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BIOLOGY (1427 journals)            First | 1 2 3 4 5 6 7 8 | Last

Showing 801 - 1000 of 1720 Journals sorted alphabetically
Journal of Fish Biology     Hybrid Journal   (Followers: 35)
Journal of Functional Biomaterials     Open Access   (Followers: 1)
Journal of Fungi     Open Access   (Followers: 2)
Journal of Genomes and Exomes     Open Access  
Journal of Great Lakes Research     Hybrid Journal   (Followers: 6)
Journal of Green Science and Technology     Full-text available via subscription   (Followers: 2)
Journal of Health and Biological Sciences     Open Access  
Journal of Heredity     Hybrid Journal   (Followers: 4)
Journal of Histology & Histopathology     Open Access   (Followers: 2)
Journal of Huazhong University of Science and Technology [Medical Sciences]     Hybrid Journal  
Journal of Human Evolution     Hybrid Journal   (Followers: 18)
Journal of Hymenoptera Research     Open Access   (Followers: 3)
Journal of Ichthyology     Hybrid Journal   (Followers: 3)
Journal of Insect Behavior     Hybrid Journal   (Followers: 8)
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: 2)
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: 17)
Journal of Law and the Biosciences     Open Access   (Followers: 4)
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: 4)
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: 11)
Journal of Mammary Gland Biology and Neoplasia     Hybrid Journal   (Followers: 2)
Journal of Marine and Aquatic Sciences     Open Access   (Followers: 1)
Journal of Marine Biology     Open Access   (Followers: 16)
Journal of Mathematical Biology     Hybrid Journal   (Followers: 11)
Journal of Mechanics in Medicine and Biology     Hybrid Journal  
Journal of Medical Primatology     Hybrid Journal   (Followers: 1)
Journal of Medical Toxicology     Hybrid Journal   (Followers: 6)
Journal of Medicine and Philosophy     Hybrid Journal   (Followers: 4)
Journal of Melittology     Open Access   (Followers: 1)
Journal of Membrane Biology     Hybrid Journal   (Followers: 2)
Journal of Membrane Science     Hybrid Journal   (Followers: 14)
Journal of Molecular Biology     Hybrid Journal   (Followers: 46)
Journal of Molecular Biology Research     Open Access   (Followers: 3)
Journal of Molecular Catalysis B: Enzymatic     Hybrid Journal   (Followers: 1)
Journal of Molecular Cell Biology     Hybrid Journal   (Followers: 14)
Journal of Molecular Evolution     Hybrid Journal   (Followers: 9)
Journal of Molecular Signaling     Open Access  
Journal of Molecular Structure     Hybrid Journal   (Followers: 8)
Journal of Molluscan Studies     Hybrid Journal   (Followers: 1)
Journal of Muscle Research and Cell Motility     Hybrid Journal   (Followers: 1)
Journal of Nanoparticle Research     Hybrid Journal   (Followers: 3)
Journal of Nanoparticles     Open Access   (Followers: 1)
Journal of Natural History     Hybrid Journal   (Followers: 10)
Journal of Natural Products     Full-text available via subscription   (Followers: 15)
Journal of Natural Science, Biology and Medicine     Open Access   (Followers: 1)
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: 14)
Journal of Parasitology and Vector Biology     Open Access   (Followers: 2)
Journal of Pharmacological and Toxicological Methods     Hybrid Journal   (Followers: 7)
Journal of Phycology     Hybrid Journal   (Followers: 7)
Journal of Physics D : Applied Physics     Hybrid Journal   (Followers: 14)
Journal of Physics: Condensed Matter     Hybrid Journal   (Followers: 6)
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: 20)
Journal of Plasma Physics     Hybrid Journal   (Followers: 20)
Journal of Pollination Ecology     Open Access  
Journal of Porphyrins and Phthalocyanines     Hybrid Journal   (Followers: 2)
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: 11)
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: 8)
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: 6)
Journal of Sustainable Bioenergy Systems     Full-text available via subscription   (Followers: 1)
Journal of Sustainable Society     Open Access   (Followers: 5)
Journal of Systematic Palaeontology     Hybrid Journal   (Followers: 7)
Journal of Systematics Evolution     Open Access   (Followers: 5)
Journal of the American Mosquito Control Association     Full-text available via subscription   (Followers: 1)
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: 23)
Journal of the Selva Andina Research Society     Open Access   (Followers: 2)
Journal of the South Carolina Academy of Science     Open Access  
Journal of Theoretical Biology     Hybrid Journal   (Followers: 14)
Journal of Thermal Biology     Hybrid Journal   (Followers: 4)
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: 20)
Journal of Vinyl & Additive Technology     Hybrid Journal  
Journal of Virological Methods     Hybrid Journal   (Followers: 7)
Journal of Virology     Hybrid Journal   (Followers: 33)
Journal of Visualized Experiments     Full-text available via subscription   (Followers: 3)
Journal of Yeast and Fungal Research     Open Access   (Followers: 1)
Journal of Zhejiang University - Science B     Hybrid Journal  
Jurnal Biologi Edukasi     Open Access  
Jurnal Fitopatologi Indonesia     Open Access  
Jurnal Pendidikan 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: 3)
Kennedy Institute of Ethics Journal     Full-text available via subscription   (Followers: 5)
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   (Followers: 1)
Le Naturaliste canadien     Full-text available via subscription  
Letters in Mathematical Physics     Hybrid Journal   (Followers: 4)
Life     Open Access   (Followers: 2)
Life Sciences in Space Research     Hybrid Journal   (Followers: 2)
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: 3)
Lipids in Health and Disease     Open Access  
Luminescence     Hybrid Journal   (Followers: 4)
mAbs     Full-text available via subscription   (Followers: 15)
Macromolecular Bioscience     Hybrid Journal   (Followers: 2)
Macromolecular Reaction Engineering     Hybrid Journal  
Madroño     Full-text available via subscription   (Followers: 1)
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: 7)
Mammal Study     Full-text available via subscription  
Mammalian Biology - Zeitschrift für Säugetierkunde     Hybrid Journal   (Followers: 4)
Mammalian Genome     Hybrid Journal   (Followers: 3)
Mammalian Species     Hybrid Journal  
Manufacturing Engineer     Hybrid Journal   (Followers: 9)
Marine Biodiversity     Hybrid Journal   (Followers: 11)
Marine Biodiversity Records     Open Access   (Followers: 5)
Marine Biology     Hybrid Journal   (Followers: 65)
Marine Biotechnology     Hybrid Journal   (Followers: 5)
Marine Mammal Science     Hybrid Journal   (Followers: 8)
Materials Science and Engineering: C     Hybrid Journal   (Followers: 19)
Materials Technology : Advanced Performance Materials     Hybrid Journal   (Followers: 4)
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: 3)
Matrix Biology     Hybrid Journal   (Followers: 1)
mBio     Open Access   (Followers: 7)
Mechanisms of Ageing and Development     Hybrid Journal   (Followers: 4)
Mechanisms of Development     Hybrid Journal   (Followers: 5)
Médecine Nucléaire     Full-text available via subscription   (Followers: 1)
médecine/sciences     Full-text available via subscription   (Followers: 2)
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: 9)
Metallomics     Full-text available via subscription  
Methods     Hybrid Journal   (Followers: 11)
Methods in Cell Biology     Full-text available via subscription   (Followers: 7)
Methods in Cell Science     Hybrid Journal   (Followers: 4)
Methods in Ecology and Evolution     Partially Free   (Followers: 38)
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: 3)
Molecular and Biochemical Parasitology     Hybrid Journal   (Followers: 2)
Molecular and Cellular Biochemistry     Hybrid Journal   (Followers: 6)
Molecular and Cellular Biology     Hybrid Journal   (Followers: 24)
Molecular Based Mathematical Biology     Open Access   (Followers: 1)
Molecular Biology     Hybrid Journal   (Followers: 12)
Molecular Biology and Evolution     Hybrid Journal   (Followers: 126)

  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  [3043 journals]
  • Development of a real-time PCR method for quantification of Prevotella
           histicola from the gut
    • Authors: Baskar Balakrishnan; David Luckey; Eric Marietta; Melissa Karau; Robin Patel; Joseph Murray; Veena Taneja
      Pages: 37 - 41
      Abstract: Publication date: December 2017
      Source:Anaerobe, Volume 48
      Author(s): Baskar Balakrishnan, David Luckey, Eric Marietta, Melissa Karau, Robin Patel, Joseph Murray, Veena Taneja
      We designed species-specific primers and developed a qPCR method for enumerating P. histicola from intestinal samples. The two designed primer sets showed specificity for the target 16S rRNA gene of P. histicola. The absolute qPCR method was sensitive to quantify as few as 103 colony-forming units (CFU) in the gut.

      PubDate: 2017-07-10T08:44:58Z
      DOI: 10.1016/j.anaerobe.2017.06.019
      Issue No: Vol. 48 (2017)
  • Prevalence and characteristics of Clostridium perfringens and Clostridium
           difficile in dogs and cats attended in diverse veterinary clinics from the
           Madrid region
    • Authors: Sergio Álvarez-Pérez; José L. Blanco; Celine Harmanus; Ed J. Kuijper; Marta E. García
      Pages: 47 - 55
      Abstract: Publication date: Available online 5 July 2017
      Author(s): Sergio Álvarez-Pérez, José L. Blanco, Celine Harmanus, Ed J. Kuijper, Marta E. García
      Despite extensive research on the epidemiology of pathogenic clostridia in dogs and cats, most published studies focus on a selected animal population and/or a single veterinary medical centre. We assessed the burden of Clostridium perfringens and C. difficile shedding by small animals in 17 veterinary clinics located within the Madrid region (Spain) and differing in size, number and features of animals attended and other relevant characteristics. In addition, we studied the genetic diversity and antibiotic susceptibility of recovered isolates. Selective culture of all fecal specimens collected during a single week from dogs (n = 105) and cats (n = 37) attended in participating clinics yielded C. perfringens/C. difficile from 31%, 4.8% of the dogs, and 20%, 0% of the cats analyzed, respectively, and three dogs yielded both species. Furthermore, 17 animals (15 dogs and two cats) that yielded a positive culture for either species were recruited for a follow-up survey and C. perfringens was again obtained from nine dogs. Considerable differences in prevalence were observed among participating clinics for both clostridial species. C. perfringens isolates (n = 109) belonged to toxinotypes A (97.2%) and E (three isolates from one dog), whereas C. difficile isolates (n = 18) belonged to the toxigenic ribotypes 106 (33.3%) and 154 (16.7%), a 009-like ribotype (33.3%) and an unknown non-toxigenic ribotype (16.7%). Amplified fragment length polymorphism-based fingerprinting classified C. perfringens and C. difficile isolates into 105 and 15 genotypes, respectively, and tested isolates displayed in vitro resistance to benzylpenicillin (2.8%, 88.8%), clindamycin (0%, 16.7%), erythromycin (0.9%, 16.7%), imipenem (1.8%, 100%), levofloxacin (0.9%, 100%), linezolid (5.5%, 0%), metronidazole (4.6%, 0%) and/or tetracycline (7.3%, 0%). All animals from which multiple isolates were retrieved yielded ≥2 different genotypes and/or antimicrobial susceptibility profiles. Future studies should focus on the seasonal and geographical variations of prevalence and diversity patterns of clostridial species in small animals.

