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BIOLOGY (1413 journals)            First | 1 2 3 4 5 6 7 8 | Last

Showing 801 - 1000 of 1720 Journals sorted alphabetically
Journal of Huazhong University of Science and Technology [Medical Sciences]     Hybrid Journal  
Journal of Human Evolution     Hybrid Journal   (Followers: 15)
Journal of Hymenoptera Research     Open Access   (Followers: 1)
Journal of Ichthyology     Hybrid Journal   (Followers: 4)
Journal of Insect Behavior     Hybrid Journal   (Followers: 8)
Journal of Insect Biodiversity     Open Access   (Followers: 2)
Journal of Insect Conservation     Hybrid Journal   (Followers: 9)
Journal of Integrated OMICS     Open Access  
Journal of Integrated Pest Management     Open Access   (Followers: 1)
Journal of Integrative Environmental Sciences     Hybrid Journal   (Followers: 4)
Journal of Intelligent Transportation Systems: Technology, Planning, and Operations     Hybrid Journal   (Followers: 4)
Journal of Invertebrate Pathology     Hybrid Journal   (Followers: 3)
Journal of Landscape Ecology     Open Access   (Followers: 9)
Journal of Law and the Biosciences     Open Access   (Followers: 2)
Journal of Leukocyte Biology     Open Access   (Followers: 2)
Journal of Life and Earth Science     Open Access  
Journal of Life Sciences Research     Open Access  
Journal of Lipid Research     Full-text available via subscription   (Followers: 7)
Journal of Lipids     Open Access  
Journal of Luminescence     Hybrid Journal   (Followers: 3)
Journal of Mammalian Evolution     Hybrid Journal   (Followers: 5)
Journal of Mammalian Ova Research     Full-text available via subscription  
Journal of Mammalogy     Full-text available via subscription   (Followers: 10)
Journal of Mammary Gland Biology and Neoplasia     Hybrid Journal   (Followers: 1)
Journal of Marine and Aquatic Sciences     Open Access  
Journal of Marine Biology     Open Access   (Followers: 11)
Journal of Mathematical Biology     Hybrid Journal   (Followers: 13)
Journal of Mechanics in Medicine and Biology     Hybrid Journal  
Journal of Medical Primatology     Hybrid Journal   (Followers: 2)
Journal of Medical Toxicology     Hybrid Journal   (Followers: 6)
Journal of Medicine and Philosophy     Hybrid Journal   (Followers: 6)
Journal of Membrane Biology     Hybrid Journal   (Followers: 1)
Journal of Membrane Science     Hybrid Journal   (Followers: 14)
Journal of Molecular Biology     Hybrid Journal   (Followers: 46)
Journal of Molecular Biology Research     Open Access   (Followers: 2)
Journal of Molecular Catalysis B: Enzymatic     Hybrid Journal   (Followers: 2)
Journal of Molecular Cell Biology     Hybrid Journal   (Followers: 10)
Journal of Molecular Evolution     Hybrid Journal   (Followers: 11)
Journal of Molecular Signaling     Open Access  
Journal of Molecular Structure     Hybrid Journal   (Followers: 6)
Journal of Molluscan Studies     Hybrid Journal   (Followers: 1)
Journal of Muscle Research and Cell Motility     Hybrid Journal  
Journal of Mycology     Open Access   (Followers: 3)
Journal of Nanoparticle Research     Hybrid Journal   (Followers: 2)
Journal of Nanoparticles     Open Access  
Journal of Natural History     Hybrid Journal   (Followers: 8)
Journal of Natural Products     Full-text available via subscription   (Followers: 10)
Journal of Natural Science, Biology and Medicine     Open Access   (Followers: 2)
Journal of Natural Sciences Research     Open Access   (Followers: 3)
Journal of Negative Results in BioMedicine     Open Access   (Followers: 1)
Journal of Nematology     Open Access   (Followers: 1)
Journal of Neuroscience and Behavioral Health     Open Access  
Journal of New Seeds     Hybrid Journal  
Journal of Nucleic Acids     Open Access  
Journal of Parasitology     Full-text available via subscription   (Followers: 11)
Journal of Parasitology and Vector Biology     Open Access   (Followers: 1)
Journal of Pharmacological and Toxicological Methods     Hybrid Journal   (Followers: 6)
Journal of Phycology     Hybrid Journal   (Followers: 6)
Journal of Physics D : Applied Physics     Hybrid Journal   (Followers: 9)
Journal of Physics: Condensed Matter     Hybrid Journal   (Followers: 7)
Journal of Physics: Conference Series     Open Access   (Followers: 2)
Journal of Phytopathology     Hybrid Journal   (Followers: 2)
Journal of Plankton Research     Hybrid Journal   (Followers: 3)
Journal of Plant Ecology     Hybrid Journal   (Followers: 14)
Journal of Plasma Physics     Hybrid Journal   (Followers: 5)
Journal of Pollination Ecology     Open Access  
Journal of Porphyrins and Phthalocyanines     Hybrid Journal   (Followers: 1)
Journal of Progressive Research in Biology     Open Access  
Journal of Proteome Research     Full-text available via subscription   (Followers: 11)
Journal of Proteomics     Hybrid Journal   (Followers: 9)
Journal of Purdue Undergraduate Research     Open Access   (Followers: 1)
Journal of Radiation Research and Applied Sciences     Open Access   (Followers: 1)
Journal of Risk Research     Hybrid Journal   (Followers: 7)
Journal of Science of the University of Kelaniya Sri Lanka     Open Access  
Journal of Seed Science     Open Access  
Journal of Signal Transduction     Open Access   (Followers: 2)
Journal of Stem Cell Research & Therapy     Open Access   (Followers: 1)
Journal of Stored Products Research     Hybrid Journal  
Journal of Structural and Functional Genomics     Hybrid Journal   (Followers: 1)
Journal of Structural Biology     Hybrid Journal   (Followers: 10)
Journal of Sustainable Bioenergy Systems     Full-text available via subscription   (Followers: 1)
Journal of Sustainable Society     Open Access   (Followers: 6)
Journal of Systematic Palaeontology     Hybrid Journal   (Followers: 7)
Journal of Systematics Evolution     Open Access   (Followers: 4)
Journal of the American Mosquito Control Association     Full-text available via subscription  
Journal of the Korean Society for Applied Biological Chemistry     Hybrid Journal  
Journal of the Renin-Angiotensin-Aldosterone System     Open Access  
Journal of the Royal Society of New Zealand     Hybrid Journal   (Followers: 1)
Journal of the Selva Andina Research Society     Open Access  
Journal of the South Carolina Academy of Science     Open Access  
Journal of Theoretical Biology     Hybrid Journal   (Followers: 12)
Journal of Thermal Biology     Hybrid Journal   (Followers: 2)
Journal of Thyroid Research     Open Access  
Journal of Tissue Engineering     Open Access   (Followers: 6)
Journal of Vacuum Science & Technology A     Full-text available via subscription   (Followers: 2)
Journal of Vacuum Science & Technology B     Full-text available via subscription   (Followers: 2)
Journal of Vector Ecology     Free   (Followers: 2)
Journal of Vegetation Science     Full-text available via subscription   (Followers: 19)
Journal of Vinyl & Additive Technology     Hybrid Journal  
Journal of Virological Methods     Hybrid Journal   (Followers: 6)
Journal of Virology     Hybrid Journal   (Followers: 31)
Journal of Visualized Experiments     Full-text available via subscription   (Followers: 2)
Journal of Wetlands Environmental Management     Open Access   (Followers: 2)
Journal of Zhejiang University - Science B     Hybrid Journal  
Journal of Zhejiang University : Agriculture & Life Sciences     Open Access  
Jurnal Biologi Indonesia     Open Access  
Jurnal Penelitian Sains (JPS)     Open Access  
Jurnal Teknosains     Open Access  
Kahramanmaras Sutcu Imam University Journal Of Natural Sciences     Open Access  
Karbala International Journal of Modern Science     Open Access   (Followers: 1)
Kennedy Institute of Ethics Journal     Full-text available via subscription   (Followers: 6)
Kew Bulletin     Hybrid Journal   (Followers: 1)
KINOME     Open Access  
Knowledge and Management of Aquatic Ecosystems     Open Access   (Followers: 3)
Koedoe : African Protected Area Conservation and Science     Open Access   (Followers: 5)
Kurtziana     Open Access  
Landscape and Ecological Engineering     Hybrid Journal   (Followers: 4)
Large Marine Ecosystems     Full-text available via subscription  
Le Naturaliste canadien     Full-text available via subscription  
Letters in Mathematical Physics     Hybrid Journal   (Followers: 2)
Life     Open Access   (Followers: 2)
Life Sciences in Space Research     Hybrid Journal  
Life Sciences, Society and Policy     Open Access  
Limnological Papers     Open Access  
Lipid Insights     Open Access  
Lipid Technology     Hybrid Journal   (Followers: 2)
Lipids     Hybrid Journal   (Followers: 2)
Lipids in Health and Disease     Open Access  
Luminescence     Hybrid Journal   (Followers: 3)
mAbs     Full-text available via subscription   (Followers: 9)
Macromolecular Bioscience     Hybrid Journal   (Followers: 1)
Macromolecular Reaction Engineering     Hybrid Journal  
Madroño     Full-text available via subscription  
Malacologia     Full-text available via subscription  
Malacologica Bohemoslovaca     Open Access   (Followers: 1)
Malawi Journal of Science and Technology     Open Access   (Followers: 6)
Mammal Review     Hybrid Journal   (Followers: 6)
Mammal Study     Full-text available via subscription  
Mammalian Biology - Zeitschrift für Säugetierkunde     Hybrid Journal   (Followers: 4)
Mammalian Genome     Hybrid Journal   (Followers: 3)
Mammalian Species     Full-text available via subscription   (Followers: 1)
Manufacturing Engineer     Hybrid Journal   (Followers: 7)
Marine Biodiversity     Hybrid Journal   (Followers: 8)
Marine Biodiversity Records     Hybrid Journal   (Followers: 4)
Marine Biology     Hybrid Journal   (Followers: 57)
Marine Biotechnology     Hybrid Journal   (Followers: 4)
Marine Mammal Science     Hybrid Journal   (Followers: 9)
Materials Science and Engineering: C     Hybrid Journal   (Followers: 19)
Materials Technology : Advanced Performance Materials     Hybrid Journal   (Followers: 6)
Mathematical Biosciences     Hybrid Journal   (Followers: 2)
Mathematical Medicine and Biology: A Journal of the IMA     Hybrid Journal   (Followers: 2)
Mathematical Physics, Analysis and Geometry     Hybrid Journal   (Followers: 1)
Mathematical Problems in Engineering     Open Access   (Followers: 2)
Matrix Biology     Hybrid Journal  
mBio     Open Access   (Followers: 6)
Mechanisms of Ageing and Development     Hybrid Journal   (Followers: 2)
Mechanisms of Development     Hybrid Journal   (Followers: 5)
Médecine Nucléaire     Full-text available via subscription  
médecine/sciences     Full-text available via subscription   (Followers: 1)
Medical and Biological Engineering and Computing     Hybrid Journal   (Followers: 2)
Medical and Biological Sciences     Open Access  
Medical Engineering & Physics     Hybrid Journal   (Followers: 8)
Membrane Protein Transport     Full-text available via subscription   (Followers: 2)
Memoirs of the Association of Australasian Palaeontologists     Full-text available via subscription   (Followers: 2)
Messenger     Full-text available via subscription  
Metabolic Engineering     Hybrid Journal   (Followers: 12)
Metabolites     Open Access  
Metabolomics     Hybrid Journal   (Followers: 7)
Metallomics     Full-text available via subscription  
Metamorfosa : Journal of Bilogical Sciences     Open Access   (Followers: 1)
Methods     Hybrid Journal   (Followers: 12)
Methods in Cell Biology     Full-text available via subscription   (Followers: 5)
Methods in Cell Science     Hybrid Journal   (Followers: 3)
Methods in Ecology and Evolution     Partially Free   (Followers: 26)
Micologia Aplicada Internacional     Open Access  
Microarrays     Open Access  
Micron     Hybrid Journal  
Mitochondrial DNA     Hybrid Journal   (Followers: 4)
Mitochondrion     Hybrid Journal   (Followers: 3)
Modelling and Simulation in Engineering     Open Access   (Followers: 3)
Modelling and Simulation in Materials Science and Engineering     Hybrid Journal   (Followers: 7)
Modern Chemotherapy     Open Access  
Molecular & Cellular Proteomics     Full-text available via subscription   (Followers: 13)
Molecular & Cellular Toxicology     Hybrid Journal   (Followers: 2)
Molecular and Biochemical Parasitology     Hybrid Journal   (Followers: 2)
Molecular and Cellular Biochemistry     Hybrid Journal   (Followers: 3)
Molecular and Cellular Biology     Hybrid Journal   (Followers: 20)
Molecular Based Mathematical Biology     Open Access  
Molecular Biology     Hybrid Journal   (Followers: 10)
Molecular Biology and Evolution     Hybrid Journal   (Followers: 78)
Molecular Biology International     Open Access   (Followers: 2)
Molecular Biology of the Cell     Partially Free   (Followers: 18)
Molecular Biology Reports     Hybrid Journal   (Followers: 4)
Molecular Brain     Open Access   (Followers: 1)
Molecular Breeding     Hybrid Journal   (Followers: 8)
Molecular Cell     Full-text available via subscription   (Followers: 43)
Molecular Ecology     Hybrid Journal   (Followers: 27)
Molecular Ecology Resources     Hybrid Journal   (Followers: 12)
Molecular Genetics and Metabolism     Hybrid Journal   (Followers: 5)
Molecular Immunology     Hybrid Journal   (Followers: 11)

