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BIOLOGY (1316 journals)            First | 1 2 3 4 5 6 7 8 | Last

Economics & Human Biology     Hybrid Journal  
Ecoprint : An International Journal of Ecology     Open Access  
Ecoscience     Full-text available via subscription   (Followers: 2)
Educational Technology Research and Development     Partially Free   (Followers: 132)
Egyptian Journal of Biology     Open Access  
Egyptian Journal of Histology     Partially Free   (Followers: 1)
Egyptian Journal of Natural History     Open Access  
EJNMMI Research     Open Access   (Followers: 1)
Electromagnetic Biology and Medicine     Hybrid Journal   (Followers: 1)
eLife     Open Access   (Followers: 14)
el–Hayah     Open Access   (Followers: 1)
Embo Molecular Medicine     Open Access   (Followers: 3)
EMBO reports     Full-text available via subscription   (Followers: 15)
Emotion Review     Hybrid Journal   (Followers: 10)
Endocrine Connections     Open Access   (Followers: 2)
Engineering & Technology     Hybrid Journal   (Followers: 15)
Engineering Economist, The     Hybrid Journal   (Followers: 2)
Engineering in Life Sciences     Hybrid Journal   (Followers: 3)
Engineering Optimization     Hybrid Journal   (Followers: 5)
Ensaios e Ciência: Ciências Biológicas, Agrárias e da Saúde     Open Access  
Environmental Biology of Fishes     Hybrid Journal   (Followers: 3)
Environmental Biosafety Research     Hybrid Journal   (Followers: 1)
Environmental Microbiology     Hybrid Journal   (Followers: 7)
Environmental Science & Technology     Full-text available via subscription   (Followers: 225)
Enzyme and Microbial Technology     Hybrid Journal   (Followers: 5)
Epidemiology & Infection     Hybrid Journal   (Followers: 12)
EPMA Journal     Open Access  
ESHRE Monographs     Hybrid Journal  
Ethiopian Journal of Biological Sciences     Open Access   (Followers: 2)
Ethnobiology and Conservation     Open Access   (Followers: 2)
Ethnobotany Research & Applications : a journal of plants, people and applied research     Open Access   (Followers: 5)
Ethology     Hybrid Journal   (Followers: 2)
Ethology Ecology & Evolution     Hybrid Journal   (Followers: 7)
Eukaryotic Cell     Full-text available via subscription   (Followers: 6)
EuPA Open Proteomics     Open Access   (Followers: 1)
EURASIP Journal on Bioinformatics and Systems Biology     Open Access   (Followers: 6)
European Journal of Cell Biology     Hybrid Journal   (Followers: 3)
European Journal of Neuroscience     Hybrid Journal   (Followers: 22)
European Journal of Phycology     Hybrid Journal   (Followers: 5)
European Journal of Protistology     Hybrid Journal   (Followers: 2)
European Journal of Soil Biology     Hybrid Journal   (Followers: 1)
European Online Journal of Natural and Social Sciences     Open Access   (Followers: 11)
European Scientific Journal     Open Access   (Followers: 2)
Evidência - Ciência e Biotecnologia - Interdisciplinar     Open Access  
EvoDevo     Open Access   (Followers: 1)
Evolução e Conservação da Biodiversidade     Open Access  
Evolution     Partially Free   (Followers: 50)
Evolution and Human Behavior     Hybrid Journal   (Followers: 8)
Evolutionary Applications     Open Access   (Followers: 2)
Evolutionary Bioinformatics     Open Access   (Followers: 14)
Evolutionary Biology     Hybrid Journal   (Followers: 15)
Evolutionary Computation     Hybrid Journal   (Followers: 9)
Experimental & Molecular Medicine     Open Access   (Followers: 2)
Experimental and Applied Acarology     Hybrid Journal   (Followers: 1)
Experimental Cell Research     Hybrid Journal   (Followers: 3)
Expert Opinion on Biological Therapy     Hybrid Journal   (Followers: 10)
Expert Opinion on Environmental Biology     Partially Free  
Expert Review of Proteomics     Full-text available via subscription   (Followers: 2)
Extreme Life, Biospeology & Astrobiology - International Journal of the Bioflux Society     Full-text available via subscription   (Followers: 2)
Extremophiles     Hybrid Journal  
F1000Research     Open Access   (Followers: 3)
Familial Cancer     Hybrid Journal   (Followers: 1)
Fatigue & Fracture of Engineering Materials and Structures     Hybrid Journal   (Followers: 12)
Fauna Norvegica     Open Access  
Febs Journal     Hybrid Journal   (Followers: 8)
Feddes Repertorium     Hybrid Journal  
Fems Yeast Research     Hybrid Journal   (Followers: 10)
Field Mycology     Full-text available via subscription   (Followers: 1)
Fish & Shellfish Immunology     Hybrid Journal   (Followers: 6)
Fitoterapia     Hybrid Journal   (Followers: 4)
Fly     Full-text available via subscription  
Folia Biologica     Full-text available via subscription  
Folia Biologica et Oecologica     Open Access   (Followers: 1)
Folia Histochemica et Cytobiologica     Open Access  
Folia Malacologica     Open Access  
Folia Microbiologica     Hybrid Journal   (Followers: 1)
Folia Primatologica     Full-text available via subscription   (Followers: 1)
Food and Bioproducts Processing     Hybrid Journal   (Followers: 1)
Forest Pathology     Hybrid Journal   (Followers: 1)
Forschung     Hybrid Journal  
Foundations of Physics     Hybrid Journal   (Followers: 1)
Free Radical Biology and Medicine     Hybrid Journal   (Followers: 5)
Free Radical Research     Hybrid Journal   (Followers: 2)
Freshwater Reviews     Full-text available via subscription   (Followers: 3)
Freshwater Science     Full-text available via subscription   (Followers: 6)
Frontiers in Ecology and Evolution     Open Access   (Followers: 2)
Frontiers in Evolutionary Neuroscience     Open Access   (Followers: 1)
Frontiers in Life Science     Hybrid Journal  
Frontiers in Marine Science     Open Access  
Frontiers in Neurogenesis     Open Access  
Frontiers in Neuroprosthetics     Open Access  
Frontiers of Biogeography     Open Access   (Followers: 1)
Frontiers of Biology     Hybrid Journal   (Followers: 1)
Frontiers of Environmental Science & Engineering     Hybrid Journal   (Followers: 3)
Fruits     Full-text available via subscription  
Functional & Integrative Genomics     Hybrid Journal   (Followers: 5)
Fundamental and Applied Limnology / Archiv für Hydrobiologie     Full-text available via subscription   (Followers: 1)
Fungal Biology     Hybrid Journal   (Followers: 4)
Fungal Biology Reviews     Full-text available via subscription   (Followers: 4)
Fungal Diversity     Hybrid Journal   (Followers: 2)

  First | 1 2 3 4 5 6 7 8 | Last

Journal Cover Anaerobe
   [6 followers]  Follow    
   Hybrid Journal Hybrid journal (It can contain Open Access articles)
     ISSN (Print) 1075-9964 - ISSN (Online) 1095-8274
     Published by Elsevier Homepage  [2563 journals]   [SJR: 0.828]   [H-I: 39]
  • Chronic botulism in a Saxony dairy farm: Sources, predisposing factors,
           development of the disease and treatment possibilities
    • Abstract: Publication date: August 2014
      Source:Anaerobe, Volume 28
      Author(s): Monika Krüger , Jürgen Neuhaus , Anke Große Herrenthey , M. Mourat Gökce , Wieland Schrödl , Awad A. Shehata
      The aim of this study is to investigate Clostridium botulinum at a Saxony dairy farm with 159 cows and 18 heifers. The animals exhibited clinical symptoms of chronic botulism. To determine the source of the infection, feces, blood, organs, and gastrointestinal fluids of dead or euthanized cows; as well as soil, water, silage and manure were tested for C. botulinum spores and BoNTs using ELISA. BoNT/C and C. botulinum type C were detected in 53% and 3% of tested animals, respectively, while BoNT/D and C. botulinum type D were detected in 18% of the animals. C. botulinum also was detected in organs, gastrointestinal fluids, drinking water and manure. To evaluate possible treatments, animals were given Jerusalem artichoke syrup (JAS), Botulism vaccine (formalinised aluminum hydroxide gel adsorbed toxoid of C. botulinum types C and D) or a suspension of Enterococcus faecalis. After four weeks treatment with JAS, BoNT/C and C. botulinum type C were not detected in feces. In contrast, BoNT/D and C. botulinum type D were not significantly influenced by the JAS treatment. Vaccination with botulism vaccine and the E. faecalis suspension significantly decreased BoNT/D and C. botulinum type D. A significant increase of Enterococci was detected in animals treated with E. faecalis. Interestingly, there was a negative correlation between the detection of both BoNT and C. botulinum with the concentration of Enterococci in feces. Although C. botulinum C and D antibodies increased significantly (p < 0.0001) after vaccination with the botulism vaccine, the reduction of C. botulinum and BoNT in feces did not result in recovery of the animals because they were deficient of trace elements [manganese (Mn), cobalt (Co), copper (Cu) and selenium (Se)]. Animals treated with trace elements recovered. It appears that intestinal microbiota dysbiosis and trace element deficiency could explain the extensive emergence of chronic Botulism.