      PubDate: 2017-07-10T08:44:58Z
      DOI: 10.1016/j.anaerobe.2017.06.023
      Issue No: Vol. 48 (2017)
  • Clostridium perfringens and C. difficile in parvovirus-positive dogs
    • Authors: Rodrigo Otávio Silveira Silva; Fernanda Alves Dorella; Henrique Cesar Pereira Figueiredo; Érica Azevedo Costa; Vanessa Pelicia; Bruna Letícia Devidé Ribeiro; Marcio Garcia Ribeiro; Antonio Carlos Paes; Jane Megid; Francisco Carlos Faria Lobato
      Pages: 66 - 69
      Abstract: Publication date: December 2017
      Source:Anaerobe, Volume 48
      Author(s): Rodrigo Otávio Silveira Silva, Fernanda Alves Dorella, Henrique Cesar Pereira Figueiredo, Érica Azevedo Costa, Vanessa Pelicia, Bruna Letícia Devidé Ribeiro, Marcio Garcia Ribeiro, Antonio Carlos Paes, Jane Megid, Francisco Carlos Faria Lobato
      The aim of this study was to investigate Clostridium difficile and Clostridium perfringens in 82 diarrheic dogs positive for canine parvovirus type 2 (CPV). Enterotoxigenic C. perfringens type A was isolated from three (3.6%) dogs. One (1.2%) strain was also positive for NetE- and NetF-encoding genes, which are commonly associated with diarrhea in dogs. Toxigenic C. difficile was isolated from one animal (1.2%), which was also positive for A/B toxins. The present study identified C. difficile and C. perfringens infection in CPV-positive dogs. Further studies are necessary to clarify if clostridial infections may predispose or potentiate CPV-infection in dogs or vice versa.

      PubDate: 2017-07-27T10:19:59Z
      DOI: 10.1016/j.anaerobe.2017.07.001
      Issue No: Vol. 48 (2017)
  • Description of Absiella argi gen. nov., sp. nov., and transfer of
           Eubacterium dolichum and Eubacterium tortuosum to the genus Absiella as
           Absiella dolichum comb. nov. and Absiella tortuosum comb. nov
    • Authors: Jayoung Paek; Yeseul Shin; Joong-Su Kim; Hongik Kim; Joong-Ki Kook; Woon Kee Paek; Young-Hyo Chang
      Pages: 70 - 75
      Abstract: Publication date: December 2017
      Source:Anaerobe, Volume 48
      Author(s): Jayoung Paek, Yeseul Shin, Joong-Su Kim, Hongik Kim, Joong-Ki Kook, Woon Kee Paek, Young-Hyo Chang
      Gram-positive, straight or slightly curved rod-shaped bacteria, designated as strains N6H1-5T and N6H1-3, were isolated from fecal samples of old dog. The analysis of 16S rRNA gene sequences indicated that the isolates belonged to the Clostridium cluster XVI and were closely related to Eubacterium dolichum KCTC 5832T, Eubacterium tortuosum DSM 3987T, Clostridium innocuum KCTC 5183T, Allobaculum stecoricanis DSM 13633T, Eubacterium limosum KCTC 3266T, and Clostridium butyricum KCTC 1871T, with 94.0%, 93.8%, 92.0%, 84.9%, 80.7%, and 80.0% sequence similarity, respectively. Chemotaxonomic data supported placement of the strains N6H1-5T and N6H1-3 in the new taxon. The strains contained m-diaminopimelic acid cell wall peptidoglycan; the major polar lipids were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), and glycolipids (GL); and the major fatty acids were C18:1 cis 9 (30.7%) and C16:0 (17.1%). The predominant metabolic end product was lactic acid. The G + C content was 35.8 mol%. The most closely related species, E. dolichum and E. tortuosum, were also assigned to the new taxon, based on the phylogenetic analysis and phenotypic data. Thus, the type strain N6H1-5T (=KCTC 15422 = JCM 30884) represents a novel genus and species, for which the name Absiella argi gen. nov., sp. nov is proposed. It is also proposed that E. dolichum KCTC 5832T and E. tortuosum DSM 3987T be transferred to this new genus, and named Absiella dolichum comb. nov. and Absiella tortuosum comb. nov., respectively.

      PubDate: 2017-08-04T19:42:55Z
      DOI: 10.1016/j.anaerobe.2017.07.006
      Issue No: Vol. 48 (2017)
  • Comparative phenotypic analysis of “Clostridium neonatale” and
           Clostridium butyricum isolates from neonates
    • Authors: S. Schönherr-Hellec; G. Klein; J. Delannoy; L. Ferraris; I. Friedel; J.C. Rozé; M.J. Butel; J. Aires
      Pages: 76 - 82
      Abstract: Publication date: December 2017
      Source:Anaerobe, Volume 48
      Author(s): S. Schönherr-Hellec, G. Klein, J. Delannoy, L. Ferraris, I. Friedel, J.C. Rozé, M.J. Butel, J. Aires
      “Clostridium neonatale” was recently described as a new species within the Cluster I of the Clostridium genus sensu stricto. In this study, we characterized “C. neonatale” isolates (n = 42) and compared their phenotypic properties with those of Clostridium butyricum (n = 26), a close related species. Strains isolated from fecal samples of healthy neonates were tested for different phenotypic characteristics. Compared to C. butyricum, “C. neonatale” showed a significant higher surface hydrophobicity (p = 0.0047), exopolysaccharide production (p = 0.0069), aero-tolerance (p = 0.0222) and viability at 30 °C (p = 0.0006). A lower swimming ability (p = 0.0146) and tolerance against bile (0.3%) (p = 0.0494), acid (pH 4.5) (p < 0.0001), osmolarity (NaCl 5%, p = 0.0188) and temperature at 50 °C (p = 0.0013) characterized “C. neonatale” strains. Our results showed that “C. neonatale” behaves very differently from C. butyricum and suggests specific responses to environmental changes. Besides it is the first study on clinical isolates for these two anaerobic members of the newborns' gut microbiota and broadens our knowledge about their phenotypic traits.

      PubDate: 2017-08-04T19:42:55Z
      DOI: 10.1016/j.anaerobe.2017.07.002
      Issue No: Vol. 48 (2017)
  • Effects of Clostridium perfringens iota toxin in the small intestine of
    • Authors: Leandro M. Redondo; Enzo A. Redondo; Gabriela C. Dailoff; Carlos L. Leiva; Juan M. Díaz-Carrasco; Octavio A. Bruzzone; Adriana Cangelosi; Patricia Geoghegan; Mariano E. Fernandez-Miyakawa
      Pages: 83 - 88
      Abstract: Publication date: December 2017
      Source:Anaerobe, Volume 48
      Author(s): Leandro M. Redondo, Enzo A. Redondo, Gabriela C. Dailoff, Carlos L. Leiva, Juan M. Díaz-Carrasco, Octavio A. Bruzzone, Adriana Cangelosi, Patricia Geoghegan, Mariano E. Fernandez-Miyakawa
      Iota toxin is a binary toxin solely produced by Clostridium perfringens type E strains, and is structurally related to CDT from C. difficile and CST from C. spiroforme. As type E causes hemorrhagic enteritis in cattle, it is usually assumed that associated diseases are mediated by iota toxin, although evidence in this regard has not been provided. In the present report, iota toxin intestinal effects were evaluated in vivo using a mouse model. Histological damage was observed in ileal loops treated with purified iota toxin after 4 h of incubation. Luminal iota toxin induced fluid accumulation in the small intestine in a dose dependent manner, as determined by the enteropooling and the intestinal loop assays. None of these changes were observed in the large intestine. These results suggest that C. perfringens iota toxin alters intestinal permeability, predominantly by inducing necrosis and degenerative changes in the mucosal epithelium of the small intestine, as well as changes in intestinal motility. The obtained results suggest a central role for iota toxin in the pathogenesis of C. perfringens type E hemorrhagic enteritis, and contribute to remark the importance of clostridial binary toxins in digestive diseases.

      PubDate: 2017-08-04T19:42:55Z
      DOI: 10.1016/j.anaerobe.2017.07.007
      Issue No: Vol. 48 (2017)
  • A multi-center ring trial for the identification of anaerobic bacteria
           using MALDI-TOF MS
    • Authors: A.C.M. Veloo; H. Jean-Pierre; U.S. Justesen; T. Morris; E. Urban; I. Wybo; H.N. Shah; A.W. Friedrich; T. Morris; H.N. Shah; H. Jean-Pierre; U.S. Justesen; E. Nagy; E. Urban; M. Kostrzewa; A. Veloo; A.W. Friedrich
      Pages: 94 - 97
      Abstract: Publication date: December 2017
      Source:Anaerobe, Volume 48
      Author(s): A.C.M. Veloo, H. Jean-Pierre, U.S. Justesen, T. Morris, E. Urban, I. Wybo, H.N. Shah, A.W. Friedrich, T. Morris, H.N. Shah, H. Jean-Pierre, U.S. Justesen, E. Nagy, E. Urban, M. Kostrzewa, A. Veloo, A.W. Friedrich
      Inter-laboratory reproducibility of Matrix Assisted Laser Desorption Time-of-Flight Mass Spectrometry (MALDI-TOF MS) of anaerobic bacteria has not been shown before. Therefore, ten anonymized anaerobic strains were sent to seven participating laboratories, an initiative of the European Network for the Rapid Identification of Anaerobes (ENRIA). On arrival the strains were cultured and identified using MALDI-TOF MS. The spectra derived were compared with two different Biotyper MALDI-TOF MS databases, the db5627 and the db6903. The results obtained using the db5627 shows a reasonable variation between the different laboratories. However, when a more optimized database is used, the variation is less pronounced. In this study we show that an optimized database not only results in a higher number of strains which can be identified using MALDI-TOF MS, but also corrects for differences in performance between laboratories.

