bacteria becomes more and more serious. Therefore, it is interesting to develop a more reasonable way to solve this issue. Because they can destroy the bacterial cell structure and then kill the infectious bacterium, the bacterial cell wall lyases are suitable candidates of antibacteria sources. Thus, it is urgent to develop an accurate and efficient computational method to predict the lyases. Based on the consideration, in this paper, a set of objective and rigorous data was collected by searching through the Universal Protein Resource (the UniProt database), whereafter a feature selection technique based on the analysis of variance (ANOVA) was used to acquire optimal feature subset. Finally, the support vector machine (SVM) was used to perform prediction. The jackknife cross-validated results showed that the optimal average accuracy of 84.82% was achieved with the sensitivity of 76.47% and the specificity of 93.16%. For the convenience of other scholars, we built a free online server called Lypred. We believe that Lypred will become a practical tool for the research of cell wall lyases and development of antimicrobial agents. PMID:27437396

  13. Bacterial infections from aquatic species: potential for and prevention of contact zoonoses.

    Science.gov (United States)

    Haenen, O L M; Evans, J J; Berthe, F

    2013-08-01

    As aquaculture production and the consumption of aquaculture products increase, the possibility of contracting zoonotic infections from either handling or ingesting these products also increases. The principal pathogens acquired topically from fish or shellfish through spine/pincer puncture or open wounds are Aeromonas hydrophila, Edwardsiella tarda, Mycobacterium marinum, Streptococcus iniae, Vibrio vulnificus and V. damsela. These pathogens, which are all indigenous to the aquatic environment, have also been associated with disease outbreaks in food fish. Outbreaks are often related to management factors, such as the quality and quantity of nutrients in the water and high stocking density, which can increase bacterial loads on the external surface of the fish. As a result, diseased fish are more likely to transmit infection to humans. This review provides an account of human cases of zoonoses throughout the world from the principal zoonotic pathogens of fish and shellfish. PMID:24547653

  14. Regeneration of Phosphorus and Nitrogen by Four Species of Heterotrophic Nanoflagellates Feeding on Three Nutritional States of a Single Bacterial Strain

    OpenAIRE

    Eccleston-Parry, J. D.; Leadbeater, B.

    1995-01-01

    Three physiological states of a single bacterial strain, namely, balanced, phosphorus-rich, and nitrogen-rich bacteria, were obtained by culturing a bacterial strain in chemostats under three different nutrient regimens. Each was shown to be distinctly different in elemental composition with respect to C/N/P ratio. These bacteria were fed to four species of heterotrophic nanoflagellates in batch culture grazing experiments, and the percent regeneration efficiencies of bacterium-bound nitrogen...

  15. The Experimental Study on the continuous Anti-bacterial Potency of Coptidis rhizoma extract on Cultivation of Staphylococcus species(S. aureus, S. epidermidis)

    OpenAIRE

    Seo, Hyeong-Sik

    2007-01-01

    Objectives This experimental study was performed to investigate the continuous anti-bacterial potency of Coptidis rhizoma extract on cultivation of Staphylococcus species(S. aureus, S. epidermidis) that induce eye disease. Methods Minimal inhibitory concentration(MIC) was measured by dropping to 50ul diluted Coptidis rhizoma extract(100%, 10%, 1%, 0.1%) on S. aureus, S. epidermidis that were cultivated from 2 to 6 days. Anti-bacterial potency was measured by the size of inhibition zone with c...

  16. Comparative identification of Candida species isolated from animals using phenotypic and PCR-RFLP methods

    Directory of Open Access Journals (Sweden)

    Nadăş George Cosmin

    2014-06-01

    Full Text Available The aim of this study was to identify 58 Candida sp. strains isolated from animals using the Chromatic Candida test, the API 20 C AUX system, and polymerase chain reaction - restriction fragment length polymorphism (PCR-RFLP. The Chromatic Candida test was able to identify only C. albicans and C. krusei. The API 20 C AUX system and PCR-RFLP had similar specificity for the identification of Candida strains. In case of both methods, Candida albicans was the most frequently isolated species - 22 (37.93% strains, followed by Candida krusei - 17 (29.31% strains, Candida famata - 10 (17.24% strains, Candida parapsilosis - five (8.62% strains, and Candida kefyr - four (6.89% strains. PCR-RFLP represents a reliable, quick and relatively inexpensive genotyping method, recommended for rapid identification of Candida spp.

  17. Identification of Meloidogyne species associated with upland ornamentals plants in Costa Rica.

    Directory of Open Access Journals (Sweden)

    Stefany Solano-González

    2015-06-01

    Full Text Available The objective of this study was to identify nematodes species of the genus Meloidogyne associated with upland ornamental plants. We sampled ten ornamental species in a commercial nursery in San Isidro, Heredia, Costa Rica between 2011-2012. Morphometric measurements of the stylet length, the tail length, and the hyaline region of J2s, as well as perineal patterns of egg-carrying females were used for identification, Genomic DNA was extracted from single J2s and molecular analyses were performed by amplifying the intergenic region between cytochrome oxidase subunit II of the COII and the long subunit of the ARN ribosomal genes by PCR-RFLP. Combining these methods allowed identification of five species of nematodes of the genus Meloidogyne (M. arenaria, M. hapla, M. hispanica, M. incognita and M. javanica, and new restriction enzyme patterns were reported for M. hapla and M. javanica using AluI. Additionally, a preliminary report of M. hispanica was described by sequencing the 28S and 18S regions.

  18. Automated identification and quantification of glycerophospholipid molecular species by multiple precursor ion scanning

    DEFF Research Database (Denmark)

    Ejsing, Christer S.; Duchoslav, Eva; Sampaio, Julio; Simons, Kai; Bonner, Ron; Thiele, Christoph; Ekroos, Kim; Shevchenko, Andrej

    2006-01-01

    We report a method for the identification and quantification of glycerophospholipid molecular species that is based on the simultaneous automated acquisition and processing of 41 precursor ion spectra, specific for acyl anions of common fatty acids moieties and several lipid class-specific fragme...... glycerophospholipids. The automated analysis of total lipid extracts was powered by a robotic nanoflow ion source and produced currently the most detailed description of the glycerophospholipidome.......We report a method for the identification and quantification of glycerophospholipid molecular species that is based on the simultaneous automated acquisition and processing of 41 precursor ion spectra, specific for acyl anions of common fatty acids moieties and several lipid class-specific fragment...... ions. Absolute quantification of identified species was linear within a concentration range of 10 nM-100 microM and was achieved by spiking into total lipid extracts a set of synthetic lipid standards with diheptadecanoyl (17:0/17:0) fatty acid moieties, representing six common classes of...

  19. New primers for sex identification in the Chinese egret and other ardeid species.

    Science.gov (United States)

    Wang, Zeng; Zhou, Xiaoping; Lin, Qingxian; Fang, Wenzhen; Chen, Xiaolin

    2011-01-01

    Using the universal P2/P8 primers, we were able to obtain the gene segments of chromo-helicase-DNA binding protein (CHD)-Z and CHD-W from ten species of ardeid birds including Chinese egret (Egretta eulophotes), little egret (E. garzetta), eastern reef egret (E. sacra), great egret (Ardea alba), grey heron (A. cinerea), Chinese pond-heron (Ardeola bacchus), cattle egret (Bubulcus ibis), black-crowned night-heron (Nycticorax nycticorax), cinnamon bittern (Ixobrychus cinnamomeus) and yellow bittern (I. sinensis). Based on conserved regions inside the P2/P8-derived sequences, we designed new PCR primers for sex identification in these ardeid species. Using agarose gel electrophoresis, the PCR products showed two bands for females (140 bp derived from CHD-W and the other 250 bp from CHD-ZW), whereas the males showed only the 250 bp band. The results indicated that our new primers could be used for accurate and convenient sex identification in ardeid species. PMID:21429119

  20. DNA barcoding and development of species-specific markers for the identification of tea mosquito bugs (Miridae: Heteroptera) in India.

    Science.gov (United States)

    Rebijith, K B; Asokan, R; Kumar, N K Krishna; Srikumar, K K; Ramamurthy, V V; Bhat, P Shivarama

    2012-10-01

    Rapid, accurate, and timely identification of insects as a group is important and challenging worldwide, as they outnumber all other animals in number and diversity. DNA barcoding is a method for the identification of species in a wide range of animal taxa, which uses the 5' region of the mitochondrial cytochrome c oxidase-I (CO-I). Yet another easy, accurate, and economical method of species discrimination is by developing species-specific markers, which produce specific amplicon for the species in question. The method is handy because it is not limited by life stages, sex, polymorphism, and other factors. Herein, we measured the usefulness of CO-I for the species discrimination of mirids in India viz. Helopeltis antonii Signoret, H. thievora Waterhouse, H. bradyi Waterhouse, and Pachypeltis maesarum Kirkaldy in their various life stages. Furthermore, our study showed the utility of species-specific markers in differentiating H. antonii (295) and H. bradyi (514) regardless of their life stages. Analysis of CO-I gene revealed <1% intraspecific divergence for all four species examined, whereas the interspecific distances ranged from 7 to 13%. This study showed that the DNA barcode and species-specific markers will aid the identification of mirids in India and will stand as a decisive tool in formulating integrated pest management (IPM) strategy, quick identification of invasive and cryptic species, haplotypes, biotypes, and other factors, if any. PMID:23068182

  1. [Identification of Microalgae Species Using Visible/Near Infrared Transmission Spectroscopy].

    Science.gov (United States)

    Zhu, Hong-yan; Shao, Yong-ni; Jiang, Lu-lu; Guo, An-que; Pan, Jian; He, Yong

    2016-01-01

    At present, the identification and classification of the microalgae and its biochemical analysis have become one of the hot spots on marine biology research. Four microalgae species, including Chlorella vulgaris, Chlorella pyrenoidosa, Nannochloropsis oculata, Chlamydomonas reinhardtii, were chosen as the experimental materials. Using an established spectral acquisition system, which consists of a portable USB 4000 spectrometer having transmitting and receiving fiber bundles connected by a fiber optic probe, a halogen light source, and a computer, the Vis/NIR transmission spectral data of 120 different samples of the microalgae with different concentration gradients were collected, and the spectral curves of fourmicroalgae species were pre-processed by different pre-treatment methods (baseline filtering, convolution smoothing, etc. ). Based on the pre-treated effects, SPA was applied to select effective wavelengths (EWs), and the selected EWs were introduced as inputs to develop and compare PLS, Least Square Support Vector Machines (LS-SVM), Extreme Learning Machine (ELM)models, so as to explore the feasibility of using Vis/NIR transmission spectroscopy technology for the rapid identification of four microalgae species in situ. The results showed that: the effect of Savitzky-Golay smoothing was much better than the other pre-treatment methods. Six EWs selected in the spectraby SPA were possibly relevant to the content of carotenoids, chlorophyll in the microalgae. Moreover, the SPA-PLS model obtained better performance than the Full-Spectral-PLS model. The average prediction accuracy of three methods including SPA-LV-SVM, SPA-ELM, and SPA-PLS were 80%, 85% and 65%. The established method in this study may identify four microalgae species effectively, which provides a new way for the identification and classification of the microalgae species. The methodology using Vis/NIR spectroscopy with a portable optic probe would be applicable to a diverse range of microalgae

  2. Identification and characterization of a bacterial hyaluronidase and its production in recombinant form.

    Science.gov (United States)

    Messina, Luciano; Gavira, Jose A; Pernagallo, Salvatore; Unciti-Broceta, Juan D; Sanchez Martin, Rosario M; Diaz-Mochon, Juan J; Vaccaro, Susanna; Conejero-Muriel, Mayte; Pineda-Molina, Estela; Caruso, Salvatore; Musumeci, Luca; Di Pasquale, Roberta; Pontillo, Angela; Sincinelli, Francesca; Pavan, Mauro; Secchieri, Cynthia

    2016-07-01

    Hyaluronidases (Hyals) are broadly used in medical applications to facilitate the dispersion and/or absorption of fluids or medications. This study reports the isolation, cloning, and industrial-scale recombinant production, purification and full characterization, including X-ray structure determination at 1.45 Å, of an extracellular Hyal from the nonpathogenic bacterium Streptomyces koganeiensis. The recombinant S. koganeiensis Hyal (rHyal_Sk) has a novel bacterial catalytic domain with high enzymatic activity, compared with commercially available Hyals, and is more thermostable and presents higher proteolytic resistance, with activity over a broad pH range. Moreover, rHyal_Sk exhibits remarkable substrate specificity for hyaluronic acid (HA) and poses no risk of animal cross-infection. PMID:27311405

  3. Identification and analysis of polyaromatic hydrocarbons (PAHs)--biodegrading bacterial strains from refinery soil of India.

    Science.gov (United States)

    Chaudhary, Priyanka; Sahay, Harmesh; Sharma, Richa; Pandey, Alok Kumar; Singh, Shashi Bala; Saxena, A K; Nain, Lata

    2015-06-01

    Polyaromatic hydrocarbons (PAHs) utilizing bacteria were isolated from soils of seven sites of Mathura refinery, India. Twenty-six bacterial strains with different morphotypes were isolated. These strains were acclimatized to utilize a mixture of four polycyclic aromatic hydrocarbons, i.e., anthracene, fluorene, phenanthrene, and pyrene, each at 50 mg/L concentration as sole carbon source. Out of total isolates, 15 potent isolates were subjected to 16S rDNA sequencing and identified as a member of diverse genera, i.e., Bacillus, Acinetobacter, Stenotrophomonas, Alcaligenes, Lysinibacillus, Brevibacterium, Serratia, and Streptomyces. Consortium of four promising isolates (Acinetobacter, Brevibacterium, Serratia, and Streptomyces) were also investigated for bioremediation of PAH mixture. This consortium was proved to be efficient PAH degrader resulting in 40-70 % degradation of PAH within 7 days. Results of this study indicated that these genera may play an active role in bioremediation of PAHs. PMID:26026847

  4. Performance of CHROMAGAR candida and BIGGY agar for identification of yeast species

    Directory of Open Access Journals (Sweden)

    Marol Serhat

    2003-10-01

    Full Text Available Abstract Background The importance of identifying the pathogenic fungi rapidly has encouraged the development of differential media for the presumptive identification of yeasts. In this study two differential media, CHROMagar Candida and bismuth sulphite glucose glycine yeast agar, were evaluated for the presumptive identification of yeast species. Methods A total number of 270 yeast strains including 169 Candida albicans, 33 C. tropicalis, 24 C. glabrata, 18 C. parapsilosis, 12 C. krusei, 5 Trichosporon spp., 4 C. kefyr, 2 C. lusitaniae, 1 Saccharomyces cerevisiae and 1 Geotrichum candidum were included. The strains were first identified by germ tube test, morphological characteristics on cornmeal tween 80 agar and Vitek 32 and API 20 C AUX systems. In parallel, they were also streaked onto CHROMagar Candida and bismuth sulphite glucose glycine yeast agar plates. The results were read according to the color, morphology of the colonies and the existance of halo around them after 48 hours of incubation at 37°C. Results The sensitivity and specificity values for C. albicans strains were found to be 99.4, 100% for CHROMagar Candida and 87.0, 75.2% for BiGGY agar, respectively. The sensitivity of CHROMagar Candida to identify C. tropicalis, C. glabrata and C. krusei ranged between 90.9 and 100% while the specificity was 100%. The sensitivity rates for BiGGY agar were 66.6 and 100% while the specificity values were found to be 95.4 and 100% for C. tropicalis and C. krusei, respectively. Conclusions It can be concluded that the use of CHROMagar Candida is an easy and reliable method for the presumptive identification of most commonly isolated Candida species especially C. albicans, C. tropicalis and C. krusei. The lower sensitivity and specificity of BiGGY agar to identify commonly isolated Candida species potentially limits the clinical usefulness of this agar.

  5. “Bacillus mediterraneensis,” a new bacterial species isolated from human gut microbiota

    OpenAIRE

    Alou, M.T.; P.-E. Fournier; Raoult, D.

    2016-01-01

    We present a brief description of “Bacillus mediterraneensis” strain Marseille-P2366T (= CSUR P2366 = DSM 102091), a new species isolated from the gastrointestinal tract of a healthy 13-month-old boy from Senegal.

  6. Using metagenomics and metatranscriptomics to study specific bacterial species involved in biological phosphorus removal from wastewater

    DEFF Research Database (Denmark)

    Albertsen, Mads; McIlroy, Simon Jon; Stokholm-Bjerregaard, Mikkel;

    to enrich for bacteria contributing to phosphorus removal and their normal competitors. To extract complete genomes we generated two metagenomes from each reactor, taken approximately 1 month apart, using the Illumina HiSeq2000 platform. Due to low micro-diversity in the reactors (2-15 dominating species...

  7. Morphological identification and COI barcodes of adult flies help determine species identities of chironomid larvae (Diptera, Chironomidae).

    Science.gov (United States)

    Failla, A J; Vasquez, A A; Hudson, P; Fujimoto, M; Ram, J L

    2016-02-01

    Establishing reliable methods for the identification of benthic chironomid communities is important due to their significant contribution to biomass, ecology and the aquatic food web. Immature larval specimens are more difficult to identify to species level by traditional morphological methods than their fully developed adult counterparts, and few keys are available to identify the larval species. In order to develop molecular criteria to identify species of chironomid larvae, larval and adult chironomids from Western Lake Erie were subjected to both molecular and morphological taxonomic analysis. Mitochondrial cytochrome c oxidase I (COI) barcode sequences of 33 adults that were identified to species level by morphological methods were grouped with COI sequences of 189 larvae in a neighbor-joining taxon-ID tree. Most of these larvae could be identified only to genus level by morphological taxonomy (only 22 of the 189 sequenced larvae could be identified to species level). The taxon-ID tree of larval sequences had 45 operational taxonomic units (OTUs, defined as clusters with >97% identity or individual sequences differing from nearest neighbors by >3%; supported by analysis of all larval pairwise differences), of which seven could be identified to species or 'species group' level by larval morphology. Reference sequences from the GenBank and BOLD databases assigned six larval OTUs with presumptive species level identifications and confirmed one previously assigned species level identification. Sequences from morphologically identified adults in the present study grouped with and further classified the identity of 13 larval OTUs. The use of morphological identification and subsequent DNA barcoding of adult chironomids proved to be beneficial in revealing possible species level identifications of larval specimens. Sequence data from this study also contribute to currently inadequate public databases relevant to the Great Lakes region, while the neighbor

  8. Testing the potential of proposed DNA barcodes for species identification of Zingiberaceae

    Institute of Scientific and Technical Information of China (English)

    Lin- Chun SHI; Yu-Lin LIN; Cai-Xiang XIE; Zhong-Zhi QIAN; Shi-Lin CHEN; Jin ZHANG; Jian-Ping HAN; Jing-Yuan SONG; Hui YAO; Ying-Jie ZHU; Jia-Chun LI; Zhen-Zhong WANG; Wei XIAO

    2011-01-01

    In 2009, the Consortium for the Barcode of Life (CBOL) recommended the combination of rbcL and matK as the plant barcode based on assessments of recoverability, sequencing quality, and levels of species discrimination. Subsequently, based on a study of more than 6600 samples belonging to 193 families from seven phyla, the internal transcribed spacer (ITS) 2 locus was proposed as a universal barcode sequence for all major plant taxa used in traditional herbal medicine. Neither of these two studies was based on a detailed analysis of a particular family. Here, Zingiberaceae plants, including many closely related species, were used to compare the genetic divergence and species identification efficiency of ITS2, rbcL, matK, psbK-psbI, trnH-psbA, and rpoB.The results indicate that ITS2 has the highest interspecific divergence and significant differences between inter- and intraspecific divergence, whereas matK and rbcL have much lower divergence values. Among 260 species belongingto 30 genera in Zingiberaceae, the discrimination ability of the ITS2 locus was 99.5% at the genus level and 73.1% at the species level. Thus, we propose that ITS2 is the preferred DNA barcode sequence for identifying Zingiberaceae plants.

  9. Species identification of Chinese medicinal plant Fallopia multiflora (Thunb.) Haraldson by suppression subtraction hybridization.