      PubDate: 2014-07-26T18:45:28Z
  • Probiotic properties of Pediococcus strains isolated from jeotgals, salted
           and fermented Korean sea-food
    • Abstract: Publication date: August 2014
      Source:Anaerobe, Volume 28
      Author(s): Kang Wook Lee , Ji Yeong Park , Hyun Deok Sa , Ji Hee Jeong , Dong Eun Jin , Ho Jin Heo , Jeong Hwan Kim
      Three Pediococcus pentosaceus strains were isolated from jeotgals, salted and fermented Korean sea-foods, and their probiotic potentials were examined. After 2 h exposure to pH 3.0, P. pentosaceus F66 survived with the survival ratio of 32.6% followed by P. pentosaceus D56 (17.2%) and P. pentosaceus A24 (7.5%). P. pentosaceus F66 also survived better (26.6%) than P. pentosaceus A24 (13.7%) and P. pentosaceus D56 (5.8%) after 2 h exposure to 0.3% bile salts. Three strains grew slowly on MRS broth with 15% NaCl (w/v), reaching the OD600 values of 0.4–0.8 in 36 h. They adhered to Caco-2 cells (10.9–13.9 CFU/cell) with similar degree of adherence of a positive control, L acto bacillus rhamnosus GG (12.8 ± 0.5 CFU/cell). Three strains possess some desirable enzyme activities such as β-galactosidase, α-glucosidase, β-glucosidase, and N-acetyl-β-glucosidase. From these results, P. pentosaceus F66 seems qualified as a probiotic and can be utilized for fermented foods including jeotgals.

      PubDate: 2014-07-26T18:45:28Z
  • Production of recombinant botulism antigens: A review of expression
    • Abstract: Publication date: August 2014
      Source:Anaerobe, Volume 28
      Author(s): G.M.S.G. Moreira , C.E.P. Cunha , F.M. Salvarani , L.A. Gonçalves , P.S. Pires , F.R. Conceição , F.C.F. Lobato
      Botulism is a paralytic disease caused by intoxication with neurotoxins produced by Clostridium botulinum. Despite their similar mechanism of action, the botulinum neurotoxins (BoNT) are classified in eight serotypes (A to H). As to veterinary medicine, the impact of this disease is essentially economic, since different species of production animals can be affected, especially by BoNT/C and D. In human health, botulism is feared in a possible biological warfare, what would involve mainly the BoNT/A, B, E and F. In both cases, the most effective way to deal with botulism is through prevention, which involves vaccination. However, the current vaccines against this disease have several drawbacks on their process of production and, besides this, can be dangerous to producers since it requires certain level of biosafety. This way, recombinant vaccines have been shown to be a great alternative for the development of vaccines against both animal and human botulism. All BoNTs have a 50-kDa light chain (LC) and a 100-kDa heavy chain (HC). The latter one presents two domains of 50 kDa, called the N-terminal (H N) and C-terminal (H C) halves. Among these regions, the H C alone seem to confer the proper immune response against intoxication. Since innumerous studies describe the expression of these distinct regions using different systems, strategies, and protocols, it is difficult to define the best option for a viable vaccine production. Thereby, the present review describes the problematic of botulism and discusses the main advances for the viable production of vaccines for both human and veterinary medicine using recombinant antigens.

      PubDate: 2014-07-26T18:45:28Z
  • Phylogeny and molecular signatures for the phylum Fusobacteria and its
           distinct subclades
    • Abstract: Publication date: August 2014
      Source:Anaerobe, Volume 28
      Author(s): Radhey S. Gupta , Mohit Sethi
      The members of the phylum Fusobacteria and its two families, Fusobacteriaceae and Leptotrichiaceae, are distinguished at present mainly on the basis of their branching in the 16S rRNA gene trees and analysis of the internal transcribed spacer sequences in the 16S-23S rDNA. However, no biochemical or molecular characteristics are known that are uniquely shared by all of most members of these groups of bacteria. We report here detailed phylogenetic and comparative analyses on 45 sequenced Fusobacteria genomes to examine their evolutionary relationships and to identify molecular markers that are specific for the members of this phylum. In phylogenetic trees based on 16S rRNA gene sequences or concatenated sequences for 17 conserved proteins, members of the families Fusobacteriaceae and Leptotrichiaceae formed strongly supported clades and were clearly distinguished. In these trees, the species from the genus Fusobacterium also formed a number of well-supported clades. In parallel, comparative analyses on Fusobacteria genomes have identified 44 conserved signature indels (CSIs) in proteins involved in a broad range of functions that are either specific for the phylum Fusobacteria or a number of distinct subclades within this phylum. Seven of these CSIs in important proteins are uniquely present in the protein homologs of all sequenced Fusobacteria and they provide potential molecular markers for this phylum. Six and three other CSIs in other protein sequences are specific for members of the families Fusobacteriaceae and Leptotrichiaceae, respectively, and they provide novel molecular means for distinguishing members of these two families. Fourteen additional CSIs in different proteins, which are specific for either members of the genera Fusobacterium or Leptotrichia, or a number of other well-supported clades of Fusobacteria at multiple phylogenetic levels, provide molecular markers for these groups and information regarding the evolutionary relationships among the members of this phylum. Lastly, the present work has also identified 14 CSIs in divergent proteins that are specific for three specific subclades of Fusobacterium species, which are also indicated to be distinct by phylogenetic analyses. The members of these three Fusobacterium subclades also differ significantly from each other in their whole genome average nucleotide identities values, suggesting that they are possible candidates for recognition as different genera. The molecular markers reported here provide novel means for the identification of members of the phylum Fusobacteria and for their classification.

      PubDate: 2014-07-26T18:45:28Z
  • Editorial board
    • Abstract: Publication date: October 2014
      Source:Anaerobe, Volume 29

      PubDate: 2014-07-26T18:45:28Z
  • Finding a robust strain for biomethanation: Anaerobic fungi
           (Neocallimastigomycota) from the Alpine ibex (Capra ibex) and their
           associated methanogens
    • Abstract: Publication date: October 2014
      Source:Anaerobe, Volume 29
      Author(s): Stefanie Leis , Philipp Dresch , Ursula Peintner , Katerina Fliegerová , Adolf Michael Sandbichler , Heribert Insam , Sabine Marie Podmirseg
      Anaerobic fungi occupy the rumen and digestive tract of herbivores, where they play an important role in enzymatic digestion of lignocellulosic and cellulosic substrates, i.e. organic material that their hosts are unable to decompose on their own. In this study we isolated anaerobic fungi from a typical alpine herbivore, the Alpine ibex (C. ibex). Three fungal strains, either as pure culture (ST2) or syntrophic co-culture with methanogens (ST3, ST4) were successfully obtained and morphologically characterised by different microscopy- and staining-techniques and by rDNA ITS gene sequencing. The isolated fungi were identified as Neocallimastix frontalis (ST2) and Caecomyces communis (ST3 and ST4). We introduce a novel field of application for lactofuchsin-staining, combined with confocal laser scanning microscopy. This approach proved as an effective method to visualize fungal structures, especially in the presence of plant biomass, generally exhibiting high autofluorescence. Moreover, we could demonstrate that fungal morphology is subject to changes depending on the carbon source used for cultivation. Oxygen tolerance was confirmed for both, C. communis-cultures for up to three, and for the N. frontalis-isolate for up to 12 h, respectively. With PCR, FISH and an oligonucleotide microarray we found associated methanogens (mainly Methanobacteriales) for C. communis, but not for N. frontalis.