      PubDate: 2017-08-15T20:13:04Z
      DOI: 10.1016/j.anaerobe.2017.07.004
      Issue No: Vol. 48 (2017)
  • Detection of enterotoxin and protease genes among Hungarian clinical
           Bacteroides fragilis isolates
    • Authors: Károly Péter Sárvári; József Sóki; Miklós Iván; Cecília Miszti; Krisztina Latkóczy; Szilvia Zsóka Melegh; Edit Urbán
      Pages: 98 - 102
      Abstract: Publication date: December 2017
      Source:Anaerobe, Volume 48
      Author(s): Károly Péter Sárvári, József Sóki, Miklós Iván, Cecília Miszti, Krisztina Latkóczy, Szilvia Zsóka Melegh, Edit Urbán
      Bacteroides fragilis as a commensal bacterium is a member of the human intestinal flora, but as an opportunistic pathogen it can cause serious infections as well. Some of them, harbouring an enterotoxin gene (bft), may cause diarrhoea mainly in young children. Recently it has been shown that a member of C11 proteases called fragipain (fpn) can activate the enterotoxin, while C10 protease (bfp) is suspected of playing an important role in the invasiveness of the B. fragilis isolates. The objective of this study was to investigate the prevalence and distribution of the bft isotypes in 200 Hungarian B. fragilis isolates collected recently; and in a subset of 72 strains, we wanted to determine the prevalence of bfp1-4 and fpn genes in bft-positive and bft-negative strains. Using the MALDI-TOF MS cfiA identification project file, 19 B. fragilis strains belonging to Division II were identified and the presence of the cfiA gene was confirmed by RT-PCR. Twenty six (13.0%) B. fragilis isolates turned out to be bft gene positive by RT-PCR; 20 isolates harboured bft-1 and six bft-2 isotypes, but no bft-3 isotype containing strains were found. A melting curve analysis and the PCR-RFLP were performed to differentiate between the bft-1 and bft-2 isotypes confirmed by sequencing. Thirty eight strains harboured bfp1, 58 isolates contained bfp2 gene, while 17 isolates proved positive for bfp3. Morever, no bfp4 positive isolate was found, and some of the B. fragilis strains tested harboured two or three bfp isotypes simultaneously. Among the 26 bft-positive strains, 24 contained the fpn gene, which confirms the role of fragipain in the activation of B. fragilis enterotoxin. In experiments, a significant negative correlation between fpn and cfiA was demonstrated (p < 0.000), a positive correlation was found between bfp2 and fpn genes (p = 0.0000803), and a negative correlation between bfp2 and cfiA genes (p = 0.011).

      PubDate: 2017-08-15T20:13:04Z
      DOI: 10.1016/j.anaerobe.2017.07.005
      Issue No: Vol. 48 (2017)
  • Pro-inflammatory cytokine responses in human gingival epithelial cells
           after stimulation with cell wall extract of Aggregatibacter
           actinomycetemcomitans subtypes
    • Authors: Nuntiya Pahumunto; Pareena Chotjumlong; Anupong Makeudom; Suttichai Krisanaprakornkit; Gunnar Dahlen; Rawee Teanpaisan
      Pages: 103 - 109
      Abstract: Publication date: December 2017
      Source:Anaerobe, Volume 48
      Author(s): Nuntiya Pahumunto, Pareena Chotjumlong, Anupong Makeudom, Suttichai Krisanaprakornkit, Gunnar Dahlen, Rawee Teanpaisan
      Varying cytokine responses of human gingival epithelial cells (HGECs) by Aggregatibacter actinomycetemcomitans subtypes have been found. Most studies have used reference strains, whereas a few has evaluated the cytokine expression in response to clinical subtypes of this bacterial species. This study aimed to examine whether there was any difference in cytokine responses of HGECs stimulated with cell wall extract (CWE) from A. actinomycetemcomitans subtypes included clinical strains from Thai adult periodontitis, various serotypes and non-serotypeable strains, strains from deep or shallow pockets, and reference serotype strains. Totally 50 clinical strains and 7 reference strains of A. actinomycetemcomitans were analyzed for the expression of IL-1β, IL-6, IL-8, and TNF-α mRNAs in HGECs by real time-PCR, and the IL-8 concentrations in cell-free supernatant measured using ELISA. An in vitro effect of released IL-8 on neutrophil migration was examined using transwell chambers. Result showed that among four cytokines studied, IL-8 mRNA was highly up-regulated by both clinical and reference strains. Serotype f revealed the highest expression compared to other serotypes. The JP2-like leukotoxin promoter gene and non-serotypeable (NS1 and NS2) demonstrated lower IL-8 responses compared to serotypeable strains, and IL-8 responses upon stimulation with clinical strains from deep pockets were also significantly lower than those isolated from shallow pockets (P < 0.01). Our findings suggest that the clinical isolates of A. actinomycetemcomitans associating with deep pockets, JP2-like leukotoxin promoter gene, NS1, and NS2 may interfere neutrophil function via minimal and immunosuppressing IL-8 responses, which may enhance their survival and virulence.

      PubDate: 2017-08-15T20:13:04Z
      DOI: 10.1016/j.anaerobe.2017.08.001
      Issue No: Vol. 48 (2017)
  • Stability and efficacy of frozen and lyophilized fecal microbiota
           transplant (FMT) product in a mouse model of Clostridium difficile
           infection (CDI)
    • Authors: Zhi-Dong Jiang; Ashley Alexander; Shi Ke; Evangelia M. Valilis; Shaofan Hu; Bingjie Li; Herbert L. DuPont
      Pages: 110 - 114
      Abstract: Publication date: December 2017
      Source:Anaerobe, Volume 48
      Author(s): Zhi-Dong Jiang, Ashley Alexander, Shi Ke, Evangelia M. Valilis, Shaofan Hu, Bingjie Li, Herbert L. DuPont
      Freezing donor fecal microbiota has simplified fecal microbiota transplantation (FMT) in the treatment of recurrent C. difficile infection (CDI). However, the optimal storage time for the frozen FMT products remains unknown. Using an established murine model of CDI, stability and efficacy of frozen and lyophilized FMT product was studied at time points from 2 months to 15 months. DNA was extracted from fecal samples from the mice with identification of specific bacterial species by real-time quantitative PCR (qPCR). FMT product stability and efficacy were measured by occurrence of diarrhea in the challenged mice together with stability of the microbiota composition. The results were analyzed and compared by SAS statistical software. All mice treated with only C. difficile developed diarrhea within 72 h. Mice treated with frozen (n = 5/group), lyophilized (n = 5/group) products stored for ≤ 7-month or fresh FMT product (n = 22) were protected from post C. difficile challenge diarrhea. There was no difference between frozen and lyophilized products (n = 5/group) stored for ≤ 7 months 95% CI 1.00 (0.38–2.64) and 1.00 (0.38–2.64), respectively. Prevention if CDI by frozen and lyophilized product was not different for storage of 9-, 11- and 15-months. qPCR results demonstrated there were no significant quantitative change in Bacteroides and Clostridium species during any of the storage times (P > 0.05). In the present study, frozen and lyophilized FMT products were stored up to 7 months without losing microbiota composition and therapeutic efficacy. The animal model described may be useful to study stability of human microbiota designed for FMT.

      PubDate: 2017-08-15T20:13:04Z
      DOI: 10.1016/j.anaerobe.2017.08.003
      Issue No: Vol. 48 (2017)
  • Antitoxin therapy of natural avian botulism outbreaks occurred in Brazil
    • Authors: Rodrigo O.S. Silva; Sandra Y.M. Gómez; Lilian B. Medeiros; Marcus V.R. Marques; Aila S.G. Silva; Elisabeth N. Mureb; Carlos A. Oliveira Junior; Samantha M. Favoretto; Francisco C.F. Lobato; Nelson R.S. Martins
      Pages: 115 - 117
      Abstract: Publication date: December 2017
      Source:Anaerobe, Volume 48
      Author(s): Rodrigo O.S. Silva, Sandra Y.M. Gómez, Lilian B. Medeiros, Marcus V.R. Marques, Aila S.G. Silva, Elisabeth N. Mureb, Carlos A. Oliveira Junior, Samantha M. Favoretto, Francisco C.F. Lobato, Nelson R.S. Martins
      Botulism commonly affects water birds and it has recently been observed to be emerging in poultry production. In the present work, outbreaks of botulism in wild native species, such as the black-fronted Piping-guan (Aburria jacutinga), wild duck (Cairina moschata) and its crosses with mallard (Anas platyrhynchos), and domestic chickens (Gallus gallus domesticus) are described. Following treatments with a commercial botulism antitoxin CD, 28 (96.5%) out of 29 animals fully recovered after 24–72 h. The antitoxin therapy was shown to be a useful option for the treatment of affected birds, including those that were severely affected.

      PubDate: 2017-08-26T20:44:49Z
      DOI: 10.1016/j.anaerobe.2017.08.005
      Issue No: Vol. 48 (2017)
  • Establishment of valnemulin susceptibility breakpoint against Clostridium
           perfringens in rabbits
    • Authors: Meng-Ting Tao; Yu-Feng Zhou; Jian Sun; Ya-Hong Liu; Xiao-Ping Liao
      Pages: 118 - 120
      Abstract: Publication date: December 2017
      Source:Anaerobe, Volume 48
      Author(s): Meng-Ting Tao, Yu-Feng Zhou, Jian Sun, Ya-Hong Liu, Xiao-Ping Liao
      Susceptibility breakpoints provide fundamental information for rational administration of antibiotics. The present investigation reports the first valnemulin susceptibility breakpoint (MIC<0.25 μg/mL) against Clostridium perfringens infections in rabbits based on the wild-type cutoff (COWT) and the pharmacokinetics/pharmacodynamic (PK/PD) cutoff (COPD). The established susceptibility breakpoint of valnemulin might be useful in resistance surveillance of pleuromutilins and development of clinical breakpoints.

      PubDate: 2017-08-26T20:44:49Z
      DOI: 10.1016/j.anaerobe.2017.08.006
      Issue No: Vol. 48 (2017)
  • Identification and characterization of Clostridium botulinum group III
           field strains by matrix-assisted laser desorption-ionization
           time-of-flight mass spectrometry (MALDI-TOF MS)
    • Authors: Luca Bano; Ilenia Drigo; Elena Tonon; Simone Pascoletti; Cinzia Puiatti; Fabrizio Anniballi; Bruna Auricchio; Florigio Lista; Cesare Montecucco; Fabrizio Agnoletti
      Pages: 126 - 134
      Abstract: Publication date: December 2017
      Source:Anaerobe, Volume 48
      Author(s): Luca Bano, Ilenia Drigo, Elena Tonon, Simone Pascoletti, Cinzia Puiatti, Fabrizio Anniballi, Bruna Auricchio, Florigio Lista, Cesare Montecucco, Fabrizio Agnoletti
      Animal botulism is primarily due to botulinum neurotoxin (BoNT) types C, D or their chimeric variants C/D or D/C, produced by Clostridium botulinum group III, which appears to include the genetically indistinguishable Clostridium haemolyticum and Clostridium novyi. In the present study, we used matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI TOF MS) to identify and characterize 81 BoNT-producing Clostridia isolated in 47 episodes of animal botulism. The instrument's default database, containing no entries for Clostridium botulinum, permitted reliable identification of 26 strains at the genus level. Although supplementation of the database with reference strains enhanced the instrument's ability to identify the neurotoxic strains at the genus level, resolution was not sufficient to recognize field strains at species level. Characterization by MALDI TOF confirmed the well-documented phenotypic and genetic differences between Clostridium botulinum strains of serotypes normally implicated in human botulism (A, B, E, F) and other Clostridium species able to produce BoNTs type C and D. The chimeric and non-chimeric field strains grouped separately. In particular, very low similarity was found between two non-chimeric type C field strains isolated in the same outbreak and the other field strains. This difference was comparable with the differences among the various Clostridia species included in the study. Characterization by MALDI TOF confirmed that BoNT-producing Clostridia isolated from animals are closely related and indistinguishable at the species level from Clostridium haemolyticum and Clostridium novyi reference strains. On the contrary, there seem to be substantial differences among chimeric and some non-chimeric type C strains.

