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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 Histology & Histopathology     Open Access   (Followers: 1)
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: 2)
Journal of Ichthyology     Hybrid Journal   (Followers: 4)
Journal of Insect Behavior     Hybrid Journal   (Followers: 9)
Journal of Insect Biodiversity     Open Access   (Followers: 3)
Journal of Insect Conservation     Hybrid Journal   (Followers: 10)
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: 12)
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: 6)
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: 12)
Journal of Mechanics in Medicine and Biology     Hybrid Journal  
Journal of Medical Primatology     Hybrid Journal   (Followers: 1)
Journal of Medical Toxicology     Hybrid Journal   (Followers: 4)
Journal of Medicine and Philosophy     Hybrid Journal   (Followers: 7)
Journal of Melittology     Open Access  
Journal of Membrane Biology     Hybrid Journal   (Followers: 1)
Journal of Membrane Science     Hybrid Journal   (Followers: 14)
Journal of Molecular Biology     Hybrid Journal   (Followers: 48)
Journal of Molecular Biology Research     Open Access   (Followers: 3)
Journal of Molecular Catalysis B: Enzymatic     Hybrid Journal   (Followers: 2)
Journal of Molecular Cell Biology     Hybrid Journal   (Followers: 12)
Journal of Molecular Evolution     Hybrid Journal   (Followers: 9)
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   (Followers: 1)
Journal of Mycology     Open Access   (Followers: 3)
Journal of Nanoparticle Research     Hybrid Journal   (Followers: 3)
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: 4)
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: 12)
Journal of Parasitology and Vector Biology     Open Access   (Followers: 1)
Journal of Pharmacological and Toxicological Methods     Hybrid Journal   (Followers: 5)
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: 15)
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: 12)
Journal of Proteomics     Hybrid Journal   (Followers: 10)
Journal of Purdue Undergraduate Research     Open Access   (Followers: 1)
Journal of Radiation Research and Applied Sciences     Open Access   (Followers: 2)
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: 2)
Journal of Stored Products Research     Hybrid Journal  
Journal of Structural and Functional Genomics     Hybrid Journal   (Followers: 1)
Journal of Structural Biology     Hybrid Journal   (Followers: 9)
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   (Followers: 1)
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: 29)
Journal of Visualized Experiments     Full-text available via subscription   (Followers: 2)
Journal of Yeast and Fungal Research     Open Access  
Journal of Zhejiang University - Science B     Hybrid Journal  
Jurnal Fitopatologi 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: 2)
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: 3)
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: 11)
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: 9)
Marine Biodiversity     Hybrid Journal   (Followers: 8)
Marine Biodiversity Records     Open Access   (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: 5)
Mathematical Biosciences     Hybrid Journal   (Followers: 3)
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: 3)
Matrix Biology     Hybrid Journal   (Followers: 1)
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: 9)
Mediterranean Journal of Biosciences     Open Access  
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: 13)
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: 6)
Methods in Cell Science     Hybrid Journal   (Followers: 3)
Methods in Ecology and Evolution     Partially Free   (Followers: 28)
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: 12)
Molecular & Cellular Toxicology     Hybrid Journal   (Followers: 2)
Molecular and Biochemical Parasitology     Hybrid Journal   (Followers: 2)
Molecular and Cellular Biochemistry     Hybrid Journal   (Followers: 4)
Molecular and Cellular Biology     Hybrid Journal   (Followers: 21)
Molecular Based Mathematical Biology     Open Access   (Followers: 1)
Molecular Biology     Hybrid Journal   (Followers: 10)
Molecular Biology and Evolution     Hybrid Journal   (Followers: 82)
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: 2)
Molecular Breeding     Hybrid Journal   (Followers: 9)
Molecular Cell     Full-text available via subscription   (Followers: 44)
Molecular Ecology     Hybrid Journal   (Followers: 29)
Molecular Ecology Resources     Hybrid Journal   (Followers: 11)
Molecular Genetics and Metabolism     Hybrid Journal   (Followers: 5)

  First | 1 2 3 4 5 6 7 8 | Last

Journal Cover Anaerobe
  [SJR: 1.066]   [H-I: 51]   [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  [3039 journals]
  • Counterselection employing mutated pheS for markerless genetic deletion in
           Bacteroides species
    • Abstract: Publication date: Available online 14 September 2016
      Author(s): Yasuhiro Kino, Haruyuki Nakayama-Imaohji, Masashi Fujita, Ayano Tada, Saori Yoneda, Kazuya Murakami, Masahito Hashimoto, Tetsuya Hayashi, Katsuichiro Okazaki, Tomomi Kuwahara
      Markerless gene deletion is necessary for multiple gene disruptions due to the limited number of antibiotic resistant markers for some bacteria. However, even in transformable strains, obtaining the expected mutation without a marker requires laborious screening of a large number of colonies. Previous studies had success in various bacteria with a counter-selection system where a conditional lethal gene was incorporated into the vector. We examined the efficacy of the mutated pheS gene (pheS*) as a counter-selective marker for gene deletion in Bacteroides. This mutation produces an amino acid substitution (A303G) in the alpha subunit of Bacteroides phenylalanyl tRNA synthetase, which in E. coli alters the specificity of the tRNA synthetase resulting in a conditional lethal mutation due to the incorporation of p-chloro-phenylalanine (p-Cl-Phe) into protein. B. fragilis YCH46 and B. thetaiotaomicron VPI-5482 transformed with a pheS*-harboring shuttle vector were clearly growth-inhibited in the presence of >5 mM p-Cl-Phe in liquid defined minimal media (DMM) and on DMM agar plates. A targeting plasmid was constructed to delete the genetic region for capsular polysaccharide PS2 in B. fragilis or PS1 in B. thetaiotaomicron. After counterselection, p-Cl-Phe-resistant colonies were generated at a frequency of 8.1 × 10−3 for B. fragilis and 1.7 × 10−3 for B. thetaiotaomicron. Of the p-Cl-Phe-resistant colonies, 4.2% and 72% harbored the correct genetic deletion for B. fragilis and B. thetaiotaomicron, respectively. These results indicate that mutated pheS is a useful counter-selective gene to construct markerless genetic deletions in Bacteroides.

      PubDate: 2016-09-15T15:08:41Z
  • A case of Bacteroides pyogenes bacteremia secondary to liver abscess
    • Abstract: Publication date: Available online 8 September 2016
      Author(s): Jong Eun Park, So-Young Park, Dong Joon Song, Hee Jae Huh, Chang-Seok Ki, Kyong Ran Peck, Nam Yong Lee
      Bacteroides pyogenes, a non-spore-forming, anaerobic, gram-negative rod, is a component of the oral flora of animals and has, on occasion, been reported to cause human infection through dog or cat bites. We report the first case of B. pyogenes bacteremia secondary to liver abscess with no history of an animal bite. The microorganism was identified by 16S rRNA sequencing.

      PubDate: 2016-09-10T14:55:45Z
  • The role of the bacterial microbiota on reproductive and pregnancy health
    • Abstract: Publication date: Available online 6 September 2016
      Author(s): Deborah B. Nelson, L. Christie Rockwell, Morgan D. Prioleau, Laura Goetzl
      Recent assessments have examined the composition of bacterial communities influencing reproductive, pregnancy and infant health. The Microbiome Project has made great strides in sequencing the microbiome and identifying the vast communities of microorganisms that inhabit our bodies and much work continues to examine the individual contribution of bacteria on health and disease to inform future therapies. This review explores the current literature outlining the contribution of important bacteria on reproductive health among sexually active men and women, outlines gaps in current research to determine causal and interventional relationships, and suggests future research initiatives. Novel treatments options to reduce adverse outcomes must recognize the heterogeneity of the bacteria within the microbiome and adequately assess long-term benefits in reducing disease burden and re-establishing a healthy Lactobacillus-dominant state. Recognizing other reservoirs outside of the lower genital track and within sexual partners as well as genetic and individual moderators may be most important for long-term cure and reduction of disease. It will be important to develop useful screening tools and comprehensively examine novel therapeutic options to promote the long-term reduction of high-risk bacteria and the re-establishment of healthy bacterial levels to considerably improve outcomes among pregnant women and sexually active men and women.