  First | 1 2 3 4 5 6 7 8 | Last

Journal Cover Anaerobe
  [SJR: 1.09]   [H-I: 44]   [4 followers]  Follow
   Hybrid Journal Hybrid journal (It can contain Open Access articles)
   ISSN (Print) 1075-9964 - ISSN (Online) 1095-8274
   Published by Elsevier Homepage  [2970 journals]
  • Clostridium difficile ribotype 027 is not evenly distributed in Hesse,
    • Abstract: Publication date: Available online 7 April 2016
      Author(s): Mardjan Arvand, Gudrun Bettge-Weller
      Clostridium difficile-isolates associated with CDI in different healthcare facilities in Hesse were analysed. The most common ribotypes were 001 (31.1%) and 027 (27.0%). The proportion of ribotype 027 among regional C. difficile-isolates was 10.8% in North Hesse, 17.2% in Middle Hesse, and 33.5% in the Rhine-Main Metropolitan Area. In the latter region, ribotype 027 was the most prevalent ribotype.

      PubDate: 2016-04-09T01:18:27Z
  • Ex vivo pharmacokinetic/pharmacodynamic relationship of valnemulin against
           Clostridium perfringens in plasma, the small intestinal and caecal
           contents of rabbits
    • Abstract: Publication date: Available online 7 April 2016
      Author(s): Yu-Feng Zhou, Yang Yu, Jian Sun, Meng-Ting Tao, Wen-Jie Zhou, Xiao Li, Xiao-Ping Liao, Ya-Hong Liu
      The pharmacokinetic (PK) and ex vivo pharmacodynamic (PD) of valnemulin against Clostridium perfringens were investigated in plasma, the small intestinal and caecal contents of rabbits following intravenous (IV) or oral administration at 3 mg/kg bodyweight (BW). The postantibiotic effect (PAE) and postantibiotic sub-MIC effect (PA-SME) of valnemulin against C. perfringens ATCC13124 were also determined. The time-kill curves were established in vitro and ex vivo to evaluate the antibacterial activity of valnemulin against C. perfringens. The elimination half-lives (T1/2λz) of valnemulin in the jejunal fluids (7.82 h) or caecal contents (14.8 h) of rabbits was significantly longer than that in plasma (2.94 h). The MIC values of valnemulin against C. perfringens ATCC13124 were both 0.063 μg/mL in the artificial medium and jejunal fluids. The PAEs of valnemulin against C. perfringens were 2.9 h (1 × MIC) and 5.03 h (4 × MIC), and the PA-SMEs ranged from 7.9 h to 11.1 h. Valnemulin exhibited rapid, time-dependent killing feature, and the ex vivo dose-response profile was closely fitted to sigmoid Emax model (r2 = 0.9985). The surrogate index of AUC24h/MIC ratios required to achieve the bactericidal and virtual bacterial elimination effects were 57.5 and 90.1 h, respectively. Accordingly, the calculated daily dosage regimens of valnemulin for the bactericidal activity (1.96 mg/kg) and bacterial elimination (3.08 mg/kg) would be therapeutically effective in rabbits against C. perfringens with MIC ≤ 0.5 μg/mL.

      PubDate: 2016-04-07T05:39:31Z
  • Neutrophil-mediated inflammation in the pathogenesis of Clostridium
           difficile infections
    • Abstract: Publication date: Available online 5 April 2016
      Author(s): Shinsmon Jose, Rajat Madan
      Clostridium difficile is the most important cause of nosocomial infectious diarrhea in the western world. C. difficile infections are a major healthcare burden with approximately 500,000 new cases every year and an estimated annual cost of nearly $1 billion in the U.S. Furthermore, the infections are no longer restricted to health care facilities, and recent studies indicate spread of C. difficile infection to the community as well. The clinical spectrum of C. difficile infection ranges from asymptomatic colonization to severe diarrhea, fulminant colitis and death. This spectrum results from a complex interplay between bacterial virulence factors, the colonic microbiome and the host inflammatory response. The overall vigor of host inflammatory response is believed to be an important determinant of C. difficile disease severity, and a more robust immune response is associated with worse outcomes. Neutrophils are the primary cells that respond to C. difficile invasion and neutrophilic inflammation is the hallmark of C. difficile-associated disease. In this review, we will focus on the role of neutrophils (infiltration to infected tissue, pathogen clearance and resolution of inflammation) in the immuno-pathogenesis of C. difficile-associated disease (CDAD).

      PubDate: 2016-04-07T05:39:31Z
  • The CpAL system regulates changes of the trans-epithelial resistance of
           human enterocytes during C. perfringens type C infection
    • Abstract: Publication date: Available online 5 April 2016
      Author(s): Porfirio Nava, Jorge E. Vidal
      Clostridium perfringens type C strains produce severe disease in humans and animals including enterotoxaemia and hemorrhagic diarrhea. Type C disease is mediated by production of toxins that damage the site of infection inducing loss of bloody fluids. Production of type C toxins, such as CPA, PFO, and, CPB is regulated by the C. perfringens Agr-like (CpAL) quorum sensing (QS) system. The CpAL system is also required to recapitulate, in vivo, intestinal signs of C. perfringens type C-induced disease, including hemorrhagic diarrhea and accumulation of fluids. The intestinal epithelium forms a physical barrier, made up of a series of intercellular junctions including tight junctions (TJs), adherens junctions (AJs) and desmosomes (DMs). This selective barrier regulates important physiological processes, including paracellular movement of ions and solutes, which, if altered, results in loss of fluids into the intestinal lumen. In this work, the effects of C. perfringens infection on the barrier function of intestinal epithelial cells was evaluated by measuring trans-epithelial resistance (TEER). Our studies demonstrate that infection of human enterocytes with C. perfringens type C strain CN3685 induced a significant drop on TEER. Changes in TEER were mediated by the CpAL system as a CN3685ΔagrB mutant did not induce such a drop. Physical contact between bacteria and enterocytes produced more pronounced changes in TEER and this phenomenon appeared also to be mediated by the CpAL system. Finally, immunofluorescence studies demonstrate that C. perfringens type C infection redistribute TJs protein occludin, and Claudin-3, and DMs protein desmoglein-2, but did not affect the AJs protein E-cadherin.

      PubDate: 2016-04-07T05:39:31Z
  • A new chromogenic medium for isolation of Bacteroides fragilis suitable
           for screening for strains with antimicrobial resistance
    • Abstract: Publication date: Available online 6 April 2016
      Author(s): Daniel Tierney, Sarah D. Copsey, Trefor Morris, John D. Perry
      There have been an increasing number of reports describing the acquisition of antimicrobial resistance by Bacteroides fragilis including the occurrence of strains with resistance to multiple antimicrobials that are relied upon for treatment of infections. The aim of this study was to design a chromogenic selective medium for isolation of B. fragilis that could be adapted for specific isolation of antimicrobial-resistant strains. Bacteroides chromogenic agar (BCA) was the result of this endeavour and allowed growth of Bacteroides spp. as black colonies and the efficient inhibition of almost all other genera tested. The medium also allowed some differentiation of B. fragilis from other members of the B. fragilis group. When compared with Bacteroides fragilis bile-esculin agar (BBE) for the isolation of B. fragilis from 100 stool samples, 30 isolates of B. fragilis were recovered on BCA compared with 19 isolates recovered on BBE (P = 0.022). When supplemented with meropenem (4 μg/ml) or metronidazole (2 μg/ml), BCA could be used to select for the growth of B. fragilis isolates with resistance to these agents. We conclude that BCA is a useful research tool for surveillance studies to assess the prevalence of B. fragilis and, in particular, the occurrence of antimicrobial-resistant strains.