      PubDate: 2014-07-26T18:45:28Z
  • In vitro evaluation of effects of gut region and fiber structure on
           the intestinal dominant bacterial diversity and functional bacterial
    • Abstract: Publication date: August 2014
      Source:Anaerobe, Volume 28
      Author(s): Jinzhen Jiao , Qi Lu , Zhiliang Tan , Leluo Guan , Chuanshe Zhou , Shaoxun Tang , Xuefeng Han
      Understanding the intestinal bacteria in ruminants and their population kinetics is essential for their ecological function, as well as their interaction with the host. In this in vitro study, we aimed to determine whether gut region and fiber structure can influence bacterial diversity and functional bacterial population, together with the kinetics of functional bacterial species in the cecal inocula using PCR-DGGE and qPCR. A split plot design was conducted with gut regions (jejunum, ileum, cecum and colon) as main plot, and substrates (neutral detergent fiber (NDF) and cellulose (CEL)) as subplot. Incubation time and gut region affected dominant bacterial diversity. The numbers of total bacteria, cellulolytic bacteria, genus Prevotella and amylolytic bacteria in the hindgut inocula were greater (P < 0.05) than those in the small intestinal inocula. Fiber structure did not significantly influence the dominant bacterial diversity and the numbers of most examined functional bacterial species. The greatest increase rate of cellulolytic bacteria occurred earlier than amylolytic bacteria except for R. albus incubated with NDF. Changes in cellulolytic bacterial populations were not coordinative with alteration of fiber disappearance as well as CMCase and xylanase activities. All these suggest that the hindgut contents have greater potential to digest fiber than small intestinal contents, and cellulolytic bacteria are of significant value at the initial stage of fiber digestion among the fiber digestive microbes in the intestine.

      PubDate: 2014-07-26T18:45:28Z
  • The identification of four histidine kinases that influence sporulation in
           Clostridium thermocellum
    • Abstract: Publication date: August 2014
      Source:Anaerobe, Volume 28
      Author(s): Elizabeth B. Mearls , Lee R. Lynd
      In this study, we sought to identify genes involved in the onset of spore formation in Clostridium thermocellum via targeted gene deletions, gene over-expression, and transcriptional analysis. We determined that three putative histidine kinases, clo1313_0286, clo1313_2735 and clo1313_1942 were positive regulators of sporulation, while a fourth kinase, clo1313_1973, acted as a negative regulator. Unlike Bacillus or other Clostridium species, the deletion of a single positively regulating kinase was sufficient to abolish sporulation in this organism. Sporulation could be restored in these asporogenous strains via overexpression of any one of the positive regulators, indicating a high level of redundancy between these kinases. In addition to having a sporulation defect, deletion of clo1313_2735 produced L-forms. Thus, this kinase may play an additional role in repressing L-form formation. This work suggests that C. thermocellum enters non-growth states based on the sensory input from multiple histidine kinases. The ability to control the development of non-growth states at the genetic level has the potential to inform strategies for improved strain development, as well as provide valuable insight into C. thermocellum biology.

      PubDate: 2014-07-26T18:45:28Z
  • Characterization of the fecal microbiome in different swine groups by
           high-throughput sequencing
    • Abstract: Publication date: August 2014
      Source:Anaerobe, Volume 28
      Author(s): Soo-Je Park , Jinu Kim , Jong-Soo Lee , Sung-Keun Rhee , Hongik Kim
      Swine have a complex microbial community within their gastrointestinal tract that plays a critical role in both health and disease. High-throughput 16S rRNA gene-based pyrosequencing was used to identify the possible core microorganisms in the gut of swine groups that differ in meat quality and weight grades (level 1 as higher meat quality and level 2 as lower meat quality). Samples were taken from the rectum and/or stool from ten animals, DNA was extracted, and the V1–V3 regions of the 16S rRNA gene were amplified. Two bacterial populations (Bacteroidetes and Firmicutes) dominated and were shared between the two groups. Significant differences between the groups were found at the genus level. The genera Lactobacillus and Oscillibacter were found in slightly higher proportions in the level 2 group (12.6 and 12.4% of the classified reads, respectively) than those of level 1 (9.6 and 7.7%, respectively). By contrast, the proportion of reads assigned to the genus Roseburia in the level 1 group (13.0%) was higher than that of level 2 (4.8%). The largest differences were related to the genera Clostridium, Oscillibacter, and Roseburia as core microorganisms. Moreover, two genera, Roseburia and Clostridium, related to level 1 produced linoleic acid or short chain fatty acids that might contribute to swine health and development. In conclusion, the presence of core bacteria in the swine gut is associated with meat quality with reduced body fat in swine.

      PubDate: 2014-07-26T18:45:28Z
  • In vitro efficacy of cefovecin against anaerobic bacteria isolated
           from subgingival plaque of dogs and cats with periodontal disease
    • Abstract: Publication date: August 2014
      Source:Anaerobe, Volume 28
      Author(s): Manouchehr Khazandi , Philip S. Bird , Jane Owens , Gary Wilson , James N. Meyer , Darren J. Trott
      Periodontal disease is a common disease of dogs and cats often requiring antimicrobial treatment as an adjunct to mechanical debridement. However, correct compliance with oral antimicrobial therapy in companion animals is often difficult. Cefovecin is a recently introduced veterinary cephalosporin that has demonstrated prolonged concentrations in extracellular fluid, allowing for dosing intervals of up to 14 days. Subgingival samples were collected from the oral cavity of 29 dogs and eight cats exhibiting grade 2 or grade 3 periodontal disease. Samples were cultivated on Wilkin Chalgrens agar and incubated in an anaerobic chamber for seven days. Selected anaerobic bacteria were isolated and identified to species level using 16S rRNA gene sequence analysis. Minimum inhibitory concentrations were determined for cefovecin and six additional antimicrobials using the agar dilution methodology recommended by the Clinical and Laboratory Standards Institute. The 65 clinical isolates were identified as Porphyromonas gulae (n = 45), Porphyromonas crevioricanis (n = 12), Porphyromonas macacae (n = 1), Porphyromonas cangingivalis (n = 1) Fusobacterium nucleatum (n = 2), Fusobacterium russii (n = 1) and Solobacterium moorei (n = 3). This is the first report of S. moorei being isolated from companion animals with periodontal disease. All isolates were highly susceptible to cefovecin, with a MIC90 of ≤0.125 μg/ml. Conversely, different resistance rates to ampicillin, amoxicillin and erythromycin between isolates were detected. Cefovecin is thus shown to be effective in vitro against anaerobic bacteria isolated from dogs and cats with periodontal disease.

      PubDate: 2014-07-26T18:45:28Z
  • In vitro activity of MCB3681 against Clostridium difficile strains
    • Abstract: Publication date: August 2014
      Source:Anaerobe, Volume 28
      Author(s): Mamun-Ur Rashid , Axel Dalhoff , Andrej Weintraub , Carl Erik Nord
      One hundred fourteen Clostridium difficile strains were collected from 67 patients and analyzed for the presence of C. difficile toxin B by the cell cytotoxoicity neutralization assay, genes for toxin A, toxin B, binary toxin and TcdC deletion by PCR. All strains were also PCR-ribotyped. The MICs of the isolates were determined against MCB3681 and nine other antimicrobial agents by the agar dilution method. All isolates were positive for toxin B as well as for toxin A and B genes. In addition, 13 isolates were positive for the binary toxin genes. Thirty-two different ribotypes were identified. No strain of ribotype 027 was found. All 114 isolates were sensitive to MCB3681 (0.008–0.5 mg/l), cadazolid (0.064–0.5 mg/l), fidaxomicin (0.008–0.125 mg/l), metronidazole (0.125–2 mg/l), vancomycin (0.125–1 mg/l) and tigecycline (0.032–0.25 mg/l). Three isolates were resistant to linezolid (8 mg/l), 12 isolates were resistant to moxifloxacin (8–32 mg/l), 87 isolates were resistant to clindamycin (8–256 mg/l) and 107 isolates were resistant to ciprofloxacin (8–256 mg/l). No association between toxins A, B and binary toxin, ribotypes and the sensitivity to MCB3681 could be found. MCB3681 has a potent in vitro activity against C. difficile.