      PubDate: 2016-09-10T14:55:45Z
  • In vitro analysis of partially hydrolyzed guar gum fermentation on
           identified gut microbiota
    • Abstract: Publication date: Available online 30 August 2016
      Author(s): Justin Carlson, Trevor Gould, Joanne Slavin
      Background Prebiotic dietary fibers resist digestion in the upper gastrointestinal tract and allow for stimulation of bacteria in the distal intestine and colon. Stimulation of bacteria among different individuals varies greatly, depending on a wide range of variables. Objective To determine the range of differences in response between individuals, a preclinical in vitro fermentation was conducted with six fecal donors. The primary objective was to compare the fecal microbiota of six individuals at baseline, 12 h and 24 h post-exposure to partially hydrolyzed guar gum (PHGG). Method Fecal donations were collected from six healthy individuals consuming a non-specific Western diet, free of antibiotic treatments in the past year, not affected by any GI diseases and not consuming any probiotic or prebiotic supplements. Fecal samples were exposed to 0.5 g of PHGG and measured for bacterial changes at 0, 12 and 24 h base on 16S rRNA sequencing. Results Parabacteroides increased from 3.48% of sequence reads to 10.62% of sequence reads after 24 h (p = 0.0181) and Bacteroidetes increased from 45.89% of sequence reads to 50.29% of sequence reads (p = 0.0008). Conclusions PHGG stimulates growth of Parabacteroides, a genus of bacteria that have been inversely associated with IBS and ulcerative colitis. PHGG provides stimulation of beneficial Bacteroidetes (Bacteroides and Parabacteroides), which may be correlated with many positive health markers and outcomes. PHGG is a prebiotic dietary fiber that is readily fermentable.

      PubDate: 2016-08-31T14:28:41Z
  • First case report of a human sepsis involving a recently identified
           anaerobic agent: Bacteroides faecis
    • Abstract: Publication date: Available online 18 August 2016
      Author(s): M. Garcia, P. Bouvet, F. Petitpas, C. Jayle, C. Legeay, J. Sautereau, A. Michaud, C. Burucoa, C. Plouzeau
      Up until now, Bacteroides faecis, a Gram-negative, anaerobic, non-motile, nonsporeforming rod has been principally described as a commensal microbe isolated from the feces of healthy adults. We report the first case of human Bacteroides faecis sepsis after removal of suspected post-colonic ischemia colonized epicardic electrodes. Electrodes and blood cultures both grew Gram-negative anaerobic rods but usual phenotypic methods and 16S rARN gene sequencing failed to ensure its species identification. B. faecis was finally identified using hsp60 gene sequencing. Because this species is not well-known and is difficult to identify, it may have been overlooked or misidentified in previous studies.

      PubDate: 2016-08-21T13:47:36Z
  • Evaluation of oral microbiota in undernourished and eutrophic children
           using checkerboard DNA-DNA hybridization
    • Abstract: Publication date: Available online 20 August 2016
      Author(s): M. Testa, S. Erbiti, A. Delgado, I.L. Cardenas
      The aim of this study was to evaluate the relationship among nutritional status, gingival health and the composition of oral microbiota in children of a public school from a very poor area of San Miguel de Tucuman. Forty-five children ranging in age from 6 to 14 years old, 13 males and 32 females were studied. Twenty of these children were undernourished (Lejarraga-Morasso Table) and twenty-five were eutrophic. A clinical study that included DMF and dmf indexes, Löe Silness Plaque Index and bleeding on probing was performed. For microbiological study, saliva samples without stimulation were taken; aliquots of them were immediately placed in TAE buffer pH 7.6, adding NaOH (N and keeping at -70 °C until processed by checkerboard DNA-DNA hybridization method to check the presence of 40 oral microorganism species. Positive bleeding on probing was present in more than 80% of children, without significant differences between eutrophic and undernourished groups. Same result were obtain for the other clinical indexes (p > 0.05, Two Way ANOVA). Significant differences were found for some oral microorganism species, with a higher percentage of undernourished children harboring them. That was the case of S. gordonii (p < 0.05), Capnocitophaga gingivalis and C. ochraceae (p < 0.01 and p < 0.10, respectively), F. nucleatum ss nucleatum (p < 0.05), P. nigrescens (p < 0.10), Campylobacter gracilis (p < 0,05), and T. denticola (p < 0.10, multiple logistic regression). Significant differences were also found between children groups for E. saborreum (p < 0.001), P. acnes (p < 0.10), G. morbillorum (p < 0.05) and L. buccalis (p < 0.10). Gingivitis and bleeding on probing would not be related to nutritional status in the groups of children studied. There were significant differences for the presence of some of the main periodontal pathogen species between eutrophic and undernourished children. It would be important to study the meaning of significant differences found for the other microorganisms more deeply.

      PubDate: 2016-08-21T13:47:36Z
  • Multidrug-resistant oral Capnocytophaga gingivalis responsible for an
           acute exacerbation of chronic obstructive pulmonary disease: Case report
           and literature review
    • Abstract: Publication date: Available online 13 August 2016
      Author(s): Elodie Ehrmann, Anne Jolivet-Gougeon, Martine Bonnaure-Mallet, Thierry Fosse
      Introduction Capnocytophaga genus was recently known to highly contribute to the beta-lactam (BL) and macrolide-lincosamide-streptogramin (MLS) resistance gene reservoir in the oral microbiota (BL: bla CSP-1 and bla CfxA; MLS: erm(F) and erm(C)). But fluoroquinolone (FQ) resistance remains uncommon in literature, without available data on resistance mechanisms. Case report For the first time, a case of acute exacerbation of chronic obstructive pulmonary disease (COPD) was described in a 78-year-old immunocompetent patient due to a multidrug-resistant Capnocytophaga gingivalis isolate with significant microbiological finding. C.gingivalis acquired resistance to third generation cephalosporins (bla CfxA3 gene), MLS (erm(F) gene), and fluoroquinolones. Genetics of the resistance, unknown as regards fluoroquinolone, was investigated and a substitution in QRDR of GyrA was described (Gly80Asn substitution) for the first time in the Capnocytophaga genus. Literature review A comprehensive literature review of Capnocytophaga spp. extra-oral infection was conducted. Including the present report, on 43 cases, 7 isolates were BL-resistant (17%), 4 isolates were MLS-resistant (9.5%) and 4 isolates were FQ-resistant (9.5%). The studied clinical isolate of C.gingivalis was the only one to combine resistance to the three groups of antibiotics BL, MLS and FQ. Four cases of Capnocytophaga lung infection were reported, including three infections involving C. gingivalis (two FQ resistant) and one involving C. sputigena. Conclusion This multidrug-resistant C. gingivalis isolate illustrated the role of oral flora as a reservoir of antibiotic resistance and its contribution to the limitation of effective antibiotics in severe respiratory infections.

      PubDate: 2016-08-16T13:27:29Z
  • First isolation of Clostridium indolis in a patient with chronic osteitis:
           A case report and literature review of human infections related to
           Clostridium saccharolyticum group species
    • Abstract: Publication date: Available online 7 August 2016
      Author(s): Romain Lotte, Laurène Lotte, Philippe Bouvet, Nicolas Degand, Antonin Bal, Michel Carles, Regis Bernard de Dompsure, Michel Popoff, Raymond Ruimy
      Clostridium indolis is an anaerobic spore-forming Gram-positive bacillus belonging to the Clostridium saccharolyticum group. Its clinical significance in human remains poorly known. We describe the first case of osteitis related to C. indolis, identified by MALDI-TOF mass spectrometry and provide a literature review of human infections related to C. saccharolyticum group species.