      PubDate: 2016-04-07T05:39:31Z
  • Bioactive fractions from the pasture legume Biserrula pelecinus L. have an
           anti-methanogenic effect against key rumen methanogens
    • Abstract: Publication date: Available online 7 April 2016
      Author(s): Bidhyut Kumar Banik, Zoey Durmic, William Erskine, Clinton Revell, Joy Vadhanabhuti, Christopher S. McSweeney, Jagadish Padmanabha, Gavin R. Flematti, Azizah A. Algreiby, Philip E. Vercoe
      Methanogenic archaea (methanogens) are common inhabitants of the mammalian intestinal tract. In ruminants, they are responsible for producing abundant amounts of methane during digestion of food, but selected bioactive plants and compounds may inhibit this activity. Recently, we have identified that, Biserrula pelecinus L. (biserrula) is one such plant and the current study investigated the specific anti-methanogenic activity of the plant. Bioassay-guided extraction and fractionation, coupled with in vitro fermentation batch culture were used to select the most bioactive fractions of biserrula. The four fractions were then tested against five species of methanogens grown in pure culture. Fraction bioactivity was assessed by measuring methane production and amplification of the methanogen mcrA gene. Treatments that showed bioactivity were subcultured in fresh broth without the bioactive fraction to distinguish between static and cidal effects. All four fractions were active against pure cultures, but the F2 fraction was the most consistent inhibitor of both methane production and cell growth, affecting four species of methanogens and also producing equivocal-cidal effects on the methanogens. Other fractions had selective activity affecting only some methanogens, or reducing either methane production or methanogenic cell growth. In conclusion, the anti-methanogenic activity of biserrula can be linked to compounds contained in selected bioactive fractions, with the F2 fraction strongly affecting key rumen methanogens. Further study is required to identify the specific plant compounds in biserrula that are responsible for the anti-methanogenic activity. These findings will help devise novel strategies to control methanogen populations and activity in the rumen, and consequently contribute in reducing e greenhouse gas emissions from ruminants.

      PubDate: 2016-04-07T05:39:31Z
  • A T-RFLP database for the rapid profiling of methanogenic communities in
           anaerobic digesters
    • Abstract: Publication date: Available online 1 April 2016
      Author(s): Franziska Bühligen, Rico Lucas, Marcell Nikolausz, Sabine Kleinsteuber
      We present a simple protocol for the cost- and time-efficient profiling of methanogens based on T-RFLP fingerprinting of mcrA amplicons. Sequence data were compiled from mesophilic lab-scale and full-scale biogas reactors operated under various conditions and fed with various substrates. The database facilitates the rapid identification of methanogens, thus reducing the need of cloning and sequencing.

      PubDate: 2016-04-03T05:26:24Z
  • Expression of arsenic resistance genes in the obligate anaerobe
           Bacteroides vulgatus ATCC 8482, a gut microbiome bacterium
    • Abstract: Publication date: Available online 31 March 2016
      Author(s): Jiajiao Li, Goutam Mandal, Barry P. Rosen
      The response of the obligate anaerobe Bacteroides vulgatus ATCC 8482, a common human gut microbiota, to arsenic was determined. B. vulgatus ATCC 8482 is highly resistant to pentavalent As(V) and methylarsenate (MAs(V)). It is somewhat more sensitive to trivalent inorganic As(III) but 100-fold more sensitive to methylarsenite (MAs(III)) than to As(III). B. vulgatus ATCC 8482 has eight continuous genes in its genome that we demonstrate form an arsenical-inducible transcriptional unit. The first gene of this ars operon, arsR, encodes a putative ArsR As(III)-responsive transcriptional repressor. The next three genes encode proteins of unknown function. The remaining genes, arsDABC, have well-characterized roles in detoxification of inorganic arsenic, but there are no known genes for MAs(III) resistance. Expression of each gene after exposure to trivalent and pentavalent inorganic and methylarsenicals was analyzed. MAs(III) was the most effective inducer. The arsD gene was the most highly expressed of the ars operon genes. These results demonstrate that this anaerobic microbiome bacterium has arsenic-responsive genes that confer resistance to inorganic arsenic and may be responsible for the organism’s ability to maintain its prevalence in the gut following dietary exposure to inorganic arsenic.
      Graphical abstract image

      PubDate: 2016-04-03T05:26:24Z
  • Detection of Clostridium botulinum neurotoxin genes (A - F) in dairy farms
           from Northern Germany using PCR: a case-control study
    • Abstract: Publication date: Available online 22 March 2016
      Author(s): Svenja Fohler, Sabrina Discher, Eva Jordan, Christian Seyboldt, Guenter Klein, Heinrich Neubauer, Martina Hoedemaker, Theresa Scheu, Amely Campe, Katharina Jensen, Amir Abdulmawjood
      Classical botulism in cattle mainly occurs after ingestion of feed contaminated with preformed toxin. In 2001 a form of botulism (“visceral botulism”) was postulated to occur after ingestion of Clostridium (C.) botulinum cells or spores, followed by colonization of the intestine, and local production of botulinum neurotoxin (BoNT) causing chronic generalized disease. To verify the potential role of C. botulinum in the described syndrome, a case-control study was conducted, including 139 farms. Fecal samples, rumen content, water and silage samples were collected on each farm. Real time BoNT gene PCR assays were conducted after enrichment in RCM (Reinforced Clostridial Medium) at 37°C and conventional PCRs after enrichment in MCM (Modified Cooked Meat Medium) at 30°C. Furthermore, a direct detection of BoNT genes without prior enrichment was attempted. BoNT A, B, C, D, E and F genes were detected in animal samples from 25 (17.99%), 3 (2.16%), 0 (0.0%), 2 (1.44%), 1 (0.72%), and 3 (2.16%) farms, respectively. Eleven feed samples were positive for BoNT A gene. By enrichment a significant increase in sensitivity was achieved. Therefore, this should be an essential part of any protocol. No significant differences regarding BoNT gene occurrence could be observed between Case and Control farms or chronically diseased and clinically healthy animals within the particular category. Thus, the postulated form of chronic botulism in cows could not be confirmed. This study supports the general opinion that C. botulinum can occasionally be found in the rumen and intestine of cows without causing disease.

      PubDate: 2016-03-25T17:51:18Z
  • Clostridium perfringens: Comparative Effects of Heat and Osmotic stress on
           non-enterotoxigenic and enterotoxigenic strains
    • Abstract: Publication date: Available online 21 March 2016
      Author(s): Cinthia Carolina Abbona, Patricia Virginia Stagnitta
      C. perfringens isolates associated with food poisoning carries a chromosomal cpe gene, while non-foodborne human gastrointestinal disease isolates carry a plasmid cpe gene. The enterotoxigenic strains tested produced vegetative cells and spores with significantly higher resistance than non-enterotoxigenic strains. These results suggest that the vegetative cells and spores have a competitive advantage over non-enterotoxigenic strains. However, no explanation has been provided for the significant associations between chromosomal cpe genotypes with the high resistance, which could explain the strong relationship between chromosomal cpe isolates and C. perfringens type A food poisoning. Here, we analyse the action of physical and chemical agent on non-enterotoxigenic and enterotoxigenic regional strains. And this study tested the relationship between the sensitivities of spores and their levels SASPs (small acid soluble proteins) production in the same strains examined.

      PubDate: 2016-03-21T17:30:47Z
  • Arthritis-induced alveolar bone loss is associated with changes in the
           composition of oral microbiota
    • Abstract: Publication date: Available online 18 March 2016
      Author(s): Jôice Dias Corrêa, Adriana Machado Saraiva, Celso Martins Queiroz-Junior, Mila Fernandes Moreira Madeira, Poliana Mendes Duarte, Mauro Martins Teixeira, Danielle Glória Souza, Tarcília Aparecida da Silva
      Rheumatoid arthritis (RA) and periodontitis (PD) are chronic inflammatory disorders that cause bone loss. PD tends to be more prevalent and severe in RA patients. Previous experimental studies demonstrated that RA triggers alveolar bone loss similarly to PD. The aim of this study was to investigate if arthritis-induced alveolar bone loss is associated with modification in the oral microbiota. Checkerboard DNA-DNA hybridization was employed to analyze forty oral bacterial species in 3 groups of C57BL/6 mice: control (n=12; without any challenge); Y4 (n=8; received oral inoculation of Aggregatibacter Actinomycetemcomitans strain FDC Y4) and AIA group (n=12; chronic antigen-induced arthritis). The results showed that AIA and Y4 group exhibited similar patterns of bone loss. The AIA group exhibited higher counts of most bacterial species analyzed with predominance of Gram-negative species similarly to infection-induced PD. Prevotella nigrescens and Treponema denticola were detected only in the Y4 group whereas Campylobacter showae, Streptococcus mitis and Streptococcus oralis were only found in the AIA group. Counts of Parvimonas micra, Selenomonas Noxia and Veillonella parvula were greater in the AIA group whereas Actinomyces viscosus and Neisseira mucosa were in large proportion in Y4 group. In conclusion, AIA is associated with changes in the composition of the oral microbiota, which might account for the alveolar bone loss observed in AIA mice.

      PubDate: 2016-03-21T17:30:47Z
  • Proteomic analysis and identification of cell surface associated proteins
           of Clostridium chauvoei
    • Abstract: Publication date: Available online 10 March 2016
      Author(s): Usharani Jayaramaiah, Neetu Singh, Sabarinath Thankappan, Ashok Kumar Mohanty, Pallab Chaudhuri, Vijendra Pal Singh, Viswas Konasagara Nagaleekar
      Blackleg is a highly fatal disease of cattle and sheep, caused by C. chauvoei, a Gram positive, anaerobic, spore forming bacteria. Cell surface-associated proteins play a major role in inducing the protective immunity. However, the identity of a majority of cell surface-associated proteins of C. chauvoei is not known. In the present investigation, we have used SDS-PAGE, 2D-gel electrophoresis and Western blotting followed by mass spectrometry to identify cell surface-associated proteins of C. chauvoei. Among the identified proteins, which have shown to offer protective antigencity in other bacteria, Enolase, Chaperonin, Ribosomal protein L10, Glycosyl Hydrolase and Flavoprotein were characterized by sequencing and their overexpression in Escherichia coli. In conclusion, cell surface-associated proteins were identified using proteomic approach and the genes for the immunoreactive proteins were expressed, which may prove to be potential diagnostic or vaccine candidates.