      PubDate: 2014-07-26T18:45:28Z
  • Bifidobacterium longum and Bifidobacterium breve isolates from preterm and
           full term neonates: Comparison of cell surface properties
    • Abstract: Publication date: August 2014
      Source:Anaerobe, Volume 28
      Author(s): Valérie Andriantsoanirina , Anne-Claire Teolis , Liu Xin Xin , Marie Jose Butel , Julio Aires
      We compared autoaggregation, surface hydrophobicity and Caco-2 cells adhesion capabilities of independent Bifidobacterium breve (n = 22) and Bifidobacterium longum (n = 25) strains isolated from preterm (n = 20) and full term neonates (n = 27). Concerning strains properties, a correlation between autoaggregation and surface hydrophobicity was found for B. longum (r = 0.40, p = 0.048), B. breve (r = 0.57, p = 0.005), and all strains independently of the species consideration (r = 0.46, p = 0.001). The absence of difference in adhesion capabilities between preterm and full term neonate strains suggests a strain-dependent property. However, B. longum strains from preterm neonates (n = 10) showed higher autoaggregation ability (p = 0.044). Additionally, independently of species consideration, preterm neonates strains showed lower surface hydrophobicity (p = 0.027). As far as species are considered, preterm neonate B. breve strains (n = 10) showed significantly lower surface hydrophobicity percentages (p = 0.043). Our results suggest the existence of variations in bifidobacteria membrane structure and/or composition that may reflect adaptation of these bacteria to the intestinal environment of either preterm or full term neonates. Such information is of interest when considering the use of bifidobacteria probiotic strains for modulation of preterm neonates gut microbiota.

      PubDate: 2014-07-26T18:45:28Z
  • Clostridium difficile and Clostridium perfringens from wild carnivore
           species in Brazil
    • Abstract: Publication date: August 2014
      Source:Anaerobe, Volume 28
      Author(s): Rodrigo Otávio Silveira Silva , Mirella Lauria D’Elia , Érika Procópio Tostes Teixeira , Pedro Lúcio Lithg Pereira , Danielle Ferreira de Magalhães Soares , Álvaro Roberto Cavalcanti , Aleksander Kocuvan , Maja Rupnik , André Luiz Quagliatto Santos , Carlos Augusto Oliveira Junior , Francisco Carlos Faria Lobato
      Despite some case reports, the importance of Clostridium perfringens and Clostridium difficile for wild carnivores remains unclear. Thus, the objective of this study was to identify C. perfringens and C. difficile strains in stool samples from wild carnivore species in Brazil. A total of 34 stool samples were collected and subjected to C. perfringens and C. difficile isolation. Suggestive colonies of C. perfringens were then analyzed for genes encoding the major C. perfringens toxins (alpha, beta, epsilon and iota) and the beta-2 toxin (cpb2), enterotoxin (cpe) and NetB (netb) genes. C. difficile strains were analyzed by multiplex-PCR for toxins A (tcdA) and B (tcdB) and a binary toxin gene (cdtB) and also submitted to a PCR ribotyping. Unthawed aliquots of samples positive for C. difficile isolation were subjected to the detection of A/B toxins by a cytotoxicity assay (CTA). C. perfringens was isolated from 26 samples (76.5%), all of which were genotyped as type A. The netb gene was not detected, whereas the cpb2 and cpe genes were found in nine and three C. perfringens strains, respectively. C. difficile was isolated from two (5.9%) samples. A non-toxigenic strain was recovered from a non-diarrheic maned wolf (Chrysocyon brachyurus). Conversely, a toxigenic strain was found in the sample of a diarrheic ocelot (Leopardus pardallis); an unthawed stool sample was also positive for A/B toxins by CTA, indicating a diagnosis of C. difficile-associated diarrhea in this animal. The present work suggests that wild carnivore species could carry C. difficile strains and that they could be susceptible to C. difficile infection.

      PubDate: 2014-07-26T18:45:28Z
  • Long-term monitoring of the human intestinal microbiota from the 2nd week
           to 13 years of age
    • Abstract: Publication date: August 2014
      Source:Anaerobe, Volume 28
      Author(s): Akihito Endo , Anna Pӓrtty , Marko Kalliomӓki , Erika Isolauri , Seppo Salminen
      Microbial contact begins prior to birth and continues rapidly thereafter. Few long term follow-up studies have been reported and we therefore characterized the development of intestinal microbiota of ten subjects from the 2nd week of life to 13 years of age. PCR-denaturing gradient gel electrophoresis combined with several bacterial group-specific primer sets demonstrated the colonization steps of defined bacterial groups in the microbiota. Bifidobacterium species were seen throughout the test period in all subjects. Bacteroides fragilis group and Blautia coccoides–Eubacterium rectale group species were not detected in several subjects during the first 6 months of life but were commonly seen after 12 months of life. Streptococcus group appeared during early life but was not seen in several subjects at the age of 13 years. Although a few species were linked with the increasing age, major bacterial species in the groups did not change dramatically. Rather considerable changes were found in the relative abundances of each bacterial species. Clustering analysis of total bacterial flora indicated that the microbiota changed considerably between 6 months and 12 months of life, and, at the age of 12 months, the intestinal microbiota was already converted toward a profile characteristic of an adult microbiota. Probiotic supplementation in the beginning of life did not have major impacts on later microbiota development.

      PubDate: 2014-07-26T18:45:28Z
  • Clostridium difficile in goats and sheep in Slovenia: Characterisation of
           strains and evidence of age-related shedding
    • Abstract: Publication date: August 2014
      Source:Anaerobe, Volume 28
      Author(s): Jana Avberšek , Tina Pirš , Mateja Pate , Maja Rupnik , Matjaž Ocepek
      Diversity of Clostridium difficile in different age groups of goats (n = 109) and sheep (n = 105) was investigated. C. difficile was detected in 9.2% of goats and 5.7% of sheep. None of the adult animals were positive. Isolates belonged to four toxinotypes (0, V, XIa, XII), six PCR-ribotypes (010, 014/020, 045, 056, SLO 061, SLO 151) and six pulsotypes. PCR-ribotypes 010, 014/020, 045 and 056 were found previously in other animal species and humans in Slovenia. Additionally, three pulsotypes were indistinguishable from restriction patterns in our PFGE database of animal isolates. All strains were susceptible to metronidazol, vancomycin, moxifloxacin, and with the exception of a single non-toxigenic strain also to clindamycin and erythromycin. While all strains were resistant to ciprofloxacin and levofloxacin, oxacillin-resistance was observed only in strains of PCR-ribotype 045. This first study on C. difficile in small ruminants in Slovenia revealed the evidence of age-related shedding as the highest was demonstrated in neonatal goats and sheep aged up to 16 days.

      PubDate: 2014-07-26T18:45:28Z
  • Skin and soft-tissue infections caused by Actinobaculum schaalii: Report
           of two cases and literature review
    • Abstract: Publication date: August 2014
      Source:Anaerobe, Volume 28
      Author(s): Daniel Tena , Cristina Fernández , María R. Lago , Marta Arias , María José Medina , Juan Antonio Sáez-Nieto
      Skin and soft-tissue infections (SSTIs) caused by Actinobaculum spp. are very rare. In the present study, we report two cases and review the literature. The first case was an immunocompromised patient with an extensive cellulitis secondary to an inguinal abscess, and the second case was a patient with a pilonidal abscess. Clinical outcomes of both patients were good after surgical drainage and treatment with cloxacillin. The review of the literature showed that SSTIs caused by Actinobaculum spp. are usually located on the perineal and inguinal regions and can be severe, particularly in immunocompromised patients. SSTIs caused by Actinobaculum spp. can be overlooked because identification is often difficult and they can be considered as contaminants.