      PubDate: 2016-08-12T13:08:31Z
  • Porphyromonas pogonae identification from a soft tissue infection: The
           first human case
    • Abstract: Publication date: December 2016
      Source:Anaerobe, Volume 42
      Author(s): Bongyoung Kim, Hyunjoo Pai, Kyu Tae Hwang, Yangsoon Lee
      We report a first human case of Porphyromonas pogonae causing soft tissue infection in a patient with open fracture. Strong β-hemolytic, aerotolerant, and non-pigmented gram-negative coccobacilli which matched Porphyromonas pogonae by PCR for 16S rRNA genes were identified from the pus specimen. The clinical course of the patient improved with repeated surgical drainage and tigecycline administration.

      PubDate: 2016-08-12T13:08:31Z
  • Robinsoniella peoriensis, originally isolated from swine manure, and early
           periprosthetic hip infection: Case report and review of the literature
    • Abstract: Publication date: Available online 30 July 2016
      Author(s): Heime Rieber, Andre Frontzek, Andreas Bell, Lars Frommelt
      We report on the first case of a periprosthetic joint infection with the anaerobic spore-forming Gram-positive rod Robinsoniella peoriensis as the causative agent. The bacterium was first isolated from a swine manure storage pit and has so far rarely been associated with human infections.

      PubDate: 2016-08-03T12:28:56Z
  • A genetic assay for gene essentiality in Clostridium
    • Abstract: Publication date: Available online 31 July 2016
      Author(s): David J.F. Walker, John T. Heap, Klaus Winzer, Nigel P. Minton
      Essential genes of pathogens are potential therapeutic targets, but are difficult to verify. Here, gene essentiality was determined by targeted knockout following engineered gene duplication. Null mutants of candidate essential genes of Clostridium difficile were viable only in the presence of a stable second copy of the gene.

      PubDate: 2016-08-03T12:28:56Z
  • Tetanus toxin production is triggered by the transition from amino acid
           consumption to peptides
    • Abstract: Publication date: Available online 1 August 2016
      Author(s): Cuauhtemoc Licona-Cassani, Jennifer A. Steen, Nicolas E. Zaragoza, Glenn Moonen, George Moutafis, Mark P. Hodson, John Power, Lars K. Nielsen, Esteban Marcellin
      Bacteria produce some of the most potent molecules known, of which many cause serious diseases such as tetanus. For prevention, billions of people and countless animals are immunised with the highly effective vaccine, industrially produced by large-scale fermentation. However, toxin production is often hampered by low yields and batch-to-batch variability. Improved productivity has been constrained by a lack of understanding of the molecular mechanisms controlling toxin production. Here we have developed a reproducible experimental framework for screening phenotypic determinants in Clostridium tetani under a process that mimics an industrial setting. We show that amino acid depletion induces production of the toxin. Using time-course transcriptomics and extracellular metabolomics to generate a ‘fermentation atlas’ that ascribe growth behaviour, nutrient consumption and gene expression to the fermentation phases, we found a subset of preferred amino acids. Exponential growth is characterised by the consumption of those amino acids followed by a slower exponential growth phase where peptides are consumed, and toxin is produced. The results aim at assisting in fermentation medium design towards the improvement of vaccine production yields and reproducibility. In conclusion, our work not only provides deep fermentation dynamics but represents the foundation for bioprocess design based on C. tetani physiological behaviour under industrial settings.

      PubDate: 2016-08-03T12:28:56Z
  • Editorial board
    • Abstract: Publication date: August 2016
      Source:Anaerobe, Volume 40

      PubDate: 2016-08-03T12:28:56Z
  • Identification and characterization of Dichelobacter nodosus serogroup H
           from ovine footrot in India
    • Abstract: Publication date: August 2016
      Source:Anaerobe, Volume 40
      Author(s): N. Vinod Kumar, D. Sreenivasulu, A. Karthik
      A total of 56 foot swabs were collected from inter digital spaces of sheep with footrot lesions were screened for 16 rRNA of Dichelobacter nodosus by PCR. Out of the 56 samples, 38(67.85%) were found to be positive. All the positive samples were subjected to multiplex PCR targeting fimA gene for identification of serogroups of D. nodosus. Serogroup H was found along with serogroup B in 12 (55.26%) samples and with serogroup I in 8 (22.2%) samples. The serogroup H was identified for the first time from the Indian subcontinent. The phylogenetic analysis of the present sequence with the available serogroup H sequences of GenBank revealed to be in close association with the serotype H1.

      PubDate: 2016-08-03T12:28:56Z
  • Analysis of the rumen bacterial diversity of goats during shift from
           forage to concentrate diet
    • Abstract: Publication date: Available online 12 July 2016
      Author(s): Diego Javier Grilli, Kateřina Fliegerová, Jan Kopečný, Sebastián Paez Lama, Vanina Egea, Noelia Sohaefer, Celia Pereyra, María Soledad Ruiz, Miguel Angel Sosa, Graciela Nora Arenas, Jakub Mrázek
      High-grain feeding used in the animal production is known to affect the host rumen bacterial community, but our understanding of consequent changes in goats is limited. This study was therefore aimed to evaluate bacterial population dynamics during 20 days adaptation of 4 ruminally cannulated goats to the high-grain diet (grain: hay – ratio of 40:60). The dietary transition of goats from the forage to the high-grain-diet resulted in the significant decrease of rumen fluid pH, which was however still higher than value established for acute or subacute ruminal acidosis was not diagnosed in studied animals. DGGE analysis demonstrated distinct ruminal microbial populations in hay-fed and grain-fed animals, but the substantial animal-to-animal variation were detected. Quantitative PCR showed for grain-fed animals significantly higher number of bacteria belonging to C. leptum group at 10 days after the incorporation of corn into the diet and significantly lower concentration of bacteria belonging to Actinobacteria phylum at the day 20 after dietary change. Taxonomic distribution analysed by NGS at day 20 revealed the similar prevalence of the phyla Firmicutes and Bacteroidetes in all goats, significantly higher presence of the unclassified genus of groups of Bacteroidales and Ruminococcaceae in grain-fed animals and significantly higher presence the genus Prevotella and Butyrivibrio in the forage-fed animals. The three different culture-independent methods used in this study show that high proportion of concentrate in goat diet does not induce any serious disturbance of their rumen ecosystem and indicate the good adaptive response of caprine ruminal bacteria to incorporation of corn into the diet.

      PubDate: 2016-07-24T11:57:37Z
  • A case of multiple recurrence of Clostridium difficile infection with
           severe hematochezia in an immunocompromised host
    • Abstract: Publication date: Available online 1 July 2016
      Author(s): Xuewu Zhang, Yunbo Chen, Silan Gu, Beiwen Zheng, Tao Lv, Yinjun Lou, Jie Jin
      Clostridium difficile infection (CDI) is increasing in incidence and severity. Clinically, diarrhea frequently occurs, but severe hematochezia is rarely seen with CDI. We describe here a hematopoietic stem cell transplantation (HSCT) recipient who experienced life-threatening gastrointestinal bleeding due to severe CDI. Subsequent stool surveillance and molecular typing observed the patient who had two episodes of recurrence with a new strain of C. difficile distinct from the initial infection. We analyze C. difficile strains obtained from the patient, and also discuss the diagnosis and treatment of this case.