    Science.gov (United States)

    Zheng, Chuan-Jin; Zhao, Shu-Jin; Shao, Li

    2014-01-01

    Fallopia multiflora (Thunb.) Haraldson, a traditional Chinese medicinal plant, has been extensively used in preparations of herbal medicine, health products and personal hygiene products. However, the clinical safety and efficiency of F. multiflora (Thunb.) Haraldson is impaired because of the existence of various adulterants. In this study, genomic DNA (gDNA) suppression subtraction hybridization (SSH) was used to authenticate F. multiflora (Thunb.) Haraldson from its adulterants. First, differential gDNA fragments between F. multiflora (Thunb.) Haraldson and its most closely related species F. multiflora var. ciliinervis (Nakai) Yonek. & H. Ohashi by SSH were identified. The differential fragments were then hybridized with arrays constructed from multiple whole genomes of several species (adulterants and/or closely related plants) to screen for the unique gDNA fragments representing F. multiflora (Thunb.) Haraldson. The unique gDNA fragments could be used to design species-specific primers for the identification of F. multiflora (Thunb.) Haraldson. Using SSH, we obtained four differential gDNA fragments, and four pairs of primers were designed. The designed primers could differentiate F. multiflora (Thunb.) Haraldson from its adulterants and/or closely related species via PCR. The results confirmed that the SSH is an efficient method for screening and designing species-specific primers. PMID:23633031

  10. Toxicity and symptomatic identification of species involved in snakebites in the Indian subcontinent

    Directory of Open Access Journals (Sweden)

    V. Kumar

    2006-01-01

    Full Text Available Snakebites, being the major occupational hazard for farm workers, claim a large number of lives in the Indian subcontinent. During the course of medical management, identification of the biting species is given a low priority, resorting to prescription of polyvalent anti-snake venom. Whereas the World Health Organization (WHO recommends monospecific anti-snake venom instead of polyvalent anti-snake venom. Thus, it is essential to identify the aggressor species either by a visual inspection or by the symptoms of the victim. Along with the four deadly venomous species (cobra, krait, Russell's viper, and saw-scaled viper, there are a number of other species of medical importance, whose venoms and bites have not been paid much attention. Thus, a misclassification resulting into erroneous treatment cannot be ruled out. This paper discusses the nature, constitution, and toxicity of venoms and their possible toxic effects on victims of snakebites. An attempt has also been made to categorize the distinctive symptoms due to the bites of the four major venomous species and their severity grading.

  11. Development of a monoclonal antibody detection assay for species-specific identification of abalone.

    Science.gov (United States)

    Lopata, Andreas L; Luijx, Thomas; Fenemore, Bartha; Sweijd, Neville A; Cook, Peter A

    2002-10-01

    Species identification based on biochemical and molecular techniques has a broad range of applications. These include compliance enforcement, the management and conservation of marine organisms, and commercial quality control. Abalone poaching worldwide and illegal trade in abalone products have increased mainly because of the attractive prices obtained and caused a sharp decline in stocks. Alleged poachers have been acquitted because of lack of evidence to correctly identify species. Therefore, a robust method is required that would identify tissue of abalone origin to species level. The aim of this study was to develop immunologic techniques, using monoclonal and polyclonal antibodies, to identify 10 different abalone species and subspecies from South Africa, the United States, Australia, and Japan. The combination of 3 developed monoclonal antibodies to South African abalone (Haliotis midae) enabled differentiation between most of the 10 species including the subspecies H. diversicolor supertexta and H. diversicolor diversicolor. In a novel approach, using antibodies of patients with allergy to abalone, the differentiation of additional subspecies, H. discus discus and H. discus hannai, was possible. A field-based immunoassay was developed to identify confiscated tissue of abalone origin. PMID:14961238

  12. Intra-Species Bacterial Quorum Sensing Studied at Single Cell Level in a Double Droplet Trapping System

    Directory of Open Access Journals (Sweden)

    Wilhelm T. S. Huck

    2013-05-01

    Full Text Available In this paper, we investigated the intra-species bacterial quorum sensing at the single cell level using a double droplet trapping system. Escherichia coli transformed to express the quorum sensing receptor protein, LasR, were encapsulated in microdroplets that were positioned adjacent to microdroplets containing the autoinducer, N-(3-oxododecanoyl-L-homoserine lactone (OdDHL. Functional activation of the LasR protein by diffusion of the OdDHL across the droplet interface was measured by monitoring the expression of green fluorescent protein (GFP from a LasR-dependent promoter. A threshold concentration of OdDHL was found to induce production of quorum-sensing associated GFP by E. coli. Additionally, we demonstrated that LasR-dependent activation of GFP expression was also initiated when the adjacent droplets contained single E. coli transformed with the OdDHL synthase gene, LasI, representing a simple quorum sensing circuit between two droplets.

  13. Biodegradation of free cyanide by bacterial species isolated from cyanide-contaminated artisanal gold mining catchment area in Burkina Faso.

    Science.gov (United States)

    Razanamahandry, Lovasoa Christine; Andrianisa, Harinaivo Anderson; Karoui, Hela; Kouakou, Koffi Marcelin; Yacouba, Hamma

    2016-08-01

    Soil and water samples were collected from a watershed in Burkina Faso where illegal artisanal gold extraction using cyanidation occurs. The samples were used to evaluate cyanide contamination and the presence of cyanide degrading bacteria (CDB). Free cyanide (F-CN) was detected in all samples, with concentrations varying from 0.023 to 0.9 mg kg(-1), and 0.7-23 μg L(-1) in the soil and water samples, respectively. Potential CDB also were present in the samples. To test the effective F-CN degradation capacity of the isolated CDB species, the species were cultivated in growth media containing 40, 60 or 80 mg F-CN L(-1), with or without nutrients, at pH 9.5 and at room temperature. More than 95% of F-CN was degraded within 25 h, and F-CN degradation was associated with bacterial growth and ammonium production. However, initial concentrations of F-CN higher than 100 mg L(-1) inhibited bacterial growth and cyanide degradation. Abiotic tests showed that less than 3% of F-CN was removed by volatilization. Thus, the degradation of F-CN occurred predominately by biological mechanisms, and such mechanisms are recommended for remediation of contaminated soil and water. The bacteria consortium used in the experiment described above exist in a Sahelian climate, which is characterized by a long hot and dry season. Because the bacteria are already adapted to the local climate conditions and show the potential for cyanide biodegradation, further applicability to other contaminated areas in West Africa, where illegal gold cyanidation is widespread, should be explored. PMID:27209555

  14. Biochemical parameters and bacterial species richness in soils contaminated by sludge-borne metals and remediated with inorganic soil amendments

    Energy Technology Data Exchange (ETDEWEB)

    Mench, M.; Renella, G.; Gelsomino, A.; Landi, L.; Nannipieri, P. [University Bordeaux, Talence (France)

    2006-11-01

    The effectiveness of two amendments for the in situ remediation of a Cd- and Ni-contaminated soil in the Louis Fargue long-term field experiment was assessed. In April 1995, one replicate plot (S1) was amended with 5% w/w of beringite (B), a coal fly ash (treatment S1 + B), and a second plot with 1% w/w zerovalent-Fe iron grit (SS) (treatment S1+SS), with the aim of increasing metal sorption and attenuating metal impacts. Long-term responses of daily respiration rates, microbial biomass, bacterial species richness and the activities of key soil enzymes (acid and alkaline phosphatase, arylsulfatase, beta-glucosidase, urease and protease activities) were studied in relation to soil metal extractability. Seven years after initial amendments, the labile fractions of Cd and Ni in both the S1 + B and S1 + SS soils were reduced to various extents depending on the metal and fractions considered. The soil microbial biomass and respiration rate were not affected by metal contamination and amendments in the S1 + B and S I + SS soils, whereas the activity of different soil enzymes was restored. The SS treatment was more effective in reducing labile pools of Cd and Ni and led to a greater recovery of soil enzyme activities than the B treatment. Bacterial species richness in the S1 soil did not alter with either treatment. It was concluded that monitoring of the composition and activity of the soil microbial community is important in evaluating the effectiveness of soil remediation practices.

  15. Biochemical parameters and bacterial species richness in soils contaminated by sludge-borne metals and remediated with inorganic soil amendments

    International Nuclear Information System (INIS)

    The effectiveness of two amendments for the in situ remediation of a Cd- and Ni-contaminated soil in the Louis Fargue long-term field experiment was assessed. In April 1995, one replicate plot (S1) was amended with 5% w/w of beringite (B), a coal fly ash (treatment S1 + B), and a second plot with 1% w/w zerovalent-Fe iron grit (SS) (treatment S1+SS), with the aim of increasing metal sorption and attenuating metal impacts. Long-term responses of daily respiration rates, microbial biomass, bacterial species richness and the activities of key soil enzymes (acid and alkaline phosphatase, arylsulfatase, β-glucosidase, urease and protease activities) were studied in relation to soil metal extractability. Seven years after initial amendments, the labile fractions of Cd and Ni in both the S1 + B and S1 + SS soils were reduced to various extents depending on the metal and fractions considered. The soil microbial biomass and respiration rate were not affected by metal contamination and amendments in the S1 + B and S1 + SS soils, whereas the activity of different soil enzymes was restored. The SS treatment was more effective in reducing labile pools of Cd and Ni and led to a greater recovery of soil enzyme activities than the B treatment. Bacterial species richness in the S1 soil did not alter with either treatment. It was concluded that monitoring of the composition and activity of the soil microbial community is important in evaluating the effectiveness of soil remediation practices. - Amendments (coal fly ash, zerovalent-Fe iron grit), reduced labile fractions of Cd and Ni in contaminated soils and restored the activity of key soil hydrolases

  16. The Value of Molecular vs. Morphometric and Acoustic Information for Species Identification Using Sympatric Molossid Bats

    Science.gov (United States)

    Gager, Yann; Tarland, Emilia; Lieckfeldt, Dietmar; Ménage, Matthieu; Botero-Castro, Fidel; Rossiter, Stephen J.; Kraus, Robert H. S.; Ludwig, Arne; Dechmann, Dina K. N.

    2016-01-01

    A fundamental condition for any work with free-ranging animals is correct species identification. However, in case of bats, information on local species assemblies is frequently limited especially in regions with high biodiversity such as the Neotropics. The bat genus Molossus is a typical example of this, with morphologically similar species often occurring in sympatry. We used a multi-method approach based on molecular, morphometric and acoustic information collected from 962 individuals of Molossus bondae, M. coibensis, and M. molossus captured in Panama. We distinguished M. bondae based on size and pelage coloration. We identified two robust species clusters composed of M. molossus and M. coibensis based on 18 microsatellite markers but also on a more stringently determined set of four markers. Phylogenetic reconstructions using the mitochondrial gene co1 (DNA barcode) were used to diagnose these microsatellite clusters as M. molossus and M. coibensis. To differentiate species, morphological information was only reliable when forearm length and body mass were combined in a linear discriminant function (95.9% correctly identified individuals). When looking in more detail at M. molossus and M. coibensis, only four out of 13 wing parameters were informative for species differentiation, with M. coibensis showing lower values for hand wing area and hand wing length and higher values for wing loading. Acoustic recordings after release required categorization of calls into types, yielding only two informative subsets: approach calls and two-toned search calls. Our data emphasizes the importance of combining morphological traits and independent genetic data to inform the best choice and combination of discriminatory information used in the field. Because parameters can vary geographically, the multi-method approach may need to be adjusted to local species assemblies and populations to be entirely informative. PMID:26943355

  17. Coral-Associated Bacterial Diversity Is Conserved across Two Deep-Sea Anthothela Species

    OpenAIRE

    Lawler, Stephanie N.; Kellogg, Christina A.; France, Scott C.; Clostio, Rachel W.; Brooke, Sandra D.; Ross, Steve W.

    2016-01-01

    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 Baltim...

  18. Characterization of a Single Magnetotactic Bacterial Species from Devil's Bathtub, Mendon Ponds Park, Honeoye Falls, NY

    Science.gov (United States)

    Wagner, C.; Tarduno, J. A.; Stein, A.; Sia, E.

    2015-12-01

    Magnetotactic bacteria (MTB) belong to a lineage of prokaryotic bacteria that synthesize magnetosomes, single domain magnetic particles (typically magnetite or greigite) with an average size of 50 nanometers. MTB utilize magnetosomes through magnetotaxis, the alignment and movement along magnetic field lines to navigate towards preferred environmental conditions. MTB are sensitive to different environments and are thought to exhibit varying magnetosome morphologies, compositions, sizes, and quantities in regards to the environments which they inhabit. These characteristics allow MTB and magnetofossils (preserved magnetosomes) to be used as modern/paleoenvironmental recorders and biomarkers for environmental change(s). Devil's Bathtub (Mendon Ponds Park, Honeoye Falls, NY) is a meromictic glacial kettle pond surrounded by deciduous tree cover. Here we examine one species of MTB based on prominence of this particular morphology at this locale. Magnetotaxis and morphology of this species have been observed using light microscopy. Micrographs have also been taken using Transmission Electron Microscopy (TEM) to verify cell morphology and to determine magnetosome morphology. TEM and magnetic hysteresis measurements were done to find and test the composition of magnetosomes. In this study we also focus on DNA sequencing and characterization of this MTB, as there are few MTB species which have been DNA sequenced successfully. Data from these experiments are directly applicable to this up-and-coming area of research as it will aid in the understanding and correlation of magnetosome and magnetofossils with environmental characteristics.

  19. ISOLATION AND IDENTIFICATION OF BACTERIAL CAUSING SOFT ROT DESEASE ON STRAWBERRY FRUIT (Fragaria x ananassa

    Directory of Open Access Journals (Sweden)

    Made Mega Yuliasari

    2015-03-01

    Full Text Available Soft rot on strawberry fruit was found in strawberry (F. x ananassa plantation in Candi Kuning, Bedugul, Bali. Soft rot on strawberry fruit can be caused by microorganism i.e. bacteria. Objectives of the research were to isolate pathogen causing soft rot on strawberry fruit with plating method and to identify bacteria causing soft rot by using Kit MicrogenTM GNA+B-ID System and Bergey’s Manual of Determinative Bacteriology reference (Holt et al., 1994. Results showed there were five isolates of bacteria (IB-1, IB-2, IB-3, IB-4, and IB-5. Positive result of Postulat Koch showed that bacteria causing soft rot on strawberry is IB-1. Identification that was done by using Kit MicrogenTM GNA+B-ID System and Bergey’s Manual of Determinative Bacteriology reference (Holt et al., 1994, showed that the isolate IB-1 is Weeksella.

  20. Six cases of Aerococcus sanguinicola infection: Clinical relevance and bacterial identification

    DEFF Research Database (Denmark)

    Ibler, K.; Jensen, K.T.; Ostergaard, C.;

    2008-01-01

    were associated with infective endocarditis. Most patients were elderly (median age 70 y) and had underlying neurological disorders including dementia, cerebral degeneration, and myelomeningocele. The primary focus of infection was the urinary tract in 3 cases and the gallbladder in 1; no focus was......Aerococcus sanguinicola is a Gram-positive coccus first described in 2001. Infections in humans are rare but the use of 16S rRNA gene sequencing and improved phenotypic methods has facilitated the identification of A. sanguinicola. We report here 6 cases of A. sanguinicola bacteraemia, 2 of which...... detected in 2 cases. Long-term prognosis was poor reflecting the frailty of the patients. All strains were susceptible to penicillin, ampicillin, cefuroxime, vancomycin, erythromycin, and rifampicin. The optimal treatment of infection with A. sanguinicola has yet to be determined Udgivelsesdato: 2008...

  1. Microfluidic system for the identification of bacterial pathogens causing urinary tract infections

    Science.gov (United States)

    Becker, Holger; Hlawatsch, Nadine; Haraldsson, Tommy; van der Wijngaart, Wouter; Lind, Anders; Malhotra-Kumar, Surbi; Turlej-Rogacka, Agata; Goossens, Herman

    2015-03-01

    Urinary tract infections (UTIs) are among the most common bacterial infections and pose a significant healthcare burden. The growing trend in antibiotic resistance makes it mandatory to develop diagnostic kits which allow not only the determination of a pathogen but also the antibiotic resistances. We have developed a microfluidic cartridge which takes a direct urine sample, extracts the DNA, performs an amplification using batch-PCR and flows the sample over a microarray which is printed into a microchannel for fluorescence detection. The cartridge is injection-molded out of COP and contains a set of two-component injection-molded rotary valves to switch between input and to isolate the PCR chamber during thermocycling. The hybridization probes were spotted directly onto a functionalized section of the outlet microchannel. We have been able to successfully perform PCR of E.coli in urine in this chip and perform a fluorescence detection of PCR products. An upgraded design of the cartridge contains the buffers and reagents in blisters stored on the chip.

  2. Identification of novel bacterial DNA gyrase inhibitors: An in silico study.

    Science.gov (United States)

    Rahimi, Hamzeh; Najafi, Ali; Eslami, Habib; Negahdari, Babak; Moghaddam, Mehrdad Moosazadeh

    2016-01-01

    Owing to essential role in bacterial survival, DNA gyrase has been exploited as a validated drug target. However, rapidly emerging resistance to gyrase-targeted drugs such as widely utilized fluoroquinolones reveals the necessity to develop novel compounds with new mechanism of actions against this enzyme. Here, an attempt has been made to identify new drug-like molecules for Shigella flexneri DNA gyrase inhibition through in silico approaches. The structural similarity search was carried out using the natural product simocyclinone D8, a unique gyrase inhibitor, to virtually screen ZINC database. A total of 11830 retrieved hits were further screened for selection of high-affinity compounds by implementing molecular docking followed by investigation of druggability according to Lipinski's rule, biological activity and physiochemical properties. Among the hits initially identified, three molecules were then confirmed to have reasonable gyrase-binding affinity and to follow Lipinski's rule. Based on these in silico findings, three compounds with different chemical structures from previously identified gyrase inhibitors were proposed as potential candidates for the treatment of fluoroquinolone-resistant strains and deserve further investigations. PMID:27499795

  3. Identification and elimination of bacterial contamination during in vitro propagation of Guadua angustifolia Kunth

    OpenAIRE

    Harleen Kaur Nadha; Richa Salwan; Ramesh Chand Kasana; Manju Anand; Anil Sood

    2012-01-01

    Background: Guadua angustifolia Kunth is a very important bamboo species with significant utility in pharmaceutical, paper, charcoal, and construction industries. Microbial contamination is a major problem encountered during establishment of in vitro cultures of Guadua. Objective: This study has been designed to analyze the identity of contaminating bacteria and to develop the strategy to eliminate them during micropropagation of Guadua. Materials and Methods: We isolated and consequently ana...

  4. Bacterial tethering analysis reveals a "run-reverse-turn" mechanism for Pseudomonas species motility.

    Science.gov (United States)

    Qian, Chen; Wong, Chui Ching; Swarup, Sanjay; Chiam, Keng-Hwee

    2013-08-01

    We have developed a program that can accurately analyze the dynamic properties of tethered bacterial cells. The program works especially well with cells that tend to give rise to unstable rotations, such as polar-flagellated bacteria. The program has two novel components. The first dynamically adjusts the center of the cell's rotational trajectories. The second applies piecewise linear approximation to the accumulated rotation curve to reduce noise and separate the motion of bacteria into phases. Thus, it can separate counterclockwise (CCW) and clockwise (CW) rotations distinctly and measure rotational speed accurately. Using this program, we analyzed the properties of tethered Pseudomonas aeruginosa and Pseudomonas putida cells for the first time. We found that the Pseudomonas flagellar motor spends equal time in both CCW and CW phases and that it rotates with the same speed in both phases. In addition, we discovered that the cell body can remain stationary for short periods of time, leading to the existence of a third phase of the flagellar motor which we call "pause." In addition, P. aeruginosa cells adopt longer run lengths, fewer pause frequencies, and shorter pause durations as part of their chemotactic response. We propose that one purpose of the pause phase is to allow the cells to turn at a large angle, where we show that pause durations in free-swimming cells positively correlate with turn angle sizes. Taken together, our results suggest a new "run-reverse-turn" paradigm for polar-flagellated Pseudomonas motility that is different from the "run-and-tumble" paradigm established for peritrichous Escherichia coli. PMID:23728820

  5. Species identification and selection to develop agroforestry at Lake Toba Catchment Area (LTCA

    Directory of Open Access Journals (Sweden)

    NURHENI WIJAYANTO

    2011-01-01

    Full Text Available Wijayanto N (2011 Species identification and selection to develop agroforestry at Lake Toba Catchment Area (LTCA. Biodiversitas 12: 52-58. In order to improve land productivity surrounding the LTCA, the existing ITTO project tries to establish agroforestry system. The system will be designed to meet consideration of both sides. on one side is to generate the people awareness of the forest and land rehabilitation, and on the other side is to support the poverty reduction. The aims of this research are: species identification and selection to develop agroforestry at LTCA. Data collecting was carried out with: interview, group discussion, field observation, divining manual study, and PRA. The diversity of the available crop kind shows the number of choices to be developed by the farmer. The farmers generally have the economic objective to develop agroforestry, including increase in net income, risk reduction, increase in environmental service, and the wealth and savings accumulation. Various types of agricultural crops, plantations and forest trees were found in LTCA. They can be the basis for building a wide variety of agroforestry systems.