      PubDate: 2017-08-26T20:44:49Z
      DOI: 10.1016/j.anaerobe.2017.08.004
      Issue No: Vol. 48 (2017)
  • Spontaneous C. septicum gas gangrene: A literature review
    • Authors: Ira Srivastava; Michael J. Aldape; Amy E. Bryant; Dennis L. Stevens
      Pages: 165 - 171
      Abstract: Publication date: December 2017
      Source:Anaerobe, Volume 48
      Author(s): Ira Srivastava, Michael J. Aldape, Amy E. Bryant, Dennis L. Stevens
      As the infectious disease paradigm undergoes a subtle shift, unusual infections associated with malignancy and immunosuppression are being increasingly reported. Spontaneous or non-traumatic Clostridium septicum infection is one such unusual infection which has gained prominence. This article aims to understand the pathophysiology, clinical manifestations and current trends in diagnosing and treating this rare but deadly infection. To understand the multifactorial causation of this infection a review of published cases of spontaneous C. septicum gas gangrene was performed and a total of 94 such cases were identified. Several factors were analyzed for each case: age, infection location and underlying illness, presenting signs and symptoms, neutropenia, gross pathology of the colon, antibiotic use, surgical intervention, and survival. A known or occult malignancy was present in 71% patients and an overall mortality of 67% was observed.

      PubDate: 2017-09-05T21:13:36Z
      DOI: 10.1016/j.anaerobe.2017.07.008
      Issue No: Vol. 48 (2017)
  • Immune discrepancies during in vitro granuloma formation in response to
           Cutibacterium (formerly Propionibacterium) acnes infection
    • Authors: Guillaume Ghislain Aubin; Grâce Ada Da Silva; Yoshinobu Eishi; Cédric Jacqueline; Frédéric Altare; Stéphane Corvec; Karim Asehnoune
      Pages: 172 - 176
      Abstract: Publication date: December 2017
      Source:Anaerobe, Volume 48
      Author(s): Guillaume Ghislain Aubin, Grâce Ada Da Silva, Yoshinobu Eishi, Cédric Jacqueline, Frédéric Altare, Stéphane Corvec, Karim Asehnoune
      Cutibacterium (formerly Propionibacterium) acnes is involved in chronic/low-grade pathologies such as sarcoidosis or prosthetic joint infection (PJI). In these diseases, granulomatous structures are frequently observed. In this study, we induced a physiological granulomatous reaction in response to different well-characterized clinical C. acnes isolates in order to investigate the cellular process during granuloma formation. Three C. acnes isolates selected according to their origin (PJI, sarcoidosis and acne) were typed by MLST. All C. acnes isolates generated granulomatous structures in our experimental conditions. The bacterial burden was better controlled by granulomas induced by the sarcoidosis C. acnes isolate. The PJI C. acnes isolate, belonging to CC36, promoted the recruitment of CD8+ lymphocytes inside the granuloma. In contrast, the acne and sarcoidosis C. acnes isolates, belonging to phylotypes IA1/CC18 and IA2/CC28, respectively, generated a higher number of granulomas and promoted the recruitment of CD4+ lymphocytes inside the granuloma. Our results provide new evidence supporting the role of C. acnes in the development of sarcoidosis and new explanations concerning the mechanisms underlying PJI due to C. acnes.

      PubDate: 2017-09-05T21:13:36Z
      DOI: 10.1016/j.anaerobe.2017.08.014
      Issue No: Vol. 48 (2017)
  • Infected breast cyst due to Prevotella buccae resistant to metronidazole
    • Authors: Fernando Cobo; Javier Rodríguez-Granger; Antonio Sampedro; José María Navarro-Marí
      Pages: 177 - 178
      Abstract: Publication date: December 2017
      Source:Anaerobe, Volume 48
      Author(s): Fernando Cobo, Javier Rodríguez-Granger, Antonio Sampedro, José María Navarro-Marí
      Prevotella buccae is a Gram-negative anaerobic rod involved in some human infections. We report the first case of an infected breast cyst in a non-puerperal women due to this pathogen. A 53-year-old woman presented with pain and a cystic lesion in the right breast. Culture of abscess drainage resulted in isolation of P. buccae. High level of resistance to metronidazole was documented. Treatment with drainage and amoxicillin-clavulanate was established, and improvement of this infection was observed.

      PubDate: 2017-09-05T21:13:36Z
      DOI: 10.1016/j.anaerobe.2017.08.015
      Issue No: Vol. 48 (2017)
  • Spatio-temporal variability of the epidemic 027 Clostridium difficile
           strains in France based on MLVA typing
    • Authors: Jeanne Couturier; Catherine Eckert; Frédéric Barbut
      Pages: 179 - 183
      Abstract: Publication date: December 2017
      Source:Anaerobe, Volume 48
      Author(s): Jeanne Couturier, Catherine Eckert, Frédéric Barbut
      MLVA analysis of 103 PCR ribotype 027 strains showed a regional specificity and the persistence of the same clone within a hospital several years apart. Capillary electrophoresis PCR ribotyping led to the identification of seven 027 variant strains and five 176 strains, four of them being implicated in an outbreak.

      PubDate: 2017-09-05T21:13:36Z
      DOI: 10.1016/j.anaerobe.2017.08.007
      Issue No: Vol. 48 (2017)
  • Dietary pomegranate extract and inulin affect gut microbiome
           differentially in mice fed an obesogenic diet
    • Authors: Song Zhang; Jieping Yang; Susanne M. Henning; Rupo Lee; Mark Hsu; Emma Grojean; Rita Pisegna; Austin Ly; David Heber; Zhaoping Li
      Pages: 184 - 193
      Abstract: Publication date: December 2017
      Source:Anaerobe, Volume 48
      Author(s): Song Zhang, Jieping Yang, Susanne M. Henning, Rupo Lee, Mark Hsu, Emma Grojean, Rita Pisegna, Austin Ly, David Heber, Zhaoping Li
      Growing evidence suggests that dysbiosis of gut microbiota is associated with pathogenesis of a variety of human diseases. Using dietary intervention to shape the composition and metabolism of the gut microbiota is increasingly recognized. In the present study, we investigated the effects of polysaccharide inulin and polyphenol-rich pomegranate extract (PomX) alone or in combination on the cecal microbiota composition and function in a diet induced obesity mouse model. Male C57BL/6 mice were randomly divided into four experimental groups and consumed either high-fat/high-sucrose [HF/HS (32% energy from fat, 25% energy from sucrose, 17% energy from protein)] diet, HF/HS diet supplemented with PomX (0.25%), or inulin (9%) or PomX and inulin in combination for 4 weeks. In mice fed the PomX-diet the proportion of Turicibacteraceae and Ruminococcaceae was significantly increased compared to the control HF/HS diet. Supplementation with inulin alone and inulin + PomX combination significantly increased the proportion of Verrucomicrobiaceae (A. muciniphila) and decreased Clostridiaceae. Only mice fed the inulin diet experienced an increase in serum lipopolysaccharide (LPS) and monocyte chemoattractant protein 1 (MCP-1), which was reversed when feeding the inulin + PomX diet. Feeding the inulin + PomX diet was associated with a significant increase in Bifidobacteriaceae and Rikenellaceae, which may have contributed to the reduction of endotoxemia markers. Inulin supplementation showed lower species richness of gut microbiota compared to mice fed with HF/HS or HF/HS/PomX, and the reduction was reversed by the addition of PomX. Inulin alone and in combination with PomX had distinct microbial clusters determined by both weighted and unweighted UniFrac Beta-Diversity principle coordinate analysis. A total of 19 KEGG biological pathways were significantly regulated in the gut microbiota with PomX and inulin alone or combined treatment. Inulin significantly enhanced KEGG infectious disease-related pathway associated with increase of serum LPS and MCP-1. No changes in gene expression of ileal proinflammatory cytokine and tight junction genes were observed in mice treated with PomX and inulin. Our results demonstrated that the gut microbiota and their biological pathways were differentially effected by dietary PomX and inulin fed combined or alone. It is therefore very important to consider the interaction among bioactive components of food when evaluating potential prebiotic effects.

      PubDate: 2017-09-18T08:44:43Z
      DOI: 10.1016/j.anaerobe.2017.08.017
      Issue No: Vol. 48 (2017)
  • Support material dictates the attached biomass characteristics during the
    • Authors: Jasmina Kerčmar; Albin Pintar
      Pages: 194 - 202
      Abstract: Publication date: December 2017
      Source:Anaerobe, Volume 48
      Author(s): Jasmina Kerčmar, Albin Pintar
      Hydrogen is considered to be an ideal energy alternative to replace environmentally burdensome fossil fuels. For its long-term production the immobilized biofilm system is the most promising and to choose the right support material the most challenging. In this respect, the anaerobic up-flow bioreactors packed with four most used support materials (polyethylene, polyurethane, activated carbon and expanded clay) were tested to investigate the crucial bacteria sensitive period-the immobilization process. Seven-day-operation was necessary and sufficient to reach metabolic and microbial stability regardless of support material used. The support material had an influence on the microbial metabolic activity as well as on quantity and quality characteristics of the immobilized microbial community, being polyethylene and expanded clay more appropriate as supports among the materials evaluated; this could be attributed to pH alteration. The obtained results suggest that the support material dictates the outcome of the immobilization process in the anaerobic continuous-flow bioreactor.

      PubDate: 2017-09-23T08:53:45Z
      DOI: 10.1016/j.anaerobe.2017.06.007
      Issue No: Vol. 48 (2017)
  • Improving gene transfer in Clostridium pasteurianum through the isolation
           of rare hypertransformable variants
    • Authors: Alexander Grosse-Honebrink; Katrin M. Schwarz; Hengzheng Wang; Nigel P. Minton; Ying Zhang
      Pages: 203 - 205
      Abstract: Publication date: December 2017
      Source:Anaerobe, Volume 48
      Author(s): Alexander Grosse-Honebrink, Katrin M. Schwarz, Hengzheng Wang, Nigel P. Minton, Ying Zhang
      Effective microbial metabolic engineering is reliant on efficient gene transfer. Here we present a simple screening strategy that may be deployed to isolate rare, hypertransformable variants. The procedure was used to increase the frequency of transformation of the solvent producing organism Clostridium pasteurianum by three to four orders of magnitude.