      PubDate: 2014-07-26T18:45:28Z
  • Antimicrobial susceptibility of clinical isolates of anaerobic bacteria in
           Ontario, 2010–2011
    • Abstract: Publication date: August 2014
      Source:Anaerobe, Volume 28
      Author(s): Alex Marchand-Austin , Prasad Rawte , Baldwin Toye , Frances B. Jamieson , David J. Farrell , Samir N. Patel
      The local epidemiology of antimicrobial susceptibility patterns in anaerobic bacteria is important in guiding the empiric treatment of infections. However, susceptibility data are very limited on anaerobic organisms, particularly among non-Bacteroides organisms. To determine susceptibility profiles of clinically-significant anaerobic bacteria in Ontario Canada, anaerobic isolates from sterile sites submitted to Public Health Ontario Laboratory (PHOL) for identification and susceptibility testing were included in this study. Using the E-test method, isolates were tested for various antimicrobials including, penicillin, cefoxitin, clindamycin, meropenem, piperacillin-tazobactam and metronidazole. The MIC results were interpreted based on guidelines published by Clinical and Laboratory Standards Institute. Of 2527 anaerobic isolates submitted to PHOL, 1412 were either from sterile sites or bronchial lavage, and underwent susceptibility testing. Among Bacteroides fragilis, 98.2%, 24.7%, 1.6%, and 1.2% were resistant to penicillin, clindamycin, piperacillin-tazobactam, and metronidazole, respectively. Clostridium perfringens was universally susceptible to penicillin, piperacillin-tazobactam, and meropenem, whereas 14.2% of other Clostridium spp. were resistant to penicillin. Among Gram-positive anaerobes, Actinomyces spp., Parvimonas micra and Propionibacterium spp. were universally susceptible to β-lactams. Eggerthella spp., Collinsella spp., and Eubacterium spp. showed variable resistance to penicillin. Among Gram-negative anaerobes, Fusobacterium spp., Prevotella spp., and Veillonella spp. showed high resistance to penicillin but were universally susceptible to meropenem and piperacillin-tazobactam. The detection of metronidazole resistant B. fragilis is concerning as occurrence of these isolates is extremely rare. These data highlight the importance of ongoing surveillance to provide clinically relevant information to clinicians for empiric management of infections caused by anaerobic organisms.

      PubDate: 2014-07-26T18:45:28Z
  • The effect of vacuum packaging, EDTA, oregano and thyme oils on the
           microbiological quality of chicken's breast
    • Abstract: Publication date: October 2014
      Source:Anaerobe, Volume 29
      Author(s): Adriana Pavelková , Miroslava Kačániová , Elena Horská , Katarína Rovná , Lukáš Hleba , Jana Petrová
      The effect of ethylenediaminetetraacetate (EDTA), oregano (Origanum vulgare) and thyme (Thymus vulgaris) oils, on the chicken breast fillets was examined in this study. The chicken breast fillets were stored under vacuum packaging (VP), at 4 ± 0.5 °C for a period of 18 days. There were used the following treatments of chicken breast fillets: Air-packaged (AC, control samples), vacuum-packaged (VPC, control samples), VP with EDTA solution 1.50% w/w (VPEC, control samples), VP with oregano oil 0.20% v/w (VP + O) and VP with thyme oil 0.20% v/w, (VP + T). The quality assessment for vacuum packaging of the product in accordance with the terms above and EDTA treatment, oregano and thyme oil was established by microbiological analyzes. The microbiological properties as the total viable counts on Plate Count Agar, after incubation for 2 days at 37 °C and coliform bacteria on Violet Red Bile Glucose agar incubated at 37 °C for 24 h, lactobacilli on Rogosa and Sharpe agar after incubation 48–78 h at 37 °C in an aerobic atmosphere supplemented with carbon dioxide (5% CO2) and Pseudomonas aeruginosa on Pseudomonas Isolation agar (PIA, Oxoid, UK) after incubation at 48 h at 35 °C were monitored. The using of oregano, thyme oil and EDTA with combination of vacuum packaging has significant effects to reduction of all followed groups of microorganisms compared with control group without vacuum packaging and untreated control group. The natural preservatives can be used as alternatives to chemical additives which could extend the meat and meat products shelf life. The knowledge about them can have an important economic feedback by reducing losses attributed to spoilage and by allowing the products to reach distant and new markets. This study shows how using of natural antimicrobials can extend the shelf-life of the meat product.

      PubDate: 2014-07-26T18:45:28Z
  • Use of fluorescent staining and flow cytometry for monitoring
           physiological changes in solventogenic clostridia
    • Abstract: Publication date: October 2014
      Source:Anaerobe, Volume 29
      Author(s): Petra Patakova , Michaela Linhova , Pavla Vykydalova , Barbora Branska , Mojmir Rychtera , Karel Melzoch
      Physiological changes in populations of Clostridium beijerinckii and Clostridium tetanomorphum were monitored by fluorescence staining and flow cytometry. To estimate the number of metabolically active cells in exponential growth, a combination of the dyes propidium iodide and carboxy fluorescein diacetate appeared to be a good choice for both species. During stationary phase, these stains did not reflect physiological changes sufficiently and therefore additional labeling with bis-(1,3-dibutylbarbituric acid) trimethineoxonol was applied. Results of fluorescence staining in solventogenic batch fermentations were compared with substrate-use data, the concentration of key metabolites and growth curves. We demonstrate that measurements by all methods were mutually compatible.

      PubDate: 2014-07-26T18:45:28Z
  • In vitro evaluation of the safety and probiotic properties of
           Lactobacilli isolated from chicken and calves
    • Abstract: Publication date: October 2014
      Source:Anaerobe, Volume 29
      Author(s): Dobroslava Bujnakova , Eva Strakova , Vladimir Kmet
      A total of 73 chicken and calves isolates were diagnosed using matrix-assisted laser desorption ionization-time-of flight mass spectrometry (Maldi-Tof MS). After a preliminary subtractive screening based on the high acid tolerance at pH 2.5 and bile resistance at 0.3% oxgall, twenty isolates belonging to the species Lactobacillus salivarius, Lactobacillus agilis, Lactobacillus reuteri, Lactobacillus murinus and Lactobacillus amylovorus were in vitro screened for the safety assessment and probiotic properties, including antibiotics susceptibility patterns, biochemical activity and potential for competitive exclusion of biofilm producing pathogens determined by crystal violet and/or quantitative Fluorescent in situ Hybridisation (FISH) assays utilizing 5′Cy 3 labelled probe Enter1432 for enteric group. Antibiotic susceptibility testing was performed according to the ISO norm 10932. The sixteen strains were susceptible to certain antimicrobial agents, except for two chicken (L. salivarius 12K, L. agilis 13K) and two calves (L. reuteri L10/1, L. murinus L9) isolates with the presence non wild-type ECOFFs (epidemiological cut-off) for gentamicin (≥256 μg ml−1), tetracycline (≥128 μg ml−1), kanamycin (≥256 μg ml−1) and streptomycin (≥96 μg ml−1). The two referenced chicken isolates gave positive aac(6′)Ie-aph(2″)Ia and tet(L) PCR results. The wild-type ECOFFs isolates were subjected to the apiZYM analysis for enzyme profile evaluation and amino acid decarboxylase activities determined by qualitative plate method and multiplex PCR for the detection of four genes involved in the production of histamine (histidine decarboxylase, hdc), tyramine (tyrosine decarboxylase, tyrdc) and putrescine (via eithers ornithine decarboxylase, odc, or agmatine deiminase, agdi). From examined strains only two chicken isolates (L. reuteri 14K; L. salivarius 15K) had no harmful β-glucuronidase, β-glucosidase activities connected with detrimental effects in the gastrointestinal tract and together no amino acid decarboxylase activities and no genes associated with biogenic amines production though only chicken L. salivarius 15K whole cells and acid supernatants shown strong suppressive potential against biofilm-forming Klebsiella and Escherichia coli. Our results highlight that above-mentioned isolate L. salivarius 15K fulfils the principle requirements of a qualified probiotic and may be seen as a reliable candidate for further validation studies in chicken.