      PubDate: 2016-07-24T11:57:37Z
  • Induction of antitoxin responses in Clostridium-difficile-infected
           patients compared to healthy blood donors
    • Abstract: Publication date: Available online 15 July 2016
      Author(s): Alice von Eichel-Streiber, Wonbeom Paik, Katherine Knight, Karina Gisch, Karolina Nadjafi, Christine Decker, Oliver Bosnjak, Adam Cheknis, Stuart Johnson, Christoph von Eichel-Streiber
      According to the literature Clostridium difficile antitoxins are present in up to 66% of humans. In a survey of ∼400 plasma samples from healthy blood donors we found that less than 6% were positive for anti-TcdA or anti-TcdB antitoxins. Using the same standard immunoassay protocol, we looked for IgG and IgA antitoxins in the blood and stool samples from 25 patients with C. difficile infection (CDI). Some patients with CDI had no antitoxin detected at all, while others had high levels of specific IgG- and IgA-antitoxins against both TcdA and TcdB in blood and IgA-anti-TcdA and -anti-TcdB antibodies in stool. Systemic responses to TcdB and mucosal responses to TcdA predominated. Among patients infected with the NAP1/027/BI strain, systemic IgG-anti-TcdB responses were particularly elevated. In contrast, patients infected with non-027 strains had more elevated mucosal IgA-anti-TcdA responses. Furthermore, high titer sera did not correlate with high neutralizing potential. We hypothesize that paradoxical killing of primed B-cells by antibody-mediated endosomal uptake of the Large Clostridial Toxins, TcdA and TcdB leads to clonal elimination of the fittest B-cells. If this hypothesis is confirmed, immune suppression rather than protective humoral immunity might be the consequence in some patients infected with toxigenic C. difficile.
      Graphical abstract image

      PubDate: 2016-07-24T11:57:37Z
  • Changes in the antibiotic susceptibility of anaerobic bacteria from
           2007–2009 to 2010–2012 based on the CLSI methodology
    • Abstract: Publication date: Available online 15 July 2016
      Author(s): Christine J. Hastey, Halsey Boyd, Audrey N. Schuetz, Karen Anderson, Diane M. Citron, Jody Dzink-Fox, Meredith Hackel, David W. Hecht, Nilda V. Jacobus, Stephen G. Jenkins, Maria Karlsson, Cynthia C. Knapp, Laura M. Koeth, Hannah Wexler, Darcie E. Roe-Carpenter
      Antimicrobial susceptibility testing of anaerobic isolates was conducted at four independent sites from 2010 to 2012 and compared to results from three sites during the period of 2007–2009. This data comparison shows significant changes in antimicrobial resistance in some anaerobic groups. Therefore, we continue to recommend institutions regularly perform susceptibility testing when anaerobes are cultured from pertinent sites. Annual generation of an institutional-specific antibiogram is recommended for tracking of resistance trends over time.

      PubDate: 2016-07-24T11:57:37Z
  • Effects of corn silage and grass silage in ruminant rations on diurnal
           changes of microbial populations in the rumen of dairy cows
    • Abstract: Publication date: Available online 20 July 2016
      Author(s): Melanie B. Lengowski, Maren Witzig, Jens Möhring, Gero M. Seyfang, Markus Rodehutscord
      Here, we examined diurnal changes in the ruminal microbial community and fermentation characteristics of dairy cows fed total mixed rations containing either corn silage (CS) or grass silage (GS) as forage. The rations, which consisted of 52% concentrate and 48% GS or CS, were offered for ad libitum intake over 20 days to three ruminal-fistulated lactating Jersey cows during three consecutive feeding periods. Feed intake, ruminal pH, concentrations of short chain fatty acids and ammonia in rumen liquid, as well as abundance change in the microbial populations in liquid and solid fractions, were monitored in 4-h intervals on days 18 and 20. The abundance of total bacteria and Fibrobacter succinogenes increased in solids in cows fed CS instead of GS, and that of protozoa increased in both solid and liquid fractions. Feeding GS favored numbers of F. succinogenes and Selenomonas ruminantium in the liquid fraction as well as the numbers of Ruminobacter amylophilus, Prevotella bryantii and ruminococci in both fractions. Minor effects of silage were detected on populations of methanogens. Despite quantitative changes in the composition of the microbial community, fermentation characteristics were less affected by forage source. These results suggest a functional adaptability of the ruminal microbiota to total mixed rations containing either GS or CS as the source of forage. Diurnal changes in microbial populations were primarily affected by feed intake and differed between species and fractions, with fewer temporal fluctuations evident in the solid than in the liquid fraction. Interactions between forage source and sampling time were of minor importance to most of the microbial species examined. Thus, diurnal changes of microbial populations and fermentative activity were less affected by the two silages.

      PubDate: 2016-07-24T11:57:37Z
  • Heat shock increases conjugation efficiency in Clostridium difficile
    • Abstract: Publication date: December 2016
      Source:Anaerobe, Volume 42
      Author(s): Joseph A. Kirk, Robert P. Fagan
      Clostridium difficile infection has increased in incidence and severity over the past decade, and poses a unique threat to human health. However, genetic manipulation of C. difficile remains in its infancy and the bacterium remains relatively poorly characterised. Low-efficiency conjugation is currently the only available method for transfer of plasmid DNA into C. difficile. This is practically limiting and has slowed progress in understanding this important pathogen. Conjugation efficiency varies widely between strains, with important clinically relevant strains such as R20291 being particularly refractory to plasmid transfer. Here we present an optimised conjugation method in which the recipient C. difficile is heat treated prior to conjugation. This significantly improves conjugation efficiency in all C. difficile strains tested including R20291. Conjugation efficiency was also affected by the choice of media on which conjugations were performed, with standard BHI media giving most transconjugant recovery. Using our optimised method greatly increased the ease with which the chromosome of R20291 could be precisely manipulated by homologous recombination. Our method improves on current conjugation protocols and will help speed genetic manipulation of strains otherwise difficult to work with.

      PubDate: 2016-07-24T11:57:37Z
  • Anaerococcus rubiinfantis sp. nov., isolated from the gut microbiota of a
           Senegalese infant with severe acute malnutrition
    • Abstract: Publication date: August 2016
      Source:Anaerobe, Volume 40
      Author(s): Maryam Tidjani Alou, Saber Khelaifia, Caroline Michelle, Claudia Andrieu, Nicholas Armstrong, Fadi Bittar, Cheikh Sokhna, Aldiouma Diallo, Pierre-Edouard Fournier, Didier Raoult, Matthieu Million
      Anaerococcus rubiinfantis sp. nov. strain mt16T is a new species within the genus Anaerococcus, which was isolated by the culturomics approach from the gut microbiota of an infant suffering from kwashiorkor. A phenotypic, biochemical and proteomic description of this strain is hereby presented alongside a complete annotation of its genome. This strictly anaerobic species forms Gram-positive non-sporeforming cocci. The major fatty acid was hexadecanoic acid. The phylogenetic analysis of strain mt16T showed a 97.9% similarity level with Anaerococcus vaginalis, the closest validly published species. Its genome is 1,929,161 bp long with 29.5% G + C content and contains 1808 protein-coding genes and 56 RNA genes, among which are six rRNA genes. Genomic analysis identified 41/1864 coding genes as ORFans (2.2%) and at least 620/1808 (34.9%) orthologous proteins which are not shared with the closest phylogenetic species. We believe that the extension of the human anaerobic gut compendium by culturomics is one of the first steps that will improve the understanding of the links between the microbiome and health or disease.