      PubDate: 2017-09-23T08:53:45Z
      DOI: 10.1016/j.anaerobe.2017.09.001
      Issue No: Vol. 48 (2017)
  • Fermentation properties of isomaltooligosaccharides are affected by human
           fecal enterotypes
    • Authors: Qinqin Wu; Xiong'e Pi; Wei Liu; Huahai Chen; Yeshi Yin; Hongwei D. Yu; Xin Wang; Liying Zhu
      Pages: 206 - 214
      Abstract: Publication date: December 2017
      Source:Anaerobe, Volume 48
      Author(s): Qinqin Wu, Xiong'e Pi, Wei Liu, Huahai Chen, Yeshi Yin, Hongwei D. Yu, Xin Wang, Liying Zhu
      Isomaltooligosaccharides (IMOs) are enzymatically synthesized oligosaccharides that have potential prebiotic effects. Five IMO substrates with 2–16° of polymerization (DP) were studied for their fermentation capacities using human microbiomes in an in vitro batch fermentation model. Eleven fecal slurries belonging to three enterotypes, including the Bacteroides-, Prevotella- and Mixed-type, exhibited different degradation rates for long chain IMOs (DP 7 to 16). In contrast, the degradation rates for short chain IMOs (DP 2 to 6) were not affected by enterotypes. Both 16S rRNA gene sequencing and quantitative PCR demonstrated that, after fermentation, the Bifidobacterium growth with IMOs was primarily detected in the Bacteroides- and Mixed-type (non-Prevotella-type), and to a lesser degree in the Prevotella-type. Interestingly, the Prevotella-type microbiome had higher levels of propionic acid and butyric acid production than non-Prevotella-type microbiome after IMOs fermentation. Moreover, principal coordinate analysis (PCoA) of both denaturing gradient gel electrophoresis (DGGE) profiling and 16S rRNA sequencing data demonstrated that the microbiome community compositions were separately clustered based on IMO chain length, suggesting significant impact of DP on the bacterial community structure. The current results clearly demonstrated that the IMO chain length could modulate the structure and composition of the human colonic microbiome. Different responses to short and long chain IMOs were observed from three human enterotypes, indicating that IMOs may be used as therapeutic substrates for directly altering human colonic bacteria.

      PubDate: 2017-09-23T08:53:45Z
      DOI: 10.1016/j.anaerobe.2017.08.016
      Issue No: Vol. 48 (2017)
  • Molecular analysis of three Clostridium difficile strain genomes isolated
           from pig farm-related samples
    • Authors: I. Martín-Burriel; S. Andrés-Lasheras; F. Harders; R.C. Mainar-Jaime; B. Ranera; P. Zaragoza; V. Falceto; Y. Bolea; E. Kuijper; R. Bolea; A. Bossers; M. Chirino-Trejo
      Pages: 224 - 231
      Abstract: Publication date: December 2017
      Source:Anaerobe, Volume 48
      Author(s): I. Martín-Burriel, S. Andrés-Lasheras, F. Harders, R.C. Mainar-Jaime, B. Ranera, P. Zaragoza, V. Falceto, Y. Bolea, E. Kuijper, R. Bolea, A. Bossers, M. Chirino-Trejo
      Clostridium difficile is an anaerobic spore-forming bacillus that usually causes gastrointestinal disorders in man and other animal species. Most of the strains isolated from animals are toxigenic being the virulent ribotype (RT) 078 predominant in several animal species. Although C. difficile is pathogenic to both humans and animals, there is no direct evidence of zoonosis. Deep genome sequencing provides sufficient resolution to analyse which strains found in animals might be related to human pathogens. So far, there are only a few fully sequenced genomes of C. difficile strains isolated from domestic and wild animals. Using Illumina technology, we have sequenced the genome of three isolates; a strain isolated from the vagina of a sow (5754), one from rat (Rattus spp) intestinal content (RC10) and a third one isolated from environmental rat faeces (RF17). Both, rat and rat faeces were sampled in fattening pig farms. Our study reveals a close genetic relationship of two of these isolates with the virulent strain M120 (RT078) isolated from a human patient. The analysis of the sequences has revealed the presence of antibiotic resistance genes, mobile elements, including the transposon linked with virulence Tn6164, and the similarity of virulence factors between these isolates and human strains. This is the first study focused on the sequencing of C. difficile genomes obtained from wild animals like rats, which can be considered as potential reservoirs for humans and other animal species. This study can help to understand the genome composition and epidemiology of this bacterium species.

      PubDate: 2017-09-30T09:30:50Z
      DOI: 10.1016/j.anaerobe.2017.09.002
      Issue No: Vol. 48 (2017)
  • Molecular epidemiology of Clostridium difficile infection in a Brazilian
           cancer hospital
    • Authors: Cecília Leite Costa; Cibele Barreto Mano de Carvalho; Rafael Holanda González; Markus Andret Cavalcante Gifoni; Ronaldo de Albuquerque Ribeiro; Carlos Quesada-Gómez; Gerly Anne de Castro Brito
      Pages: 232 - 236
      Abstract: Publication date: December 2017
      Source:Anaerobe, Volume 48
      Author(s): Cecília Leite Costa, Cibele Barreto Mano de Carvalho, Rafael Holanda González, Markus Andret Cavalcante Gifoni, Ronaldo de Albuquerque Ribeiro, Carlos Quesada-Gómez, Gerly Anne de Castro Brito
      Clostridium difficile is a Gram-positive spore forming anaerobic bacterium and the main cause of healthcare-associated diarrhea. This study aimed to perform the phenotypic characterization and molecular typing of Clostridium difficile isolates among patients at a cancer hospital in Brazil. During 18 months, 48 diarrheic fecal samples were collected, of these 48% were positive in either one or both of the performed tests: detection of toxins A/B and culture. Clostridium difficile was recovered from four samples (17%). All strains carried toxin A and B genes, and the isolates belonged to PCR-ribotype 014/020, PGFE-type NAP4 and toxinotype XVIII. On the other hand, one isolate belonged to a novel PCR-ribotype, and PFGE-type, likewise to toxinotype IXb. The isolates showed susceptibility to metronidazole, vancomycin and moxifloxacin, and were resistant to ciprofloxacin. Finally, the findings indicate high positivity between the samples tested, suggesting an expressive importance of this infection, including detection of a novel ribotype/PFGE-type of Clostridium difficile, and show for the first time the detection of community-associated Clostridium difficile infection (CA-CDI) in these patients in Northeast Brazil. These data emphasize the importance to a better understanding of the epidemiological situation of this infection in Brazilian hospitals.

      PubDate: 2017-10-14T03:45:39Z
      DOI: 10.1016/j.anaerobe.2017.10.001
      Issue No: Vol. 48 (2017)
  • Evaluation of the genus of Caldicellulosiruptor for production of
           1,2-propanediol from methylpentoses
    • Authors: Eva Maria Ingvadottir; Sean Michael Scully; Johann Orlygsson
      Pages: 86 - 88
      Abstract: Publication date: October 2017
      Source:Anaerobe, Volume 47
      Author(s): Eva Maria Ingvadottir, Sean Michael Scully, Johann Orlygsson
      Caldicellulosiruptor species degrade l-rhamnose and l-fucose to 1,2-propanediol. Six of the nine species within the genus produced 1,2-propanediol from l-rhamnose and three utilized l-fucose to produce the compound. Yields of 1,2-propanediol up to 40.5% of the theoretical yield were observed from methylpentoses catabolism.

      PubDate: 2017-05-02T12:45:07Z
      DOI: 10.1016/j.anaerobe.2017.04.015
      Issue No: Vol. 47 (2017)
  • Antimicrobial susceptibility profiles of oral Treponema species
    • Authors: Kazuko Okamoto-Shibayama; Jin Sekino; Kouki Yoshikawa; Atsushi Saito; Kazuyuki Ishihara
      Abstract: Publication date: Available online 13 October 2017
      Author(s): Kazuko Okamoto-Shibayama, Jin Sekino, Kouki Yoshikawa, Atsushi Saito, Kazuyuki Ishihara
      Treponemes occur in the microflora of the dental plaque. Certain Treponema species that are frequently isolated from chronic periodontitis lesions are involved in its initiation and progression. In addition to mechanical instrumentation, antimicrobial agents are used as an adjunctive treatment modality for periodontitis. Despite its importance for successful antimicrobial treatment, information about susceptibility is limited for Treponema species. The aim of this study was to assess the susceptibility of two Treponema denticola strains, Treponema socranskii, and Treponema vincentii to eleven antimicrobial agents. The minimum inhibitory and minimum bactericidal concentrations of these antimicrobial agents revealed strain-specific variation. Doxycycline, minocycline, azithromycin, and erythromycin were very effective against all Treponema species tested in this study, whereas fluoroquinolones only exhibited an equivalent effectiveness on T. socranskii. The susceptibility of one T. denticola strain, T. socranskii, and T. vincentii to kanamycin was influenced by prior exposure to aerobic conditions. The susceptibility to quinolone drugs varied among strains of T. denticola, although they share an amino acid sequence identity of greater than 99% for DNA gyrase (type II topoisomerase) subunit A. In addition, an ATP-binding cassette (ABC) transporter inhibitor assay for T. denticola indicated that the transport of quinolone drugs is partially related to this transporter, although there may be parallel transport mechanisms. Our results provide important insights into antimicrobial agent-Treponema dynamics and establish a basis for developing an appropriate adjunctive therapy for periodontal disease.

      PubDate: 2017-10-14T03:45:39Z
      DOI: 10.1016/j.anaerobe.2017.10.005
  • The role of purified Clostridium difficile glucosylating toxins in disease
           pathogenesis utilizing a murine cecum injection model
    • Authors: Yongrong Zhang; Zhiyong Yang; Si Gao; Therwa Hamza; Harris G. Yfantis; Michael Lipsky; Hanping Feng
      Abstract: Publication date: Available online 12 October 2017
      Author(s): Yongrong Zhang, Zhiyong Yang, Si Gao, Therwa Hamza, Harris G. Yfantis, Michael Lipsky, Hanping Feng
      Most pathogenic Clostridium difficile produce two major exotoxins TcdA and TcdB, in the absence of which the bacterium is non-pathogenic. While it is important to investigate the role of each toxin in the pathogenesis of C. difficile infection (CDI) using isogenic strains, it is impossible to precisely control the expression levels of individual toxins and exclude bacterial factors that may contribute to the toxins' effects during infection. In this study, we utilized an acute intestinal disease model by injecting purified toxins directly into mouse cecum after a midline laparotomy. We evaluated the physical condition of mice by clinical score and survival, and the intestinal tissue damage and inflammation by histology. Depending on the dose of the toxins, mice developed mild to severe colitis, experienced diarrhea or rapidly died. We found that both purified TcdA and TcdB were able to induce clinical disease, intestinal inflammation, and tissue damage that resembled CDI. TcdA was significantly faster in inducing intestinal inflammation and tissue damage, and was approximately five times more potent than TcdB in terms of inducing severe gut disease and death outcomes in mice. Moreover, we found that the two toxins had significant synergistic effects on disease induction. Comparison of the in vivo toxicity of TcdB from clinical strains revealed that TcdB from an epidemic RT 027 strain was more toxic than the others. Our study thus demonstrates that both TcdA and TcdB, independent of other factors from C. difficile bacterium, are able to cause disease that resembles CDI and highlights the importance of targeting both toxins for vaccines and therapeutics against the disease.