      PubDate: 2014-07-26T18:45:28Z
  • Isolation and characterization of faecal bifidobacteria and lactobacilli
           isolated from dogs and primates
    • Abstract: Publication date: October 2014
      Source:Anaerobe, Volume 29
      Author(s): Viola Strompfová , Andrea Lauková
      Although bifidobacteria and lactobacilli have been suggested beneficial for the host and are components of many probiotics and competitive exclusion mixtures, the knowledge on abundance, metabolic and probiotic characteristics in isolates from dogs and monkeys is still limited. The present study was aimed to isolate Bifidobacterium and Lactobacillus strains (faeces of 22 dogs and of 5 primates: Cebus apella, Eulemur fulvus, Erythrocebus patas, Macaca fascicularis, Papio hamadryas) with the MALDI-TOF identification system Lactobacillus murinus, Bifidobacterium animalis and Pediococcus acidilactici were more frequently isolated species in dogs while Lactobacillus plantarum was isolated in several species of primates. Ten strains of 6 species were assayed for enzymatic activities (only Lactobacillus reuteri strains showed no undesirable enzymatic activity), antimicrobial susceptibility (detected higher minimum inhibitory concentration levels for tetracycline and gentamicin), and inhibitory activity against 15 indicator bacteria. All strains inhibited Gram-negative indicators while lactobacilli showed larger inhibition zones than bifidobacteria. L. reuteri II/3b/a (isolate from M. fascicularis) showed the best antimicrobial properties. Resistance to bile (0.3% w/v) was observed in all tested strains (no decrease of CFU/ml) whereas the decrease of 68.4–94.4% (after 90 min exposition) and 78.4–99.9% CFU/ml (after 180 min) depending on the strain was detected in the artificial gastric juice.

      PubDate: 2014-07-26T18:45:28Z
  • Eremophila glabra reduces methane production and methanogen populations
           when fermented in a Rusitec
    • Abstract: Publication date: October 2014
      Source:Anaerobe, Volume 29
      Author(s): XiXi Li , Zoey Durmic , ShiMin Liu , Chris S. McSweeney , Philip E. Vercoe
      Eremophila glabra Juss. (Scrophulariaceae), a native Australian shrub, has been demonstrated to have low methanogenic potential in a batch in vitro fermentation system. The present study aimed to test longer-term effects of E. glabra on rumen fermentation characteristics, particularly methane production and the methanogen population, when included as a component of a fermentation substrate in an in vitro continuous culture system (Rusitec). E. glabra was included at 150, 250, 400 g/kg DM (EG15, EG25, and EG40) with an oaten chaff and lupin-based substrate (control). Overall, the experiment lasted 33 days, with 12 days of acclimatization, followed by two periods during which fermentation characteristics (total gas, methane and VFA productions, dry matter disappearance, pH) were measured. The number of copies of genes specifically associated with total bacteria and cellulolytic bacteria (16S rRNA gene) and total ruminal methanogenic archaeal organisms (the methyl coenzyme M reductase A gene (mcrA)) was also measured during this time using quantitative real-time PCR. Total gas production, methane and volatile fatty acid concentrations were significantly reduced with addition of E. glabra. At the end of the experiment, the overall methane reduction was 32% and 45% for EG15 and EG25 respectively, compared to the control, and the reduction was in a dose-dependent manner. Total bacterial numbers did not change, but the total methanogen population decreased by up to 42.1% (EG40) when compared to the control substrate. The Fibrobacter succinogenes population was reduced at all levels of E. glabra, while Ruminococcus albus was reduced only by EG40. Our results indicate that replacing a portion of a fibrous substrate with E. glabra maintained a significant reduction in methane production and methanogen populations over three weeks in vitro, with some minor inhibition on overall fermentation at the lower inclusion levels.

      PubDate: 2014-07-26T18:45:28Z
  • Influences of the substrate feeding regime on methanogenic activity in
           biogas reactors approached by molecular and stable isotope methods
    • Abstract: Publication date: October 2014
      Source:Anaerobe, Volume 29
      Author(s): Z. Lv , A.F. Leite , H. Harms , H.H. Richnow , J. Liebetrau , M. Nikolausz
      In order to better understand the effects of the substrate feeding regime on methanogenesis during anaerobic digestion in biogas reactors, four continuous stirred tank reactors operated under mesophilic conditions were investigated. In addition to standard physicochemical parameters, the stable isotopic signatures of CH4 and CO2 before and after daily feeding were analyzed. The activity of the methanogens was assessed by methyl coenzyme M reductase alpha-subunit (mcrA/mrtA) gene transcript analysis. Two different feeding regimes i.e. single vs. double consecutive feeding of the otherwise same daily maize silage load were investigated. During the first phase, a single feeding of the whole daily dose increased the biogas production within 70–80 min from around 0.5 to 2.0 L/h. This increase was associated with a transient increase of the acetic acid concentration and a corresponding decrease of the pH. Only moderate increase in biogas yield and VFA concentration (mainly acetate) was observed when the daily substrate was apportioned into two feedings. However, the overall daily gas production was similar in both cases. Regardless of the feeding regime, significantly depleted δ 13CH4 and minor changes in the CO2 content of biogas were observed after feeding, which were followed by enrichment of δ 13CH4. This period was associated with detectable changes in activity of methanogenic communities monitored by terminal restriction fragment length polymorphism analysis based on the transcripts of mcrA/mrtA genes. Methanoculleus and Methanobacterium spp. were the predominant methanogens in all reactors, while Methanosarcina spp. activity was only significant in two reactors. The activity of Methanoculleus and Methanosarcina spp. increased after the feeding in these reactors, which was followed by a depletion of δ 13C in the produced gas. In both reactors, the less depleted isotopic values were detected before the second feeding, when Methanobacterium was the most active genus. Variations in reactor performance and methanogenic community characteristics were attributed to inoculum heterogeneity and stochastic factors during the reactor set up.

      PubDate: 2014-07-26T18:45:28Z
  • Efficiency of RNA extraction from selected bacteria in the context of
           biogas production and metatranscriptomics
    • Abstract: Publication date: October 2014
      Source:Anaerobe, Volume 29
      Author(s): Lucy Stark , Tina Giersch , Röbbe Wünschiers
      Understanding the microbial population in anaerobic digestion is an essential task to increase efficient substrate use and process stability. The metabolic state, represented e.g. by the transcriptome, of a fermenting system can help to find markers for monitoring industrial biogas production to prevent failures or to model the whole process. Advances in next-generation sequencing make transcriptomes accessible for large-scale analyses. In order to analyze the metatranscriptome of a mixed-species sample, isolation of high-quality RNA is the first step. However, different extraction methods may yield different efficiencies in different species. Especially in mixed-species environmental samples, unbiased isolation of transcripts is important for meaningful conclusions. We applied five different RNA-extraction protocols to nine taxonomic diverse bacterial species. Chosen methods are based on various lysis and extraction principles. We found that the extraction efficiency of different methods depends strongly on the target organism. RNA isolation of gram-positive bacteria was characterized by low yield whilst from gram-negative species higher concentrations can be obtained. Transferring our results to mixed-species investigations, such as metatranscriptomics with biofilms or biogas plants, leads to the conclusion that particular microorganisms might be over- or underrepresented depending on the method applied. Special care must be taken when using such metatranscriptomics data for, e.g. process modeling.