  6. Performance of chromogenic media for Candida in rapid presumptive identification of Candida species from clinical materials

    Directory of Open Access Journals (Sweden)

    M V Pravin Charles

    2015-01-01

    Full Text Available Background: In perspective of the worldwide increase in a number of immunocompromised patients, the need for identification of Candida species has become a major concern. The development of chromogenic differential media, introduced recently, facilitate rapid speciation. However, it can be employed for routine mycology workup only after an exhaustive evaluation of its benefit and cost effectiveness. This study was undertaken to evaluate the benefit and cost effectiveness of chromogenic media for speciation of Candida clinical isolates. Materials and Methods: Sputum samples of 382 patients were screened for the presence of Candida spp. by Gram stain and culture on sabouraud dextrose agar. Candida species were identified using Gram stain morphology, germ tube formation, cornmeal agar with Tween-80, sugar fermentation tests and morphology on HiCrome Candida differential agar. All the Candida isolates were inoculated on HiCrome Candida agar (HiMedia, Mumbai, India. Results: The sensitivity and specificity of HiCrome agar for identification of Candida albicans were 90% and 96.42%, respectively whereas sensitivity and specificity of carbohydrate fermentation test were 86.67% and 74.07%, respectively. Sensitivity and specificity values of HiCrome agar for detection of C. albicans, Candida parapsilosis and Candida glabrata were above 90%. Conclusions: We found HiCrome agar has high sensitivity and specificity comparable to that of the conventional method. In addition, use of this differential media could significantly cut down the turnaround time as well as cost of sample processing.

  7. Comparison of tryptophan biosynthetic operon regulation in different Gram-positive bacterial species.

    Science.gov (United States)

    Gutiérrez-Preciado, Ana; Yanofsky, Charles; Merino, Enrique

    2007-09-01

    The tryptophan biosynthetic operon has been widely used as a model system for studying transcription regulation. In Bacillus subtilis, the trp operon is primarily regulated by a tryptophan-activated RNA-binding protein, TRAP. Here we show that in many other Gram-positive species the trp operon is regulated differently, by tRNA(Trp) sensing by the RNA-based T-box mechanism, with T-boxes arranged in tandem. Our analyses reveal an apparent relationship between trp operon organization and the specific regulatory mechanism(s) used. PMID:17555843

  8. The fur Gene as a New Phylogenetic Marker for Vibrionaceae Species Identification

    DEFF Research Database (Denmark)

    Machado, Henrique; Gram, Lone

    2015-01-01

    Microbial taxonomy is essential in all areas of microbial science. The 16S rRNA gene sequence is one of the main phylogenetic species markers; however, it does not provide discrimination in the family Vibrionaceae, where other molecular techniques allow better interspecies resolution. Although...... multilocus sequence analysis (MLSA) has been used successfully in the identification of Vibrio species, the technique has several limitations. They include the fact that several locus amplifications and sequencing have to be performed, which still sometimes lead to doubtful identifications. Using an in...... silico approach based on genomes from 103 Vibrionaceae strains, we demonstrate here the high resolution of the fur gene in the identification of Vibrionaceae species and its usefulness as a phylogenetic marker. The fur gene showed within-species similarity higher than 95%, and the relationships inferred...

  9. Use of Wood Characters in the Identification of Selected Timber Species in Nigeria.

    Directory of Open Access Journals (Sweden)

    Adeniyi Akanni JAYEOLA

    2009-11-01

    Full Text Available Ten popular timber species belonging to seven families in Nigeria were identified in the Herbarium. Wood samples of each species were studied anatomically in search of stable taxonomic micromorphological attributes. Characters of the treachery elements, in particular, the vessel; fibre and ray structure; intercellular canal and phloem parenchyma are diagnostic among the species. The invariable presence of non-septate fibres in Afzelia africana (Sm. and Milicia excelsa (Welsh. and C. C. Berg. delimits them from other woods which all posses septate fibres. Occurrence of tyloses in the metaxylem of Cordia millenii (Bak., Antiaris toxicaria(Lesch., Tectona grandis (L. F., Terminalia ivorensis (A. Chev. and Triplochiton scleroxylon (K. Schum. separates them from Anogeissus leiocarpus (Guill. and Perr., Khaya ivorensis (A. Chev. and Mansonia altissima (A. Chev.. A detailed study of the wood structure of the commercial Nigerian timber species may provide an invaluable tool for determination, identification of fragments and thereby assisting in promoting quality assurance as well as detecting adulteration in wood trade and detecting camouflage and substitution of CITES-listed trees.

  10. Clinical significance, antimicrobial susceptibility and molecular identification of Nocardia species isolated from children with cystic fibrosis.

    Science.gov (United States)

    Betrán, Ana; Villuendas, M Cruz; Rezusta, Antonio; Pereira, Javier; Revillo, M José; Rodríguez-Nava, Verónica

    2016-01-01

    Nocardia is an opportunistic pathogen that causes respiratory infections in immunocompromised patients. The aim of this study was to analyze the epidemiology, clinical significance and antimicrobial susceptibility of Nocardia species isolated from eight children with cystic fibrosis. The isolated species were identified as Nocardia farcinica, Nocardia transvalensis, Nocardia pneumoniae, Nocardia veterana and Nocardia wallacei. N. farcinica was isolated in three patients and all of them presented lung affectation with a chronic colonization and pneumonia. N. farcinica showed resistance against gentamicin, tobramycin, cefotaxime, but was susceptible to trimethoprim-sulfamethoxazole and amikacin. N. transvalensis, which was isolated from two patients, showed an association with chronic colonization. N. transvalensis was resistant to tobramycin and amikacin, but susceptible to ciprofloxacin, trimethoprim-sulfamethoxazole and cefotaxime. N. veterana, N. pneumoniae and N. wallacei were isolated from three different patients and appeared in transitory lung colonization. N. veterana and N. pneumoniae were susceptible to imipenem, trimethoprim-sulfamethoxazole, amikacin, tobramycin, and cefotaxime. N. wallacei was resistant to amikacin, tobramycin, imipenem, and trimethoprim-sulfamethoxazole and susceptible to ciprofloxacin and cefotaxime. All the isolates were identified up to species level by 16S rRNA gene sequencing. The presence of Nocardia in the sputum of patients with cystic fibrosis is not always an indication of an active infection; therefore, the need for a treatment should be evaluated on an individual basis. The detection of multidrug-resistant species needs molecular identification and susceptibility testing, and should be performed for all Nocardia infections. PMID:27155949

  11. Scolex morphology of monozoic cestodes (Caryophyllidea) from the Palaearctic Region: a useful tool for species identification.

    Science.gov (United States)

    Oros, Mikulás; Scholz, Tomás; Hanzelová, Vladimíra; Mackiewicz, John S

    2010-03-01

    A comparative study of the scoleces of caryophyllidean tapeworms (Cestoda: Caryophyllidea), parasitic in cypriniform fishes in the Palaearctic Region, was carried out using light and scanning electron microscopy. Three-dimensional pictures of the scoleces of 18 species of caryophyllidean cestodes of the Capingentidae (1 species), Caryophyllaeidae (7) and Lytocestidae (10), and outlines of the scoleces and anterior extent of the testes and vitelline follicles of 19 Palaearctic taxa were documented. Both species of Atractolytocestus Anthony, 1957 possess a bulboacuminate scolex, whereas species of Archigetes Leuckart, 1876 have fossate scoleces of the bothrioloculodiscate type, with loculi, bothrium-like depressions and an apical disc. Breviscolex orientalis Kulakovskaya, 1962, the only member of the Capingentidae, has a cuneiform scolex, as do both taxa of the lytocestid genus Caryophyllaeides Nybelin, 1922. The scoleces of two species of Caryophyllaeus Gmelin, 1790 are flabellate, whereas that of the congeneric C. fimbriceps Annenkova-Chlopina, 1919 is cuneicrispitate. Khawia Hsü, 1935, the most specious Palaearctic genus, with seven taxa that we consider to be valid, has the highest diversity in scolex morphology: semi-bulbate, flabellate, cuneiform, cuneifimbriate, truncated cuneiform-flabellate and festoon-like. Species of Monobothrium Nybelin, 1922 have either a digitiform scolex with widened posterior part or cuneiform, with lateral auricular extensions. Paracaryophyllaeus gotoi (Motomura, 1927) is characteristic in its possessing a bulbate scolex, whereas Paraglaridacris limnodrili (Yamaguti, 1934) has a fossate scolex of the bulboloculate type with bothrium-like depressions and feebly developed lateral loculi. Anterior extent of the testes and vitelline follicles and their mutual position show a somewhat higher variability than scolex shape, with intraspecific variation in some taxa, such as Atractolytocestus sagittatus (Kulakovskaya et Akhmerov, 1965), B

  12. Identification of a bacterial pathogen associated with Porites white patch syndrome in the Western Indian Ocean.

    Science.gov (United States)

    Séré, Mathieu G; Tortosa, Pablo; Chabanet, Pascale; Quod, Jean-Pascal; Sweet, Michael J; Schleyer, Michael H

    2015-09-01

    Porites white patch syndrome (PWPS) is a coral disease recently described in the Western Indian Ocean. This study aimed to isolate and identify potential pathogens associated with PWPS utilizing both culture and nonculture screening techniques and inoculation trials. A total of 14 bacterial strains (those dominant in disease lesions, absent or rare in healthy tissues and considered potential pathogens in a previous study) were cultured and used to experimentally inoculate otherwise healthy individuals in an attempt to fulfil Henle-Koch's postulates. However, only one (P180R), identified as closely related (99-100% sequence identity based on 1.4 kb 16S RNA sequence) to Vibrio tubiashii, elicited signs of disease in tank experiments. Following experimental infection (which resulted in a 90% infection rate), the pathogen was also successfully re-isolated from the diseased tissues and re-inoculated in healthy corals colonies, therefore fulfilling the final stages of Henle-Koch's postulates. Finally, we report that PWPS appears to be a temperature-dependent disease, with significantly higher tissue loss (anova: d.f. = 2, F = 39.77, P < 0.01) occurring at 30 °C [1.45 ± 0.85 cm(2) per day (mean ± SE)] compared to ambient temperatures of 28 and 26 °C (0.73 ± 0.80 cm(2) per day (mean ± SE) and 0.51 ± 0.50 cm(2) per day (mean ± SE), respectively). PMID:26193772

  13. Rapid label-free identification of mixed bacterial infections by surface plasmon resonance

    Directory of Open Access Journals (Sweden)

    Fu Weiling

    2011-06-01

    Full Text Available Abstract Background Early detection of mixed aerobic-anaerobic infection has been a challenge in clinical practice due to the phenotypic changes in complex environments. Surface plasmon resonance (SPR biosensor is widely used to detect DNA-DNA interaction and offers a sensitive and label-free approach in DNA research. Methods In this study, we developed a single-stranded DNA (ssDNA amplification technique and modified the traditional SPR detection system for rapid and simultaneous detection of mixed infections of four pathogenic microorganisms (Pseudomonas aeruginosa, Staphylococcus aureus, Clostridium tetani and Clostridium perfringens. Results We constructed the circulation detection well to increase the sensitivity and the tandem probe arrays to reduce the non-specific hybridization. The use of 16S rDNA universal primers ensured the amplification of four target nucleic acid sequences simultaneously, and further electrophoresis and sequencing confirmed the high efficiency of this amplification method. No significant signals were detected during the single-base mismatch or non-specific probe hybridization (P 2 values of >0.99. The lowest detection limits were 0.03 nM for P. aeruginosa, 0.02 nM for S. aureus, 0.01 nM for C. tetani and 0.02 nM for C. perfringens. The SPR biosensor had the same detection rate as the traditional culture method (P Conclusions Our method can rapidly and accurately identify the mixed aerobic-anaerobic infection, providing a reliable alternative to bacterial culture for rapid bacteria detection.

  14. Nucleic Acid-Based Detection and Identification of Bacterial and Fungal Plant Pathogens - Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Kingsley, Mark T.

    2001-03-13

    The threat to American interests from terrorists is not limited to attacks against humans. Terrorists might seek to inflict damage to the U.S. economy by attacking our agricultural sector. Infection of commodity crops by bacterial or fungal crop pathogens could adversely impact U.S. agriculture, either directly from damage to crops or indirectly from damage to our ability to export crops suspected of contamination. Recognizing a terrorist attack against U.S. agriculture, to be able to prosecute the terrorists, is among the responsibilities of the members of Hazardous Material Response Unit (HMRU) of the Federal Bureau of Investigation (FBI). Nucleic acid analysis of plant pathogen strains by the use of polymerase chain reaction (PCR) amplification techniques is a powerful method for determining the exact identity of pathogens, as well as their possible region of origin. This type of analysis, however, requires that PCR assays be developed specific to each particular pathogen strain, and analysis protocols developed that are specific to the particular instrument used for detection. The objectives of the work described here were threefold: 1) to assess the potential terrorist threat to U.S. agricultural crops, 2) to determine whether suitable assays exist to monitor that threat, and 3) where assays are needed for priority plant pathogen threats, to modify or develop those assays for use by specialists at the HMRU. The assessment of potential threat to U.S. commodity crops and the availability of assays for those threats were described in detail in the Technical Requirements Document (9) and will be summarized in this report. This report addresses development of specific assays identified in the Technical Requirements Document, and offers recommendations for future development to ensure that HMRU specialists will be prepared with the PCR assays they need to protect against the threat of economic terrorism.

  15. Bacterial metabolism of methylated amines and identification of novel methylotrophs in Movile Cave.

    Science.gov (United States)

    Wischer, Daniela; Kumaresan, Deepak; Johnston, Antonia; El Khawand, Myriam; Stephenson, Jason; Hillebrand-Voiculescu, Alexandra M; Chen, Yin; Colin Murrell, J

    2015-01-01

    Movile Cave, Romania, is an unusual underground ecosystem that has been sealed off from the outside world for several million years and is sustained by non-phototrophic carbon fixation. Methane and sulfur-oxidising bacteria are the main primary producers, supporting a complex food web that includes bacteria, fungi and cave-adapted invertebrates. A range of methylotrophic bacteria in Movile Cave grow on one-carbon compounds including methylated amines, which are produced via decomposition of organic-rich microbial mats. The role of methylated amines as a carbon and nitrogen source for bacteria in Movile Cave was investigated using a combination of cultivation studies and DNA stable isotope probing (DNA-SIP) using (13)C-monomethylamine (MMA). Two newly developed primer sets targeting the gene for gamma-glutamylmethylamide synthetase (gmaS), the first enzyme of the recently-discovered indirect MMA-oxidation pathway, were applied in functional gene probing. SIP experiments revealed that the obligate methylotroph Methylotenera mobilis is one of the dominant MMA utilisers in the cave. DNA-SIP experiments also showed that a new facultative methylotroph isolated in this study, Catellibacterium sp. LW-1 is probably one of the most active MMA utilisers in Movile Cave. Methylated amines were also used as a nitrogen source by a wide range of non-methylotrophic bacteria in Movile Cave. PCR-based screening of bacterial isolates suggested that the indirect MMA-oxidation pathway involving GMA and N-methylglutamate is widespread among both methylotrophic and non-methylotrophic MMA utilisers from the cave. PMID:25050523

  16. Species identification of tephritids across a broad taxonomic range using ribosomal D

    International Nuclear Information System (INIS)

    International trade and passenger travel are significant factors in the spread of economically important fruit fly species. The risk of accidental introduction via infested fruit is high, and in New Zealand the recent Medfly incursion in Auckland demonstrated the reality of this threat (Frampton, 2000). There are no economically important species of fruit fly established in New Zealand at present, but 31 are considered high risk in terms of their potential colonisation (refer to the Biosecurity (Notifiable Organisms) Amendment Order 1997). These are amongst a background of non-pest and low risk pest species that may also arrive in fruit from neighbouring countries or trading partners. Quarantine officials closely monitor fruit fly host material at the New Zealand borders (Frampton, 2000). In terms of the action to be taken should an infestation be discovered, there is significant benefit from being able to accurately identify species from the immature life stages, or at least to distinguish the high and low risk groups (Armstrong et al. 1997a). The need for this quarantine application was also highlighted by White (1996) at the previous fruit fly symposium in Sand Keys, Florida, where he summarised the advances made in larval taxonomy over the last decade. Despite this, morphological keys such as those of Steck et al. (1990) and White and Elson Harris (1992), are still only available for about a third of ca. 250 pest species. For those species, even so, identification is not easy and only possible for good quality late instar larvae; there are no morphological characters for early instars or eggs. Until recently in New Zealand, the identification of immature life stages depended entirely on rearing through to adults. This was time consuming and often unsuccessful (Armstrong et al. 1997b). A rapid molecular technique has since been described as a feasible alternative or supplementary quarantine tool (Armstrong et al. 1997a). The method is based on the polymerase

  17. Impact of sampling depth and plant species on local environmental conditions, microbiological parameters and bacterial composition in a mercury contaminated salt marsh

    International Nuclear Information System (INIS)

    Highlights: ► Vegetated habitat contained distinct bacterial communities. ► Variation in bacterial composition with depth differed between plant species. ► There is evidence of an effect of mercury concentration on bacterial composition. ► Depth and sampling depth explained almost 70% of the variation in bacterial composition. - Abstract: We compare the environmental characteristics and bacterial communities associated with two rushes, Juncus maritimus and Bolboschoenus maritimus, and adjacent unvegetated habitat in a salt marsh subjected to historical mercury pollution. Mercury content was higher in vegetated than unvegetated habitat and increased with sampling depth. There was also a significant relationship between mercury concentration and bacterial composition. Habitat (Juncus, Bolboschoenus or unvegetated), sample depth, and the interaction between both, however, explained most of the variation in composition (∼70%). Variation in composition with depth was most prominent for the unvegetated habitat, followed by Juncus, but more constrained for Bolboschoenus habitat. This constraint may be indicative of a strong plant–microbe ecophysiological adaptation. Vegetated habitat contained distinct bacterial communities associated with higher potential activity of aminopeptidase, β-glucosidase and arylsulphatase and incorporation rates of 14C-glucose and 14C-acetate. Communities in unvegetated habitat were, in contrast, associated with both higher pH and proportion of sulphate reducing bacteria.

  18. A unique DNA repair and recombination gene (recN) sequence for identification and intraspecific molecular typing of bacterial wilt pathogen Ralstonia solanacearum and its comparative analysis with ribosomal DNA sequences

    Indian Academy of Sciences (India)

    Aundy Kumar; Thekkan Puthiyaveedu Prameela; Rajamma Suseelabhai

    2013-06-01

    Ribosomal gene sequences are a popular choice for identification of bacterial species and, often, for making phylogenetic interpretations. Although very popular, the sequences of 16S rDNA and 16-23S intergenic sequences often fail to differentiate closely related species of bacteria. The availability of complete genome sequences of bacteria, in the recent years, has accelerated the search for new genome targets for phylogenetic interpretations. The recently published full genome data of nine strains of R. solanacearum, which causes bacterial wilt of crop plants, has provided enormous genomic choices for phylogenetic analysis in this globally important plant pathogen. We have compared a gene candidate recN, which codes for DNA repair and recombination function, with 16S rDNA/16-23S intergenic ribosomal gene sequences for identification and intraspecific phylogenetic interpretations in R. solanacearum. recN gene sequence analysis of R. solanacearum revealed subgroups within phylotypes (or newly proposed species within plant pathogenic genus, Ralstonia), indicating its usefulness for intraspecific genotyping. The taxonomic discriminatory power of recN gene sequence was found to be superior to ribosomal DNA sequences. In all, the recN-sequence-based phylogenetic tree generated with the Bayesian model depicted 21 haplotypes against 15 and 13 haplotypes obtained with 16S rDNA and 16-23S rDNA intergenic sequences, respectively. Besides this, we have observed high percentage of polymorphic sites (S 23.04%), high rate of mutations (Eta 276) and high codon bias index (CBI 0.60), which makes the recN an ideal gene candidate for intraspecific molecular typing of this important plant pathogen.

  19. Identification and characterization of pathogen to bacterial septicaemia in cultured turbot, Scophthalmus maximus

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Bacteria-infected turbots Scophthalmus maximus with septicaemia were examined between 2001 and 2004 in aspects of the conditions of disease occurrence, clinical syndromes and pathological changes. The phenotypic information of pathogenic bacteria was studied, including morphology,physiological and biochemical characteristics, and the mol% G+C of the DNA. In addition, representative strains (S010623-1, LH031120-1) were selected for molecular identification by partial 16S rRNA gene sequencing. The results show that the isolates (LH031120-1 to LH031120-6, HT040308-1 to HT040308-6,HT040620-1 to HT040620-6) from three farms were identified as Edwardsiella tarda. The isolates (S010610-1 to S010610-10, S010623-1 to S010623-20) from one farm were identified as Listonella anguillarum. We conducted studies on the pathogenicity of isolates by artificial infection, and revealed all infected groups in morbidity and mortality. The septicaemia infected turbot showed a syndrome similar to that of the naturally infected fish. Antibiotic sensitivity showed that of 37 antimicrobial agents, E. tarda was sensitive to 27 agents, and L. anguillarum was sensitive to 21 agents.

  20. Peracetic Acid Treatment Generates Potent Inactivated Oral Vaccines from a Broad Range of Culturable Bacterial Species.