      PubDate: 2017-10-14T03:45:39Z
      DOI: 10.1016/j.anaerobe.2017.10.006
  • Identification of CfiA coding genes in Bacteroides fragilis isolates
           recovered in Argentina. Inconsistencies in CfiA organization and
    • Authors: Mirta R. Litterio; Daniela Cejas; Gabriel Gutkind; Marcela Radice
      Abstract: Publication date: Available online 7 October 2017
      Author(s): Mirta R. Litterio, Daniela Cejas, Gabriel Gutkind, Marcela Radice
      CfiA (CcrA) metallo-β-lactamase is the main carbapenem resistance mechanism in B. fragilis. From cfiA positive isolates detected in a previous surveillance study, 3 displayed resistance to imipenem while the remaining were susceptible. The aim of this study was to identify the cfiA alleles and to analyze the presence of IS elements in their upstream regions. CfiA-1, CfiA-4, CfiA-13, CfiA-19 and CfiA-22 were detected. IS elements belonging to IS21 family and IS942 group were identified upstream to cfiA in the 3 imipenem resistant isolates. We present an exhaustive analysis of cfiA/CfiA registers in databases, illustrating the inconsistencies in both organization and nomenclature. According to this analysis CfiA family comprises nowadays 15 different CfiA variants coded by 24 cfiA sequences. Curation of CfiA database is mandatory, if not new cfiA admission at GenBank will contribute to make this classification more complex.

      PubDate: 2017-10-14T03:45:39Z
      DOI: 10.1016/j.anaerobe.2017.10.003
  • Rifaximin-resistant Clostridium difficile strains isolated from
           symptomatic patients
    • Authors: Reigadas Martin; Bouza
      Abstract: Publication date: Available online 6 October 2017
      Author(s): E. Reigadas, P. Muñoz-Pacheco, L. Alcalá, M. Marín, A. Martin, E. Bouza
      Background Rifaximin has been proposed as an alternative treatment for specific cases of Clostridium difficile infection (CDI) and intestinal decontamination. Rifaximin-resistant C. difficile has occasionally been reported. Antibiotic susceptibility testing relies on anaerobic agar dilution (reference method), which is cumbersome and not routinely used. There is no commercial test for detection of resistance to rifaximin. Objectives To assess resistance to rifaximin by C. difficile and to evaluate the correlation between the results of the rifampicin E-test and susceptibility to rifaximin. Methods We compared the in vitro susceptibility of clinical CDI isolates to rifaximin over a 6-month period using the agar dilution method with susceptibility to rifampicin using the E-test. All isolates were characterized using PCR-ribotyping. Clinical data were recorded prospectively. Results We recovered 276 consecutive C. difficile isolates and found that 32.2% of episodes were caused by rifaximin-resistant strains. The MICs for rifaximin ranged from <0.0009–256 mg/L, with a geometric mean (GM) of 0.256 mg/L, an MIC50/90 of 0.015/>256 mg/L. Rifaximin and rifampicin MICs were comparable, and all strains classed as resistant by agar dilution were correctly classified as resistant by E-test. The most common ribotypes were 001 (37.2%), 078/126 (14.3%), and 014 (12.0%). Ribotype 001 exhibited the highest MICs for rifaximin. Conclusions Resistance to rifaximin was common; resistance rates were higher in ribotype 001 strains. Susceptibility to rifaximin determined by agar dilution correlated with susceptibility to rifampicin determined using the E-test, including rifaximin-resistant strains. Our results suggest that the rifampicin E-test is a valid method for the prediction of rifaximin-resistant C. difficile.

      PubDate: 2017-10-08T02:40:16Z
  • First described case of prosthetic joint infection with Clostridium
    • Authors: Joseph A. McBride; Alana K. Sterkel; William M. Rehrauer; Jeannina A. Smith
      Abstract: Publication date: Available online 1 July 2017
      Author(s): Joseph A. McBride, Alana K. Sterkel, William M. Rehrauer, Jeannina A. Smith
      An orthopedic hardware infection with Clostridium disporicum is described. C. disporicum is a gram positive anaerobic bacillus which can contain two subterminal spores. C. disporicum had not previously been reported in musculoskeletal infections. Gram stains demonstrating gram positive bacilli with two subterminal spores should alert practitioners to the possibility of C. disporicum infection.
      Graphical abstract image

      PubDate: 2017-07-01T15:30:53Z
      DOI: 10.1016/j.anaerobe.2017.06.022
  • Is Clostridium difficile infection a risk factor for subsequent
           bloodstream infection'
    • Authors: Robert J. Ulrich; Kavitha Santhosh; Jill A. Mogle; Vincent B. Young; Krishna Rao
      Abstract: Publication date: Available online 29 June 2017
      Author(s): Robert J. Ulrich, Kavitha Santhosh, Jill A. Mogle, Vincent B. Young, Krishna Rao
      Background Clostridium difficile infection (CDI) is a common nosocomial diarrheal illness increasingly associated with mortality in United States. The underlying factors and mechanisms behind the recent increases in morbidity from CDI have not been fully elucidated. Murine models suggest a mucosal barrier breakdown leads to bacterial translocation and subsequent bloodstream infection (BSI). This study tests the hypothesis that CDI is associated with subsequent BSI in humans. Methods We conducted a retrospective cohort study on 1132 inpatients hospitalized >72 h with available stool test results for toxigenic C. difficile. The primary outcome was BSI following CDI. Secondary outcomes included 30-day mortality, colectomy, readmission, and ICU admission. Unadjusted and adjusted logistic regression models were developed. Results CDI occurred in 570 of 1132 patients (50.4%). BSI occurred in 86 (7.6%) patients. Enterococcus (14%) and Klebsiella (14%) species were the most common organisms. Patients with BSI had higher comorbidity scores and were more likely to be male, on immunosuppression, critically ill, and have a central venous catheter in place. Of the patients with BSI, 36 (42%) had CDI. CDI was not associated with subsequent BSI (OR 0.69; 95% CI 0.44–1.08; P = 0.103) in unadjusted analysis. In multivariable modeling, CDI appeared protective against subsequent BSI (OR 0.57; 95% CI 0.34–0.96; P = 0.036). Interaction modeling suggests a complicated relationship among CDI, BSI, antibiotic exposure, and central venous catheter use. Conclusions In this cohort of inpatients that underwent testing for CDI, CDI was not a risk factor for developing subsequent BSI.
      Teaser Key Points: Clostridium difficile infection is not associated with subsequent bloodstream infection. It is associated with male gender, immunosuppression, comorbid disease burden, and systemic inflammatory response syndrome.

      PubDate: 2017-07-01T15:30:53Z
      DOI: 10.1016/j.anaerobe.2017.06.020
  • A case of severe empyema with acute respiratory distress syndrome caused
           by Slackia exigua requiring veno-venous extracorporeal membrane
    • Authors: M.Y. Man; H.P. Shum; Alan Wu; R.A. Lee; W.W. Yan
      Abstract: Publication date: Available online 28 June 2017
      Author(s): M.Y. Man, H.P. Shum, Alan Wu, R.A. Lee, W.W. Yan
      Slackia exigua (S. exigua) is an obligatory anaerobic coccobacillus under the family of Coriobacteriaceae. It is a rare cause of pyogenic extraoral infections. We report a 58-year-old lady with good past health presented with fulminant community-acquired pneumonia causing acute respiratory distress syndrome caused by S. exigua requiring veno-venous extra-corporeal membrane oxygenation (VV-ECMO). Bacterial identification can be challenging and often require 16 S rRNA and MALDI-TOF MS. The patient was treated with amoxicillin-clavulanic acid according to sensitivity and made significant recovery.

      PubDate: 2017-07-01T15:30:53Z
      DOI: 10.1016/j.anaerobe.2017.06.017
  • Dose-response effects of dietary pequi oil on fermentation characteristics
           and microbial population using a rumen simulation technique (Rusitec)
    • Authors: Andrea Camacho Duarte; Zoey Durmic; Philip E. Vercoe; Alexandre V. Chaves
      Abstract: Publication date: Available online 28 June 2017
      Author(s): Andrea Camacho Duarte, Zoey Durmic, Philip E. Vercoe, Alexandre V. Chaves
      The effect of increasing the concentration of commercial pequi (Caryocar brasiliense) oil on fermentation characteristics and abundance of methanogens and fibrolityc bacteria was evaluated using the rumen simulation technique (Rusitec). In vitro incubation was performed over 15 days using a basal diet consisting of ryegrass, maize silage and concentrate in equal proportions. Treatments consisted of control diet (no pequi oil inclusion, 0 g/kg DM), pequi dose 1 (45 g/kg DM), and pequi dose 2 (91 g/kg DM). After a 7 day adaptation period, samples for fermentation parameters (total gas, methane, and VFA production) were taken on a daily basis. Quantitative real time PCR (q-PCR) was used to evaluate the abundance of the main rumen cellulolytic bacteria, as well as abundance of methanogens. Supplementation with pequi oil did not reduce overall methane production (P = 0.97), however a tendency (P = 0.06) to decrease proportion of methane in overall microbial gas was observed. Increasing addition of pequi oil was associated with a linear decrease (P < 0.01) in dry matter disappearance of maize silage. The abundance of total methanogens was unchanged by the addition of pequi oil, but numbers of those belonging to Methanomassiliicoccaceae decreased in liquid-associated microbes (LAM) samples (P < 0.01) and solid-associated microbes (SAM) samples (P = 0.09) respectively, while Methanobrevibacter spp. increased (P < 0.01) only in SAM samples. Fibrobacter succinogenes decreased (P < 0.01) in both LAM and SAM samples when substrates were supplemented with pequi oil. In conclusion, pequi oil was ineffective in mitigating methane emissions and had some adverse effects on digestibility and selected fibrolytic bacteria.