      PubDate: 2016-03-13T17:18:54Z
  • Differential proteomic analysis of outer membrane enriched extracts of
           Bacteroides fragilis grown under bile salts stress
    • Abstract: Publication date: Available online 4 March 2016
      Author(s): Renata F. Boente, Heidi Pauer, Deborah N.S. Silva, Joaquim Santos Filho, Vanessa Sandim, Luis Caetano M. Antunes, Rosana Barreto Rocha Ferreira, Russolina B. Zingali, Regina M.C.P. Domingues, Leandro A. Lobo
      Bacteroides fragilis is the anaerobic bacteria most commonly isolated anaerobic bacteria from infectious processes. Several virulence traits contribute to the pathogenic nature of this bacterium, including the ability to tolerate the high concentrations of bile found in the gastrointestinal tract (GIT). The activity of bile salts is similar to detergents and may lead to membrane permeabilization and cell death. Modulation of outer membrane proteins (OMPs) is considered a crucial event to bile salts resistance. The primary objective of the current work was to identify B. fragilis proteins associated with the stress induced by high concentration of bile salts. The outer membrane of B. fragilis strain 638R was isolated after growth either in the presence of 2% conjugated bile salts or without bile salts. The membrane fractions were separated on SDS-PAGE and analyzed by ESI-Q/TOF tandem mass spectrometry. A total of 37 proteins were identified; among them nine were found to be expressed exclusively in the absence of bile salts whereas eight proteins were expressed only in the presence of bile salts. These proteins are related to cellular functions such as transport through membrane, nutrient uptake, and protein-protein interactions. This study demonstrates the alteration of OMPs composition in B. fragilis during bile salts stress resistance and adaptation to environmental changes. Proteomics of OMPs was also shown to be a useful approach in the identification of new targets for functional analyses.

      PubDate: 2016-03-04T16:33:31Z
  • Isolation and whole genome sequencing of a Ruminococcus-like bacterium,
           associated with irritable bowel syndrome
    • Abstract: Publication date: Available online 2 March 2016
      Author(s): Ulla Hynönen, Pia Rasinkangas, Reetta Satokari, Lars Paulin, Willem M. de Vos, Taija E. Pietilä, Ravi Kant, Airi Palva
      In our previous studies on the intestinal microbiota in irritable bowel syndrome (IBS), we identified a bacterial phylotype with higher abundance in patients suffering from diarrhea than in healthy controls. In the present work, we have isolated in pure culture strain RT94, belonging to this phylotype, determined its whole genome sequence and performed an extensive genomic analysis and phenotypical testing. This revealed strain RT94 to be a strict anaerobe apparently belonging to a novel species with only 94 % similarity in the 16S rRNA gene sequence to the closest relatives Ruminococcus torques and Ruminococcus lactaris. The G + C content of strain RT94 is 45.2 mol% and the major long-chain cellular fatty acids are C16:0, C18:0 and C14:0. The isolate is metabolically versatile but not a mucus or cellulose utilizer. It produces acetate, ethanol, succinate, lactate and formate, but very little butyrate, as end products of glucose metabolism. The mechanisms underlying the association of strain RT94 with diarrhea-type IBS are discussed.

      PubDate: 2016-03-04T16:33:31Z
  • Elucidating the richness of bacterial groups in the gut of nicobarese
           tribal community – Perspective on their lifestyle transition
    • Abstract: Publication date: Available online 3 March 2016
      Author(s): Maile Anwesh, K. Vinod Kumar, Muruganandam Nagarajan, M. Punnam Chander, C. Kartick, Vijayachari Paluru
      Lifestyle and dietary habits are crucial features that can alter the gut microbiome of humans. Humans, along with their gut microbes, have coevolved in order to sustain themselves in different environments. They were able to adapt themselves to the dietary sources available in their environment. The relation between humans and their gut microbiota and the link with coevolution forms an interesting aspect of research. To understand this association, the participation of ancient communities with less exposure to urbanisation is a prerequisite. The current study quantifies the richness of bacterial groups in the gut of Nicobarese. This group of population is an ethnic community of Nicobar group of islands, who have migrated from the remote to rural and urban areas. Alterations in the dominant bacterial groups in relation to their lifestyle transition were emphasized, by comparing the participants from remote, rural and urban settings. The remote cohort remains diverse and stable than the other two cohorts and had higher numbers of Bacteroidetes. Prevotella forms the dominant genus in the Bacteroidetes phylum, indicating the carbohydrate-rich diet of remote Nicobarese. Whereas, the urban cohort is dominated by Bifidobacterium group rather than the Bacteroidetes. Implications of dietary patterns, the transition to different lifestyles and their impact on the microbiota among these cohorts are discussed.

      PubDate: 2016-03-04T16:33:31Z
  • Improving the reproducibility of the NAP1/B1/027 epidemic strain R20291 in
           the hamster model of infection
    • Abstract: Publication date: Available online 2 March 2016
      Author(s): Michelle L. Kelly, Yen Kuan Ng, Stephen T. Cartman, Mark M. Collery, Alan Cockayne, Nigel P. Minton
      Comparative analysis of the Clostridium difficile BI/NAP1/027 strain R20291 and ClosTron-derived ermB mutants in the hamster infection model are compromised by the clindamycin susceptibility of the parent. Mutants can appear more virulent. We have rectified this anomaly by genome engineering. The variant created (CRG20291) represents an ideal control strain for virulence assays of ClosTron mutants.

      PubDate: 2016-03-04T16:33:31Z
  • Morphological and Functional Adaptations of Fusobacterium nucleatum
           Exposed to Human Neutrophil Peptide-1
    • Abstract: Publication date: Available online 23 February 2016
      Author(s): Ahmed Ali Musrati, Dareen Fteita, Jorma Paranko, Eija Könönen, Ulvi Kahraman Gürsoy
      Background and objective We recently demonstrated that Fusobacterium nucleatum can resist to human neutrophil peptide (HNP)-1 by decreasing its membrane permeability and increasing its proliferation and biofilm formation. In this continuation study, we aimed to further evaluate and explain these resistance properties by determining the morphological and functional adaptations of F. nucleatum, using transmission electron microscopy (TEM). Materials and Methods Cultures of the type strain of F. nucleatum (ssp. nucleatum ATCC 25586) and two clinical strains (ssp. polymorphum AHN 9910 and ssp. nucleatum AHN 9508) were incubated without (0 μg/ml) or with four different test concentrations of recombinant HNP-1 (1, 5, 10 and 20 μg/ml). Membrane morphology and thickness, and cell (visualized by TEM), planktonic growth (measured in colony forming units), and biofilm formation (measured as total mass) were analyzed. Scrambled HNP-1 was used in planktonic growth and biofilm formation studies as a negative control. Results TEM analyses revealed a decrease in the outer membrane surface corrugations and roughness of the strain AHN 9508 with increasing HNP-1 concentrations. In higher concentrations of HNP-1, the strain AHN 9910 showed thicker outer membranes with a number of associated rough vesicles attached to the outer surface. Intracellular granules became increasingly visible in the strain ATCC 25586 with increasing peptide concentrations. With increased concentrations of HNP-1, planktonic growth of the two clinical strains was significantly enhanced ( P<0.001) and of the type strain significantly suppressed (P<0.01). HNP-1 decreased the biofilm formation of the two clinical strains, AHN 9910 (P<0.01) and 9508 ( P<0.001) significantly. Scrambled HNP-1 showed no effect on planktonic growth or biofilm formation of the tested strains. Discussion F. nucleatum has the ability to withstand the lethal effects of HNP-1, and the ultrastructural changes on bacterial membrane and cytoplasm may play role in this adaptive process.

      PubDate: 2016-02-28T16:07:28Z
  • Complete genome sequences and analysis of the Fusobacterium nucleatum
           subspecies animalis 7-1 bacteriophage ɸFunu1 and ɸFunu2
    • Abstract: Publication date: April 2016
      Source:Anaerobe, Volume 38
      Author(s): Kyla Cochrane, Abigail Manson McGuire, Margaret E. Priest, Amr Abouelleil, Gustavo C. Cerqueira, Reggie Lo, Ashlee M. Earl, Emma Allen-Vercoe
      Fusobacterium nucleatum is a strictly anaerobic, Gram negative bacterial species that has been associated with dental infections, pre-term labor, appendicitis, inflammatory bowel disease, and, more recently, colorectal cancer. The species is unusual in its phenotypic and genotypic heterogeneity, with some strains demonstrating a more virulent phenotype than others; however, as yet the genetic basis for these differences is not understood. Bacteriophage are known to contribute to the virulence phenotype of several bacterial species. In this work, we set out to characterize the bacteriophage associated with F. nucleatum subsp. animalis strain 7-1, a highly invasive isolate from the human gastrointestinal tract. As well, we used computational approaches to predict and compare bacteriophage signatures across available sequenced F. nucleatum genomes.

      PubDate: 2016-02-28T16:07:28Z
  • Comparison of culture-dependent and independent approaches to characterize
           fecal bifidobacteria and lactobacilli
    • Abstract: Publication date: April 2016
      Source:Anaerobe, Volume 38
      Author(s): Andrea Quartieri, Marta Simone, Caterina Gozzoli, Mina Popovic, Giuseppe D'Auria, Alberto Amaretti, Stefano Raimondi, Maddalena Rossi
      Different culture-dependent and independent methods were applied to investigate the population of bifidobacteria and lactobacilli in the feces of five healthy subjects. Bacteria were isolated on MRS, a complex medium supporting growth of lactobacilli and bifidobacteria, and on three selective media for bifidobacteria and two for lactobacilli. Taxonomic characterization of the isolates was carried out by RAPD-PCR and partial 16S sequencing. The selectivity of genus-specific media was also investigated by challenging colonies from MRS plates to grow onto each medium. In parallel, a quantitative and qualitative description of bifidobacteria and lactic acid bacteria was obtained by FISH, qPCR, TRFLP, and 16S rRNA gene sequencing. Bifidobacteria did not fail to grow on their specific media and were easily isolated and enumerated, showing comparable quantitative data among culture-dependent and -independent techniques. The Bifidobacterium species identified on plates and those extracted from TRFLP and 16S rRNA gene sequencing were mostly overlapping. Selective media for lactobacilli gave unsuitable results, being too stringent or too permissive. The quantification of lactobacilli through selective plates, qPCR, FISH, and 16S rRNA gene sequencing gave unreliable results. Therefore, unlike bifidobacteria, intestinal lactobacilli are still problematic in terms of quantification and accurate profiling at level of species and possibly of strains by both culture-dependent and culture-independent techniques.