      PubDate: 2016-07-24T11:57:37Z
  • Reclassification of Clostridium difficile as Clostridioides difficile
           (Hall and O’Toole 1935) Prévot 1938
    • Abstract: Publication date: August 2016
      Source:Anaerobe, Volume 40
      Author(s): Paul A. Lawson, Diane M. Citron, Kerin L. Tyrrell, Sydney M. Finegold
      The recent proposal by Lawson and Rainey (2015) to restrict the genus Clostridium to Clostridium butyricum and related species has ramifications for the members of the genera that fall outside this clade that should not be considered as Clostridium sensu stricto. One such organism of profound medical importance is Clostridioides difficile that is a major cause of hospital-acquired diarrhea and mortality in individuals. Based on 16S rRNA gene sequence analysis, the closest relative of Clostridium difficile is Clostridium mangenotii with a 94.7% similarity value and both are located within the family Peptostreptococcaceae that is phylogenetically far removed from C. butyricum and other members of Clostridium sensu stricto. Clostridium difficile is Clostridium mangenotii each produce abundant H2 gas when grown in PYG broth and also produce a range of straight and branched chain saturated and unsaturated fatty acids with C16:0 as a major product. The cell wall peptidoglycan contains meso-DAP as the diagnostic diamino acid. Based on phenotypic, chemotaxonomic and phylogenetic analyses, novel genus Clostridioides gen. nov. is proposed for Clostridium difficile as Clostridioides difficile gen. nov. comb. nov. and that Clostridium mangenotii be transferred to this genus as Clostridioides mangenotii comb. nov. The type species of Clostridioides is Clostridioides difficile.

      PubDate: 2016-07-24T11:57:37Z
  • New insights into Clostridium perfringens epsilon toxin activation and
           action on the brain during enterotoxemia
    • Abstract: Publication date: Available online 16 June 2016
      Author(s): John C. Freedman, Bruce A. McClane, Francisco A. Uzal
      Epsilon toxin (ETX), produced by Clostridium perfringens types B and D, is responsible for diseases that occur mostly in ruminants. ETX is produced in the form of an inactive prototoxin that becomes proteolytically-activated by several proteases. A recent ex vivo study using caprine intestinal contents demonstrated that ETX prototoxin is processed in a step-wise fashion into a stable, active ∼27 kDa band on SDS-PAGE. When characterized further by mass spectrometry, the stable ∼27 kDa band was shown to contain three ETX species with varying C-terminal residues; each of these ETX species is cytotoxic. This study also demonstrated that, in addition to trypsin and chymotrypsin, proteases such as carboxypeptidases are involved in processing ETX prototoxin. Once absorbed, activated ETX species travel to several internal organs, including the brain, where this toxin acts on the vasculature to cross the blood-brain barrier, produces perivascular edema and affects several types of brain cells including neurons, astrocytes, and oligodendrocytes. In addition to perivascular edema, affected animals show edema within the vascular walls. This edema separates the astrocytic end-feet from affected blood vessels, causing hypoxia of nervous system tissue. Astrocytes of rats and sheep affected by ETX show overexpression of aquaporin-4, a membrane channel protein that is believed to help remove water from affected perivascular spaces in an attempt to resolve the perivascular edema. Amyloid precursor protein, an early astrocyte damage indicator, is also observed in the brains of affected sheep. These results show that ETX activation in vivo seems to be more complex than previously thought and this toxin acts on the brain, affecting vascular permeability, but also damaging neurons and other cells.

      PubDate: 2016-06-18T18:01:24Z
  • Development of SYN-004, an oral beta-lactamase treatment to protect the
           gut microbiome from antibiotic-mediated damage and prevent Clostridium
           difficile infection
    • Abstract: Publication date: Available online 2 June 2016
      Author(s): Michael Kaleko, J. Andrew Bristol, Steven Hubert, Todd Parsley, Giovanni Widmer, Saul Tzipori, Poorani Subramanian, Nur Hasan, Perrti Koski, John Kokai-Kun, Joseph Sliman, Annie Jones, Sheila Connelly
      The gut microbiome, composed of the microflora that inhabit the gastrointestinal tract and their genomes, make up a complex ecosystem that can be disrupted by antibiotic use. The ensuing dysbiosis is conducive to the emergence of opportunistic pathogens such as Clostridium difficile. A novel approach to protect the microbiome from antibiotic-mediated dysbiosis is the use of beta-lactamase enzymes to degrade residual antibiotics in the gastrointestinal tract before the microflora are harmed. Here we present the preclinical development and early clinical studies of the beta-lactamase enzymes, P3A, currently referred to as SYN-004, and its precursor, P1A. Both P1A and SYN-004 were designed as orally-delivered, non-systemically available therapeutics for use with intravenous beta-lactam antibiotics. SYN-004 was engineered from P1A, a beta-lactamase isolated from Bacillus licheniformis, to broaden its antibiotic degradation profile. SYN-004 efficiently hydrolyses penicillins and cephalosporins, the most widely used IV beta-lactam antibiotics. In animal studies, SYN-004 degraded ceftriaxone in the GI tract of dogs and protected the microbiome of pigs from ceftriaxone-induced changes. Phase I clinical studies demonstrated SYN-004 safety and tolerability. Phase 2 studies are in progress to assess the utility of SYN-004 for the prevention of antibiotic-associated diarrhea and Clostridium difficile disease.

      PubDate: 2016-06-15T02:04:32Z
  • Editorial board
    • Abstract: Publication date: June 2016
      Source:Anaerobe, Volume 39

      PubDate: 2016-06-15T02:04:32Z
  • Gene regulation by the VirS/VirR system in Clostridium perfringens
    • Abstract: Publication date: Available online 11 June 2016
      Author(s): Kaori Ohtani
      The Gram-positive anaerobic spore-forming rod, Clostridium perfringens, is widely distributed in nature, especially in soil and the gastrointestinal tract of humans and animals. C. perfringens produces many secreted toxins and enzymes that are involved in the pathogenesis of gas gangrane and gastrointestinal disease. One of the most important systems regulating the production of these proteins in C. perfringens is the VirS/VirR-VR-RNA signal transduction cascade. The Agr system also important for the regulation of toxin genes. VirS appears to sense the peptide produced by the Agr (accessory gene regulator) system. The VirS/VirR-VR-RNA cascade controls the pathogenesis of C. perfringens infections by regulating virulence related genes and genes for energy metabolism. These systems are important for the host cell-induced upregulation of toxin production.

      PubDate: 2016-06-15T02:04:32Z
  • Zoonotic potential of the Clostridium difficile RT078 family in Taiwan
    • Abstract: Publication date: Available online 9 June 2016
      Author(s): Bo-Yang Tsai, Wen-Chien Ko, Ter-Hsin Chen, Ying-Chen Wu, Po-Han Lan, Yi-Hsuan Chen, Yuan-Pin Hung, Pei-Jane Tsai
      Clostridium difficile is the major cause of nosocomial diarrhea. We have previously demonstrated that in southern Taiwan, severe C. difficile-associated diarrhea (CDAD) cases were due to the C. difficile RT 126 strain infection, indicating the arrival of an epidemic C. difficile clone in southern Taiwan. RT126 has a close genetic relationship with RT078. However, the RT078 family is the predominant strain of C. difficile in animals worldwide, particularly in swine. In this study, we surveyed C. difficile strains isolated from swine at several farms in Taiwan from August 2011 to March 2015. We found that all swine strains, namely RT078 (32.5%, 37 of 114), RT126 (28.9%, 33 of 114) and RT127 (37.7%, 43 of 114), belonged to the toxigenic RT078 family. All strains had high gyrA mutation rate (57.9%, 66/114), which was linked to quinolone resistance. Notably, Rep-PCR revealed that 3 RT078 animal strains had the same fingerprint as human RT078 clinical isolates; their phylogenic relationship was closely related to the whole gene sequences of tcdB, thus suggesting zoonotic potential for C. difficile infection in Taiwan.