      PubDate: 2017-07-01T15:30:53Z
      DOI: 10.1016/j.anaerobe.2017.06.013
  • Microbial analysis of root canal and periradicular lesion associated to
           teeth with endodontic failure
    • Authors: R.S. Pereira; V.A.A. Rodrigues; W.T. Furtado; S. Gueiros; G.S. Pereira; M.J. Avila-Campos
      Abstract: Publication date: Available online 27 June 2017
      Author(s): R.S. Pereira, V.A.A. Rodrigues, W.T. Furtado, S. Gueiros, G.S. Pereira, M.J. Avila-Campos
      The quantification of ten microorganisms at the root ends and in the surrounding periradicular lesions was performed. Thirty 3 mm samples root ends and 30 samples of the surrounding chronic periapical infection were collected during apical microsurgery. Samples were triturated, and the bacterial DNA was obtained. The bacterial quantification was performed by using the SYBR Green system. At least one microorganism was detected in all patients. In both the root end and periapical samples, Fusobacterium nucleatum (71.6%), Dialister pneumosintes (58.3%) and Tannerella forsythia (48.3%) were the most prevalent species. Dialister pneumosintes showed statistically significant values in the root end, and F. nucleatum was also significant in the apical periodontitis samples. A statistically significant association between T. forsythia and Porphyromonas gingivalis in the root ends was observed. Bacterial associations from 2 to 7 species were observed in most samples. Extra-radicular and/or intra-radicular infections were present in all teeth with failed endodontic treatment, and showed polymicrobial infection in most cases, with a predominance of F. nucleatum, D. pneumosintes and T. forsythia. When present, Enterococcus faecalis was never found to be the most prevalent species. The presence of a microbial diversity in post-treatment apical periodontitis confirms the polymicrobial and synergistic characteristic of this process. Our results show that the bacterial array associated with the 3 mm root ends and periradicular lesions in post-treatment apical periodontitis are complex and with a high inter-individual variability. These results might be useful to delineate treatment strategies for microbial elimination in apical periodontitis. Further studies are necessary to elucidate the role of these microorganisms in endodontic treatment failures.

      PubDate: 2017-07-01T15:30:53Z
      DOI: 10.1016/j.anaerobe.2017.06.016
  • Prevalence of Clostridium perfringens toxin in patients suspected of
           having antibiotic-associated diarrhea
    • Authors: Young Jin Kim; Si Hyun Kim; Junggu Ahn; Soongmoon Cho; Dongchun Kim; Kwanghyun Kim; Heegun Lee; Hyunwoo Son; Hee Joo Lee; Dongeun Yong; Jun Yong Choi; Hye Ran Kim; Jeong Hwan Shin
      Abstract: Publication date: Available online 26 June 2017
      Author(s): Young Jin Kim, Si Hyun Kim, Junggu Ahn, Soongmoon Cho, Dongchun Kim, Kwanghyun Kim, Heegun Lee, Hyunwoo Son, Hee Joo Lee, Dongeun Yong, Jun Yong Choi, Hye Ran Kim, Jeong Hwan Shin
      Background Although Clostridium perfringens has been reported as a cause of antibiotic-associated diarrhea (AAD), it is uncommon to detect this pathogen in clinical microbiology laboratories in Korea. The aim of this study was to investigate the prevalence of C. perfringens toxin in patients suspected of having AAD. Methods A total of 135 stool specimens submitted to a clinical microbiology laboratory for C. difficile toxin assay were tested. We tried to detect both C. difficile and C. perfringens toxins using the Seeplex Diarrhea ACE Detection kit (Seegene, Seoul, Korea). We evaluated the prevalence of 10 bacteria and 5 viruses. Results A total of 40 Clostridium spp. were detected in 34 specimens (29.6%). The C. perfringens toxin was detected in 14 of 135 specimens (10.4%), while C. difficile toxin was detected in 26 specimens (19.3%). Other bacteria and viruses, including 8 Aeromonas spp., were detected in 15 specimens. All tests were negative in 92 of the 135 specimens (68.1%). Conclusion Clostridium. perfringens toxin is relatively common, and we should consider the possibility of its presence in patients suspected of having AAD, especially if C. difficile tests are negative.

      PubDate: 2017-07-01T15:30:53Z
      DOI: 10.1016/j.anaerobe.2017.06.015
  • Actinomyces radicidentis and Actinomyces haliotis, coccoid Actinomyces
           species isolated from the human oral cavity
    • Authors: Rolf Claesson; Ulf Sjögren; Anders Esberg; Malin Brundin; Margareta Granlund
      Abstract: Publication date: Available online 21 June 2017
      Author(s): Rolf Claesson, Ulf Sjögren, Anders Esberg, Malin Brundin, Margareta Granlund
      There are few reports on the bacterial species Actinomyces radicidentis in the literature. In this study, putative A. radicidentis isolates were collected from 16 root canal samples from 601 examined patients. The isolates were examined by biochemical tests, 16S rRNA gene sequencing, Arbitrarily-primed (AP-) PCR, antibiotic susceptibility testing, and MALDI-TOF analyses. In parallel, two A. radicidentis reference strains and two putative A. radicidentis isolates from United Kingdom were tested. Sixteen of the 18 isolates were confirmed as A. radicidentis. The remaining two isolates, both of which were isolated from root canals (one from Sweden and the other from the UK), but were identified as Actinomyces haliotis by sequencing ∼ 1300 base pairs of the 16S rRNA-gene. This isolates had a divergent, but between them similar, AP-PCR pattern, and a common distribution of sequence signatures in the 16S rRNA gene, but were not identified by MALDI-TOF. A. haliotis is a close relative to A. radicidentis, hitherto only been described from a sea-snail. The identity of A. haliotis was confirmed by a phylogenetic tree based on 16S rRNA gene sequences with species specific sequences included, and by additional biochemical tests. The examined bacteria exhibited similar antibiotic susceptibility patterns when tested for 10 separate antibiotic classes with E-tests (bioMérieux). The MIC90 for β-lactams (benzylpenicillin and cefuroxime) and vancomycin was 0.5 mg/L, for colistin and ciprofloxacin 8 mg/mL and for the other antibiotic classes ≤ 25 mg/mL The isolation of A. haliotis from infected dental root canals cast doubt on the accepted opinion that all Actinomyces infections have an endogenous source.

      PubDate: 2017-07-01T15:30:53Z
      DOI: 10.1016/j.anaerobe.2017.06.011
  • Temporal microbiota changes of high-protein diet intake in a rat model
    • Authors: Chunlong Mu; Yuxiang Yang; Zhen Luo; Weiyun Zhu
      Abstract: Publication date: Available online 17 June 2017
      Author(s): Chunlong Mu, Yuxiang Yang, Zhen Luo, Weiyun Zhu
      Alterations of specific microbes serve as important indicators that link gut health with specific diet intake. Although a six-week high-protein diet (45% protein) upregulates the pro-inflammatory response and oxidative stress in colon of rats, the dynamic alteration of gut microbiota remains unclear. To dissect temporal changes of microbiota, dynamic analyses of fecal microbiota were conducted using a rat model. Adult rats were fed a normal-protein diet or an HPD for 6 weeks, and feces collected at different weeks were used for microbiota and metabolite analysis. The structural alteration of fecal microbiota was observed after 4 weeks, especially for the decreased appearance of bands related to Akkermansia species. HPD increased numbers of Escherichia coli while decreased Akkermansia muciniphila, Bifidobacterium, Prevotella, Ruminococcus bromii, and Roseburia/Eubacterium rectale (P < 0.05), compared to the normal-protein diet. HPD also decreased the copies of genes encoding butyryl-CoA:acetate CoA-transferase and and Prevotella-associated methylmalonyl-CoA decarboxylase α-subunit (P < 0.05). The concentrations of acetate, propionate, and butyrate were decreased by HPD (P < 0.05). Additionally, HPD tended to decrease (P = 0.057) the concentration of IgG in the colonic lumen, which was positively correlated with fecal butyrate at week 6 (P < 0.05). Collectively, this study found the temporal alteration of fecal microbiota related to the decreased numbers and activity of propionate- and butyrate-producing bacteria in feces after the HPD. These findings may provide important reference for linking changes of specific fecal microbes with gut health under high-protein diet.
      Graphical abstract image

      PubDate: 2017-06-21T15:01:25Z
      DOI: 10.1016/j.anaerobe.2017.06.003
  • Changes in faecal bacteria during fattening in finishing swine
    • Authors: T. Ban-Tokuda; S. Maekawa; T. Miwa; S. Ohkawara; H. Matsui
      Abstract: Publication date: Available online 10 June 2017
      Author(s): T. Ban-Tokuda, S. Maekawa, T. Miwa, S. Ohkawara, H. Matsui
      Body fat accumulation in mice and human is linked to the percentage of Firmicutes and Bacteroidetes, two bacterial phyla dominant in the large intestine. However, little is known about the relationship between the composition of the gut microbiota and fattening in pig. This study aimed to investigate the abundance of Firmicutes, Bacteroidetes, and Bacteroides, which is the major genus within Bacteroidetes, in porcine faeces during fattening. Ten 4-month-old crossbred pigs were given free access to commercial feed for fattening and water for 14 weeks. Daily feed intake and body weight were measured every 2 weeks. Faecal samples were collected at 0, 4, 8, and 14 weeks, and plasma samples were collected every 2 weeks. Daily feed intake increased until 8 weeks, and then decreased. Body weight increased with fattening during the experimental period. Feed efficiency showed high values at 0–4 and 6–8 weeks. The level of Firmicutes increased (P < 0.05), whereas those of Bacteroides and Bacteroidetes decreased (P < 0.05) with fattening. The total short chain fatty acid content in the faeces increased (P < 0.05) with fattening until 8 weeks and then decreased (P < 0.05) at 14 weeks. There were no significant relationships between the level of Firmicutes and feed intake or plasma leptin concentration. The levels of Bacteroidetes and Bacteroides correlated with feed intake, body weight, and plasma leptin or plasma urea nitrogen (PUN) concentration. Our results suggested that the level of Firmicutes increased and those of Bacteroidetes and Bacteroides decreased with increase in feed intake and body weight, similar to previous results obtained for mice and human. However, energy extraction from feed was not influenced by compositional alteration of gut flora, because daily gain and feed efficiency did not show high values towards the end of the fattening period. Manipulating the gut microbiota might help improve fattening performance, although further studies are necessary to understand the relationships between the composition of gut microbiota and energy absorption.

      PubDate: 2017-06-12T14:33:00Z
      DOI: 10.1016/j.anaerobe.2017.06.006
  • The gut bacterium and pathobiont Bacteroides vulgatus activates NF-κB in
           a human gut epithelial cell line in a strain and growth phase dependent
    • Authors: Páraic Ó Cuív; Tomas de Wouters; Rabina Giri; Stanislas Mondot; Wendy J. Smith; Hervé M. Blottière; Jakob Begun; Mark Morrison
      Abstract: Publication date: Available online 3 June 2017
      Author(s): Páraic Ó Cuív, Tomas de Wouters, Rabina Giri, Stanislas Mondot, Wendy J. Smith, Hervé M. Blottière, Jakob Begun, Mark Morrison
      The gut microbiota is increasingly implicated in the pathogenesis of Crohn's disease (CD) and ulcerative colitis (UC) although the identity of the bacteria that underpin these diseases has remained elusive. The pathobiont Bacteroides vulgatus has been associated with both diseases although relatively little is known about how its growth and functional activity might drive the host inflammatory response. We identified an ATP Binding Cassette (ABC) export system and lipoprotein in B. vulgatus ATCC 8482 and B. vulgatus PC510 that displayed significant sequence similarity to an NF-κB immunomodulatory regulon previously identified on a CD-derived metagenomic fosmid clone. Interestingly, the ABC export system was specifically enriched in CD subjects suggesting that it may be important for colonization and persistence in the CD gut environment. Both B. vulgatus ATCC 8482 and PC510 activated NF-κB in a strain and growth phase specific manner in a HT-29/kb-seap-25 enterocyte like cell line. B. vulgatus ATCC 8482 also activated NF-κB in Caco-2-NF-κBluc enterocyte like and LS174T-NF-κBluc goblet cell like cell lines and induced NF-κB-p65 subunit nuclear translocation and IL-6, IL-8, CXCL-10 and MCP-1 gene expression. Despite this, NF-κB activation was not coincident with maximal expression of the ABC exporter or lipoprotein in B. vulgatus PC510 suggesting that the regulon may be necessary but not sufficient for the immunomodulatory effects.