      PubDate: 2016-02-28T16:07:28Z
  • Missing microbes – A must-read written by an influential pioneer
    • Abstract: Publication date: April 2016
      Source:Anaerobe, Volume 38
      Author(s): Lars Engstrand

      PubDate: 2016-02-28T16:07:28Z
  • Antagonistic activities of some Bifidobacterium sp. strains isolated from
           resident infant gastrointestinal microbiota on Gram-negative enteric
    • Abstract: Publication date: Available online 26 February 2016
      Author(s): Cristina Delcaru, Ionela Alexandru, Paulina Podgoreanu, Violeta Corina Cristea, Coralia Bleotu, Mariana Carmen Chifiriuc, Eugenia Bezirtzoglou, Veronica Lazar
      The gastrointestinal microbiota contributes to the consolidation of the anti-infectious barrier against enteric pathogens. The purpose of this study was to investigate the influence of Bifidobacterium sp. strains, recently isolated from infant gastrointestinal microbiota on the in vitro growth and virulence features expression of enteropathogenic bacterial strains. The antibacterial activity of twelve Bifidobacterium sp. strains isolated from human feces was examined in vitro against a wide range of Gram negative pathogenic strains isolated from 30 infant patients (3 days - 5 years old) with diarrhea. Both potential probiotic strains (Bifidobacterium longum, B pseudocatenulatum, B. catenulatum, B. breve, B. ruminantium) and enteropathogenic strains (EPEC, EIEC, Klebsiella pneumoniae, Salmonella sp., Yersinia enterocolitica, P. aeruginosa) were identified by MALDI-TOF and confirmed serologically when needed. The bactericidal activity, growth curve, adherence to the cellular HEp-2 substratum and production of soluble virulence factors have been assessed in the presence of different Bifidobacterium sp. cultures and fractions (whole culture and free-cell supernatants). Among the twelve Bifidobacterium sp. strains, the largest spectrum of antimicrobial activity against 9 of the 18 enteropathogenic strains was revealed for a B. breve strain recently isolated from infant intestinal feces. The whole culture and free-cell supernatant of B. breve culture decreased the multiplication rate, shortened the log phase and the total duration of the growth curve, with an earlier entrance in the decline phase and inhibited the adherence capacity to a cellular substratum and the swimming/swarming motility too. These results indicate the significant probiotic potential of the B. breve strain.

      PubDate: 2016-02-28T16:07:28Z
  • Anaerococcus nagyae sp. nov., isolated from human clinical specimens
    • Abstract: Publication date: April 2016
      Source:Anaerobe, Volume 38
      Author(s): A.C.M. Veloo, E.D. de Vries, H. Jean-Pierre, A.J. van Winkelhoff
      We describe a new Anaerococcus species isolated from human clinical specimens. Analyses of 16S rRNA gene sequences of three strains showed <98% similarity with its closest relative Anaerococcus octavius. Phylogenetically the isolated strains form a cluster and can be differentiated from other species of the genus Anaerococcus based on its phenotypic characteristics and its MALDI-TOF MS profile. We propose the name Anaerococcus nagyae, with A. nagyae DSM101193 (accession number KU043522) as the type strain.

      PubDate: 2016-02-28T16:07:28Z
  • Editorial board
    • Abstract: Publication date: April 2016
      Source:Anaerobe, Volume 38

      PubDate: 2016-02-28T16:07:28Z
  • Anaerobic bacteraemia: a 10-year retrospective epidemiological survey
    • Abstract: Publication date: Available online 23 February 2016
      Author(s): Steven de Keukeleire, Ingrid Wybo, Anne Naessens, Fedoua Echahidi, Mieke Van der Beken, Kristof Vandoorslaer, Stefan Vermeulen, Denis Piérard
      In order to identify current trends in anaerobic bacteraemia, a 10-year retrospective study was performed in the University Hospital Brussel, Belgium. All clinically relevant bacteraemia detected from 2004 until 2013 were included. Medical records were reviewed in an attempt to define clinical parameters that might be associated with the occurrence of anaerobic bacteraemia. 437 of the isolated organisms causing anaerobic bacteraemia were thawed, subcultured and reanalyzed using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF). There were an average of 33 cases of anaerobic bacteraemia per year during 2004 to 2008 compared to an average of 27 cases per year during 2009-2013 (P= 0.017), corresponding to a decrease by 19% between the first and the latter period. Also, the total number of cases of anaerobic bacteraemia per 100,000 patient days decreased from 17.3 in the period from 2004 to 2008 to 13.7 in the period 2009 to 2013 (P= 0.023). Additionally, the mean incidence of anaerobic bacteraemia decreased during the study period (1.27/1,000 patients in 2004 vs. 0.94/1,000 patients in 2013; P= 0.008). In contrast, the proportion of isolated anaerobic bacteraemia compared to the number of all bacteraemia remained stable at 5%. Bacteroides spp. and Parabacteroides spp. accounted for 47.1% of the anaerobes, followed by 14.4% Clostridium spp., 12.6% non-spore-forming Gram-positive rods, 10.5% anaerobic cocci, 8.2% Prevotella spp. and other Gram-negative rods and 7.1% Fusobacterium spp. The lower gastrointestinal tract (47%) and wound infections (10%) were the two most frequent sources for bacteraemia, with the origin remaining unknown in 62 cases (21%). The overall mortality rate was 14%. Further studies focusing on the antimicrobial susceptibility and demographic background of patients are needed to further objectify the currently observed trends.

      PubDate: 2016-02-23T15:48:14Z
  • Clinical characteristics associated with mortality of patients with
           anaerobic bacteremia
    • Abstract: Publication date: Available online 20 February 2016
      Author(s): Takumi Umemura, Yukihiro Hamada, Yuka Yamagishi, Hiroyuki Suematsu, Hiroshige Mikamo
      The presence of anaerobes in the blood stream is known to be associated with a higher rate of mortality. However, few prognostic risk factor analyses examining whether a patient’s background characteristics are associated with the prognosis have been reported. We performed a retrospective case-controlled study to assess the prognostic factors associated with death from anaerobic bacteremia. Seventy-four patients with anaerobic bacteremia were treated between January 2005 and December 2014 at Aichi Medical University Hospital. The clinical information included drug susceptibility was used for analysis of prognostic factors for 30-day mortality. Multivariate logistic analyses revealed an association between the 30-day mortality rate and malignancy (OR: 3.64, 95% CI: 1.08–12.31) and clindamycin resistance (OR: 7.93, 95% CI: 2.33–27.94). The result of Kaplan-Meier analysis of mortality showed that the 30-day survival rate was 83% in clindamycin susceptible and 38.1% in clindamycin resistant anaerobes causing bacteremia. The result of log-rank test also showed that susceptibility to clindamycin affected mortality (P < 0.001). Our results indicated that malignancy and clindamycin susceptibility could be used to identify subgroups of patients with anaerobic bacteremia with a higher risk of 30-day mortality. The results of this study are important for the early and appropriate management of patients with anaerobic bacteremia.

      PubDate: 2016-02-23T15:48:14Z
  • Place of diagnostic tools in the identification of Anaerobiospirillum
           succiniproducens bacteraemia
    • Abstract: Publication date: Available online 16 February 2016
      Author(s): V. Decroix, E. Pluquet, M. Choquet, N. Ammenouche, S. Castelain, R. Guiheneuf
      Anaerobiospirillum succiniproducens is a rare but potentially lethal pathogen. We report a case of A. succiniproducens bloodstream infection in a 55-year-old man hospitalized for pelvic trauma. The strain was identified by 16sRNA sequencing after several failures of identification by MALDI-TOF MS. The strain was susceptible to beta-lactam antibiotics and ciprofloxacin, but resistant to macrolides and clindamycin. Identification tools must be improved to enhance our knowledge on this rare pathogen and to define optimal therapy.

      PubDate: 2016-02-19T15:12:31Z
  • In vitro fermentation of alginate and its derivatives by human gut
    • Abstract: Publication date: Available online 16 February 2016
      Author(s): Miaomiao Li, Guangsheng Li, Qingsen Shang, Xiuxia Chen, Wei Liu, Xiong’e Pi, Liying Zhu, Yeshi Yin, Guangli Yu, Xin Wang
      Alginate (Alg) has a long history as a food ingredient in East Asia. However, the human gut microbes responsible for the degradation of alginate and its derivatives have not been fully understood yet. Here, we report that alginate and the low molecular polymer derivatives of mannuronic acid oligosaccharides (MO) and guluronic acid oligosaccharides (GO) can be completely degraded and utilized at various rates by fecal microbiota obtained from six Chinese individuals. However, the derivative of propylene glycol alginate sodium sulfate (PSS) was not hydrolyzed. The bacteria having a pronounced ability to degrade Alg, MO and GO were isolated from human fecal samples and were identified as Bacteroides ovatus, Bacteroides xylanisolvens, and Bacteroides thetaiotaomicron. Alg, MO and GO can increase the production level of short chain fatty acids (SCFA), but GO generates the highest level of SCFA. Our data suggest that alginate and its derivatives could be degraded by specific bacteria in the human gut, providing the basis for the impacts of alginate and its derivates as special food additives on human health.

      PubDate: 2016-02-19T15:12:31Z
  • Parvimonas micra: A Rare Cause of Native Joint Septic Arthritis
    • Abstract: Publication date: Available online 18 February 2016
      Author(s): Adam Baghban, Shaili Gupta
      Parvimonas micra is a fastidious, anaerobic, gram positive coccus, which is found in normal human oral and gastrointestinal flora. It has also been known as Peptostreptococcus micros and Micromonas micros with its most recent re-classification in 2006. It has been described in association with hematogenous seeding of prosthetic joints [1, 2]. Several cases of discitis and osteomyelitis have been described in association with dental procedures and periodontal disease often with a subacute presentation. However, cases of native joint septic arthritis are limited [3-5]. Per our literature review, there is one case of native knee septic arthritis described in 1999, with a prolonged time to diagnosis and treatment due to difficulty culturing P. micra. The previously reported patient experienced significant joint destruction and morbidity [6]. Advances in culture techniques and new methods of organism identification including MALDI-TOF and 16s rRNA sequencing have lead to increased identification of this organism, which may be a more frequent bone and joint pathogen than previously realized.