    Science.gov (United States)

    Moor, Kathrin; Wotzka, Sandra Y; Toska, Albulena; Diard, Médéric; Hapfelmeier, Siegfried; Slack, Emma

    2016-01-01

    Our mucosal surfaces are the main sites of non-vector-borne pathogen entry, as well as the main interface with our commensal microbiota. We are still only beginning to understand how mucosal adaptive immunity interacts with commensal and pathogenic microbes to influence factors such as infectivity, phenotypic diversity, and within-host evolution. This is in part due to difficulties in generating specific mucosal adaptive immune responses without disrupting the mucosal microbial ecosystem itself. Here, we present a very simple tool to generate inactivated mucosal vaccines from a broad range of culturable bacteria. Oral gavage of 10(10) peracetic acid-inactivated bacteria induces high-titer-specific intestinal IgA in the absence of any measurable inflammation or species invasion. As a proof of principle, we demonstrate that this technique is sufficient to provide fully protective immunity in the murine model of invasive non-typhoidal Salmonellosis, even in the face of severe innate immune deficiency. PMID:26904024

  1. Interaction of legionella pneumophila and helicobacter pylori with bacterial species isolated from drinking water biofilms

    Directory of Open Access Journals (Sweden)

    Azevedo Nuno F

    2011-03-01

    Full Text Available Abstract Background It is well established that Legionella pneumophila is a waterborne pathogen; by contrast, the mode of Helicobacter pylori transmission remains unknown but water seems to play an important role. This work aims to study the influence of five microorganisms isolated from drinking water biofilms on the survival and integration of both of these pathogens into biofilms. Results Firstly, both pathogens were studied for auto- and co-aggregation with the species isolated from drinking water; subsequently the formation of mono and dual-species biofilms by L. pneumophila or H. pylori with the same microorganisms was investigated. Neither auto- nor co-aggregation was observed between the microorganisms tested. For biofilm studies, sessile cells were quantified in terms of total cells by SYTO 9 staining, viable L. pneumophila or H. pylori cells were quantified using 16 S rRNA-specific peptide nucleic acid (PNA probes and cultivable cells by standard culture techniques. Acidovorax sp. and Sphingomonas sp. appeared to have an antagonistic effect on L. pneumophila cultivability but not on the viability (as assessed by rRNA content using the PNA probe, possibly leading to the formation of viable but noncultivable (VBNC cells, whereas Mycobacterium chelonae increased the cultivability of this pathogen. The results obtained for H. pylori showed that M. chelonae and Sphingomonas sp. help this pathogen to maintain cultivability for at least 24 hours. Conclusions It appears that M. chelonae may have an important role in the survival of both pathogens in drinking water. This work also suggests that the presence of some microorganisms can decrease the cultivability of L. pneumophila but not the viability which indicates that the presence of autochthonous microorganisms can lead to misleading results when the safety of water is assessed by cultivable methods alone.

  2. A Multi-Unit Project for Building Scientific Confidence via Authentic Research in Identification of Environmental Bacterial Isolates

    Directory of Open Access Journals (Sweden)

    Christa Chatfield

    2014-08-01

    Full Text Available This authentic research project is designed to identify environmental isolates by metabolic phenotypes and 16s sequence analysis and with an investigation of biofilm growth is presented as implemented in an upper-level microbiology lab course. Three units were used in the lab: one for basic metabolic identification, one for the 16s rDNA sequencing and a third for biofilm growth analysis. Assessment was by weekly notebook entries detailing the outcomes of each day in lab, providing relatively on-time feedback on student understanding and learning to both the student and the instructor. The intent for these units was for each to increase the uncertainty of the project outcomes and to challenge students to design projects with open-ended results. All student groups have been able to obtain DNA sequence data in the limited 6-7 weeks of the lab project. Students report increased confidence in their abilities and a general excitement about the project methods and results. The data produced by the students can be incorporated into larger research questions posed by the faculty running the course as determined by the source of the unknown bacterial isolates.

  3. An X-ray Absorption Fine Structure study of Au adsorbed onto the non-metabolizing cells of two soil bacterial species

    Energy Technology Data Exchange (ETDEWEB)

    Song, Zhen; Kenney, Janice P.L.; Fein, Jeremy B.; Bunker, Bruce A. (Notre)

    2015-02-09

    Gram-positive and Gram-negative bacterial cells can remove Au from Au(III)-chloride solutions, and the extent of removal is strongly pH dependent. In order to determine the removal mechanisms, X-ray Absorption Fine Structure (XAFS) spectroscopy experiments were conducted on non-metabolizing biomass of Bacillus subtilis and Pseudomonas putida with fixed Au(III) concentrations over a range of bacterial concentrations and pH values. X-ray Absorption Near Edge Structure (XANES) and Extended X-ray Absorption Fine Structure (EXAFS) data on both bacterial species indicate that more than 90% of the Au atoms on the bacterial cell walls were reduced to Au(I). In contrast to what has been observed for Au(III) interaction with metabolizing bacterial cells, no Au(0) or Au-Au nearest neighbors were observed in our experimental systems. All of the removed Au was present as adsorbed bacterial surface complexes. For both species, the XAFS data suggest that although Au-chloride-hydroxide aqueous complexes dominate the speciation of Au in solution, Au on the bacterial cell wall is characterized predominantly by binding of Au atoms to sulfhydryl functional groups and amine and/or carboxyl functional groups, and the relative importance of the sulfhydryl groups increases with increasing pH and with decreasing Au loading. The XAFS data for both microorganism species suggest that adsorption is the first step in the formation of Au nanoparticles by bacteria, and the results enhance our ability to account for the behavior of Au in bacteria-bearing geologic systems.

  4. Increasing the dynamic control space of mammalian transcription devices by combinatorial assembly of homologous regulatory elements from different bacterial species.

    Science.gov (United States)

    Bacchus, William; Weber, Wilfried; Fussenegger, Martin

    2013-01-01

    Prokaryotic transcriptional regulatory elements are widely utilized building blocks for constructing regulatory genetic circuits adapted for mammalian cells and have found their way into a broad range of biotechnological applications. Prokaryotic transcriptional repressors, fused to eukaryotic transactivation or repression domains, compose the transcription factor, which binds and adjusts transcription from chimeric promoters containing the repressor-specific operator sequence. Escherichia coli and Chlamydia trachomatis share common features in the regulatory mechanism of the biosynthesis of l-tryptophan. The repressor protein TrpR of C. trachomatis regulates the trpRBA operon and the TrpR of E. coli regulates the trpEDCBA operon, both requiring l-tryptophan as a co-repressor. Fusion of these bacterial repressors to the VP16 transactivation domain of Herpes simplex virus creates synthetic transactivators that could bind and activate chimeric promoters, assembled by placing repressor-specific operator modules adjacent to a minimal promoter, in an l-tryptophan-adjustable manner. Combinations of different transactivator and promoter variants from the same or different bacterial species resulted in a multitude of regulatory systems where l-tryptophan regulation properties, background noise, and maximal gene expression levels were significantly diverse. Different l-tryptophan analogues showed diverse regulatory capacity depending on the promoter/transactivator combination. We believe the systems approach to rationally choose promoters, transactivators and inducer molecules, to obtain desired and predefined genetic expression dynamics and control profiles, will significantly advance the design of new regulatory circuits as well as improving already existing ones. PMID:23178502

  5. Optimization and evaluation of Flexicult® Vet for detection, identification and antimicrobial susceptibility testing of bacterial uropathogens in small animal veterinary practice

    OpenAIRE

    Guardabassi, Luca; Hedberg, Sandra; Jessen, Lisbeth Rem; Damborg, Peter Panduro

    2015-01-01

    BACKGROUND: Urinary tract infection (UTI) is a common reason for antimicrobial prescription in dogs and cats. The objective of this study was to optimize and evaluate a culture-based point-of-care test for detection, identification and antimicrobial susceptibility testing of bacterial uro-pathogens in veterinary practice.METHODS: Seventy-two urine samples from dogs and cats with suspected UTI presenting to seven veterinary facilities were used by clinical staff and an investigator to estimate...

  6. Comparative analysis of midgut bacterial communities in three aedine mosquito species from dengue-endemic and non-endemic areas of Rajasthan, India.

    Science.gov (United States)

    Charan, S S; Pawar, K D; Gavhale, S D; Tikhe, C V; Charan, N S; Angel, B; Joshi, V; Patole, M S; Shouche, Y S

    2016-09-01

    Dengue viruses are transmitted to humans through the bites of infected female aedine mosquitoes. Differences in the composition and structure of bacterial communities in the midguts of mosquitoes may affect the vector's ability to transmit the disease. To investigate and analyse the role of midgut bacterial communities in viral transmission, midgut bacteria from three species, namely Stegomyia aegypti (= Aedes aegypti), Fredwardsius vittatus (= Aedes vittatus) and Stegomyia albopicta (= Aedes albopictus) (all: Diptera: Culicidae), from dengue-endemic and non-endemic areas of Rajasthan, India were compared. Construction and analyses of six 16S rRNA gene libraries indicated that Serratia spp.-related phylotypes dominated all clone libraries of the three mosquito species from areas in which dengue is not endemic. In dengue-endemic areas, phylotypes related to Aeromonas, Enhydrobacter spp. and uncultivated bacterium dominated the clone libraries of S. aegypti, F. vittatus and S. albopicta, respectively. Diversity indices analysis and real-time TaqMan polymerase chain reaction assays showed bacterial diversity and abundance in the midguts of S. aegypti to be higher than in the other two species. Significant differences observed among midgut bacterial communities of the three mosquito species from areas in which dengue is and is not endemic, respectively, may be related to the vectorial capacity of mosquitoes to carry dengue viruses and, hence, to the prevalence of disease in some areas. PMID:27094337

  7. Comparative Genomics between Two Xenorhabdus bovienii Strains Highlights Differential Evolutionary Scenarios within an Entomopathogenic Bacterial Species.

    Science.gov (United States)

    Bisch, Gaëlle; Ogier, Jean-Claude; Médigue, Claudine; Rouy, Zoé; Vincent, Stéphanie; Tailliez, Patrick; Givaudan, Alain; Gaudriault, Sophie

    2016-01-01

    Bacteria of the genus Xenorhabdus are symbionts of soil entomopathogenic nematodes of the genus Steinernema. This symbiotic association constitutes an insecticidal complex active against a wide range of insect pests. Within Xenorhabdus bovienii species, the X. bovienii CS03 strain (Xb CS03) is nonvirulent when directly injected into lepidopteran insects, and displays a low virulence when associated with its Steinernema symbiont. The genome of Xb CS03 was sequenced and compared with the genome of a virulent strain, X. bovienii SS-2004 (Xb SS-2004). The genome size and content widely differed between the two strains. Indeed, Xb CS03 had a large genome containing several specific loci involved in the inhibition of competitors, including a few NRPS-PKS loci (nonribosomal peptide synthetases and polyketide synthases) producing antimicrobial molecules. Consistently, Xb CS03 had a greater antimicrobial activity than Xb SS-2004. The Xb CS03 strain contained more pseudogenes than Xb SS-2004. Decay of genes involved in the host invasion and exploitation (toxins, invasins, or extracellular enzymes) was particularly important in Xb CS03. This may provide an explanation for the nonvirulence of the strain when injected into an insect host. We suggest that Xb CS03 and Xb SS-2004 followed divergent evolutionary scenarios to cope with their peculiar life cycle. The fitness strategy of Xb CS03 would involve competitor inhibition, whereas Xb SS-2004 would quickly and efficiently kill the insect host. Hence, Xenorhabdus strains would have widely divergent host exploitation strategies, which impact their genome structure. PMID:26769959

  8. Survival of added bacterial species and metabolism of toxic compounds in natural environments

    International Nuclear Information System (INIS)

    Bacteria able to degrade either 2,4-dichlorophenol (DCP) or phenanthrene (PHEN) were isolated from polluted freshwater environments. Two isolates able to degrade each compound were tested for mineralization with a sensitive 14C assay and for survival in lake water and sewage using a selective medium. One DCP isolate was identified as Alcaligenes paradoxus and the other as Alcaligenes sp. One PHEN isolate was identified as Pseudomonas fluorescens and the other as Pseudomonas sp. All four isolates survived and grew in sterile environments which indicated that starvation would not be a factor in survival of these strains. The number of organisms declined immediately in number in nonsterile lake water. However, they did survive or even grow in nonsterile sewage for a short period before declining in number. Biotic factors appeared to be influential for survival and mineralization of target compounds in many environments. The removal of protozoa, which prey on bacteria, improved survival of the added cells, but had no influence on the mineralization of 10 μg DCP/L. In comparison, degradation of 10 and 25 mg DCP/L stopped after a few days. Yeast nitrogen base appeared to overcome the lack of nutrient regeneration, a function attributed to protozoa. The additional nutrients increased toxicant mineralization, especially when seeded with appropriate species. Thus, protozoa may limit growth of added cells but appear to be needed for mineralization of higher concentrations of DCP

  9. A cross-sectional survey of bacterial species in plaque from client owned dogs with healthy gingiva, gingivitis or mild periodontitis.

    Science.gov (United States)

    Davis, Ian J; Wallis, Corrin; Deusch, Oliver; Colyer, Alison; Milella, Lisa; Loman, Nick; Harris, Stephen

    2013-01-01

    Periodontal disease is the most widespread oral disease in dogs which if left untreated results in significant pain to the pet and loss of dentition. The objective of this study was to identify bacterial species in canine plaque that are significantly associated with health, gingivitis and mild periodontitis (plaque samples were collected from 223 dogs with healthy gingiva, gingivitis and mild periodontitis with 72 to 77 samples per health status. DNA was extracted from the plaque samples and subjected to PCR amplification of the V1-V3 region of the 16S rDNA. Pyrosequencing of the PCR amplicons identified a total of 274 operational taxonomic units after bioinformatic and statistical analysis. Porphyromonas was the most abundant genus in all disease stages, particularly in health along with Moraxella and Bergeyella. Peptostreptococcus, Actinomyces, and Peptostreptococcaceae were the most abundant genera in mild periodontitis. Logistic regression analysis identified species from each of these genera that were significantly associated with health, gingivitis or mild periodontitis. Principal component analysis showed distinct community profiles in health and disease. The species identified show some similarities with health and periodontal disease in humans but also major differences. In contrast to human, healthy canine plaque was found to be dominated by Gram negative bacterial species whereas Gram positive anaerobic species predominate in disease. The scale of this study surpasses previously published research and enhances our understanding of the bacterial species present in canine subgingival plaque and their associations with health and early periodontal disease. PMID:24349448

  10. Identification and Phylogeny of the First T Cell Epitope Identified from a Human Gut Bacteroides Species.

    Directory of Open Access Journals (Sweden)

    Maria Elisa Perez-Muñoz

    Full Text Available Host T cell reactivity toward gut bacterial epitopes has been recognized as part of disease pathogenesis. However, the specificity of T cells that recognize this vast number of epitopes has not yet been well described. After colonizing a C57BL/6J germ-free mouse with the human gut symbiotic bacteria Bacteroides thetaiotaomicron, we isolated a T cell that recognized these bacteria in vitro. Using this T cell, we mapped the first known non-carbohydrate T cell epitope within the phylum Bacteroidetes. The T cell also reacted to two other additional Bacteroides species. We identified the peptide that stimulated the T cell by using a genetic approach. Genomic data from the epitope-positive and epitope-negative bacteria explain the cross-reactivity of the T cell to multiple species. This epitope degeneracy should shape our understanding of the T cell repertoire stimulated by the complex microbiome residing in the gastrointestinal tract in both healthy and disease states.

  11. Virome analysis for identification of novel mammalian viruses in bat species from Chinese provinces.

    Science.gov (United States)

    Wu, Zhiqiang; Ren, Xianwen; Yang, Li; Hu, Yongfeng; Yang, Jian; He, Guimei; Zhang, Junpeng; Dong, Jie; Sun, Lilian; Du, Jiang; Liu, Liguo; Xue, Ying; Wang, Jianmin; Yang, Fan; Zhang, Shuyi; Jin, Qi

    2012-10-01

    Bats are natural hosts for a large variety of zoonotic viruses. This study aimed to describe the range of bat viromes, including viruses from mammals, insects, fungi, plants, and phages, in 11 insectivorous bat species (216 bats in total) common in six provinces of China. To analyze viromes, we used sequence-independent PCR amplification and next-generation sequencing technology (Solexa Genome Analyzer II; Illumina). The viromes were identified by sequence similarity comparisons to known viruses. The mammalian viruses included those of the Adenoviridae, Herpesviridae, Papillomaviridae, Retroviridae, Circoviridae, Rhabdoviridae, Astroviridae, Flaviridae, Coronaviridae, Picornaviridae, and Parvovirinae; insect viruses included those of the Baculoviridae, Iflaviridae, Dicistroviridae, Tetraviridae, and Densovirinae; fungal viruses included those of the Chrysoviridae, Hypoviridae, Partitiviridae, and Totiviridae; and phages included those of the Caudovirales, Inoviridae, and Microviridae and unclassified phages. In addition to the viruses and phages associated with the insects, plants, and bacterial flora related to the diet and habitation of bats, we identified the complete or partial genome sequences of 13 novel mammalian viruses. These included herpesviruses, papillomaviruses, a circovirus, a bocavirus, picornaviruses, a pestivirus, and a foamy virus. Pairwise alignments and phylogenetic analyses indicated that these novel viruses showed little genetic similarity with previously reported viruses. This study also revealed a high prevalence and diversity of bat astroviruses and coronaviruses in some provinces. These findings have expanded our understanding of the viromes of bats in China and hinted at the presence of a large variety of unknown mammalian viruses in many common bat species of mainland China. PMID:22855479

  12. A contribution to the identification of charcoal origin in Brazil II - Macroscopic characterization of Cerrado species.

    Science.gov (United States)

    Gonçalves, Thaís A P; Nisgoski, Silvana; Oliveira, Julia S; Marcati, Carmen R; Ballarin, Adriano W; Muñiz, Graciela I B

    2016-05-13

    The Brazilian Cerrado is the richest savanna in the world. It is also one of the biomes more threatened in the country and a hotspot for conservation priorities. The main causes of deforestation in Cerrado are agricultural practices, livestock and charcoal production. Although charcoal has a minor impact, its consumption represents the deforestation of 16.000 Km² of the Cerrado. To contribute for the biomes's conservation it is very important to improve forestry supervision. Thus, in this work we present the macroscopic characterization of charcoal from 25 Cerrado's species. We simulate the real conditions of forest controllers by using the magnifications of 10x, 25x and 65x. Likewise, the charcoals micrographs are all of transverse sections due to the larger amount of anatomical information. We also analyzed texture, brightness, vitrification, ruptures and some special features. The species present several differences in their anatomical structure. Although some of them are very unique, this work does not intent to identify charcoals only by macroscopic analyses. But it might give directions to future identification of genera or species. It also provides knowledge for government agents to verify the documents of forestry origin by fast analyzing a sample of charcoal itself. PMID:27192198

  13. Crop species identification using machine vision of computer extracted individual leaves

    Science.gov (United States)

    Camargo Neto, João; Meyer, George E.

    2005-11-01

    An unsupervised method for plant species identification was developed which uses computer extracted individual whole leaves from color images of crop canopies. Green canopies were isolated from soil/residue backgrounds using a modified Excess Green and Excess Red separation method. Connected components of isolated green regions of interest were changed into pixel fragments using the Gustafson-Kessel fuzzy clustering method. The fragments were reassembled as individual leaves using a genetic optimization algorithm and a fitness method. Pixels of whole leaves were then analyzed using the elliptic Fourier shape and Haralick's classical textural feature analyses. A binary template was constructed to represent each selected leaf region of interest. Elliptic Fourier descriptors were generated from a chain encoding of the leaf boundary. Leaf template orientation was corrected by rotating each extracted leaf to a standard horizontal position. This was done using information provided from the first harmonic set of coefficients. Textural features were computed from the grayscale co-occurrence matrix of the leaf pixel set. Standardized leaf orientation significantly improved the leaf textural venation results. Principle component analysis from SAS (R) was used to select the best Fourier descriptors and textural indices. Indices of local homogeneity, and entropy were found to contribute to improved classification rates. A SAS classification model was developed and correctly classified 83% of redroot pigweed, 100% of sunflower 83% of soybean, and 73% of velvetleaf species. An overall plant species correct classification rate of 86% was attained.