      PubDate: 2016-06-15T02:04:32Z
  • A MLST Clade 2 Clostridium difficile strain with a variant TcdB induces
           severe inflammatory and oxidative response associated with mucosal
    • Abstract: Publication date: Available online 14 June 2016
      Author(s): Cecília Leite Costa, Diana López-Ureña, Thiago de Oliveira Assis, Ronaldo A. Ribeiro, Rodrigo Otávio Silveira Silva, Maja Rupnik, Mark H. Wilcox, Alex Fiorini de Carvalho, Anderson Oliveira do Carmo, Adriana Abalen Martins Dias, Cibele Barreto Mano de Carvalho, Esteban Chaves-Olarte, César Rodríguez, Carlos Quesada-Gómez, Gerly Anne de Castro Brito
      The epidemiology of Clostridium difficile infections is highly dynamic as new strains continue to emerge worldwide. Here we present a detailed analysis of a new C. difficile strain (ICC-45) recovered from a cancer patient in Brazil that died from severe diarrhea. A polyphasic approach assigned a new PCR-ribotype and PFGE macrorestriction pattern to strain ICC-45, which is toxigenic (tcdA + , tcdB + and ctdB + ) and classified as ST41 from MLST Clade 2 and toxinotype IXb. Strain ICC-45 encodes for a variant TcdB that induces a distinct CPE in agreement with its toxinotype. Unlike epidemic NAP1/027 strains, which are also classified to MLST Clade 2, strain ICC-45 is susceptible to fluoroquinolones and does not overproduce toxins TcdA and TcdB. However, supernatants from strain ICC-45 and a NAP1/027 strain produced similar expression of pro-inflammatory cytokines, epithelial damage, and oxidative stress response in the mouse ileal loop model. These results highlight inflammation and oxidative stress as common features in the pathogenesis of C. difficile Clade 2 strains. Finally, this work contributes to the description of differences in virulence among various C. difficile strains.

      PubDate: 2016-06-15T02:04:32Z
  • MALDI-TOF MS is more accurate than VITEK II ANC card and API Rapid ID 32 A
           system for the identification of Clostridium species
    • Abstract: Publication date: Available online 11 June 2016
      Author(s): Young Jin Kim, Si Hyun Kim, Hyun-Jung Park, Hae-Geun Park, Dongchul Park, Sae Am Song, Hee Joo Lee, Dongeun Yong, Jun Yong Choi, Joong-Ki Kook, Hye Ran Kim, Jeong Hwan Shin
      All 50 C. difficile strains were definitely identified by Vitek2 system, Rapid ID 32A system, and MALDI-TOF. For 18 non-difficile Clostridium strains, the identification results were correct in 0, 2, and 17 strains by Vitek2, Rapid ID 32A, and MALDI-TOF, respectively. MALDI-TOF could be used as the primary tool for identification of Clostridium species.

      PubDate: 2016-06-15T02:04:32Z
  • Propionibacterium acnes biofilm – A sanctuary for Staphylococcus
    • Abstract: Publication date: August 2016
      Source:Anaerobe, Volume 40
      Author(s): Harmony Tyner, Robin Patel
      The purpose of this study was to measure the effect of combined culture of Propionibacterium acnes and Staphylococcus aureus on biofilm formation under different oxygen concentrations. We measured planktonic growth and biofilm formation of P. acnes and S. aureus alone and together under aerobic and anaerobic conditions. Both P. acnes and S. aureus grew under anaerobic conditions. When grown under anaerobic conditions, P. acnes with or without S. aureus formed a denser biomass biofilm than did S. aureus alone. Viable S. aureus was recovered from a16-day old combined P. acnes and S. aureus biofilm, but not a monomicrobial S. aureus biofilm.

      PubDate: 2016-06-15T02:04:32Z
  • Fatal Clostridium perfringens sepsis due to emphysematous gastritis and
           literature review
    • Abstract: Publication date: August 2016
      Source:Anaerobe, Volume 40
      Author(s): Karoly Peter Sarvari, Bela Vasas, Ildiko Kiss, Andrea Lazar, Istvan Horvath, Marianna Simon, Zoltan Peto, Edit Urban
      A 76-year-old female patient was admitted to the Level I Emergency Department of University of Szeged with severe abdominal pain and vomiting. The clinical assessment with laboratory tests and radiological investigations confirmed severe sepsis associated with intravascular hemolysis and multiorgan failure and acute pancreatitis. On the abdominal CT, besides of other abnormalities, the presence of gas bubbles in the stomach, small intestines and liver were seen. The gastric alterations pointed to emphysematous gastritis. Despite of the medical treatment, the patient's condition quickly deteriorated and eight hours after admission the patient died. The autopsy evaluation revealed systemic infection of abdominal origin caused by gas-producing Gram-positive bacteria, and the post-mortem microbiological cultures confirmed the presence of Cloctridium perfringens in many abdominal organs. Emphysematous gastritis seemed to be the primary infectious focus.

      PubDate: 2016-06-15T02:04:32Z
  • Serological identification of botulinum neurotoxins: A critical overview
    • Abstract: Publication date: August 2016
      Source:Anaerobe, Volume 40
      Author(s): Domingo F. Giménez
      The reasons that gave rise to the controversy over the serological method (SerM) and genetics regarding the identification of an alleged novel botulinum neurotoxin (BoNT), type H, have been concisely examined. This discussion will remain opened inasmuch as the SerM is not performed according to the recommended procedures outlined in this overview and thoroughly discussed on previous publications. If correctly performed and interpreted, the SerM will keep its preeminence in the identification, typing and taxonomy of BoNTs.

      PubDate: 2016-06-15T02:04:32Z
  • Screening for enterotoxigenic Bacteroides fragilis in stool samples
    • Abstract: Publication date: August 2016
      Source:Anaerobe, Volume 40
      Author(s): Jacqueline I. Keenan, Alan Aitchison, Rachel V. Purcell, Rosie Greenlees, John F. Pearson, Frank A. Frizelle
      Bacteroides fragilis is a commensal bacterium found in the gut of most humans, however enterotoxigenic B. fragilis strains (ETBF) have been associated with diarrhoea and colorectal cancer (CRC). The purpose of this study was to establish a method of screening for the Bacteroides fragilis toxin (bft) gene in stool samples, as a means of determining if carriage of ETBF is detected more often in CRC patients than in age-matched healthy controls. Stool samples from 71 patients recently diagnosed with CRC, and 71 age-matched controls, were screened by standard and quantitative PCR using primers specific for the detection of the bft gene. Bacterial template DNA from stool samples was prepared by two methods: a sweep, where all colonies growing on Bacteroides Bile Esculin agar following stool culture for 48 h at 37 °C in an anaerobic environment were swept into sterile water and heat treated; and a direct DNA extraction from each stool sample. The bft gene was detected more frequently from DNA isolated from bacterial sweeps than from matched direct DNA extractions. qPCR was found to be more sensitive than standard PCR in detecting bft. The cumulative total of positive qPCR assays from both sample types revealed that 19 of the CRC patients had evidence of the toxin gene in their stool sample (27%), compared to seven of the age-matched controls (10%). This difference was significant (P = 0.016). Overall, ETBF carriage was detected more often in CRC patient stool samples compared to controls, but disparate findings from the different DNA preparations and testing methods suggests that poor sensitivity may limit molecular detection of ETBF in stool samples.