      PubDate: 2016-02-19T15:12:31Z
  • Clostridium kogasensis sp. nov., a novel member of the genus Clostridium,
           isolated from soil under a corroded gas pipeline
    • Abstract: Publication date: Available online 17 February 2016
      Author(s): Yeseul Shin, Seok-Seong Kang, Jayoung Paek, Tae Eun Jin, Hong Seok Song, Hongik Kim, Hee-Moon Park, Young-Hyo Chang
      Two bacterial strains, YHK0403T and YHK0508, isolated from soil under a corroded gas pipe line, were revealed as Gram-negative, obligately anaerobic, spore-forming and mesophilic bacteria. The cells were rod-shaped and motile by means of peritrichous flagella. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolates were members of the genus Clostridium and were the most closely related to C. scatologenes KCTC 5588T (95.8% sequence similarity), followed by C. magnum KCTC 15177T (95.8%), C. drakei KCTC 5440T (95.7%) and C. tyrobutyricum KCTC 5387T (94.9%). The G+C contents of the isolates were 29.6 mol%. Peptidoglycan in the cell wall was of the A1γ type with meso-diaminopimelic acid. The major polar lipid was diphosphatidylglycerol (DPG), and other minor lipids were revealed as phosphatidylglycerol (PG), phosphatidylethanolamine (PE), two unknown glycolipids (GL1 and GL2), an unknown aminoglycolipid (NGL), two unknown aminophospholipids (PN1 and PN2) and four unknown phospholipids (PL1 to PL4). Predominant fatty acids were C16:0 and C16:1 cis9 DMA. The major end products from glucose fermentation were identified as butyrate (12.2 mmol) and acetate (9.8 mmol). Collectively, the results from a wide range of phenotypic tests, chemotaxonomic tests, and phylogenetic analysis indicated that the two isolates represent novel species of the genus Clostridium, for which the name Clostridium kogasensis sp. nov. (type strain, YHK0403T =KCTC 15258T=JCM 18719T) is proposed.

      PubDate: 2016-02-19T15:12:31Z
  • Rumen microbial abundance and fermentation profile during severe subacute
           ruminal acidosis and its modulation by plant derived alkaloids in vitro
    • Abstract: Publication date: Available online 8 February 2016
      Author(s): Elsayed Mickdam, Ratchaneewan Khiaosa-ard, Barbara U. Metzler-Zebeli, Fenja Klevenhusen, Remigius Chizzola, Qendrim Zebeli
      Rumen microbiota have important metabolic functions for the host animal. This study aimed at characterizing changes in rumen microbial abundances and fermentation profiles using a severe subacute ruminal acidosis (SARA) in vitro model, and to evaluate a potential modulatory role of plant derived alkaloids (PDA), containing quaternary benzophenanthridine and protopine alkaloids, of which sanguinarine and chelerythrine were the major bioactive compounds. Induction of severe SARA strongly affected the rumen microbial composition and fermentation variables without suppressing the abundance of total bacteria. Protozoa and fungi were more sensitive to the low ruminal pH condition than bacteria. Induction of severe SARA clearly depressed degradation of fiber (P < 0.001), which came along with a decreased relative abundance of fibrolytic Ruminococcus albus and Fibrobacter succinogenes (P < 0.001). Under severe SARA conditions, the genus Prevotella, Lactobacillus group, Megasphaera elsdenii, and Entodinium spp. (P < 0.001) were more abundant, whereas Ruminobacter amylophilus was less abundant. SARA largely suppressed methane formation (-70%, P < 0.001), although total methanogenic 16S rRNA gene abundance was not affected. According to principal component analysis, Methanobrevibacter spp. correlated to methane concentration. Addition of PDA modulated ruminal fermentation under normal conditions such as enhanced (P < 0.05) concentration of total SCFA, propionate and valerate, and increased (P < 0.05) degradation of crude protein compared with the unsupplemented control diet. Our results indicate strong shifts in the microbial community during severe SARA compared to normal conditions. Supplementation of PDA positively modulates ruminal fermentation under normal ruminal pH conditions.
      Graphical abstract image

      PubDate: 2016-02-10T17:47:36Z
  • Case series of patients with Fusobacterium nucleatum bacteremia with
           emphasis on the presence of cancer
    • Abstract: Publication date: June 2016
      Source:Anaerobe, Volume 39
      Author(s): Erlangga Yusuf, Ingrid Wybo, Denis Piérard
      Fusobacterium nucleatum is anaerobic oral microbiota that might be associated with cancer. We reported 22 consecutive cases of patients (mean age of 63.8 years (range 34–89), 59.1% male) with F. nucleatum bacteremia that were admitted to a university hospital over a 10-year period. In 17 (77.2%) of these patients, F. nucleatum was the sole possible pathogen. Seven of the 22 patients (31.8%) had active cancer: esophagus carcinoma (n = 3), hematologic malignancies (n = 1), gastrointestinal stromal tumor (n = 1), melanoma (n = 1), and breast cancer (n = 1). In six out of seven patients (85.7%), the F. nucleatum was found within six months of the diagnosis of cancer. Four of seven (57.1%), patients with cancer were on chemotherapy. Three of 22 patients (13.4%) died within 1 month of F. nucleatum bacteremia due to cancer. In conclusion, F. nucleatum bacteremia occurs rarely and when it is found, it is often in patients with cancer, especially those with a recent diagnosis.

      PubDate: 2016-02-10T17:47:36Z
  • Clostridium difficile recurrences in Stockholm
    • Abstract: Publication date: Available online 21 January 2016
      Author(s): Staffan Sandell, Mamun-Ur Rashid, Christina Jorup-Rönström, Kristina Ellström, Carl Erik Nord, Andrej Weintraub
      Sixty-eight hospital-admitted patients with a first episode of Clostridium difficile infection (CDI) were included and followed up during 1 year. Faeces samples were collected at 1, 2, 6 and 12 months after inclusion and analyzed for the presence of C. difficile toxin B, genes for toxin A, toxin B, binary toxin and TcdC deletion by PCR. All strains were also PCR-ribotyped and the MICs of the isolates were determined against eight antimicrobial agents. In 68 patients initially included, antibiotics, clinical signs and co-morbidities were analyzed and 56 were evaluable for recurrences. The mean number of different antibiotics given during 3 months prior to inclusion was 2.6 (range 0-6). Six patients had not received any antibiotics and three of them had diagnosed inflammatory bowel disease. Thirty-two patients (57%) had either a microbiological or clinical recurrence, 16 of whom had clinical recurrences that were confirmed microbiologically (13, 23%) or unconfirmed by culture (3, 5%). Twenty-nine patients were positive in at least one of the follow-up tests, 16 had the same ribotype in follow-up tests, i.e. relapse, and 13 a different ribotype, i.e., reinfection. Most common ribotypes were 078/126, 020, 023, 026, 014/077, 001 and 005. No strain of ribotype 027 was found. Strains ribotype 078/126 and 023 were positive for binary toxin and were the strains most prone to cause recurrence. All strains were sensitive to vancomycin and metronidazole. Patients with recurrences were significantly older (p=0.02) and all patients had a high burden of comorbidities, which could explain the high fatality rate, 26 (38%) patients died during the 1-year follow-up.

      PubDate: 2016-01-21T16:21:49Z
  • A novel murine model of Clostridium sordellii myonecrosis: Insights into
           the pathogenesis of disease
    • Abstract: Publication date: Available online 21 January 2016
      Author(s): Michael J. Aldape, Clifford R. Bayer, Amy E. Bryant, Dennis L. Stevens
      Clostridium sordellii infections have been reported in women following natural childbirth and spontaneous or medically-induced abortion, injection drug users and patients with trauma. Death is rapid and mortality ranges from 70-100%. Clinical features include an extreme leukemoid reaction, the absence of fever, and only minimal pain or erythema at the infected site. In the current study, we developed a murine model of C. sordellii soft tissue infection to elucidate the pathogenic mechanisms. Mice received 0.5, 1.0 or 2.0 x 106 CFU C. sordellii (ATCC 9714 type strain) in the right thigh muscle. All doses caused fatal infection characterized by intense swelling of the infected limb but no erythema or visible perfusion deficits. Survival rates and time to death were inoculum dose-dependent. Mice developed a granulocytic leukocytosis with left shift, the onset of which directly correlated with disease severity. Histopathology of infected tissue showed widespread edema, moderate muscle damage and minimal neutrophil infiltration. Circulating levels of granulocyte colony-stimulating factor (G-CSF), soluble tumor necrosis factor receptor I (sTNF-RI) and interlukin-6 (IL-6) were significantly increased in infected animals, while TNF-α, and IL-1β levels were only mildly elevated, suggesting these host factors likely mediate the leukocytosis and innate immune dysfunction characteristic of this infection. Thus, this model mimics many of the salient features of this infection in humans and has allowed us to identify novel targets for intervention.

      PubDate: 2016-01-21T16:21:49Z
  • Corrigendum to “Cloning and characterization of l-lactate
           dehydrogenase gene of Staphylococcus aureus” [Anaerobe 24 (2013)
    • Abstract: Publication date: Available online 14 January 2016
      Author(s): Sthanikam Yeswanth, Yellapu Nanda Kumar, Uppu Venkateswara Prasad, Vimjam Swarupa, Valasani Koteswara Rao, Potukuchi Venkata Gurunadha Krishna Sarma

      PubDate: 2016-01-17T16:07:36Z
  • Clostridium difficile flagella predominantly activate TLR5-linked
           NF-κB pathway in epithelial cells
    • Abstract: Publication date: Available online 11 January 2016
      Author(s): Jameel Batah, Cécile Denève-Larrazet, Pierre-Alain Jolivot, Sarah Kuehne, Anne Collignon, Jean-Christophe Marvaud, Imad Kansau
      Clostridium difficile has become the most common enteropathogen responsible for intestinal nosocomial post-antibiotic infections. This has coincided with the appearance of serious cases related to the emergence of hypervirulent strains. The toxins are the main virulence factors and elicit an inflammatory response during C. difficile infection. However, other bacterial components appear to be involved in the inflammatory process. In some pathogens, flagella play a role in pathogenesis through abnormal stimulation of the TLR5-mediated host immune response. To date, few studies have addressed this role for C. difficile flagella. In the current study, we confirm in two different epithelial cell models that C. difficile thanks to its FliC flagellin interact with TLR5. In addition, thanks to inhibition and transcriptomic studies we demonstrate that the interaction of flagellin and TLR5 predominantly activates the NF-κB and, in a lesser degree, the MAPK pathways, via TLR5, leading to up-regulation of pro-inflammatory gene expression and synthesis of pro-inflammatory mediators. These results suggest a role for C. difficile flagella in contributing to inflammatory response in host intestinal cells.