      PubDate: 2014-07-26T18:45:28Z
  • Cultivation of moonmilk-born non-extremophilic Thaum and
           Euryarchaeota in mixed culture
    • Abstract: Publication date: October 2014
      Source:Anaerobe, Volume 29
      Author(s): Christoph Reitschuler , Philipp Lins , Andreas Otto Wagner , Paul Illmer
      PCR-DGGE, qPCR and sequencing highlighted a quite homogenous archaeal community prevailing in secondary calcite deposits, so-called moonmilk, within the cold alpine Hundalm cave in Tyrol (Austria). Furthermore, the depth profile of this moonmilk could prove that the Archaea are located in oxygen-rich near- and oxygen-depleted sub-surface layers. To gather these communities we therefore applied an aerobic and anaerobic cultivation approach in oligotrophic and methanotrophic media. The mixed moonmilk community was analyzed with a combination of molecular methods using qPCR, PCR-DGGE and sequencing. Anaerobic and aerobic cultures were additionally investigated with GC and HPLC analyses. It was possible to initially cultivate and enrich the supposed aerobic/microaerophilic and anaerobic archaeal fraction, representing the natural archaeal community. While the naturally less abundant near-surface Archaea are closely related to members of the Thaumarchaeota (Nitrosopumilus maritimus), the highly abundant anaerobic Archaea are more distantly related to members within the Euryarchaeota. It is possible that these cultivable moonmilk-born Archaea represent new ecotypes or are so far undescribed. Based on the sequencing results and the production of very low amounts of methane, a corresponding methanogenic community is thought to represent only a minor abundant archaeal fraction. On a physiological level the cultivated moonmilk community is cold-adapted and basically of oligotrophic and organotrophic character.

      PubDate: 2014-07-26T18:45:28Z
  • Effect of DNA extraction and sample preservation method on rumen bacterial
    • Abstract: Publication date: October 2014
      Source:Anaerobe, Volume 29
      Author(s): Katerina Fliegerova , Ilma Tapio , Aurelie Bonin , Jakub Mrazek , Maria Luisa Callegari , Paolo Bani , Alireza Bayat , Johanna Vilkki , Jan Kopečný , Kevin J. Shingfield , Frederic Boyer , Eric Coissac , Pierre Taberlet , R. John Wallace
      The comparison of the bacterial profile of intracellular (iDNA) and extracellular DNA (eDNA) isolated from cow rumen content stored under different conditions was conducted. The influence of rumen fluid treatment (cheesecloth squeezed, centrifuged, filtered), storage temperature (RT, −80 °C) and cryoprotectants (PBS-glycerol, ethanol) on quality and quantity parameters of extracted DNA was evaluated by bacterial DGGE analysis, real-time PCR quantification and metabarcoding approach using high-throughput sequencing. Samples clustered according to the type of extracted DNA due to considerable differences between iDNA and eDNA bacterial profiles, while storage temperature and cryoprotectants additives had little effect on sample clustering. The numbers of Firmicutes and Bacteroidetes were lower (P < 0.01) in eDNA samples. The qPCR indicated significantly higher amount of Firmicutes in iDNA sample frozen with glycerol (P < 0.01). Deep sequencing analysis of iDNA samples revealed the prevalence of Bacteroidetes and similarity of samples frozen with and without cryoprotectants, which differed from sample stored with ethanol at room temperature. Centrifugation and consequent filtration of rumen fluid subjected to the eDNA isolation procedure considerably changed the ratio of molecular operational taxonomic units (MOTUs) of Bacteroidetes and Firmicutes. Intracellular DNA extraction using bead-beating method from cheesecloth sieved rumen content mixed with PBS-glycerol and stored at −80 °C was found as the optimal method to study ruminal bacterial profile.

      PubDate: 2014-07-26T18:45:28Z
  • Can fungal zoospores be the source of energy for the rumen protozoa
           Eudiplodinium maggii?
    • Abstract: Publication date: October 2014
      Source:Anaerobe, Volume 29
      Author(s): Renata Miltko , Grzegorz Bełżecki , Barbara Kowalik , Tadeusz Michałowski
      Results of our earlier studies showed the ability of ciliates Eudiplodinium maggii to digest and metabolize commercial chitin. The natural source of this polysaccharide in the rumen are fungi. The objectives of present research were to determine the effect of fungal zoospores on the survival and population density of E. maggii to quantify the concentration of chitin in the cells of protozoa and to examine the ability of E. maggii, to ferment chitin of fungal zoospores. The cultivation experiment showed that the survival of protozoa was shorter than 4 days when the culture medium was composed of buffer solution and lyophilized fungal spores. An enrichment of this medium with wheat gluten prolonged the survival of ciliates up to 8 days. The supplementation of the last medium with meadow hay enabled the protozoa to survive for 28 days but a positive effect was observed only during the last 8 days of experiment. The chitin content was 0.27 ng and 0.21–0.35 ng per single zoospore and ciliate, respectively. An increase in the concentration of volatile fatty acids (VFA) was found when protozoa were incubated with zoospores. The production rate of VFA was 46.3 pM/protozoan per h whereas the endogenous production did not exceed 31 pM/protozoan per h. The molar proportion of acetic acid was 77.7% and these of butyric and propionic acids–12.2 and 11.0%, respectively. The obtained results make it evident that carbohydrates present in fungal zoospores were utilized by protozoa in energy yielding processes.

      PubDate: 2014-07-26T18:45:28Z
  • Molecular comparative assessment of the microbial ecosystem in rumen and
           faeces of goats fed alfalfa hay alone or combined with oats
    • Abstract: Publication date: October 2014
      Source:Anaerobe, Volume 29
      Author(s): Hamid Mohammadzadeh , David R. Yáñez-Ruiz , Gonzalo Martínez-Fernandez , Leticia Abecia
      The objective of this work was to compare the biomass and community structure of bacteria, protozoa and archaea communities in samples of rumen and faeces of goats and to what extent the diet (alfalfa hay with or without supplemented oats) offered to them exert an influence. Four cannulated adult goats fistulated in the rumen were used in a cross over design experiment in two experimental periods of 26 days, consisting in 14 days of adaptation, 7 days of sampling rumen contents and 5 days of digestibility measurement. Bacterial, protozoa and archaeal biomass and the communities' structure was assessed by real time PCR (qPCR) and denaturing gradient gel electrophoresis (DGGE), respectively. The numbers of archaea and bacteria in both rumen and faeces were higher and lower, respectively, in animals fed AH diet (P < 0.005). Contrary, protozoal numbers were not affected by the diet but were lower (P < 0.001) in faeces than in rumen. The analysis of the community structure revealed a consistently different population in structure in rumen and faeces for the three studied microbial groups and that supplementing alfalfa hay with oats led to a decrease in the similarity between sites in the rumen and faeces: similarity indexes for bacteria (57 and 27%), archaea (26 and 9%) and protozoa (62 and 22%) in animals fed AH and AHO diets, respectively.

      PubDate: 2014-07-26T18:45:28Z
  • Sample prefractionation with liquid isoelectric focusing enables in depth
           microbial metaproteome analysis of mesophilic and thermophilic biogas
    • Abstract: Publication date: October 2014
      Source:Anaerobe, Volume 29
      Author(s): F. Kohrs , R. Heyer , A. Magnussen , D. Benndorf , T. Muth , A. Behne , E. Rapp , R. Kausmann , M. Heiermann , M. Klocke , U. Reichl
      Biogas production from energy crops and biodegradable waste is one of the major sources for renewable energies in Germany. Within a biogas plant (BGP) a complex microbial community converts biomass to biogas. Unfortunately, disturbances of the biogas process occur occasionally and cause economic losses of varying extent. Besides technical failures the microbial community itself is commonly assumed as a reason for process instability. To improve the performance and efficiency of BGP, a deeper knowledge of the composition and the metabolic state of the microbial community is required and biomarkers for monitoring of process deviations or even the prediction of process failures have to be identified. Previous work based on 2D-electrophoresis demonstrated that the analysis of the metaproteome is well suited to provide insights into the apparent metabolism of the microbial communities. Using SDS-PAGE with subsequent mass spectrometry, stable protein patterns were evaluated for a number of anaerobic digesters. Furthermore, it was shown that severe changes in process parameters such as acidification resulted in significant modifications of the metaproteome. Monitoring of changing protein patterns derived from anaerobic digesters, however, is still a challenge due to the high complexity of the metaproteome. In this study, different combinations of separation techniques to reduce the complexity of proteomic BGP samples were compared with respect to the subsequent identification of proteins by tandem mass spectrometry (MS/MS): (i) 1D: proteins were tryptically digested and the resulting peptides were separated by reversed phase chromatography prior to MS/MS. (ii) 2D: proteins were separated by GeLC-MS/MS according to proteins molecular weights before tryptic digestion, (iii) 3D: proteins were separated by gel-free fractionation using isoelectric focusing (IEF) conducted before GeLC-MS/MS. For this study, a comparison of two anaerobic digesters operated at mesophilic and at thermophilic conditions was conducted. The addition of further separation dimensions before protein identification increased the number of identified proteins. On the other hand additional fractionation steps increased the experimental work load and the time required for LC-MS/MS measurement. The high resolution of the 3D-approach enabled the detection of approximately 750 to 1650 proteins covering the main pathways of hydrolysis, acidogenesis, acetogenesis and methanogenesis. Methanosarcinales dominated in the mesophilic BGP, whereas Methanomicrobiales were highly abundant in the thermophilic BGP. Pathway analysis confirmed the taxonomic results and revealed that the acetoclastic methanogenesis occurred preferentially at mesophilic conditions, whereas exclusively hydrogenotrophic methanogenesis was detected in thermophilic BGP. However, for the identification of process biomarkers by comprehensive screening of BGP it will be indispensable to find a balance between the experimental efforts and analytical resolution.