  14. Identification of meat species by using laser-induced breakdown spectroscopy.

    Science.gov (United States)

    Bilge, Gonca; Velioglu, Hasan Murat; Sezer, Banu; Eseller, Kemal Efe; Boyaci, Ismail Hakki

    2016-09-01

    The aim of the present study is to identify meat species by using laser-induced breakdown spectroscopy (LIBS). Elemental composition differences between meat species were used for meat identification. For this purpose, certain amounts of pork, beef and chicken were collected from different sources and prepared as pellet form for LIBS measurements. The obtained LIBS spectra were evaluated with some chemometric methods, and meat species were qualitatively discriminated with principal component analysis (PCA) method with 83.37% ratio. Pork-beef and chicken-beef meat mixtures were also analyzed with partial least square (PLS) method quantitatively. Determination coefficient (R(2)) and limit of detection (LOD) values were found as 0.994 and 4.4% for pork adulterated beef, and 0.999 and 2.0% for chicken adulterated beef, respectively. In the light of the findings, it was seen that LIBS can be a valuable tool for quality control measurements of meat as a routine method. PMID:27179147

  15. Identification of a potential fungal species by 18S rDNA for ligninases production.

    Science.gov (United States)

    Ferhan, M; Santos, S N; Melo, I S; Yan, N; Sain, M

    2013-12-01

    Fungal species for ligninases production was investigated by 18S ribosomal DNA sequence analysis. Two primer sets were chosen to amplify a major part of the 18S rDNA, which resulted in intense PCR product of approximately 550-820 bp in size per sample. The results suggest that the 18S rDNA-based approach is a useful tool for identification of unknown potential fungal species for ligninases production. The isolated fungal species produces mainly manganese peroxidase (MnP). The enzyme oxidized a variety of the usual MnP substrates, including lignin related polyphenols. Time course studies showed that maximum production of ligninolytic enzymes MnP (64 IU L⁻¹), lignin peroxidase (26.35 IU L⁻¹), and laccase (5.44 IU L⁻¹), respectively, were achieved after 10 days of cultivation under optimum conditions. Furthermore, the biological decolorization of Remazol Brilliant Blue R dye following 10 days of cultivation was 94 %. NCBI BLAST was used to search for closest matched sequences in the GenBank database and based on sequence homology the first BLAST hit was Dothioraceae sp. LM572 with accession number EF060858.1. PMID:23744034

  16. HG/LT-GC/ICP-MS coupling for identification of metal(loid) species in human urine after fish consumption

    Energy Technology Data Exchange (ETDEWEB)

    Kresimon, J.; Grueter, U.M.; Hirner, A.V. [Inst. of Environmental Analytical Chemistry, University of Essen (Germany)

    2001-11-01

    Human urine samples after fish consumption have been investigated by low-temperature gas chromatography with inductively coupled plasma mass spectrometric detection after sample derivatization by hydride generation (HG/LT-GC/ICP-MS). This analytical technique enabled the identification of organometal(loid) compounds in human urine; species of the six elements germanium, arsenic, selenium, tin, antimony, and mercury were determined.Three different organic selenium species, two germanium species, seven arsenic species, four tin species, five antimony species, and one species of mercury were found; 18 of the 22 species detected could be identified. The relative detection limits ranged between 2 and 12 pg x L{sup -1} (x=element). These organometal(loid) compounds probably build up in the human body under the influence of micro-organisms, in the presence of hydrogen sulfide and methane, in the human intestine. (orig.)

  17. Use of Molecular Diagnostic Tools for the Identification of Species Responsible for Snakebite in Nepal: A Pilot Study

    Science.gov (United States)

    Sharma, Sanjib Kumar; Kuch, Ulrich; Höde, Patrick; Bruhse, Laura; Pandey, Deb P.; Ghimire, Anup; Chappuis, François; Alirol, Emilie

    2016-01-01

    Snakebite is an important medical emergency in rural Nepal. Correct identification of the biting species is crucial for clinicians to choose appropriate treatment and anticipate complications. This is particularly important for neurotoxic envenoming which, depending on the snake species involved, may not respond to available antivenoms. Adequate species identification tools are lacking. This study used a combination of morphological and molecular approaches (PCR-aided DNA sequencing from swabs of bite sites) to determine the contribution of venomous and non-venomous species to the snakebite burden in southern Nepal. Out of 749 patients admitted with a history of snakebite to one of three study centres, the biting species could be identified in 194 (25.9%). Out of these, 87 had been bitten by a venomous snake, most commonly the Indian spectacled cobra (Naja naja; n = 42) and the common krait (Bungarus caeruleus; n = 22). When both morphological identification and PCR/sequencing results were available, a 100% agreement was noted. The probability of a positive PCR result was significantly lower among patients who had used inadequate “first aid” measures (e.g. tourniquets or local application of remedies). This study is the first to report the use of forensic genetics methods for snake species identification in a prospective clinical study. If high diagnostic accuracy is confirmed in larger cohorts, this method will be a very useful reference diagnostic tool for epidemiological investigations and clinical studies. PMID:27105074

  18. Identification of a bacterial pectin acetyl esterase in Erwinia chrysanthemi 3937.

    Science.gov (United States)

    Shevchik, V E; Hugouvieux-Cotte-Pattat, N

    1997-06-01

    Erwinia chrysanthemi causes soft-rot diseases of various plants by enzymatic degradation of the pectin in plant cell walls. The structural complexity of pectin requires the combined action of several pectinases for its efficient breakdown. Three types of pectinases have so far been identified in E. chrysanthemi: two pectin methyl esterases (PemA, PemB), a polygalacturonase (PehX), and eight pectate lyases (PelA, PelB, PelC, PelD, PelE, PelL, PelZ, PelX). We report in this paper the analysis of a novel enzyme, the pectin acetyl esterase encoded by the paeY gene. No bacterial form of pectin acetyl esterases has been described previously, while plant tissues and some pectinolytic fungi were found to produce similar enzymes. The paeY gene is present in a cluster of five pectinase-encoding genes, pelA-pelE-pelD-paeY-pemA. The paeY open reading frame is 1650 bases long and encodes a 551-residue precursor protein of 60704Da, including a 25-amino-acid signal peptide. PaeY shares one region of homology with a rhamnogalacturonan acetyl esterase of Aspergillus aculeatus. To characterize the enzyme, the paeY gene was overexpressed and its protein product was purified. PaeY releases acetate from sugar-beet pectin and from various synthetic substrates. Moreover, the enzyme was shown to act in synergy with other pectinases. The de-esterification rate by PaeY increased after previous demethylation of the pectins by PemA and after depolymerization of the pectin by pectate lyases. In addition, the degradation of sugar-beet pectin by pectate lyases is favoured after the removal of methyl and acetyl groups by PemA and PaeY, respectively. The paeY gene was first identified on the basis of its regulation, which shares several characteristics with that of other pectinases. Analysis of the paeY transcription, using gene fusions, revealed that it is induced by pectic catabolic products and is affected by growth phase, oxygen limitation and catabolite repression. Regulation of pae

  19. Single-Step PCR Using (GACA)4 Primer: Utility for Rapid Identification of Dermatophyte Species and Strains▿

    OpenAIRE

    Shehata, Atef S.; Mukherjee, Pranab K.; Aboulatta, Hassan N.; El Akhras, Atef I.; Abbadi, Said H.; Ghannoum, Mahmoud A.

    2008-01-01

    Dermatophytes are fungi that belong to three genera: Epidermophyton, Microsporum, and Trichophyton. Identification of dermatophyte species is essential for appropriate diagnosis and treatment of dermatophytosis. Routine identification depends on macroscopic and microscopic morphology, which is time-consuming and does not identify dermatophyte strains. In this study, two PCR-based methods were compared for their abilities to identify 21 dermatophyte isolates obtained from Egyptian patients to ...

  20. PCR amplification of species-specific repeat for meat DNA identification via genetic markers in cattle and sheep

    OpenAIRE

    Ahmed M.M.

    2005-01-01

    The designed and evaluated four assays based upon PCR amplification of species-specific repeat (SSR) for detection, identification and authentication of cattle and sheep on the DNA level. SSR primers were applied in the polymerase chain reaction (PCR), the products has been used for the specific identification of cattle and sheep meat. PCR amplification size of the gene encoding SSR region in cattle and sheep meat was 603 bp and 374 bp respectively. The results showed that SSR analysis produc...

  1. In silico identification of conserved microRNAs in large number of diverse plant species

    Directory of Open Access Journals (Sweden)

    Jagadeeswaran Guru

    2008-04-01

    Full Text Available Abstract Background MicroRNAs (miRNAs are recently discovered small non-coding RNAs that play pivotal roles in gene expression, specifically at the post-transcriptional level in plants and animals. Identification of miRNAs in large number of diverse plant species is important to understand the evolution of miRNAs and miRNA-targeted gene regulations. Now-a-days, publicly available databases play a central role in the in-silico biology. Because, at least ~21 miRNA families are conserved in higher plants, a homology based search using these databases can help identify orthologs or paralogs in plants. Results We searched all publicly available nucleotide databases of genome survey sequences (GSS, high-throughput genomics sequences (HTGS, expressed sequenced tags (ESTs and nonredundant (NR nucleotides and identified 682 miRNAs in 155 diverse plant species. We found more than 15 conserved miRNA families in 11 plant species, 10 to14 families in 10 plant species and 5 to 9 families in 29 plant species. Nineteen conserved miRNA families were identified in important model legumes such as Medicago, Lotus and soybean. Five miRNA families – miR319, miR156/157, miR169, miR165/166 and miR394 – were found in 51, 45, 41, 40 and 40 diverse plant species, respectively. miR403 homologs were found in 16 dicots, whereas miR437 and miR444 homologs, as well as the miR396d/e variant of the miR396 family, were found only in monocots, thus providing large-scale authenticity for the dicot- and monocot-specific miRNAs. Furthermore, we provide computational and/or experimental evidence for the conservation of 6 newly found Arabidopsis miRNA homologs (miR158, miR391, miR824, miR825, miR827 and miR840 and 2 small RNAs (small-85 and small-87 in Brassica spp. Conclusion Using all publicly available nucleotide databases, 682 miRNAs were identified in 155 diverse plant species. By combining the expression analysis with the computational approach, we found that 6 miRNAs and 2

  2. Oligonucleotide indexing of DNA barcodes: identification of tuna and other scombrid species in food products

    Directory of Open Access Journals (Sweden)

    Botti Sara

    2010-08-01

    Full Text Available Abstract Background DNA barcodes are a global standard for species identification and have countless applications in the medical, forensic and alimentary fields, but few barcoding methods work efficiently in samples in which DNA is degraded, e.g. foods and archival specimens. This limits the choice of target regions harbouring a sufficient number of diagnostic polymorphisms. The method described here uses existing PCR and sequencing methodologies to detect mitochondrial DNA polymorphisms in complex matrices such as foods. The reported application allowed the discrimination among 17 fish species of the Scombridae family with high commercial interest such as mackerels, bonitos and tunas which are often present in processed seafood. The approach can be easily upgraded with the release of new genetic diversity information to increase the range of detected species. Results Cocktail of primers are designed for PCR using publicly available sequences of the target sequence. They are composed of a fixed 5' region and of variable 3' cocktail portions that allow amplification of any member of a group of species of interest. The population of short amplicons is directly sequenced and indexed using primers containing a longer 5' region and the non polymorphic portion of the cocktail portion. A 226 bp region of CytB was selected as target after collection and screening of 148 online sequences; 85 SNPs were found, of which 75 were present in at least two sequences. Primers were also designed for two shorter sub-fragments that could be amplified from highly degraded samples. The test was used on 103 samples of seafood (canned tuna and scomber, tuna salad, tuna sauce and could successfully detect the presence of different or additional species that were not identified on the labelling of canned tuna, tuna salad and sauce samples. Conclusions The described method is largely independent of the degree of degradation of DNA source and can thus be applied to

  3. Collaborative processes in species identification using an internet-based taxonomic resource

    Science.gov (United States)

    Kontkanen, Jani; Kärkkäinen, Sirpa; Dillon, Patrick; Hartikainen-Ahia, Anu; Åhlberg, Mauri

    2016-01-01

    Visual databases are increasingly important resources through which individuals and groups can undertake species identification. This paper reports research on the collaborative processes undertaken by pre-service teacher students when working in small groups to identify birds using an Internet-based taxonomic resource. The student groups are conceptualised as 'knowledge-building communities' working in a 'joint problem space' comprising the collective knowledge of the participants interacting with the taxonomic database. Collaborative group work and associated dialogue were recorded with digital video. The recordings were analysed for the categories of dialogue and the categories of knowledge used by the students as they interacted with the taxonomic database and how they drew on their previous experiences of identifying birds. The outcomes are discussed in the context of the interplay of individual and social processes and the interplay between abstraction and lived experience in the joint problem space.

  4. Simultaneous Identification of Neutral and Anionic Species in Complex Mixtures without Separation.

    Science.gov (United States)

    Zhao, Yanchuan; Chen, Lily; Swager, Timothy M

    2016-01-18

    A chemosensory system is reported that operates without the need for separation techniques and is capable of identifying anions and structurally similar bioactive molecules. In this strategy, the coordination of analytes to a metal complex with an open binding cleft generates "static structures" on the NMR timescale. Unique signals are created by strategically placing fluorine atoms in close proximity to bound analytes so that small structural differences induce distinct (19)F NMR shifts that can be used to identify each analyte. The utility of this method is illustrated by quantifying caffeine levels in coffee, by identifying ingredients in tea and energy drinks, and by discriminating between multiple biogenic amines with remote structural differences six carbon atoms away from the binding site. We further demonstrate the simultaneous identification of multiple neutral and anionic species in a complex mixture. PMID:26756442

  5. Sea cucumber species identification of family Caudinidae from Surabaya based on morphological and mitochondrial DNA evidence

    Science.gov (United States)

    Amin, Muhammad Hilman Fu'adil; Pidada, Ida Bagus Rai; Sugiharto, Widyatmoko, Johan Nuari; Irawan, Bambang

    2016-03-01

    Species identification and taxonomy of sea cucumber remains a challenge problem in some taxa. Caudinidae family of sea cucumber was comerciallized in Surabaya, and it was used as sea cucumber chips. Members of Caudinid sea cucumber have similiar morphology, so it is hard to identify this sea cucumber only from morphological appearance. DNA barcoding is useful method to overcome this problem. The aim of this study was to determine Caudinid specimen of sea cucumber in East Java by morphological and molecular approach. Sample was collected from east coast of Surabaya, then preserved in absolute ethanol. After DNA isolation, Cytochrome Oxydase I (COI) gene amplification was performed using Echinoderm universal primer and PCR product was sequenced. Sequencing result was analyzed and identified in NCBI database using BLAST. Results showed that Caudinid specimen in have closely related to Acaudina molpadioides sequence in GenBank with 86% identity. Morphological data, especially based on ossicle, also showed that the specimen is Acaudina molpadioides.

  6. Fish species identification based on its acoustic target strength using in situ measurement

    Directory of Open Access Journals (Sweden)

    Raja-Bidin Raja-Hassan

    2010-11-01

    Full Text Available The purpose of this study is fish species identification using acoustic target strength (TS. Insitu measurement has been deployed at the South China Sea of Terengganu Malaysia using Furuno FQ-80 Scientific Echo Sounder which included in the research vessel of KK Senangin II. The transducer isplaced 2.8 meter under sea surface while fish put in the net cage under the vessel. TS data have beencollected independently for commercial fish in Malaysia, there are Selar boops (Oxeye scad, Alepesdjedaba (Shrimp scad, Megalaspis cordyla (Torpedo scad, and Decapterus maruadsi/b> (Japanese scad.TS value, depth, and position of specific target have been observed using echogram. TS of every speciesis different although similar size and at the similar range from transducer. Thus, the specific fish specieshas been identified based on its acoustic target strength.

  7. Candida colonization and species identification by two methods in NICU newborn

    Directory of Open Access Journals (Sweden)

    Narges Sadat Taherzadeh

    2016-02-01

    Full Text Available Background: Over the last two decades invasive candidiasis has become an increasing problem in neonatal intensive care units (NICUs. Colonization of skin and mucous membranes with Candida spp. is important factor in the pathogenesis of neonatal infection and several colonized sites are major risk factors evoking higher frequencies of progression to invasive candidiasis. The aim of this study was to detect Candida colonization in NICU patients. Methods: This cross-sectional study was conducted on 93 neonates in NICUs at Imam Khomeini and Children Medical Center Hospitals in Tehran. Cutaneous and mucous membrane samples obtained at first, third, and seventh days of patients’ stay in NICUs during nine months from August 2013 to May 2014. The samples were primarily cultured on CHROMagar Candida medium. The cultured media were incubated at 35°C for 48h and evaluated based on colony color produced on CHROMagar Candida. In addition, isolated colonies were cultured on Corn Meal Agar medium supplemented with tween 80 for identification of Candida spp. based on their morphology. Finally, polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP method was performed for definite identification of isolated species. Results: Colonization by Candida spp. was occurred in 20.43% of neonates. Fifteen and four patients colonized with one and two different Candida spp., respectively. Isolated Candida spp. identified as; C. parapsilosis (n: 10, C. albicans (n: 7, C. tropicalis (n: 3, C. guilliermondii (n: 2, and C. krusei (n: 1. In present study non-albicans Candia species were dominant (69.56% and C. parapsilosis was the most frequent isolate (43.47%. Using Fisher's exact test, the correlation between fungal colonization with low birth weight, low gestational age, and duration of hospital stay was found to be statistically significant (P=0.003. Conclusion: The results of this study imply to the candida species colonization of neonates

  8. Species-specific diversity of novel bacterial lineages and differential abundance of predicted pathways for toxic compound degradation in scorpion gut microbiota.

    Science.gov (United States)

    Bolaños, Luis M; Rosenblueth, Mónica; Castillo-Ramírez, Santiago; Figuier-Huttin, Gilles; Martínez-Romero, Esperanza

    2016-05-01

    Scorpions are considered 'living fossils' that have conserved ancestral anatomical features and have adapted to numerous habitats. However, their gut microbiota diversity has not been studied. Here, we characterized the gut microbiota of two scorpion species, Vaejovis smithi and Centruroides limpidus. Our results indicate that scorpion gut microbiota is species-specific and that food deprivation reduces bacterial diversity. 16S rRNA gene phylogenetic analysis revealed novel bacterial lineages showing a low level of sequence identity to any known bacteria. Furthermore, these novel bacterial lineages were each restricted to a different scorpion species. Additionally, our results of the predicted metagenomic profiles revealed a core set of pathways that were highly abundant in both species, and mostly related to amino acid, carbohydrate, vitamin and cofactor metabolism. Notably, the food-deprived V. smithi shotgun metagenome matched almost completely the metabolic features of the prediction. Finally, comparisons among predicted metagenomic profiles showed that toxic compound degradation pathways were more abundant in recently captured C. limpidus scorpions. This study gives a first insight into the scorpion gut microbiota and provides a reference for future studies on the gut microbiota from other arachnid species. PMID:26058415

  9. Antimicrobial activity of plant essential oils against bacterial and fungal species involved in food poisoning and/or food decay.

    Science.gov (United States)

    Lixandru, Brînduşa-Elena; Drăcea, Nicoleta Olguţa; Dragomirescu, Cristiana Cerasella; Drăgulescu, Elena Carmina; Coldea, Ileana Luminiţa; Anton, Liliana; Dobre, Elena; Rovinaru, Camelia; Codiţă, Irina

    2010-01-01

    The currative properties of aromatic and medicinal plants have been recognized since ancient times and, more recently, the antimicrobial activity of plant essential oils has been used in several applications, including food preservation. The purpose of this study was to create directly comparable, quantitative data on the antimicrobial activity of some plant essential oils prepared in the National Institute of Research-Development for Chemistry and Petrochemistry, Bucharest to be used for the further development of food packaging technology, based on their antibacterial and antifungal activity. The essential oils extracted from thyme (Thymus vulgaris L.), basil (Ocimum basilicum L.), coriander (Coriandrum sativum L.), rosemary (Rosmarinus officinalis L.), sage (Salvia officinalis L.), fennel (Foeniculum vulgare L.), spearmint (Mentha spicata L.) and carraway (Carum carvi L.) were investigated for their antimicrobial activity against eleven different bacterial and three fungal strains belonging to species reported to be involved in food poisoning and/or food decay: S. aureus ATCC 25923, S. aureus ATCC 6538, S. aureus ATCC 25913, E. coli ATCC 25922, E. coli ATCC 35218, Salmonella enterica serovar Enteritidis Cantacuzino Institute Culture Collection (CICC) 10878, Listeria monocytogenes ATCC 19112, Bacillus cereus CIP 5127, Bacillus cereus ATCC 11778, Candida albicans ATCC 10231, Aspergillus niger ATCC 16404, Penicillium spp. CICC 251 and two E. coli and Salmonella enterica serovar Enteritidis clinical isolates. The majority of the tested essential oils exibited considerable inhibitory capacity against all the organisms tested, as supported by growth inhibition zone diameters, MICs and MBC's. Thyme, coriander and basil oils proved the best antibacterial activity, while thyme and spearmint oils better inhibited the fungal species. PMID:21462837

  10. Performance of optimized McRAPD in identification of 9 yeast species frequently isolated from patient samples: potential for automation

    Directory of Open Access Journals (Sweden)

    Koukalova Dagmar

    2009-11-01

    Full Text Available Abstract Background Rapid, easy, economical and accurate species identification of yeasts isolated from clinical samples remains an important challenge for routine microbiological laboratories, because susceptibility to antifungal agents, probability to develop resistance and ability to cause disease vary in different species. To overcome the drawbacks of the currently available techniques we have recently proposed an innovative approach to yeast species identification based on RAPD genotyping and termed McRAPD (Melting curve of RAPD. Here we have evaluated its performance on a broader spectrum of clinically relevant yeast species and also examined the potential of automated and semi-automated interpretation of McRAPD data for yeast species identification. Results A simple fully automated algorithm based on normalized melting data identified 80% of the isolates correctly. When this algorithm was supplemented by semi-automated matching of decisive peaks in first derivative plots, 87% of the isolates were identified correctly. However, a computer-aided visual matching of derivative plots showed the best performance with average 98.3% of the accurately identified isolates, almost matching the 99.4% performance of traditional RAPD fingerprinting. Conclusion Since McRAPD technique omits gel electrophoresis and can be performed in a rapid, economical and convenient way, we believe that it can find its place in routine identification of medically important yeasts in advanced diagnostic laboratories that are able to adopt this technique. It can also serve as a broad-range high-throughput technique for epidemiological surveillance.