      PubDate: 2017-06-06T14:11:11Z
      DOI: 10.1016/j.anaerobe.2017.06.002
  • Quantification, isolation and characterization of Bifidobacterium from the
           vaginal microbiomes of reproductive aged women
    • Authors: Aline C. Freitas; Janet E. Hill
      Abstract: Publication date: Available online 25 May 2017
      Author(s): Aline C. Freitas, Janet E. Hill
      The vaginal microbiome plays an important role in women's reproductive health. Imbalances in this microbiota, such as the poorly defined condition of bacterial vaginosis, are associated with increased susceptibility to sexually transmitted infections and negative reproductive outcomes. Currently, a “healthy” vaginal microbiota in reproductive aged women is understood to be dominated by Lactobacillus, although “atypical” microbiomes, such as Bifidobacterium-dominated profiles, have been described. Despite these observations, vaginal bifidobacteria remain relatively poorly characterized, and questions remain regarding their actual abundance in the microbiome. In this study, we used quantitative PCR to confirm the relative abundance of Bifidobacterium in the vaginal microbiomes of healthy reproductive aged women (n = 42), previously determined by deep sequencing. We also isolated and phenotypically characterized vaginal bifidobacteria (n = 40) in the context of features thought to promote reproductive health. Most isolates were identified as B. breve or B. longum based on cpn60 barcode sequencing. Fermentation patterns of vaginal bifidobacteria did not differ substantially from corresponding type strains of gut or oral origin. Lactic acid was produced by all vaginal isolates, with B. longum strains producing the highest levels, but only 32% of isolates produced hydrogen peroxide. Most vaginal bifidobacteria were also able to tolerate high levels of lactic acid (100 mM) and low pH (4.5 or 3.9), conditions typical of vaginal fluid of healthy women. Most isolates were resistant to metronidazole but susceptible to clindamycin, the two most common antibiotics used to treat vaginal dysbiosis. These findings demonstrate that Bifidobacterium is the dominant member of some vaginal microbiomes and suggest that bifidobacteria have the potential to be as protective as lactobacilli according to the current understanding of a healthy vaginal microbiome.

      PubDate: 2017-05-27T13:18:29Z
      DOI: 10.1016/j.anaerobe.2017.05.012
  • Rumen microbial and fermentation characteristics are affected differently
           by acarbose addition during two nutritional types of simulated severe
           subacute ruminal acidosis in vitro
    • Authors: Yue Wang; Junhua Liu; Yuyang Yin; Weiyun Zhu; Shengyong Mao
      Abstract: Publication date: Available online 7 April 2017
      Author(s): Yue Wang, Junhua Liu, Yuyang Yin, Weiyun Zhu, Shengyong Mao
      Little information is available on whether or not the effect of an alpha-glucosidase inhibitor on the prevention of ruminal acidosis is influenced by the type of diet during ruminant feeding. This study was conducted to explore the effect of acarbose addition on the prevention of severe subacute ruminal acidosis induced by either cracked wheat or beet pulp in vitro. Cracked wheat and beet pulp were fermented in vitro by rumen microorganisms obtained from three dairy cows. When cracked wheat was used as the substrate and fermented for 24 h, compared with the control, acarbose addition decreased the concentrations of acetate, propionate, butyrate, total volatile fatty acids, and lactate (P < 0.05), while linearly increasing the ratio of acetate to propionate, pH value and, the ammonia-nitrogen level (P < 0.05). Applying Illumina MiSeq sequencing of a fragment of the 16S rRNA gene revealed that the relative abundance of Firmicutes and Bacteroidetes as well as the ACE (abundance-based coverage estimator) value, Chao 1 value, and Shannon index increased significantly (P < 0.05), while there was a significant reduction (P < 0.05) in the relative abundance of Tenericutes as well as Proteobacteria after adding acarbose compared to the control. On the other hand, when beet pulp was used as the substrate, acarbose addition had no significant effects (P > 0.05) on the fermentation parameters and the Chao 1 value, the Shannon index, and the proportion of Firmicutes and Bacteroidetes. In general, these findings indicate that acarbose had more effects on ruminal fermentation when wheat was used as the substrate, whereas it exhibited little effect on ruminal fermentation when beet pulp was used as the substrate.

      PubDate: 2017-04-11T11:45:07Z
      DOI: 10.1016/j.anaerobe.2017.04.003
  • The effect of penicillin administration in early life on murine gut
           microbiota and blood lymphocyte subsets
    • Authors: Jaroslaw Daniluk; Urszula Daniluk; Malgorzata Rusak; Milena Dabrowska; Joanna Reszec; Magdalena Garbowicz; Kinga Humińska; Andrzej Dabrowski
      Abstract: Publication date: Available online 18 March 2017
      Author(s): Jaroslaw Daniluk, Urszula Daniluk, Malgorzata Rusak, Milena Dabrowska, Joanna Reszec, Magdalena Garbowicz, Kinga Humińska, Andrzej Dabrowski
      Background and aim Antibiotics have many beneficial effects but their uncontrolled use may lead to increased risk of serious diseases in the future. Our hypothesis is that an early antibiotic exposition may affect immune system by altering gut microbiota. Therefore, the aim of the study was to determine the effect of penicillin treatment on gut microorganisms and immune system of mice. Methods: 21-days old C57BL6/J/cmdb male mice were treated with low-dose of penicillin (study group) or water only (control group) for 4 weeks. Tissue and stool samples for histology or microbiome assessment and peripheral blood for CBC and flow cytometry evaluation were collected. Results: We found high variability in microbiota composition at different taxonomic levels between littermate mice kept in the same conditions, independently of treatment regimen. Interestingly, low-dose of penicillin caused significant increase of Parabacteroides goldsteinii in stool and in colon tissue in comparison to control group (9.5% vs. 4.9%, p = 0.008 and 10.7% vs. 6.1%, p = 0.008, respectively). Moreover, mice treated with penicillin demonstrated significantly elevated percentage of B cells (median 10.5% vs 8.0%, p = 0.01) and decrease in the percentage of total CD4+ cell (median 75.4% vs 82.5%, p = 0.0039) with subsequent changes among subsets - increased percentage of regulatory T cells (Treg), T helper 1 (Th1) and T helper 2 (Th2) cells. Conclusion: Our study showed significant effect of penicillin on B and T cells in peripheral blood of young mice. This effect may be mediated through changes in gut microbiota represented by the expansion of Parabacteroides goldsteinii.

      PubDate: 2017-03-20T21:19:39Z
      DOI: 10.1016/j.anaerobe.2017.03.015
  • Effect of operating temperature on anaerobic digestion of the Brazilian
           waterweed Egeria densa and its microbial community
    • Authors: Keiko Watanabe; Mitsuhiko Koyama; Junko Ueda; Syuhei Ban; Norio Kurosawa; Tatsuki Toda
      Abstract: Publication date: Available online 16 March 2017
      Author(s): Keiko Watanabe, Mitsuhiko Koyama, Junko Ueda, Syuhei Ban, Norio Kurosawa, Tatsuki Toda
      To develop an effective treatment for the globally invasive Brazilian waterweed Egeria densa, anaerobic digestion was observed at 37 °C, 55 °C, and 65 °C. The average methane production rate at 55 °C was 220 mL L−1 day−1, which was two-fold that at 37 °C and 65 °C. Volatile fatty acid accumulation was detected under thermophilic conditions; however, although there was methane production, the system did not shutdown. The microbial communities differed between mesophilic (37 °C) and thermophilic (55 °C and 65 °C) conditions. A bacterial community consisting of the phyla Bacteroidetes (43%), Firmicutes (37%), Proteobacteria (9%), Synergistetes (5%), Spirochaetes (1%), and unclassified bacteria (5%) were detected under mesophilic condition. In contrast, the phylum Firmicutes was dominant under thermophilic conditions. In the archaeal community, Methanosaeta concilii (40%), Methanolinea sp. (17%), and unclassified euryarchaeota (43%) were detected under mesophilic condition. Methanosarcina thermophila (87% at 55 °C, 54% at 65 °C) and Methanothermobacter thermautotrophicus (13% at 55 °C, 46% at 65 °C) were detected under thermophilic conditions. At both 37 °C and 55 °C, acetoclastic methanogenesis likely occurred because of the lower abundance of hydrogenotrophic methanogens. At 65 °C, the growth of the acetoclastic methanogen Methanosarcina thermophila was limited by the high temperature, therefore, acetate oxidation and hydrogenotrophic methanogenesis may have occurred.

      PubDate: 2017-03-20T21:19:39Z
      DOI: 10.1016/j.anaerobe.2017.03.014
  • Characterization of vaginal Lactobacillus species by rplK -based multiplex
           qPCR in Russian women
    • Authors: Vladimir V. Demkin; Stanislav I. Koshechkin
      Abstract: Publication date: Available online 14 March 2017
      Author(s): Vladimir V. Demkin, Stanislav I. Koshechkin
      We describe a multiplex qPCR assay for identification and quantitative assessment of a set of vaginal Lactobacillus species, including L. acidophilus, L. crispatus, L. gasseri, L. helveticus, L. iners, and L. jensenii. The assay extends the previously developed qPCR method for Lactobacillus detection and total quantification based on targeting the rplK gene. Both assays use only single pair of primers and a set of probes combined in three reactions, comprising a vaginal Lactobacillus diagnostic assay panel. The utility of the diagnostic panel was evaluated by analyzing of vaginal swab specimens from 145 patients with different status of vaginal health. Most frequently, only one Lactobacillus species was dominant (68,9%), mostly L. crispatus (18,6%) or L. iners (33,1%), but two or three Lactobacillus species were also being simultaneously detected (24,9%). The diagnostic panel will facilitate investigations of the role of Lactobacillus species in the health of the female reproductive system and promote studies of variability of the vaginal microbiota.

      PubDate: 2017-03-20T21:19:39Z
      DOI: 10.1016/j.anaerobe.2017.03.011
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