      PubDate: 2016-01-13T15:55:30Z
  • Clostridium perfringens type A netF and netE positive and C. difficile
           co-infection in two adult dogs
    • Abstract: Publication date: Available online 4 January 2016
      Author(s): Amanda Nádia Diniz, Rodrigo Otávio Silveira Silva, Carlos Augusto Oliveira Junior, Felipe Pierezan, Francisco Carlos Faria Lobato
      The aim of this study was to report two cases of Clostridium perfringens type A and C. difficile co-infection in adult dogs. Both animals were positive for A/B toxin. Toxigenic C. difficile and C. perfringens type A positive for NetE and NetF-encoding genes were isolated. This report reinforces the necessity of studying a possible synergism of C. difficile and C. perfringens in enteric disorders.

      PubDate: 2016-01-05T14:30:13Z
  • Multidrug resistance in Clostridium perfringens isolated from diarrheal
           neonatal piglets in Thailand
    • Abstract: Publication date: Available online 2 January 2016
      Author(s): Bhinyada Ngamwongsatit, Wimonrat Tanomsridachchai, Orasa Suthienkul, Supanee Urairong, Wichian Navasakuljinda, Tavan Janvilisri
      Clostridium perfringens causes diarrhea in neonatal piglets, thereby affecting commercial swine farming. The objective of this study was to determine the prevalence and characterize antimicrobial resistance in C. perfringens isolated from diarrheal neonatal piglets in Thailand. A total of 260 rectal swab samples were collected from 13 farms and were subjected to C. perfringens isolation. A total of 148 samples were PCR-positive for C. perfringens toxin genes, from which 122 were recovered. All isolates were cpb2-encoding C. perfringens type A and enterotoxin gene negative. Most of the isolates were susceptible to ampicillin, bacitracin, chlorotetracycline, doxycycline, and oxytetracycline with MIC50 values ranging from 0.32 – 8 μg/ml. The high resistance rates were observed for ceftiofur, enrofloxacin, erythromycin, lincomycin, and tylosin. Among resistant isolates, 82% were resistant to more than one type of antibiotics. The distinct pattern of multiple drug resistance in C. perfringens was observed in different regions, potentially reflecting the farm specific usage of these agents.

      PubDate: 2016-01-05T14:30:13Z
  • Survival of the ovine footrot pathogen Dichelobacter nodosus in different
    • Abstract: Publication date: Available online 30 December 2015
      Author(s): Mohd Muzafar, Laura E. Green, Leo A. Calvo-Bado, Esther Tichauer, Hayley King, Philip James, Elizabeth M.H. Wellington
      Dichelobacter nodosus (D. nodosus) is the causative agent of footrot in sheep; one of the most important health and welfare issues of sheep worldwide. For control programmes to be effective, it is essential that the transmission cycle of D. nodosus is understood and bacterial reservoirs in the environment are better defined. This study evaluated the survival of D. nodosus in different soils using soil microcosms. Cultivation independent and dependent methods were used to detect D. nodosus over 40 days from seeding in soil. A D. nodosus specific probe was used for quantification by qPCR and viability was assessed by cell permeability to an intercalating dye, PMA, and by culture. Survival varied dramatically depending on soil type, matric potential (MP) and temperature. Our findings indicate that D. nodosus survival was higher at 5 oC compared with 25 o C in all soils and significantly longer at both temperatures in clay soil (>44% clay) compared with other soil types. Survival under all conditions was longer than 30 days for both culture independent and dependent methods, this is substantially longer than previous studies and, if this is an infectious dose, longer than the current recommendation of resting a field for 14 days to prevent onward infection.

      PubDate: 2016-01-01T14:13:40Z
  • Clostridium difficile associated reactive arthritis: case report and
           literature review
    • Abstract: Publication date: Available online 30 December 2015
      Author(s): Paul Legendre, Valérie Lalande, Catherine Eckert, Fréderic Barbut, Laurence Fardet, Jean-Luc Meynard, Laure Surgers
      Introduction Extra-gastro-intestinal tract manifestations associated with Clostridium difficile infection (CDI), including reactive arthritis (ReA), are uncommon. Method We report a case of ReA associated with a relapse of CDI in a 46-year-old woman. A toxigenic C. difficile strain was isolated from stools and characterized as PCR-ribotype 014/020/077. We conducted a comprehensive literature review of ReA associated with CDI (ReA-CDI). Diagnostic criteria for ReA-CDI were: (i) evidence of aseptic synovitis (confirmed by culture) developing during or immediately after colitis, (ii) presence of a toxigenic C. difficile strain in stool samples, and (iii) absence of other causes of colitis and arthritis. Results Forty-nine cases of ReA-CDI (excluding the present report) have already been described since 1976. Of these reports, Mean age of patients was 38 years (SD: 18.5), 46% were male, and 68% had HLA B27 genotype. Sixty-nine percent of patients received a β-lactamin treatment before CDI. ReA-CDI occurred a median 10 days (range 0-55 days) after CDI. Outcome was favorable in 90% of patients and oral non anti-inflammatory drugs were required for 55%. Conclusion ReA-CDI remains uncommon. Compared to the general population, it is more likely observed in younger patients with HLA B27-positive genotype.

      PubDate: 2016-01-01T14:13:40Z
  • Effects of the dietary protein level on the microbial composition and
           metabolomic profile in the hindgut of the pig
    • Abstract: Publication date: Available online 24 December 2015
      Author(s): Liping Zhou, Lingdong Fang, Yue Sun, Yong Su, Weiyun Zhu
      The aim of this study was to investigate the effects of a long-term low protein diet on the microbial composition and metabolomic profile in the hindgut of the pig. Thirty-six Duroc × Landrace × Large White growing barrows (70 days of age, 23.57 ± 1.77 kg) were randomly allocated to normal protein diet (NP) and low protein diet (LP) groups using a randomized block design. At the age of 170 days, the digesta in the hindguts of the pigs were collected for microbial and metabolomic analysis. The results showed that there were no significant differences in the average daily gain, average daily feed intake, or feed:gain ratio between the NP and LP groups. The concentrations of isobutyrate, isovalerate, and branched-chain fatty acids (BCFAs)/short-chain fatty acids (SCFAs) in the cecum decreased with the reduction of dietary protein. Pyrosequencing of the V1–V3 region of the 16S rRNA genes showed that LP diet significantly decreased the relative abundance of Lactobacillus in the cecum, and Streptococcus in the colon; however, the relative abundance of Prevotella and Coprococcus in the LP group was significantly higher than in the NP group in the cecum, and Sarcina, Peptostreptococcaceae incertae sedis, Mogibacterium, Subdoligranulum, and Coprococcus was higher in the colon. The gas chromatography–mass spectrometry (GC–MS) analysis showed that the dietary protein level mainly affected phenylalanine metabolism; glycine, serine, and threonine metabolism; the citrate cycle; pyruvate metabolism; and the alanine, aspartate, and glutamate metabolism. Moreover, the correlation analysis of the combined datasets revealed some potential relationships between the colonic metabolites and certain microbial species. These results suggest that a low protein diet may modulate the microbial composition and metabolites of the hindgut, without affecting the growth performance of pigs; however, potential roles of this modulation to the health of pigs remains unknown.

      PubDate: 2015-12-28T13:49:25Z
  • Metagenomic assessment of the functional potential of the rumen microbiome
           in Holstein dairy cows
    • Abstract: Publication date: Available online 15 December 2015
      Author(s): Dipti W. Pitta, Nagaraju Indugu, Sanjay Kumar, Bonnie Vecchiarelli, Rohini Sinha, Linda D. Baker, Bhima Bhukya, James D. Ferguson
      The microbial ecology of the rumen microbiome is influenced by the diet and the physiological status of the dairy cow and can have tremendous influence on the yield and components of milk. There are significant differences in milk yields between first and subsequent lactations of dairy cows, but information on how the rumen microbiome changes as the dairy cow gets older has received little attention. We characterized the rumen microbiome of the dairy cow for phylogeny and functional pathways by lactation group and stage of lactation using a metagenomics approach. Our findings revealed that the rumen microbiome was dominated by Bacteroidetes (70%), Firmicutes (15-20%) and Proteobacteria (7%). The abundance of Firmicutes and Proteobacteria were independently influenced by diet and lactation. Bacteroidetes contributed to a majority of the metabolic functions in first lactation dairy cows while the contribution from Firmicutes and Proteobacteria increased incrementally in second and third lactation dairy cows. We found that nearly 70% of the CAZymes were oligosaccharide breaking enzymes which reflect the higher starch and fermentable sugars in the diet. The results of this study suggest that the rumen microbiome continues to evolve as the dairy cow advances in lactations and these changes may have a significant role in milk production.

      PubDate: 2015-12-16T12:47:41Z
  • Diversity of Clostridium perfringens isolates from various sources and
           prevalence of conjugative plasmids
    • Abstract: Publication date: April 2016
      Source:Anaerobe, Volume 38
      Author(s): Miseon Park, Joanna Deck, Steven L. Foley, Rajesh Nayak, J. Glenn Songer, Janice R. Seibel, Saeed A. Khan, Alejandro P. Rooney, David W. Hecht, Fatemeh Rafii
      Clostridium perfringens is an important pathogen, causing food poisoning and other mild to severe infections in humans and animals. Some strains of C. perfringens contain conjugative plasmids, which may carry antimicrobial resistance and toxin genes. We studied genomic and plasmid diversity of 145 C. perfringens type A strains isolated from soils, foods, chickens, clinical samples, and domestic animals (porcine, bovine and canine), from different geographic areas in the United States between 1994 and 2006, using multiple-locus variable-number tandem repeat analysis (MLVA) and/or pulsed-field gel electrophoresis (PFGE). MLVA detected the genetic diversity in a majority of the isolates. PFGE, using SmaI and KspI, confirmed the MLVA results but also detected differences among the strains that could not be differentiated by MLVA. All of the PFGE profiles of the strains were different, except for a few of the epidemiologically related strains, which were identical. The PFGE profiles of strains isolated from the same domestic animal species were clustered more closely with each other than with other strains. However, a variety of C. perfringens strains with distinct genetic backgrounds were found among the clinical isolates. Variation was also observed in the size and number of plasmids in the strains. Primers for the internal fragment of a conjugative tcpH gene of C. perfringens plasmid pCPF4969 amplified identical size fragments from a majority of strains tested; and this gene hybridized to the various-sized plasmids of these strains. The sequences of the PCR-amplified tcpH genes from 12 strains showed diversity among the tcpH genes. Regardless of the sources of the isolates, the genetic diversity of C. perfringens extended to the plasmids carrying conjugative genes.