  11. Bacterial Conjunctivitis

    OpenAIRE

    Köhle, Ülkü; Kükner, Şahap

    2003-01-01

    Conjunctivitis is an infection of the conjunctiva, generally characterized by irritation, itching, foreign body sensation, tearing and discharge. Bacterial conjunctivitis may be distinguished from other types of conjunctivitis by the presence of yellow–white mucopurulent discharge. It is the most common form of ocular infection all around the world. Staphylococcus species are the most common bacterial pathogenes, followed by Streptococcus pneumoniae and Haemophilus i...

  12. Stealth Proteins: In Silico Identification of a Novel Protein Family Rendering Bacterial Pathogens Invisible to Host Immune Defense.

    Directory of Open Access Journals (Sweden)

    2005-11-01

    Full Text Available There are a variety of bacterial defense strategies to survive in a hostile environment. Generation of extracellular polysaccharides has proved to be a simple but effective strategy against the host's innate immune system. A comparative genomics approach led us to identify a new protein family termed Stealth, most likely involved in the synthesis of extracellular polysaccharides. This protein family is characterized by a series of domains conserved across phylogeny from bacteria to eukaryotes. In bacteria, Stealth (previously characterized as SacB, XcbA, or WefC is encoded by subsets of strains mainly colonizing multicellular organisms, with evidence for a protective effect against the host innate immune defense. More specifically, integrating all the available information about Stealth proteins in bacteria, we propose that Stealth is a D-hexose-1-phosphoryl transferase involved in the synthesis of polysaccharides. In the animal kingdom, Stealth is strongly conserved across evolution from social amoebas to simple and complex multicellular organisms, such as Dictyostelium discoideum, hydra, and human. Based on the occurrence of Stealth in most Eukaryotes and a subset of Prokaryotes together with its potential role in extracellular polysaccharide synthesis, we propose that metazoan Stealth functions to regulate the innate immune system. Moreover, there is good reason to speculate that the acquisition and spread of Stealth could be responsible for future epidemic outbreaks of infectious diseases caused by a large variety of eubacterial pathogens. Our in silico identification of a homologous protein in the human host will help to elucidate the causes of Stealth-dependent virulence. At a more basic level, the characterization of the molecular and cellular function of Stealth proteins may shed light on fundamental mechanisms of innate immune defense against microbial invasion.

  13. Stealth proteins: in silico identification of a novel protein family rendering bacterial pathogens invisible to host immune defense.

    Directory of Open Access Journals (Sweden)

    Peter Sperisen

    2005-11-01

    Full Text Available There are a variety of bacterial defense strategies to survive in a hostile environment. Generation of extracellular polysaccharides has proved to be a simple but effective strategy against the host's innate immune system. A comparative genomics approach led us to identify a new protein family termed Stealth, most likely involved in the synthesis of extracellular polysaccharides. This protein family is characterized by a series of domains conserved across phylogeny from bacteria to eukaryotes. In bacteria, Stealth (previously characterized as SacB, XcbA, or WefC is encoded by subsets of strains mainly colonizing multicellular organisms, with evidence for a protective effect against the host innate immune defense. More specifically, integrating all the available information about Stealth proteins in bacteria, we propose that Stealth is a D-hexose-1-phosphoryl transferase involved in the synthesis of polysaccharides. In the animal kingdom, Stealth is strongly conserved across evolution from social amoebas to simple and complex multicellular organisms, such as Dictyostelium discoideum, hydra, and human. Based on the occurrence of Stealth in most Eukaryotes and a subset of Prokaryotes together with its potential role in extracellular polysaccharide synthesis, we propose that metazoan Stealth functions to regulate the innate immune system. Moreover, there is good reason to speculate that the acquisition and spread of Stealth could be responsible for future epidemic outbreaks of infectious diseases caused by a large variety of eubacterial pathogens. Our in silico identification of a homologous protein in the human host will help to elucidate the causes of Stealth-dependent virulence. At a more basic level, the characterization of the molecular and cellular function of Stealth proteins may shed light on fundamental mechanisms of innate immune defense against microbial invasion.

  14. Calibrating snakehead diversity with DNA barcodes: expanding taxonomic coverage to enable identification of potential and established invasive species.

    Directory of Open Access Journals (Sweden)

    Natasha R Serrao

    Full Text Available Detecting and documenting the occurrence of invasive species outside their native range requires tools to support their identification. This can be challenging for taxa with diverse life stages and/or problematic or unresolved morphological taxonomies. DNA barcoding provides a potent method for identifying invasive species, as it allows for species identification at all life stages, including fragmentary remains. It also provides an efficient interim taxonomic framework for quantifying cryptic genetic diversity by parsing barcode sequences into discontinuous haplogroup clusters (typical of reproductively isolated species and labelling them with unique alphanumeric identifiers. Snakehead fishes are a diverse group of opportunistic predators endemic to Asia and Africa that may potentially pose significant threats as aquatic invasive species. At least three snakehead species (Channa argus, C. maculata, and C. marulius are thought to have entered North America through the aquarium and live-food fish markets, and have established populations, yet their origins remain unclear. The objectives of this study were to assemble a library of DNA barcode sequences derived from expert identified reference specimens in order to determine the identity and aid invasion pathway analysis of the non-indigenous species found in North America using DNA barcodes. Sequences were obtained from 121 tissue samples representing 25 species and combined with public records from GenBank for a total of 36 putative species, which then partitioned into 49 discrete haplogroups. Multiple divergent clusters were observed within C. gachua, C. marulius, C. punctata and C. striata suggesting the potential presence of cryptic species diversity within these lineages. Our findings demonstrate that DNA barcoding is a valuable tool for species identification in challenging and under-studied taxonomic groups such as snakeheads, and provides a useful framework for inferring invasion pathway

  15. Calibrating snakehead diversity with DNA barcodes: expanding taxonomic coverage to enable identification of potential and established invasive species.

    Science.gov (United States)

    Serrao, Natasha R; Steinke, Dirk; Hanner, Robert H

    2014-01-01

    Detecting and documenting the occurrence of invasive species outside their native range requires tools to support their identification. This can be challenging for taxa with diverse life stages and/or problematic or unresolved morphological taxonomies. DNA barcoding provides a potent method for identifying invasive species, as it allows for species identification at all life stages, including fragmentary remains. It also provides an efficient interim taxonomic framework for quantifying cryptic genetic diversity by parsing barcode sequences into discontinuous haplogroup clusters (typical of reproductively isolated species) and labelling them with unique alphanumeric identifiers. Snakehead fishes are a diverse group of opportunistic predators endemic to Asia and Africa that may potentially pose significant threats as aquatic invasive species. At least three snakehead species (Channa argus, C. maculata, and C. marulius) are thought to have entered North America through the aquarium and live-food fish markets, and have established populations, yet their origins remain unclear. The objectives of this study were to assemble a library of DNA barcode sequences derived from expert identified reference specimens in order to determine the identity and aid invasion pathway analysis of the non-indigenous species found in North America using DNA barcodes. Sequences were obtained from 121 tissue samples representing 25 species and combined with public records from GenBank for a total of 36 putative species, which then partitioned into 49 discrete haplogroups. Multiple divergent clusters were observed within C. gachua, C. marulius, C. punctata and C. striata suggesting the potential presence of cryptic species diversity within these lineages. Our findings demonstrate that DNA barcoding is a valuable tool for species identification in challenging and under-studied taxonomic groups such as snakeheads, and provides a useful framework for inferring invasion pathway analysis. PMID

  16. Identification of a Cryptic Bacterial Promoter in Mouse (mdr1a P-Glycoprotein cDNA.

    Directory of Open Access Journals (Sweden)

    Kristen M Pluchino

    Full Text Available The efflux transporter P-glycoprotein (P-gp is an important mediator of various pharmacokinetic parameters, being expressed at numerous physiological barriers and also in multidrug-resistant cancer cells. Molecular cloning of homologous cDNAs is an important tool for the characterization of functional differences in P-gp between species. However, plasmids containing mouse mdr1a cDNA display significant genetic instability during cloning in bacteria, indicating that mdr1a cDNA may be somehow toxic to bacteria, allowing only clones containing mutations that abrogate this toxicity to survive transformation. We demonstrate here the presence of a cryptic promoter in mouse mdr1a cDNA that causes mouse P-gp expression in bacteria. This expression may account for the observed toxicity of mdr1a DNA to bacteria. Sigma 70 binding site analysis and GFP reporter plasmids were used to identify sequences in the first 321 bps of mdr1a cDNA capable of initiating bacterial protein expression. An mdr1a M107L cDNA containing a single residue mutation at the proposed translational start site was shown to allow sub-cloning of mdr1a in E. coli while retaining transport properties similar to wild-type P-gp. This mutant mdr1a cDNA may prove useful for efficient cloning of mdr1a in E. coli.

  17. Biotic stress protein markers of Aquilaria sp. for gaharu species identification in Malaysia

    International Nuclear Information System (INIS)

    Gaharu trees (Aquilaria) is in danger of extinction in the wild due to illegal logging. Its resin (Gaharu) is used for the production of highly valued incense throughout Asia. In Aquilaria sp. systemic induction of defense genes in response to mechanical wounding in nature is regulated by an 18-amino-acid peptide signal protein called systemin. This protein is produced in response to the natural stress at the vicinity of the wound and is also influenced by its genetic background. As the protein can be differentiated by its locality, the protein expressed is also found to be significantly different which, in turn, can be used for identification of this plant species. In this work, A. malaccensis and A. hirta were evaluated based on the targeted genes related to systemin. Targeted gene refers to specific sequence in genomic DNA. Sequence mining from public databases is part of the crucial process in getting the specific genes. The sequences will go through alignment step to identify conserved region prior to primer design. The primers were used in Polymerase Chain Reaction (PCR) techniques to amplify the conserved regions. It was found that both samples can be differentiated. This would be useful for plant breeders, trader and planter in ensuring authentic planting materials. This paper will describe the use of targeted genes primers as markers in identifying the Aquilaria species. (author)

  18. Environmental isolation, biochemical identification, and antifungal drug susceptibility of Cryptococcus species

    Directory of Open Access Journals (Sweden)

    Valter Luis Iost Teodoro

    2013-12-01

    Full Text Available Introduction The incidence of opportunistic fungal infections has increased in recent years and is considered an important public health problem. Among systemic and opportunistic mycoses, cryptococcosis is distinguished by its clinical importance due to the increased risk of infection in individuals infected by human immunodeficiency virus. Methods To determine the occurrence of pathogenic Cryptococcus in pigeon excrement in the City of Araraquara, samples were collected from nine environments, including state and municipal schools, abandoned buildings, parks, and a hospital. The isolates were identified using classical tests, and susceptibility testing for the antifungal drugs (fluconazole, itraconazole, voriconazole, and amphotericin B independently was also performed. After collection, the excrement samples were plated on Niger agar and incubated at room temperature. Results A total of 87 bird dropping samples were collected, and 66.6% were positive for the genus Cryptococcus. The following species were identified: Cryptococcus neoformans (17.2%, Cryptococcus gattii (5.2%, Cryptococcus ater (3.5%, Cryptococcus laurentti (1.7%, and Cryptococcus luteolus (1.7%. A total of 70.7% of the isolates were not identified to the species level and are referred to as Cryptococcus spp. throughout the manuscript. Conclusions Although none of the isolates demonstrated resistance to antifungal drugs, the identification of infested areas, the proper control of birds, and the disinfection of these environments are essential for the epidemiological control of cryptococcosis.

  19. Plasma polymerization chemistry of unsaturated hydrocarbons: neutral species identification by mass spectrometry

    International Nuclear Information System (INIS)

    Radio frequency discharges ignited in low-pressure and pure hydrocarbon gases were investigated by mass spectrometry. The plasma process was applied to four unsaturated monomers: styrene C8H8, benzene C6H6, ethylene C2H4 and acetylene C2H2. The remote mass spectrometer location restricted species identification to neutral closed-shell molecules in their respective plasmas. Among the peaks in the mass spectra, those directly due to neutrals produced in the plasma were determined following a successful two-step methodology. Firstly, the use of low electron impact energy limited the fragmentation and strongly simplified the cracking patterns. Secondly, attribution of peaks directly due to neutrals was confirmed or ruled out by systematically measuring their appearance potential. In the case of styrene, not less than 48 new molecules were detected. The discussion of the observed stable by-products in each discharge suggested several radicals responsible for their production. Comparing the set of species among the four plasmas showed that the repeated addition of intermediates with one or two carbon atoms and with low H content dominated the chemistry. Under our conditions of intermediate to high W/FM (power over mass flow ratio), the gas-phase plasma polymerization then preferentially occurred through significant fragmentation and recombination. Finally, the measured appearance potentials during plasma provided estimation for the threshold ionization energy of several highly unsaturated hydrocarbons, useful for modeling. (paper)

  20. Identification and analysis of copine/BONZAI proteins among evolutionarily diverse plant species.

    Science.gov (United States)

    Zou, Baohong; Hong, Xuexue; Ding, Yuan; Wang, Xiang; Liu, He; Hua, Jian

    2016-08-01

    Copines are evolutionarily conserved calcium-dependent membrane-binding proteins with potentially critical biological functions. In plants, the function of these proteins has not been analyzed except for in Arabidopsis thaliana where they play critical roles in development and disease resistance. To facilitate functional studies of copine proteins in crop plants, genome-wide identification, curation, and phylogeny analysis of copines in 16 selected plant species were conducted. All the identified 32 plant copines have conserved features of the two C2 domains (C2A and C2B) and the von Willebrand factor A (vWA) domain. Different from animal and protozoa copines, plant copines have glycine at the second residue potentially acquiring a unique protein myristoylation modification. Phylogenetic analysis suggests that copine was present as one copy when evolving from green algae to basal flowering plants, and duplicated before the divergence of monocots and dicots. In addition, gene expression and protein localization study of rice copines suggests both conserved and different properties of copines in dicots and monocots. This study will contribute to uncovering the role of copine genes in different plant species. PMID:27484220

  1. Identification of Aspergillus species in Central Europe able to produce G-type aflatoxins.

    Science.gov (United States)

    Baranyi, Nikolett; Despot, Daniela Jakšić; Palágyi, Andrea; Kiss, Noémi; Kocsubé, Sándor; Szekeres, András; Kecskeméti, Anita; Bencsik, Ottó; Vágvölgyi, Csaba; Klarić, Maja Šegvić; Varga, János

    2015-09-01

    The occurrence of potential aflatoxin producing fungi was examined in various agricultural products and indoor air in Central European countries including Hungary, Serbia and Croatia. For species identification, both morphological and sequence based methods were applied. Aspergillus flavus was detected in several samples including maize, cheese, nuts, spices and indoor air, and several isolates were able to produce aflatoxins. Besides, three other species of Aspergillus section Flavi, A. nomius, A. pseudonomius and A. parasiticus were also isolated from cheese, maize and indoor air, respectively. This is the first report on the occurrence of A. nomius and A. pseudonomius in Central Europe. All A. nomius, A. pseudonomius and A. parasiticus isolates were able to produce aflatoxins B1, B2, G1 and G2. The A. nomius isolate came from cheese produced very high amounts of aflatoxins (above 1 mg ml⁻¹). All A. nomius, A. pseudonomius and A. parasiticus isolates produced much higher amounts of aflatoxin G1 then aflatoxin B1. Further studies are in progress to examine the occurrence of producers of these highly carcinogenic mycotoxins in agricultural products and indoor air in Central Europe. PMID:26344029

  2. Determination of 16S rRNA Sequences of Enterococci and Application to Species Identification of Nonmotile Enterococcus gallinarum Isolates

    OpenAIRE

    Patel, Robin; Piper, Kerryl E.; Rouse, Mark S; Steckelberg, James M.; Uhl, Jim R.; Kohner, Peggy; Hopkins, Marlene K.; Cockerill, Franklin R.; Kline, Bruce C.

    1998-01-01

    The 16S rRNA sequences of enterococcal species E. faecium, E. faecalis, E. gallinarum, E. casseliflavus/flavescens, E. dispar, E. pseudoavium, E. sulfureus, E. malodoratus, E. raffinosus, E. cecorum, E. hirae, E. saccharolyticus, E. seriolicida, E. mundtii, E. avium, E. durans, E. columbae, and E. solitarius are presented herein. These data were utilized to confirm the species identification of two nonmotile E. gallinarum isolates which had been previously phenotypically identified as E. faec...

  3. Phylogeny and Identification of Pantoea Species and Typing of Pantoea agglomerans Strains by Multilocus Gene Sequencing ▿ †

    OpenAIRE

    Delétoile, Alexis; Decré, Dominique; Courant, Stéphanie; Passet, Virginie; Audo, Jennifer; Grimont, Patrick; Arlet, Guillaume; Brisse, Sylvain

    2008-01-01

    Pantoea agglomerans and other Pantoea species cause infections in humans and are also pathogenic to plants, but the diversity of Pantoea strains and their possible association with hosts and disease remain poorly known, and identification of Pantoea species is difficult. We characterized 36 Pantoea strains, including 28 strains of diverse origins initially identified as P. agglomerans, by multilocus gene sequencing based on six protein-coding genes, by biochemical tests, and by antimicrobial ...

  4. Comprehensive characterization of indoor airborne bacterial profile

    Institute of Scientific and Technical Information of China (English)

    P.L.Chan; P.H.F.Yu; Y.W.Cheng; C.Y.Chan; P.K.Wong

    2009-01-01

    This is the first detailed characterization of the air-borne bacterial profiles in indoor environments and two restaurants were selected for this study.Fifteen genera of bacteria were isolated from each restaurant and identified by three different bacterial identification systems including MIDI, Biolog and Riboprinter?.The dominant bacteria of both restaurants were Gram-positive bacteria in which Micrococcus and Bacillus species were the most abundant species.Most bacteria identified were representative species of skin and respiratory tract of human, and soil.Although the bacterial levels in these restaurants were below the limit of the Hong Kong Indoor Air Quality Objective (HKIAQO) Level 1 standard (i.e., < 500 cfu/m3), the majority of these bacteria were opportunistic pathogens.These results suggested that the identity of airborne bacteria should also be included in the IAQ to ensure there is a safety guideline for the public.

  5. Identification of cephalopod species from the North and Baltic Seas using morphology, COI and 18S rDNA sequences

    Science.gov (United States)

    Gebhardt, Katharina; Knebelsberger, Thomas

    2015-09-01

    We morphologically analyzed 79 cephalopod specimens from the North and Baltic Seas belonging to 13 separate species. Another 29 specimens showed morphological features of either Alloteuthis mediaor Alloteuthis subulata or were found to be in between. Reliable identification features to distinguish between A. media and A. subulata are currently not available. The analysis of the DNA barcoding region of the COI gene revealed intraspecific distances (uncorrected p) ranging from 0 to 2.13 % (average 0.1 %) and interspecific distances between 3.31 and 22 % (average 15.52 %). All species formed monophyletic clusters in a neighbor-joining analysis and were supported by bootstrap values of ≥99 %. All COI haplotypes belonging to the 29 Alloteuthis specimens were grouped in one cluster. Neither COI nor 18S rDNA sequences helped to distinguish between the different Alloteuthis morphotypes. For species identification purposes, we recommend the use of COI, as it showed higher bootstrap support of species clusters and less amplification and sequencing failure compared to 18S. Our data strongly support the assumption that the genus Alloteuthis is only represented by a single species, at least in the North Sea. It remained unclear whether this species is A. subulata or A. media. All COI sequences including important metadata were uploaded to the Barcode of Life Data Systems and can be used as reference library for the molecular identification of more than 50 % of the cephalopod fauna known from the North and Baltic Seas.

  6. Identification of forensically important blow fly species (Diptera: Calliphoridae) in China by mitochondrial cytochrome oxidase I gene differentiation

    Institute of Scientific and Technical Information of China (English)

    Qin-Lai Liu; Li Yang; Kun-Lu Wu; Ling-mei Lan; Jiang-Feng Wang; Yao-Qing Chen; Ji-Feng Cai; Yun-Feng Chang; Yan Gu; Ya-Dong Guo; Xing-Hua Wang; Ji-FangWeng; Ming Zhong; Xiang Wang

    2011-01-01

    Unambiguous and rapid sarcosaphagous insect species identification is an essential requirement for forensic investigations. Although some insect species are difficult to classify morphologically, they can be effectively identified using molecular methods based on similarity with abundant authenticated reference DNA sequences in local databases.However, local databases are still relatively incomplete in China because of the large land area with distinct regional conditions. In this study, 75 forensically important blow flies were collected from 23 locations in 16 Chinese provinces, and a 278-bp segment of the cytochrome oxidase subunit Ⅰ gene of all specimens was successfully sequenced. Phylogenetic analysis of the sequenced segments showed that all Calliphorid specimens were properly assigned into nine species with relatively strong supporting values, thus indicating that the 278-bp cytochrome oxidase subunit one region is suitable for identification of Calliphorid species. The clear difference between intraspecific threshold and interspecific divergence confirmed the potential of this region for Calliphorid species identification,especially for distinguishing between morphologically similar species. Intraspecific geographic variations were observed in Lucilia sericata (Meigen, 1826) and Lucilia caesar (Linnaeus, 1758).