      PubDate: 2016-06-15T02:04:32Z
  • Copaifera reticulata oleoresin: Chemical characterization and
           antibacterial properties against oral pathogens
    • Abstract: Publication date: August 2016
      Source:Anaerobe, Volume 40
      Author(s): Danae Kala Rodríguez Bardají, Jonas Joaquim Mangabeira da Silva, Thamires Chiquini Bianchi, Daniele de Souza Eugênio, Pollyanna Francielli de Oliveira, Luís Fernando Leandro, Hervé Louis Ghislain Rogez, Rodrigo Cassio Sola Venezianni, Sergio Ricardo Ambrosio, Denise Crispim Tavares, Jairo Kenupp Bastos, Carlos Henrique G. Martins
      Oral infections such as periodontitis and tooth decay are the most common diseases of humankind. Oleoresins from different copaifera species display antimicrobial and anti-inflammatory activities. Copaifera reticulata is the commonest tree of this genus and grows abundantly in several Brazilian states, such as Pará, Amazonas, and Ceará. The present study has evaluated the chemical composition and antimicrobial potential of the Copaifera reticulata oleoresin (CRO) against the causative agents of tooth decay and periodontitis and has assessed the CRO cytotoxic potential. Cutting edge analytical techniques (GC-MS and LC-MS) aided the chemical characterization of CRO. Antimicrobial assays included determination of the Minimum Inhibitory Concentration (MIC), determination of the Minimum Bactericidal Concentration (MBC), determination of the Minimum Inhibitory Concentration of Biofilm (MICB50), Time Kill Assay, and Checkerboard Dilution. Conduction of XTT assays on human lung fibroblasts (GM07492-A cells) helped to examine the CRO cytotoxic potential. Chromatographic analyses revealed that the major constituents of CRO were β-bisabolene, trans-α-bergamotene, β-selinene, α-selinene, and the terpene acids ent-agathic-15-methyl ester, ent-copalic acid, and ent-polyalthic acid. MIC and MBC results ranged from 6.25 to 200 μg/mL against the tested bacteria. The time-kill assay conducted with CRO at concentrations between 50 and 100 μg/mL showed bactericidal activity against Fusobacterium nucleatum (ATCC 25586) and Streptococcus mitis (ATCC 49456) after 4 h, Prevotella nigrescens (ATCC 33563) after 6 h, Porphyromonas gingivalis (ATCC 33277) and Lactobacillus casei (clinical isolate) after 12 h, and Streptococcus salivarius (ATCC 25975) and Streptococcus mutans (ATCC 25175) after 18 h. The fractional inhibitory concentration indexes (FICIs) revealed antagonistic interaction for Lactobacillus casei (clinical isolate), indifferent effect for Porphyromonas gingivalis (ATCC 33277), Fusobacterium nucleatum (ATCC 25586), Prevotella nigrescens (ATCC 33563), and Streptococcus salivarius (ATCC 25975), and additive effect for Streptococcus mutans (ATCC 25175) and Streptococcus mitis (ATCC 49456). Treatment of GM07492-A cells with CRO demonstrated that concentrations up to 39 μg/mL significantly reduced cell viability as compared to the negative control, being IC50 equal to 51.85 ± 5.4 μg/mL. These results indicated that CRO plays an important part in the search for novel sources of agents that can act against oral pathogens.

      PubDate: 2016-06-15T02:04:32Z
  • Evaluation of the VIDAS glutamate dehydrogenase assay for the detection of
           Clostridium difficile
    • Abstract: Publication date: August 2016
      Source:Anaerobe, Volume 40
      Author(s): Bo-Moon Shin, Eun Joo Lee, Jung Wha Moon, Seon Yeong Lee
      We evaluated the performance of the VIDAS GDH assay for the detection of Clostridium difficile. In total, 350 fecal specimens collected from patients clinically suspected of having CDI were analyzed by C. difficile culture and enzyme-linked fluorescent immunoassay (VIDAS GDH); the results were compared with those of toxigenic C. difficile culture (TC), PCR (Xpert C. difficile assay), and toxin AB EIA (VIDAS CDAB). The numbers of culture-positive and culture-negative samples were 108 and 242, respectively. The concordance between the GDH assay and C. difficile culture was 90.3%. With PCR, 12 more samples were found to be positive in GDH-positive/C. difficile culture-negative specimens. Thus, the concordance between GDH assay and C. difficile culture/PCR was 93.7%. The sensitivity, specificity, positive predictive value, and negative predictive value of the VIDAS GDH assay were 97.2%, 87.2%, 77.2%, and 98.6%, respectively, based on the C. difficile culture, and 97.5%, 91.7%, 86.0%, and 98.6%, respectively, based on C. difficile culture/PCR. Positivity rates of the GDH assay were partially associated with those of semi-quantitative C. difficile cultures, which were maximized in grade 3 (>100 colony-forming unit [CFU]) compared with grade 1 (<10 CFU). We evaluated the two-step or three-step algorithm using GDH assay as a first step. No toxin EIA-positive case was found among GDH-negative samples, and 60.8% (48/79) were TC- and/or PCR-positive among the GDH-positive/toxin EIA-negative samples. Thus, approximately 25% of the 350 samples required a confirmatory test (TC or PCR) in the GDH-toxin EIA algorithm, whereas only 2.3% of the total samples in GDH-PCR algorithm was discrepant and required another confirmatory test like TC.

      PubDate: 2016-06-15T02:04:32Z
  • Clostridium difficile ribotype 176 – A predictor for high mortality and
           risk of nosocomial spread'
    • Abstract: Publication date: August 2016
      Source:Anaerobe, Volume 40
      Author(s): Sylvia Polivkova, Marcela Krutova, Katarina Petrlova, Jiri Benes, Otakar Nyc
      Purpose The objective of this survey was to determine the incidence of Clostridium difficile infections (CDI) at the Department of Infectious Diseases, Bulovka Hospital, and to evaluate clinical and epidemiological data on CDI patients together with a detailed molecular characterisation of C. difficile isolates. The patient outcomes were correlated to causative C. difficile PCR-ribotype. Methods The twelve-month study (2013) comprised patients two years of age and older with CDI. CDI severity was estimated using ESCMID criteria and ATLAS scoring. C. difficile isolates were further characterized using ribotyping, Multiple-Locus Variable Tandem-Repeats analysis (MLVA) and investigation of antibiotic-resistance determinants (gyrA, gyrB, rpoB, ermB). Results A total of 619 diarrhoeal stools were investigated. Seventy-two stool samples were GDH and toxin A/B positive, and 39 samples were GDH positive only and subsequently toxigenic C. difficile was cultured. In total, 111 C. difficile isolates were characterized, of which 64 (57.7%) belonged to PCR-ribotype 176. MLVA analysis of PCR-ribotype 176 isolates revealed 11 clonal complexes. Seventy-two isolates (64.9%) showed amino acid substitution Thr82Ile in the GyrA, and sixty-two isolates (55.9%) showed amino acid substitutions Arg505Lys together with His502Asn, or Asp492Glu together with Arg505Lys in the RpoB. Twelve isolates (10.8%) were ermB positive. Severe CDI according to the ESCMID criteria was recorded in forty-two patients (37.8%), and sixteen patients (14.4%) had ATLAS score ≥ 6. Twenty-nine patients (26.1%) had recurrent CDI and twenty-four patients (21.6%) died during the study period. Conclusions A higher rate of severe CDI, recurrences and mortality in association with PCR-ribotype 176 infections were observed. The high incidence of PCR-ribotype 176 in the study, and the presence of clonal relatedness between PCR-ribotype 176 isolates, indicate its higher capacity to spread in a hospital setting, which in turn highlights the need to implement strict epidemic measures when PCR-ribotype 176 occurs.

      PubDate: 2016-06-15T02:04:32Z
  • Administration of probiotic kefir to mice with Clostridium difficile
           infection exacerbates disease
    • Abstract: Publication date: August 2016
      Source:Anaerobe, Volume 40
      Author(s): Jennifer K. Spinler, Aaron Brown, Caná L. Ross, Prapaporn Boonma, Margaret E. Conner, Tor C. Savidge
      Lifeway® kefir, a fermented milk product containing 12 probiotic organisms, is reported to show promise as an alternative to fecal microbiota transplantation for recurrent Clostridium difficile infection (CDI). We employed a murine CDI model to study the probiotic protective mechanisms and unexpectedly determined that kefir drastically increased disease severity. Our results emphasize the need for further independent clinical testing of kefir as alternative therapy in recurrent CDI.