      PubDate: 2015-12-03T08:37:45Z
  • A case of bacteremia caused by Dialister pneumosintes and Slackia exigua
           in a patient with periapical abscess
    • Abstract: Publication date: April 2016
      Source:Anaerobe, Volume 38
      Author(s): Min Young Lee, Young Jin Kim, Hyun Jung Gu, Hee Joo Lee
      Dialister pneumosintes and Slackia exigua are both obligatory anaerobe and known to be associated with periodontal diseases and other oral infection. We report a case of blood stream infection caused by D. pneumosintes and S. exigua. This occurred in a 78-year-old female patient that presented with general weakness and fever. We revealed that she had a periapical absecess. The blood culture was positive for D. pneumosintes and S. exigua; however, identifying them was challenging. Ultimately, 16S rRNA sequencing was used to identify the organisms. The patient recovered after being treated with ceftriaxone and clindamycin. To the best of our knowledge, this is the first report of bacteremia caused by mixed infection of D. pneumosintes and S. exigua.

      PubDate: 2015-12-03T08:37:45Z
  • Microbial colonization of normal skin: direct visualization of 194 skin
    • Abstract: Publication date: Available online 2 December 2015
      Author(s): Anika C. Jahns, Oleg A. Alexeyev
      Recent genetic studies have suggested the presence of numerous microbial species on and in the skin. We characterised microbial colonization of a large collection of skin biopsies from 194 healthy subjects by fluorescence assay. Forty per cent of all biopsies did not show any evidence for microbial colonization. Propionibacterium acnes was the sole predominant bacterial species in both sebaceous and non-sebaceous areas. Non- P. acnes species were present in 20% of all biopsies. Only hair follicles and stratum corneum were colonized. Understanding of cutaneous microbiota requires validation from a variety of approaches and techniques.

      PubDate: 2015-12-03T08:37:45Z
  • Robust and effective methodologies for cryopreservation and DNA extraction
           from anaerobic gut fungi
    • Abstract: Publication date: Available online 24 November 2015
      Author(s): Kevin V. Solomon, John K. Henske, Michael K. Theodorou, Michelle A. O’Malley
      Cell storage and DNA isolation are essential to developing an expanded suite of microorganisms for biotechnology. However, many features of non-model microbes, such as an anaerobic lifestyle and rigid cell wall, present formidable challenges to creating strain repositories and extracting high quality genomic DNA. Here, we establish accessible, high efficiency, and robust techniques to store lignocellulolytic anaerobic gut fungi long term without specialized equipment. Using glycerol as a cryoprotectant, gut fungal isolates were preserved for a minimum of 23 months at -80°C. Unlike previously reported approaches, this improved protocol is non-toxic and rapid, with samples surviving twice as long with negligible growth impact. Genomic DNA extraction for these isolates was optimized to yield samples compatible with next generation sequencing platforms (e.g. Illumina, PacBio). Popular DNA isolation kits and precipitation protocols yielded preps that were unsuitable for sequencing due to carbohydrate contaminants from the chitin-rich cell wall and extensive energy reserves of gut fungi. To address this, we identified a proprietary method optimized for hardy plant samples that rapidly yielded DNA fragments in excess of 10 kb with minimal RNA, protein or carbohydrate contamination. Collectively, these techniques serve as fundamental tools to manipulate powerful biomass-degrading gut fungi and improve their accessibility among researchers.

      PubDate: 2015-11-29T08:26:10Z
  • Microbiological diagnosis of Eggerthella lenta blood culture isolates in a
           Swedish tertiary hospital: Rapid identification and antimicrobial
           susceptibility profile
    • Abstract: Publication date: Available online 22 November 2015
      Author(s): Karin Liderot, Paul Ratcliffe, Petra Lüthje, Ellinor Tidholm, Volkan Özenci
      Eggerthella lenta is a Gram-positive anaerobic bacillus. Improved diagnostics and increased awareness of rare pathogens have revealed its potential to cause serious invasive infections. In this study, 18 clinical E. lenta isolates derived from positive blood cultures were included. Underlying problems of the patients were in the majority of cases related to the gastrointestinal tract. The performance of two MALDI-TOF MS systems, i.e. Bruker and Vitek MS, in identification of E. lenta was analyzed. In addition, the minimal inhibitory concentrations for clinically relevant antimicrobial agents were determined by routine procedures using E-test. 17 of the 18 E. lenta isolates investigated in this study were correctly identified to species level by the Bruker MS system, while the Vitek MS system identified all 18 isolates. Antimicrobial sensitivity towards the tested agents was in general good. However, high resistance rates were observed for penicillin G and piperacillin-tazobactam based on EUCAST breakpoints.

      PubDate: 2015-11-24T23:24:19Z
  • Comparison of vaginal microbial community structure in healthy and
           endometritis dairy cows by PCR-DGGE and Real-time PCR
    • Abstract: Publication date: Available online 10 November 2015
      Author(s): Jun Wang, Chengtao Sun, Chang Liu, Yujiang Yang, Wenfa Lu
      The normal vaginal microflora provides protection against infections of the reproductive tract. Previous studies have focused on the isolation and screening of probiotic strains from the vagina of cows; however, the vaginal microflora of postpartum cows is poorly characterized. The present study was conducted to evaluate and characterize the vaginal microflora of healthy postpartum cows in relation to postpartum cows with endometritis by using PCR followed by denaturing gradient gel electrophoresis (PCR-DGGE) and Real-time PCR. The study population comprised 5 healthy cows and 5 cows with endometritis. The results indicated that the vaginal bacterial microflora of healthy postpartum cows was dominated by Lactobacillus sakei subsp. and Weissella koreensis, while there were no dominant bacterial species in the vaginal microflora of postpartum cows with endometritis. Common microorganisms such as Bacteroides spp., Fusobacterium spp., Enterococcus spp., Prevotella spp., Clostridium perfringens strains, and Escherichia coli were detected in both groups of cows by Real-time PCR. The bacterial diversity in the vagina of cows with endometritis was significantly higher than that in healthy cows. The results indicated that the vaginal microflora of cows with endometritis was more diverse and lacked dominant bacterial species as compared to that of the healthy cows, suggesting that disruption of the normal vaginal microflora may contribute to the onset of endometritis. This microbial community analysis provided information that might be used to develop probiotics to treat endometritis in cows; however, further investigation is needed.

      PubDate: 2015-11-12T22:21:15Z
  • Inactivation of Clostridium difficile spores by microwave irradiation
    • Abstract: Publication date: Available online 4 November 2015
      Author(s): Suvash Chandra Ojha, Surang Chankhamhaengdecha, Sombat Singhakaew, Puey Ounjai, Tavan Janvilisri
      Spores are a potent agent for C. difficile transmission. Therefore, factors inhibiting spores have been of continued interest. In the present study, we investigated the influence of microwave irradiation in addition to conductive heating for C. difficile spore inactivation in aqueous suspension. The spores of 15 C. difficile isolates from different host origins were exposed to conductive heating and microwave irradiation. The complete inhibition of spore viability at 107 CFU/ml was encountered following microwave treatment at 800W for 60 seconds, but was not observed in the conductive-heated spores at the same time-temperature exposure. The distinct patterns of ultrastructural alterations following microwave and conductive heat treatment were observed and the degree of damages by microwave was in the exposure time-dependent manner. Microwave would therefore be a simple and time-efficient tool to inactivate C. difficile spores, thus reducing the risk of C. difficile transmission.
      Graphical abstract image

      PubDate: 2015-11-05T15:40:39Z
  • Livers provide a reliable matrix for real-time PCR confirmation of avian
    • Abstract: Publication date: Available online 3 November 2015
      Author(s): Caroline Le Maréchal, Valentine Ballan, Sandra Rouxel, Marie-Hélène Bayon-Auboyer, Marie-Agnès Baudouard, Hervé Morvan, Emmanuelle Houard, Typhaine Poëzevara, Rozenn Souillard, Cédric Woudstra, Sophie Le Bouquin, Patrick Fach, Marianne Chemaly
      Diagnosis of avian botulism is based on clinical symptoms, which are indicative but not specific. Laboratory investigations are therefore required to confirm clinical suspicions and establish a definitive diagnosis. Real-time PCR methods have recently been developed for the detection of Clostridium botulinum group III producing type C, D, C/D or D/C toxins. However, no study has been conducted to determine which types of matrices should be analyzed for laboratory confirmation using this approach. This study reports on the comparison of different matrices (pooled intestinal contents, livers, spleens and cloacal swabs) for PCR detection of C. botulinum. Between 2013 and 2015, 63 avian botulism suspicions were tested and 37 were confirmed as botulism. Analysis of livers using real-time PCR after enrichment led to the confirmation of 97% of the botulism outbreaks. Using the same method, spleens led to the confirmation of 90 % of botulism outbreaks, cloacal swabs of 93 % and pooled intestinal contents of 46%. Liver appears to be the most reliable type of matrix for laboratory confirmation using real-time PCR analysis.

      PubDate: 2015-11-05T15:40:39Z
  • Polymicrobial infection alter inflammatory microRNA in rat salivary glands
           during periodontal disease
    • Abstract: Publication date: Available online 22 October 2015
      Author(s): Gautam Nayar, Adrienne Gauna, Sasanka Chukkapalli, Irina Velsko, Lakshmyya Kesavalu, Seunghee Cha
      Periodontal disease initiated by subgingival pathogens is linked with diminished secretion of saliva, and implies pathogenic bacteria dissemination to or affects secondary sites such as the salivary glands. MicroRNAs activated in response to bacteria may modulate immune responses against pathogens. Therefore, Sprague-Dawley rats were infected by oral lavage consisting of polymicrobial inocula, namely Porphyromonas gingivalis, Tannerella forsythia, and Treponema denticola, or sham-infected for 12 weeks (n=6). We quantified inflammatory miRNA expression levels of miRNA-132, miR-146a, and miR-155 at secondary sites to the primary infection of the gingiva, including submandibular salivary glands, lacrimal glands, and pancreas. The presence of bacteria was detected in situ at secondary sites. Infected rat gingiva showed increased relative expression of miR-155. In contrast, miRNA-155 expression was decreased in submandibular salivary glands, along with positive identification of P. gingivalis in 2/6 and T. denticola in 1/6 rat salivary glands. Furthermore, miRNA-132 and miRNA-146a were significantly decreased in the pancreas of infected rats. This study is the first to show primary periodontal infections can alter miRNA profiles in secondary sites such as the salivary gland and pancreas. Whether these alterations contribute to pathologies of salivary glands in Sjögren’s syndrome or of pancreas in diabetes warrants further investigation.

      PubDate: 2015-10-24T07:48:54Z
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