  7. Genotypic and phenotypic applications for the differentiation and species-level identification of achromobacter for clinical diagnoses.

    Science.gov (United States)

    Gomila, Margarita; Prince-Manzano, Claudia; Svensson-Stadler, Liselott; Busquets, Antonio; Erhard, Marcel; Martínez, Deny L; Lalucat, Jorge; Moore, Edward R B

    2014-01-01

    The Achromobacter is a genus in the family Alcaligenaceae, comprising fifteen species isolated from different sources, including clinical samples. The ability to detect and correctly identify Achromobacter species, particularly A. xylosoxidans, and differentiate them from other phenotypically similar and genotypically related Gram-negative, aerobic, non-fermenting species is important for patients with cystic fibrosis (CF), as well as for nosocomial and other opportunistic infections. Traditional phenotypic profile-based analyses have been demonstrated to be inadequate for reliable identifications of isolates of Achromobacter species and genotypic-based assays, relying upon comparative 16S rRNA gene sequence analyses are not able to insure definitive identifications of Achromobacter species, due to the inherently conserved nature of the gene. The uses of alternative methodologies to enable high-resolution differentiation between the species in the genus are needed. A comparative multi-locus sequence analysis (MLSA) of four selected 'house-keeping' genes (atpD, gyrB, recA, and rpoB) assessed the individual gene sequences for their potential in developing a reliable, rapid and cost-effective diagnostic protocol for Achromobacter species identifications. The analysis of the type strains of the species of the genus and 46 strains of Achromobacter species showed congruence between the cluster analyses derived from the individual genes. The MLSA gene sequences exhibited different levels of resolution in delineating the validly published Achromobacter species and elucidated strains that represent new genotypes and probable new species of the genus. Our results also suggested that the recently described A. spritinus is a later heterotypic synonym of A. marplatensis. Strains were analyzed, using whole-cell Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight mass spectrometry (MALDI-TOF MS), as an alternative phenotypic profile-based method with the potential to

  8. Genotypic and phenotypic applications for the differentiation and species-level identification of achromobacter for clinical diagnoses.

    Directory of Open Access Journals (Sweden)

    Margarita Gomila

    Full Text Available The Achromobacter is a genus in the family Alcaligenaceae, comprising fifteen species isolated from different sources, including clinical samples. The ability to detect and correctly identify Achromobacter species, particularly A. xylosoxidans, and differentiate them from other phenotypically similar and genotypically related Gram-negative, aerobic, non-fermenting species is important for patients with cystic fibrosis (CF, as well as for nosocomial and other opportunistic infections. Traditional phenotypic profile-based analyses have been demonstrated to be inadequate for reliable identifications of isolates of Achromobacter species and genotypic-based assays, relying upon comparative 16S rRNA gene sequence analyses are not able to insure definitive identifications of Achromobacter species, due to the inherently conserved nature of the gene. The uses of alternative methodologies to enable high-resolution differentiation between the species in the genus are needed. A comparative multi-locus sequence analysis (MLSA of four selected 'house-keeping' genes (atpD, gyrB, recA, and rpoB assessed the individual gene sequences for their potential in developing a reliable, rapid and cost-effective diagnostic protocol for Achromobacter species identifications. The analysis of the type strains of the species of the genus and 46 strains of Achromobacter species showed congruence between the cluster analyses derived from the individual genes. The MLSA gene sequences exhibited different levels of resolution in delineating the validly published Achromobacter species and elucidated strains that represent new genotypes and probable new species of the genus. Our results also suggested that the recently described A. spritinus is a later heterotypic synonym of A. marplatensis. Strains were analyzed, using whole-cell Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight mass spectrometry (MALDI-TOF MS, as an alternative phenotypic profile-based method with the

  9. Identification of Burkholderia spp. in the clinical microbiology laboratory: comparison of conventional and molecular methods

    NARCIS (Netherlands)

    C. van Pelt (Cindy); C.M. Verduin (Cees); W.H.F. Goessens (Wil); M.C. Vos (Margreet); B. Tummler; C. Segonds; F. Reubsaet; A.F. van Belkum (Alex); H.A. Verbrugh (Henri)

    1999-01-01

    textabstractCystic fibrosis (CF) predisposes patients to bacterial colonization and infection of the lower airways. Several species belonging to the genus Burkholderia are potential CF-related pathogens, but microbiological identification may be complicated. This situat

  10. DNA-based identification of forensically important species of Sarcophagidae (Insecta: Diptera) from Rio de Janeiro, Brazil.

    Science.gov (United States)

    Napoleão, K S; Mello-Patiu, C A; Oliveira-Costa, J; Takiya, D M; Silva, R; Moura-Neto, R S

    2016-01-01

    Sarcophagidae, or flesh flies, are of great importance in forensic entomology, but their effective application requires precise taxonomic identification, which relies almost exclusively on characteristics of the male genitalia. Given that female flies and larvae are most abundant in animal carcasses or on corpses, precise morphological identification can be difficult; therefore, DNA sequencing can be an additional tool for use in taxonomic identification. This paper analyzes part of the mitochondrial cytochrome c oxidase subunit I (COI) gene from three Sarcophagidae species of forensic importance in the City of Rio de Janeiro: Oxysarcodexia fluminensis, Peckia chrysostoma, and Peckia intermutans. COI fragments of 400 bp from 36 specimens of these three species were sequenced. No intraspecific differences were found among specimens of O. fluminensis, but P. chrysostoma and P. intermutans each had two haplotypes, ranging from 0 to 0.7%. The interspecific divergence was 8.5-11.6%, corroborating previously reported findings. PMID:27173314

  11. Detection and identification of human Plasmodium species with real-time quantitative nucleic acid sequence-based amplification

    NARCIS (Netherlands)

    P.F. Mens; G.J. Schoone; P.A. Kager; H.D.F.H. Schallig

    2006-01-01

    Background: Decisions concerning malaria treatment depend on species identification causing disease. Microscopy is most frequently used, but at low parasitaemia (< 20 parasites/mu l) the technique becomes less sensitive and time consuming. Rapid diagnostic tests based on Plasmodium antigen detection

  12. Molecular species identification of Central European ground beetles (Coleoptera: Carabidae using nuclear rDNA expansion segments and DNA barcodes

    Directory of Open Access Journals (Sweden)

    Raupach Michael J

    2010-09-01

    Full Text Available Abstract Background The identification of vast numbers of unknown organisms using DNA sequences becomes more and more important in ecological and biodiversity studies. In this context, a fragment of the mitochondrial cytochrome c oxidase I (COI gene has been proposed as standard DNA barcoding marker for the identification of organisms. Limitations of the COI barcoding approach can arise from its single-locus identification system, the effect of introgression events, incomplete lineage sorting, numts, heteroplasmy and maternal inheritance of intracellular endosymbionts. Consequently, the analysis of a supplementary nuclear marker system could be advantageous. Results We tested the effectiveness of the COI barcoding region and of three nuclear ribosomal expansion segments in discriminating ground beetles of Central Europe, a diverse and well-studied invertebrate taxon. As nuclear markers we determined the 18S rDNA: V4, 18S rDNA: V7 and 28S rDNA: D3 expansion segments for 344 specimens of 75 species. Seventy-three species (97% of the analysed species could be accurately identified using COI, while the combined approach of all three nuclear markers provided resolution among 71 (95% of the studied Carabidae. Conclusion Our results confirm that the analysed nuclear ribosomal expansion segments in combination constitute a valuable and efficient supplement for classical DNA barcoding to avoid potential pitfalls when only mitochondrial data are being used. We also demonstrate the high potential of COI barcodes for the identification of even closely related carabid species.

  13. Performance of Candida ID, a New Chromogenic Medium for Presumptive Identification of Candida Species, in Comparison to CHROMagar Candida

    OpenAIRE

    Willinger, Birgit; Hillowoth, Cornelia; Selitsch, Brigitte; Manafi, Mammad

    2001-01-01

    Candida ID agar allows identification of Candida albicans and differentiation of other Candida species. In comparison with CHROMagar Candida, we evaluated the performance of this medium directly from 596 clinical specimens. In particular, detection of C. albicans after 24 h of incubation was easier on Candida ID (sensitivity, 96.8%) than on CHROMagar (sensitivity, 49.6%).

  14. A PCR-based method for identification of bifidobacteria from the human alimentary tract at the species level

    NARCIS (Netherlands)

    Venema, K.; Maathuis, A.J.H.

    2003-01-01

    A polymerase chain reaction (PCR)-based method was developed for the identification of isolates of Bifidobacterium at the species level. Using two Bifidobacterium-specific primers directed against the 16S ribosomal gene (Bif164 and Bif662), a PCR product was obtained from the type strains of 12 diff

  15. Raw Cow Milk Bacterial Population Shifts Attributable to Refrigeration

    OpenAIRE

    Lafarge, Véronique; Ogier, Jean-Claude; Girard, Victoria; Maladen, Véronique; Leveau, Jean-Yves; Gruss, Alexandra; Delacroix-Buchet, Agnès

    2004-01-01

    We monitored the dynamic changes in the bacterial population in milk associated with refrigeration. Direct analyses of DNA by using temporal temperature gel electrophoresis (TTGE) and denaturing gradient gel electrophoresis (DGGE) allowed us to make accurate species assignments for bacteria with low-GC-content (low-GC%) (55%) genomes, respectively. We examined raw milk samples before and after 24-h conservation at 4°C. Bacterial identification was facilitated by comparison with an extensive b...

  16. [Development of a real-time polymerase chain reaction method for the identification of Candida species].

    Science.gov (United States)

    Ağca, Harun; Dalyan Cilo, Burcu; Özmerdiven, Gülşah Ece; Sağlam, Sezcan; Ener, Beyza

    2015-01-01

    Candida species are one of the major causes of nosocomial infections and are the fourth most common agent involved in bloodstream infections. The impact of non-albicans Candida species is increasing, however C.albicans is still the most common species. Since the antifungal susceptibility pattern among Candida spp. may be different, rapid diagnosis and identification of non-albicans Candida spp. are important for the determination of antifungal agents that will be used for treatment. The aim of the study was to describe a real-time polymerase chain reaction (Rt-PCR) assay that rapidly detects, identifies and quantitates Candida species from blood culture samples. A total of 50 consecutive positive blood culture bottles (BACTEC, Beckton Dickinson, USA) identified at our laboratory between June-November 2013, were included in the study. Reference strains of Candida spp. (C.albicans ATCC 10231, C.glabrata ATCC 90030, C.tropicalis ATCC 1021, C.krusei ATCC 6258, C.parapsilosis ATCC 22019 and C. dubliniensis CD36) grown on Sabouraud dextrose agar were used for quality control. BACTEC bottles that were positive for Escherichia coli, Pseudomonas aeruginosa and Staphylococcus aureus were also studied to search the cross-reactivity. A commercial kit (Zymo Research, USA) was used for DNA extraction. Real-time PCR was performed on LightCycler 480 (Roche, Germany) with primers and probes specific for 18S rRNA of Candida species. Twenty microlitres of the reaction mix contained 2 μl of extracted DNA, 2 μl of LightCycler Fast Start DNA Master Probe (Roche Diagnostics, Germany), 2 μl of MgCl(2) (5 mmol), 2 μl of 10x PCR buffer (Roche Diagnostics, Germany), 0.5 μl of each primer (0.01 nmol/μl) and 1 μl of each probe (0.1 μmol/μl) (TibMolBiol, Germany). Amplification was performed using the following conditions; 95°C for 10 mins and 50 cycles of denaturation at 95°C for 10 secs, annealing at 62°C for 10 secs and polymerisation at 72°C for 20 secs. A melting curve was

  17. Identification of pets and raccoons as sources of bacterial contamination of urban storm sewers using a sequence-based bacterial source tracking method.

    Science.gov (United States)

    Ram, Jeffrey L; Thompson, Brooke; Turner, Carrie; Nechvatal, Jordan M; Sheehan, Harry; Bobrin, Janis

    2007-08-01

    In urbanized areas, contaminated storm sewers can feed high bacterial levels into free-flowing streams and rivers. Although illicit connections sometimes cause contamination, urban wildlife and free-roaming domesticated or feral pets may be another source. After eliminating illicit connections as sources of high levels of Escherichia coli in two storm sewers tributary to the Huron River in southeast Michigan, the roles of urban wildlife, pets, humans, and birds were investigated using a sequence-based bacterial source tracking technology. After enumeration, E. coli were isolated from water samples collected during spring to fall, 2005. Sequences in the gene beta-glucuronidase of each isolate were compared to sequences of reference strains from humans, raccoons, pets (cats and dogs), and birds. The highest percentage source for six of ten events was pets (ANOVA, p=0.005). Among isolates attributed to pets, strains from cats occurred more frequently on seven of nine events in which pets had a non-zero probability. High raccoon percentages (up to 60%) occurred in late summer and fall, and varied significantly more than in the spring (F-test), possibly reflecting urban raccoon den-site mobility. The sequence-based bacterial source tracking method suggests that feces from pets and raccoons are important contributors to urban storm sewers. PMID:17540431

  18. Detection and species identification of Campylobacter in stool samples of children and animals from Vellore, south India

    Directory of Open Access Journals (Sweden)

    P Rajendran

    2012-01-01

    Full Text Available Campylobacter spp. are an important cause of bacterial gastroenteritis frequently isolated from animal, poultry and environmental samples. In this study, we investigated the zoonotic potential of Campylobacter spp. by comparing prevalence rates and species in 394 children with diarrhoea and 652 animals in Vellore using PCR-based tools. Eighteen children (4.5% had campylobacteriosis, a majority of whom had co-pathogens (15/18 and most were infected with Campylobacter jejuni (16/18. A few C. coli and mixed infections with both species were also seen. Among the animal samples, 16/25 chicken samples (64% were positive and all were found to be C. jejuni.

  19. Identification of polyvalent protective immunogens from outer membrane proteins in Vibrio parahaemolyticus to protect fish against bacterial infection.

    Science.gov (United States)

    Peng, Bo; Ye, Jin-Zhou; Han, Yi; Zeng, Li; Zhang, Jian-Ying; Li, Hui

    2016-07-01

    Vaccination is one of the most effective and economic way to prevent infectious diseases in aquaculture. The development of effective vaccines, however, is still limited, especially for polyvalent vaccines, which are against multiple species. With this regard, identification of polyvalent protective immunogens, serving as polyvalent vaccines, became a key step in vaccine development. In the current study, 17 outer membrane proteins from Vibrio parahaemolyticus were identified as immunogens. Further, four of the 17 proteins including VP2309, VP0887, VPA0548 and VP1019 were characterized as efficiently protective immunogens against V. parahaemolyticus' infection through passive and active immunizations in zebrafish. Importantly, these four proteins showed cross-protective capability against infections by Aeromonas hydrophila or/and Pseudomonas fluorescens, which shared similar epitopes with V. parahaemolyticus in homology of these proteins. Further investigation showed that the expression level of the four protective immunogens elevated in response to fish plasma in a dose-dependent manner. These results indicate that the four protective immunogens are polyvalent vaccine candidates in aquaculture. PMID:27071519

  20. Rapid and Accurate Identification of Animal Species in Natural Leather Goods by Liquid Chromatography/Mass Spectrometry

    Science.gov (United States)

    Izuchi, Yukari; Takashima, Tsuneo; Hatano, Naoya

    2016-01-01

    The demand for leather goods has grown globally in recent years. Industry revenue is forecast to reach $91.2 billion by 2018. There is an ongoing labelling problem in the leather items market, in that it is currently impossible to identify the species that a given piece of leather is derived from. To address this issue, we developed a rapid and simple method for the specific identification of leather derived from cattle, horses, pigs, sheep, goats, and deer by analysing peptides produced by the trypsin-digestion of proteins contained in leather goods using liquid chromatography/mass spectrometry. We determined species-specific amino acid sequences by liquid chromatography/tandem mass spectrometry analysis using the Mascot software program and demonstrated that collagen α-1(I), collagen α-2(I), and collagen α-1(III) from the dermal layer of the skin are particularly useful in species identification. PMID:27313979

  1. Identification and Preliminary Analysis of Several Centromere-associated Bacterial Artificial Chromosome Clones from a Diploid Wheat Library

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Although the centromeres of some plants have been investigated previously, our knowledge of the wheat centromere is still very limited. To understand the structure and function of the wheat centromere, we used two centromeric repeats (RCS1 and CCS1-5ab) to obtain some centromere-associated bacterial artificial chromosome (BAC) clones in 32 RCS1-related BAC clones that had been screened out from a diploid wheat (Triticum boeoticum Boiss.; 2n=2x=14) BAC library. Southern hybridization results indicated that, of the 32 candidates,there were 28 RCS1-positive clones. Based on gel blot patterns, the frequency of RCS1 was approximately one copy every 69.4 kb in these 28 RCS1-positive BAC clones. More bands were detected when the same filter was probed with CCS1-5ab. Furthermore, the CCS1 bands covered all the bands detected by RCS1, which suggests that some CCS1 repeats were distributed together with RCS1. The frequency of CCS1 families was once every 35.8 kb, nearly twice that of RCS1. Fluorescence in situ hybridization (FISH) analysis indicated that the five BAC clones containing RCS1 and CCS1 sequences all detected signals at the centromeric regions in hexaploid wheat, but the signal intensities on the A-genome chromosomes were stronger than those on the B- and/or D-genome chromosomes. The FISH analysis among nine Triticeae cereals indicated that there were A-genomespecific (or rich) sequences dispersing on chromosome arms in the BAC clone TbBAC5. In addition, at the interphase cells, the centromeres of diploid species usually clustered at one pole and formed a ring-like allocation in the period before metaphase.

  2. Comparative proteome analysis of psychrophilic versus mesophilic bacterial species: Insights into the molecular basis of cold adaptation of proteins

    OpenAIRE

    Reddy Boojala; Metpally Raghu

    2009-01-01

    Abstract Background Cold adapted or psychrophilic organisms grow at low temperatures, where most of other organisms cannot grow. This adaptation requires a vast array of sequence, structural and physiological adjustments. To understand the molecular basis of cold adaptation of proteins, we analyzed proteomes of psychrophilic and mesophilic bacterial species and compared the differences in amino acid composition and substitution patterns to investigate their likely association with growth temp...

  3. Oligotyping reveals differences between gut microbiomes of free-ranging sympatric Namibian carnivores (Acinonyx jubatus, Canis mesomelas) on a bacterial species-like level

    Science.gov (United States)

    Menke, Sebastian; Wasimuddin; Meier, Matthias; Melzheimer, Jörg; Mfune, John K. E.; Heinrich, Sonja; Thalwitzer, Susanne; Wachter, Bettina; Sommer, Simone

    2014-01-01

    Recent gut microbiome studies in model organisms emphasize the effects of intrinsic and extrinsic factors on the variation of the bacterial composition and its impact on the overall health status of the host. Species occurring in the same habitat might share a similar microbiome, especially if they overlap in ecological and behavioral traits. So far, the natural variation in microbiomes of free-ranging wildlife species has not been thoroughly investigated. The few existing studies exploring microbiomes through 16S rRNA gene reads clustered sequencing reads into operational taxonomic units (OTUs) based on a similarity threshold (e.g., 97%). This approach, in combination with the low resolution of target databases, generally limits the level of taxonomic assignments to the genus level. However, distinguishing natural variation of microbiomes in healthy individuals from “abnormal” microbial compositions that affect host health requires knowledge of the “normal” microbial flora at a high taxonomic resolution. This gap can now be addressed using the recently published oligotyping approach, which can resolve closely related organisms into distinct oligotypes by utilizing subtle nucleotide variation. Here, we used Illumina MiSeq to sequence amplicons generated from the V4 region of the 16S rRNA gene to investigate the gut microbiome of two free-ranging sympatric Namibian carnivore species, the cheetah (Acinonyx jubatus) and the black-backed jackal (Canis mesomelas). Bacterial phyla with proportions >0.2% were identical for both species and included Firmicutes, Fusobacteria, Bacteroidetes, Proteobacteria and Actinobacteria. At a finer taxonomic resolution, black-backed jackals exhibited 69 bacterial taxa with proportions ≥0.1%, whereas cheetahs had only 42. Finally, oligotyping revealed that shared bacterial taxa consisted of distinct oligotype profiles. Thus, in contrast to 3% OTUs, oligotyping can detect fine-scale taxonomic differences between microbiomes

  4. Recognition and identification of bumblebee species in the Bombus lucorum-complex (Hymenoptera, Apidae – A review and outlook

    Directory of Open Access Journals (Sweden)

    Silas Bossert

    2015-02-01

    Full Text Available The recognition of cryptic species represents one of the major challenges in current taxonomy and affects our understanding of global diversity. In practice, the process from discovery to acceptance in the scientific community can take an extensive length of time. A prime example is the traditionally difficult taxonomy of the cryptic bumblebee species belonging to the Bombus lucorum-complex. The status of the three European species in the group – Bombus lucorum and the closely related Bombus cryptarum and Bombus magnus – has recently become widely accepted, primarily due to investigations of nucleotide sequences and marking pheromones. In contrast, doubts prevail concerning the validity of species identification based on morphology. As a consequence, our knowledge of the species is muddled in a mire of unreliable and confusing literature data from a large number of authors over the centuries. To clarify this issue, this paper provides a recapitulation of the historical literature and highlights the milestones in the process of species recognition. Further, the possibility of a morphologically based species identification is discussed in the context of new molecular data. Finally, this review outlines the current challenges and provides directions for future issues.