      PubDate: 2016-06-15T02:04:32Z
  • Infections caused by Tissierella praeacuta: A report of two cases and
           literature review
    • Abstract: Publication date: August 2016
      Source:Anaerobe, Volume 40
      Author(s): F. Caméléna, B. Pilmis, B. Mollo, A. Hadj, A. Le Monnier, A. Mizrahi
      Herein we report two cases of infections caused by Tissierella praeacuta and a review of the literature. The first case was a septic pseudarthrosis of the left femur after multiple fractures. Two per-operative samples were positive with T. praeacuta. The patient was successfully treated by piperacillin – tazobactam and metronidazole. The second case was a bacteremia in a patient suffering from pyonephrosis and a hepatic abscess. The treatment was meropenem. No relapses were observed in both cases. Identification of the strains using MALDI-TOF coupled to mass spectrometry (MS) (Beckman coulter, France) was inconclusive in the two cases. Identification by 16S rRNA sequencing was then performed. This bacterium was susceptible to beta-lactams, chloramphenicol, rifampicine and metronidazole.

      PubDate: 2016-06-15T02:04:32Z
  • A novel method for imaging the pharmacological effects of antibiotic
           treatment on Clostridium difficile
    • Abstract: Publication date: August 2016
      Source:Anaerobe, Volume 40
      Author(s): Bradley T. Endres, Eugénie Bassères, Ali Memariani, Long Chang, M. Jahangir Alam, Richard J. Vickers, Ioannis A. Kakadiaris, Kevin W. Garey
      Clostridium difficile is a significant cause of nosocomial-acquired infection that results in severe diarrhea and can lead to mortality. Treatment options for C. difficile infection (CDI) are limited, however, new antibiotics are being developed. Current methods for determining efficacy of experimental antibiotics on C. difficile involve antibiotic killing rates and do not give insight into the drug's pharmacologic effects. Considering this, we hypothesized that by using scanning electron microscopy (SEM) in tandem to drug killing curves, we would be able to determine efficacy and visualize the phenotypic response to drug treatment. To test this hypothesis, supraMIC kill curves were conducted using vancomycin, metronidazole, fidaxomicin, and ridinilazole. Following collection, cells were either plated or imaged using a scanning electron microscope (SEM). Consistent with previous reports, we found that the tested antibiotics had significant bactericidal activity at supraMIC concentrations. By SEM imaging and using a semi-automatic pipeline for image analysis, we were able to determine that vancomycin and to a lesser extent fidaxomicin and ridinilazole significantly affected the cell wall, whereas metronidazole, fidaxomicin, and ridinilazole had significant effects on cell length suggesting a metabolic effect. While the phenotypic response to drug treatment has not been documented previously in this manner, the results observed are consistent with the drug's mechanism of action. These techniques demonstrate the versatility and reliability of imaging and measurements that could be applied to other experimental compounds. We believe the strategies laid out here are vital for characterizing new antibiotics in development for treating CDI.

      PubDate: 2016-06-15T02:04:32Z
  • Determination of the extent of Clostridium difficile colonisation and
           toxin accumulation in sows and neonatal piglets
    • Abstract: Publication date: August 2016
      Source:Anaerobe, Volume 40
      Author(s): Łukasz Grześkowiak, Jürgen Zentek, Wilfried Vahjen
      Clostridium difficile is an important spore-forming, opportunistic pathogen in animal husbandry and health care. In pig farming, only neonatal piglets are affected, and diarrhoea and necrotising lesions are common symptoms leading to dehydration and in some cases death. This study aimed at the assessment of the quantitative development of C. difficile colonisation in neonatal piglets by determining the shedding of spores and C. difficile toxins A (TcdA) and B (TcdB) concentrations in sow (n = 5–6) and piglet pen faeces (n = 5–6) at different time points. Spores were quantified on selective agar plates and toxins using ELISA method. C. difficile was not detected in the faeces of all but one sow during the perinatal period. Faeces of 2- and 4-day-old piglets contained 0.65 log cells/g and 5.88 log cells/g of C. difficile, respectively. Toxins were detected on day 4 at a concentration of 2.13 log ng/g (TcdA) and 2.06 log ng/g (TcdB). On day 6, concentration of C. difficile reached 6.14 log CFU/g and toxins 2.02 log ng/g (TcdA) and 2.20 log ng/g (TcdB). Two-week-old piglets showed 4.72 log CFU/g of C. difficile but toxins could not be detected. At 21 days of age, both C. difficile and toxins were undetectable. The concentration and the prevalence of C. difficile were positively associated with the prevalence of toxins in piglets. A very short time window for colonisation by C. difficile, including toxin-producing strains can be observed in neonatal piglets. The significance for animal health and the risk of a carrier status need to be addressed in future studies.

      PubDate: 2016-06-15T02:04:32Z
  • Protective potential of recombinant non-purified botulinum neurotoxin
           serotypes C and D
    • Abstract: Publication date: August 2016
      Source:Anaerobe, Volume 40
      Author(s): Clóvis Moreira, Carlos Eduardo Pouey da Cunha, Gustavo Marçal Schmidt Garcia Moreira, Marcelo Mendonça, Felipe Masiero Salvarani, Ângela Nunes Moreira, Fabricio Rochedo Conceição
      Botulinum neurotoxin (BoNT) serotypes C and D are responsible for cattle botulism, a fatal paralytic disease that results in great economic losses in livestock production. Vaccination is the main approach to prevent cattle botulism. However, production of commercially available vaccines (toxoids) involves high risk and presents variation of BoNT production between batches. Such limitations can be attenuated by the development of novel nontoxic recombinant vaccines through a simple and reproducible process. The aim of this study was to evaluate the protective potential of recombinant non-purified botulinum neurotoxin serotypes C and D. Bivalent vaccines containing 200 μg rHCC and rHCD each were formulated in three different ways: (1) purified antigens; (2) recombinant Escherichia coli bacterins; (3) recombinant E. coli cell lysates (supernatant and inclusion bodies). Guinea pigs immunized subcutaneously with recombinant formulations developed a protective immune response against the respective BoNTs as determined by a mouse neutralization bioassay with pooled sera. Purified recombinant antigens were capable of inducing 13 IU/mL antitoxin C and 21 IU/mL antitoxin D. Similarly, both the recombinant bacterins and the cell lysate formulations were capable of inducing 12 IU/mL antitoxin C and 20 IU/mL antitoxin D. These values are two times as high as compared to values induced by the commercial toxoid used as control, and two to ten times as high as the minimum amount required by the Brazilian Ministry of Agriculture, Livestock and Food Supply (MAPA), respectively. Therefore, we used a practical, industry-friendly, and efficient vaccine production process that resulted in formulations capable of inducing protective immune response (neutralizing antitoxins) against botulism serotypes C and D.

      PubDate: 2016-06-15T02:04:32Z
  • The bacteriocin bactofencin A subtly modulates gut microbial populations
    • Abstract: Publication date: August 2016
      Source:Anaerobe, Volume 40
      Author(s): Caitriona M. Guinane, Elaine M. Lawton, Paula M. O'Connor, Órla O'Sullivan, Colin Hill, R. Paul Ross, Paul D. Cotter
      The diverse and dynamic microbiota of the gastrointestinal tract represents a vast source of bioactive substances. These include bacteriocins, which are antimicrobial peptides with the potential to modulate gut populations to impact positively on human health. Although several gut-derived bacteriocins have been isolated, there remain only a few exceptional studies in which their influence on microbial populations within the gut has been investigated. To facilitate such investigations, in vitro faecal fermentation systems can be used to simulate the anaerobic environment of the colon. In this instance, such a system was employed to explore the impact of bactofencin A, a novel broad spectrum class IId bacteriocin produced by gut isolates of Lactobacillus salivarius, on intestinal populations and overall microbial diversity. The study reveals that, although bactofencin A is a broad spectrum bacteriocin, it has a relatively subtle influence on intestinal communities, with a potentially positive impact on anaerobic populations such as Bacteroides, Clostridium and Bifidibacterium spp. The strategy taken is an important first step in investigating the merits of using bactofencin A to manipulate the gut microbiota in a beneficial way for health.

      PubDate: 2016-06-15T02:04:32Z
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
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