  5. Identification guide to some Diaptomid species (Crustacea, Copepoda, Calanoida, Diaptomidae of “de la Plata” River Basin (South America

    Directory of Open Access Journals (Sweden)

    Gilmar Perbiche-Neves

    2015-04-01

    Full Text Available An identification guide is presented for species of calanoid copepod family Diaptomidae from “de la Plata” River Basin (Argentina, Brazil, Bolivia, Paraguay and Uruguay. It was based on material collected during the summer and winter of 2010 from 43 sites across the eastern part and the lower stretches of this basin, the second largest in South America and the fourth in the world. The guide contains identification keys and species diagnoses for males and females, richly supported by scanning electronic micrographs and/or line drawings of 19 species. It also includes some general remarks on the taxonomy and phylogenetic relationships of these species. The key was adjusted to be useful for these species only, with separate keys for each sex, and is the first for females of South America. One species classified herein as incertae sedis was not included in the analysis. At least ten other species have previously been recorded in the basin but were not present in our samples. This is the first attempt to compile comprehensive taxonomic information on this group of copepods in this region, and it is expected to become a useful tool for biologists and young taxonomists interested in the crustacean biota of the Neotropical region.

  6. Identification guide to some Diaptomid species (Crustacea, Copepoda, Calanoida, Diaptomidae) of "de la Plata" River Basin (South America).

    Science.gov (United States)

    Perbiche-Neves, Gilmar; Boxshall, Geoffrey Allan; Previattelli, Daniel; Nogueira, Marcos Gomes; da Rocha, Carlos Eduardo Falavigna

    2015-01-01

    An identification guide is presented for species of calanoid copepod family Diaptomidae from "de la Plata" River Basin (Argentina, Brazil, Bolivia, Paraguay and Uruguay). It was based on material collected during the summer and winter of 2010 from 43 sites across the eastern part and the lower stretches of this basin, the second largest in South America and the fourth in the world. The guide contains identification keys and species diagnoses for males and females, richly supported by scanning electronic micrographs and/or line drawings of 19 species. It also includes some general remarks on the taxonomy and phylogenetic relationships of these species. The key was adjusted to be useful for these species only, with separate keys for each sex, and is the first for females of South America. One species classified herein as incertae sedis was not included in the analysis. At least ten other species have previously been recorded in the basin but were not present in our samples. This is the first attempt to compile comprehensive taxonomic information on this group of copepods in this region, and it is expected to become a useful tool for biologists and young taxonomists interested in the crustacean biota of the Neotropical region. PMID:25931959

  7. Identification guide to some Diaptomid species (Crustacea, Copepoda, Calanoida, Diaptomidae) of “de la Plata” River Basin (South America)

    Science.gov (United States)

    Perbiche-Neves, Gilmar; Boxshall, Geoffrey Allan; Previattelli, Daniel; Nogueira, Marcos Gomes; da Rocha, Carlos Eduardo Falavigna

    2015-01-01

    Abstract An identification guide is presented for species of calanoid copepod family Diaptomidae from “de la Plata” River Basin (Argentina, Brazil, Bolivia, Paraguay and Uruguay). It was based on material collected during the summer and winter of 2010 from 43 sites across the eastern part and the lower stretches of this basin, the second largest in South America and the fourth in the world. The guide contains identification keys and species diagnoses for males and females, richly supported by scanning electronic micrographs and/or line drawings of 19 species. It also includes some general remarks on the taxonomy and phylogenetic relationships of these species. The key was adjusted to be useful for these species only, with separate keys for each sex, and is the first for females of South America. One species classified herein as incertae sedis was not included in the analysis. At least ten other species have previously been recorded in the basin but were not present in our samples. This is the first attempt to compile comprehensive taxonomic information on this group of copepods in this region, and it is expected to become a useful tool for biologists and young taxonomists interested in the crustacean biota of the Neotropical region. PMID:25931959

  8. 76 FR 64074 - Schedules for Atlantic Shark Identification Workshops and Protected Species Safe Handling...

    Science.gov (United States)

    2011-10-17

    ... National Oceanic and Atmospheric Administration RIN 0648-XA670 Schedules for Atlantic Shark Identification... Shark Identification workshop scheduled for November 17, 2011, in Charleston, SC, has been changed. This.... Atlantic Shark Identification workshops are mandatory for Atlantic Shark Dealer permit holders or...

  9. A cross-sectional survey of bacterial species in plaque from client owned dogs with healthy gingiva, gingivitis or mild periodontitis.

    Directory of Open Access Journals (Sweden)

    Ian J Davis

    Full Text Available Periodontal disease is the most widespread oral disease in dogs which if left untreated results in significant pain to the pet and loss of dentition. The objective of this study was to identify bacterial species in canine plaque that are significantly associated with health, gingivitis and mild periodontitis (<25% attachment loss. In this survey subgingival plaque samples were collected from 223 dogs with healthy gingiva, gingivitis and mild periodontitis with 72 to 77 samples per health status. DNA was extracted from the plaque samples and subjected to PCR amplification of the V1-V3 region of the 16S rDNA. Pyrosequencing of the PCR amplicons identified a total of 274 operational taxonomic units after bioinformatic and statistical analysis. Porphyromonas was the most abundant genus in all disease stages, particularly in health along with Moraxella and Bergeyella. Peptostreptococcus, Actinomyces, and Peptostreptococcaceae were the most abundant genera in mild periodontitis. Logistic regression analysis identified species from each of these genera that were significantly associated with health, gingivitis or mild periodontitis. Principal component analysis showed distinct community profiles in health and disease. The species identified show some similarities with health and periodontal disease in humans but also major differences. In contrast to human, healthy canine plaque was found to be dominated by Gram negative bacterial species whereas Gram positive anaerobic species predominate in disease. The scale of this study surpasses previously published research and enhances our understanding of the bacterial species present in canine subgingival plaque and their associations with health and early periodontal disease.

  10. High-resolution bacterial growth inhibition profiling combined with HPLC-HRMS-SPE-NMR for identification of antibacterial constituents in Chinese plants used to treat snakebites

    DEFF Research Database (Denmark)

    Liu, Yueqiu; Nielsen, Mia; Stærk, Dan;

    2014-01-01

    Ethnopharmacogical relevance Bacterial infection is one of the main secondary infections caused by snakebite. The 88 plant species investigated in this study have been used as folk remedies for treatment of snakebite, and it is therefore the aim of this study to investigate whether the plants...... contain compounds with bacterial growth inhibition. Materials and methods The water and ethanol extracts of 88 plant species were screened at 200 μg/mL against Bacillus subtilis, Staphylococcus aureus, Escherichia coli and Pseudomonas aeruginosa for their antibacterial activity by micro-broth dilution...... assay. The most active extracts were fractionated into microplates using analytical-scale RP-HPLC, and subsequently growth inhibition was assessed for each well. The biochromatograms constructed from these assays were used to identify compounds responsible for antibacterial activity. The structures of...

  11. Assessing the effect of litter species on the dynamic of bacterial and fungal communities during leaf decomposition in microcosm by molecular techniques.

    Directory of Open Access Journals (Sweden)

    Wenjing Xu

    Full Text Available Although bacteria and fungi are well-known to be decomposers of leaf litter, few studies have examined their compositions and diversities during the decomposition process in tropical stream water. Xishuangbanna is a tropical region preserving one of the highest floristic diversity areas in China. In this study, leaf litter of four dominant plant species in Xishuangbanna was incubated in stream water for 42 days during which samples were taken regularly. Following DNA extraction, PCR-DGGE (denaturing gradient gel electrophoresis and clone-sequencing analyses were performed using bacterial and fungal specific primers. Leaf species have slightly influences on bacterial community rather than fungal community. The richness and diversity of bacteria was higher than that of fungi, which increased towards the end of the 42-day-incubation. The bacterial community was initially more specific upon the type of leaves and gradually became similar at the later stage of decomposition with alpha-proteobacteria as major component. Sequences affiliated to methanotrophs were obtained that indicates potentially occurrence of methane oxidation and methanogenesis. For the fungal community, sequences affiliated to Aspergillus were predominant at the beginning and then shifted to Pleosporales. Our results suggest that the microorganisms colonizing leaf biofilm in tropical stream water were mostly generalists that could exploit the resources of leaves of various species equally well.

  12. Characterization of Viral Communities of Biting Midges and Identification of Novel Thogotovirus Species and Rhabdovirus Genus.

    Science.gov (United States)

    Temmam, Sarah; Monteil-Bouchard, Sonia; Robert, Catherine; Baudoin, Jean-Pierre; Sambou, Masse; Aubadie-Ladrix, Maxence; Labas, Noémie; Raoult, Didier; Mediannikov, Oleg; Desnues, Christelle

    2016-01-01

    More than two thirds of emerging viruses are of zoonotic origin, and among them RNA viruses represent the majority. Ceratopogonidae (genus Culicoides) are well-known vectors of several viruses responsible for epizooties (bluetongue, epizootic haemorrhagic disease, etc.). They are also vectors of the only known virus infecting humans: the Oropouche virus. Female midges usually feed on a variety of hosts, leading to possible transmission of emerging viruses from animals to humans. In this context, we report here the analysis of RNA viral communities of Senegalese biting midges using next-generation sequencing techniques as a preliminary step toward the identification of potential viral biohazards. Sequencing of the RNA virome of three pools of Culicoides revealed the presence of a significant diversity of viruses infecting plants, insects and mammals. Several novel viruses were detected, including a novel Thogotovirus species, related but genetically distant from previously described tick-borne thogotoviruses. Novel rhabdoviruses were also detected, possibly constituting a novel Rhabdoviridae genus, and putatively restricted to insects. Sequences related to the major viruses transmitted by Culicoides, i.e., African horse sickness, bluetongue and epizootic haemorrhagic disease viruses were also detected. This study highlights the interest in monitoring the emergence and circulation of zoonoses and epizooties using their arthropod vectors. PMID:26978389

  13. The Bergen multifrequency analyzer (BMA): A new toolbox for acoustic categorization and species identification

    Science.gov (United States)

    Ona, Egil; Korneliussen, Rolf; Knudsen, Hans Petter; Rang, Kjell; Eliassen, Inge; Heggelund, Yngve; Patel, Daniel

    2001-05-01

    Multifrequency split-beam echo sounders with nearly identical and overlapping acoustic beams have been regularly used in acoustic surveys for fish stock abundance estimation. Calibrated raw data from up to six simultaneously working echo sounders at 18, 38, 70, 120, 200, and 364 kHz were applied for developing a new processing tool for real-time acoustic target categorization and acoustic species identification. The system now handles raw data from the Simrad EK500 and EK60 split-beam echo sounders, and performs a stepwise, modular sequence of analysis, like bottom detection, noise quantification and removal, target categorization, and school detection in near-real time. Direct generation of new, synthetic echograms, based upon the measured frequency response of the targets, is also one of the most useful features of the system. This information may significantly increase the accuracy of acoustic survey estimates of fish and zooplankton. New routines for noise removal, target categorization, and school detection will be presented, as well as new methods for training and building the artificial experience of the analyzer.

  14. Bacterial lipases

    NARCIS (Netherlands)

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

    1994-01-01

    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, mea

  15. Feather barbs as a good source of mtDNA for bird species identification in forensic wildlife investigations

    Directory of Open Access Journals (Sweden)

    Speller Camilla F

    2011-07-01

    Full Text Available Abstract Background The ability to accurately identify bird species is crucial for wildlife law enforcement and bird-strike investigations. However, such identifications may be challenging when only partial or damaged feathers are available for analysis. Results By applying vigorous contamination controls and sensitive PCR amplification protocols, we found that it was feasible to obtain accurate mitochondrial (mtDNA-based species identification with as few as two feather barbs. This minimally destructive DNA approach was successfully used and tested on a variety of bird species, including North American wild turkey (Meleagris gallopavo, Canada goose (Branta canadensis, blue heron (Ardea herodias and pygmy owl (Glaucidium californicum. The mtDNA was successfully obtained from 'fresh' feathers, historic museum specimens and archaeological samples, demonstrating the sensitivity and versatility of this technique. Conclusions By applying appropriate contamination controls, sufficient quantities of mtDNA can be reliably recovered and analyzed from feather barbs. This previously overlooked substrate provides new opportunities for accurate DNA species identification when minimal feather samples are available for forensic analysis.

  16. Practical identification of human originated Lactobacillus species by amplified ribosomal DNA restriction analysis (ARDRA) for probiotic use.

    Science.gov (United States)

    Öztürk, Mehmet; Meterelliyöz, Merve

    2015-08-01

    Probiotics are gaining popularity and increasing the importance of their accurate speciation. Lactobacillus species are commonly used as probiotic strains mostly of clinical importance. Present knowledge indicates that at least 14 Lactobacillus species are associated with the human intestinal tract. Currently, researchers are interested in developing efficient techniques for screening and selecting probiotics bacteria, but unfortunately most of these methods are time-consuming, labor-intensive and costly. The aim of this study is to develop reliable, rapid and accurate method to identify 14 references Lactobacillus species that could have been found in the human alimentary tract by 16S ribosomal DNA restriction analysis. In this study, to develop an effective method for the genotype-based identification of the reference Lactobacillus species, 1.5 kb of 16S rRNA nucleotide sequences of 14 Lactobacillus were collected from the Gene Bank aligned, in silico restricted and analyzed in respect to their 16S-rRNA restriction fragment polymorphism. In silico restriction profiles of 16S-rRNA indicated that FspBI, HinfI and DraI restriction enzymes (RE) are convenient for differentiation of 14 Lactobacillus species in human intestinal tract except Lb. casei and Lb. paracasei. The patterns of our experimental findings obtained from 16S PCR-ARDRA completely confirmed our in silico patterns. The present work demonstrated that 16S PCR-ARDRA method with FspBI, HinfI and DraI RE is a rapid, accurate and reliable method for the identification of Lactobacillus species from human alimentary tract, especially during the identification of large numbers of isolates and any laboratory equipped with a thermo cycler for probiotic use. PMID:25860079

  17. Evaluation of the bacterial microbiome of two flea species using different DNA-isolation techniques provides insights into flea host ecology.

    Science.gov (United States)

    Lawrence, Andrea L; Hii, Sze-Fui; Chong, Rowena; Webb, Cameron E; Traub, Rebecca; Brown, Graeme; Šlapeta, Jan

    2015-12-01

    Fleas (Siphonaptera) are ubiquitous blood-sucking pests of animals worldwide and are vectors of zoonotic bacteria such as Rickettsia and Bartonella. We performed Ion Torrent PGM amplicon sequencing for the bacterial 16S rRNA gene to compare the microbiome of the ubiquitous cat flea (Ctenocephalides f. felis) and the host-specific echidna stickfast flea (Echidnophaga a. ambulans) and evaluated potential bias produced during common genomic DNA-isolation methods. We demonstrated significant differences in the bacterial community diversity between the two flea species but not between protocols combining surface sterilisation with whole flea homogenisation or exoskeleton retention. Both flea species were dominated by obligate intracellular endosymbiont Wolbachia, and the echidna stickfast fleas possessed the endosymbiont Cardinium. Cat fleas that were not surface sterilised showed presence of Candidatus 'Rickettsia senegalensis' DNA, the first report of its presence in Australia. In the case of Rickettsia, we show that sequencing depth of 50 000 was required for comparable sensitivity with Rickettsia qPCR. Low-abundance bacterial genera are suggested to reflect host ecology. The deep-sequencing approach demonstrates feasibility of pathogen detection with simultaneous quantitative analysis and evaluation of the inter-relationship of microbes within vectors. PMID:26542076

  18. PCR Identification for Equus przewalsrii Species%普氏野马物种的PCR鉴定

    Institute of Scientific and Technical Information of China (English)

    郑小龙; 王群; 岳志芹; 朱来华; 梁成珠; 邓明俊; 肖西志; 姜帆; 于业锋

    2013-01-01

    为建立鉴定普氏野马的PCR方法,根据线粒体D-Loop区序列,设计了针对普氏野马的特异性扩增引物,通过优化反应体系和扩增条件,建立了能够鉴定普氏野马的PCR方法。该方法检测灵敏度较高,可扩增10-3 ng的DNA ,与蒙古马、伊犁马、哈萨克马、阿拉伯马、驴、骡、牛和羊等动物均不发生交叉反应,具有很好的特异性。结果表明,建立的普氏野马物种鉴定的PCR方法特异性好,灵敏度较高,简单可靠,可作为普氏野马的一种有效鉴定方法,对普氏野马的保护起到重要的作用。%To develop the species-specific PCR assay for the identification of Equus przewalsrii ,primers were designed from mitochondria D-loop region after alignment of the available sequences in the GenBank database .The primers generated specific fragments of 315 bp length for Equus przewalsrii .The results showed that the PCR was established .The sensitivity analysis showed that the developed PCR could detect 10-3 ng DNA ,and no cross reaction with Mongolia horse ,Ili horse ,Kazakh horse ,Arabian horse ,Don-key ,Mule ,Bovine and Ovine .The results demonstrated that this species-specific PCR provided a useful , specific ,sensitive and simple technique to identify Equus przewalsrii .This assay could play an important role in conservation of Equus p rz ew alsrii .

  19. An illustrated guide to the identification of the known species of Diatraea Guilding (Lepidoptera, Crambidae, Crambinae) based on genitalia.

    Science.gov (United States)

    Solis, M Alma; Metz, Mark A

    2016-01-01

    The genus Diatraea Guilding is one of the most economically important groups of moths in the Western Hemisphere. The larvae are stem borers that feed on species of Poaceae, or grasses, such as sugarcane, corn, rice, and sorghum, as well as many other native grasses. Interest in this group has risen considerably since sugarcane and other grasses have been utilized and/or investigated as biofuels. This is the first modern study to treat all 41 valid described species. Most type specimens were examined and we provide a checklist with 19 new synonyms. We provide keys for the identification of most species in this genus based on morphology of the male and female genitalia and modern illustrations of male and female genitalia. We also provide an updated table of species distribution by country. PMID:27081337

  20. Four-locus phylogeny of Fusarium avenaceum and related species and their species-specific identification based on partial phosphate permease gene sequences.

    Science.gov (United States)

    Stakheev, Alexander A; Khairulina, Dina R; Zavriev, Sergey K

    2016-05-16

    The fungus Fusarium avenaceum and its closest relatives are responsible for contamination of agricultural plants and their products by mycotoxins such as enniatins and moniliformin. Precise identification of mycotoxin producers is necessary for estimation of the accumulation risk of those compounds and for preventing the consumption of highly contaminated products. Nucleic acids amplification-based techniques proved to be the most rapid and reliable approach for pathogen diagnostics and identification. In this study partial phosphate permease gene (PHO) sequences were determined for Fusarium avenaceum (including one isolate identified as F. arthrosporioides), F. tricinctum, F. acuminatum and F. torulosum. Phylogenetic analysis of 40 isolates of those species from different climates and geographical regions of Russia and some neighboring countries based on sequences of PHO, translation elongation factor 1 alpha (TEF1α), beta-tubulin (β-TUB), enniatin synthetase (Esyn1) genes and combined data set demonstrated that the PHO gene possesses the highest rate of variability among them and can be considered as an informative marker for phylogenetic studies of these species. According to the combined data set phylogeny, the isolates of each species formed clusters with a high bootstrap support. Analysis of PHO sequences revealed a high intraspecific variability of F. avenaceum: there were 5 independent clusters on the dendrogram, including one cluster which was closer to F. torulosum than to other F. avenaceum isolates. Variable sites in PHO sequences have been used for the design of species-specific primers and a fluorescent hydrolysis probe. The specificity of the assay was shown for DNA samples extracted from 68 isolates of 23 Fusarium species. Quantitative PCR approach was applied to estimate the contamination rate of 17 naturally infected oat and barley samples, previously characterized by microbiological procedures. PMID:26974249