      PubDate: 2014-07-26T18:45:28Z
  • Dynamics of biofilm formation during anaerobic digestion of organic waste
    • Abstract: Publication date: October 2014
      Source:Anaerobe, Volume 29
      Author(s): Susanne Langer , Daniel Schropp , Frank R. Bengelsdorf , Maazuza Othman , Marian Kazda
      Biofilm-based reactors are effectively used for wastewater treatment but are not common in biogas production. This study investigated biofilm dynamics on biofilm carriers incubated in batch biogas reactors at high and low organic loading rates for sludge from meat industry dissolved air flotation units. Biofilm formation and dynamics were studied using various microscopic techniques. Resulting micrographs were analysed for total cell numbers, thickness of biofilms, biofilm-covered surface area, and the area covered by extracellular polymeric substances (EPS). Cell numbers within biofilms (1011 cells ml−1) were up to one order of magnitude higher compared to the numbers of cells in the fluid reactor content. Further, biofilm formation and structure mainly correlated with the numbers of microorganisms present in the fluid reactor content and the organic loading. At high organic loading (45 kg VS m−3), the thickness of the continuous biofilm layer ranged from 5 to 160 μm with an average of 51 μm and a median of 26 μm. Conversely, at lower organic loading (15 kg VS m−3), only microcolonies were detectable. Those microcolonies increased in their frequency of occurrence during ongoing fermentation. Independently from the organic loading rate, biofilms were embedded completely in EPS within seven days. The maturation and maintenance of biofilms changed during the batch fermentation due to decreasing substrate availability. Concomitant, detachment of microorganisms within biofilms was observed simultaneously with the decrease of biogas formation. This study demonstrates that biofilms of high cell densities can enhance digestion of organic waste and have positive effects on biogas production.

      PubDate: 2014-07-26T18:45:28Z
  • Clostridium difficile infection among immunocompromised patients in Rio de
           Janeiro - Brazil and detection of moxifloxacin resistance in a ribotype
           014 strain
    • Abstract: Publication date: Available online 5 June 2014
      Author(s): Danielle Angst Secco , Ilana Teruszkin Balassiano , Renata Ferreira Boente , Karla Rodrigues Miranda , Jon Brazier , Val Hall , Joaquim dos Santos-Filho , Leandro Araujo Lobo , Simone Aranha Nouér , Regina Maria Cavalcanti Pilotto Domingues
      Clostridium difficile is a Gram-positive spore forming anaerobic bacterium, often associated with nosocomial diarrhea and pseudomembranous colitis. The acquisition of this organism occurs primarily in hospitals through accidental ingestion of spores, and its establishment and proliferation in the colon results from the removal of members of the normal intestinal flora during or after antibiotic therapy. In this study, stool samples from patients admitted to the University Hospital Clementino Fraga Filho (HUCCF / UFRJ) were screened for C. difficile toxins with an ELISA test and cultured with standard techniques for C. difficile isolation. A total of 74 stool samples were collected from patients undergoing antibiotic therapy between August 2009 and November 2010, only two (2,7%) were positive in the ELISA test and culture. A third isolate was obtained from a negative ELISA test sample. All cases of CDI were identified in patients with acute lymphoid or myeloid leukemia. Genotypic and phenotypic characterization showed that all strains carried toxins A and B genes, and belonged to PCR-ribotypes 014, 043 and 046. The isolated strains were sensitive to metronidazole and vancomycin, and resistant to ciprofloxacin and levofloxacin. Resistance to moxifloxacin, was present in the strain from PCR-ribotype 014, that showed an amino acid substitution in gyrB gene (Asp 426 → Asn). This is the first time that this mutation in a PCR-ribotype 014 strain has been described in Brazil.

      PubDate: 2014-06-06T14:44:06Z
  • Porphyromonas gingivalis stimulates IL-6 and IL-8 secretion in GMSM-K,
           HSC-3 and H413 oral epithelial cells
    • Abstract: Publication date: Available online 1 June 2014
      Author(s): Michael Yee , Shawn Kim , Pushpinder Sethi , Nejat Düzgüneş , Krystyna Konopka
      Introduction Infection of oral epithelial cells with periodontopathogenic bacteria results in the production of pro-inflammatory cytokines involved in the initiation and progression of periodontal disease. The purpose of this study was to examine the release of interleukin (IL)-6 and IL-8 by oral epithelial cells after exposure to Porphyromonas gingivalis. Methods Non-tumor-derived, immortalized human GMSM-K cells, and human oral squamous cell carcinoma, HSC-3 and H413 cells, were co-cultured with live and heat-inactivated P. gingivalis 2561 (ATCC 33277) and W83 (ATCC BAA-308™). IL-6 and IL-8 were quantified in the culture supernatants after 6 and 24 h. Results The basal levels of both cytokines and the responses to P. gingivalis were strongly dependent on cell type. GMSM-K cells produced less IL-8 than HSC-3 and H413 cells. Live P. gingivalis induced significant IL-6 and IL-8 secretion in GMSM-K and HSC-3 cells, and heat-inactivation of bacteria enhanced greatly IL-6 and IL-8 stimulation in these cells. Uninfected H413 cells produced high levels of IL-6 and IL-8, but were not responsive to live P. gingivalis; heat-inactivated P. gingivalis up-regulated IL-6 and IL-8 secretion in these cells. Conclusions Since base-line secretion of IL-6 and IL-8, and responses to P. gingivalis depend on the cell type, conclusions on the responses to P. gingivalis should not be based on studies with a single cell type.

      PubDate: 2014-06-06T14:44:06Z
  • Clostridium perfringens and Clostridium difficile in cooked beef sold in
           Côte d’Ivoire and their antimicrobial susceptibility
    • Abstract: Publication date: Available online 2 June 2014
      Author(s): Kra Athanase Kouassi , Adjéhi Thomas Dadie , Kouadio Florent N’Guessan , Koffi Marcellin Dje , Yao Guillaume Loukou
      The aim of this study was to evaluate the prevalence of Clostridium difficile and Clostridium perfringens in cooked beef sold in the streets in Côte d’Ivoire and their antimicrobial susceptibility. A total of 395 kidney and flesh samples of cooked beef were collected from vendors at Abidjan and subjected to C. difficile and C. perfringens isolation and identification by using biochemical tests, API 20A system and PCR detection. Subsequently, the antimicrobial susceptibility test was performed for confirmed isolates. Our results showed the prevalence of 12.4% for C. difficile (11.04% in kidney and 13.45% in flesh) and 5.06% for C. perfringens (2.32% in kidney and 7.17% in flesh). Metronidazole and vancomycin remained the most potent antimicrobial agents against C. difficile while metronidazole and penicillin G were the most potent agents against C. perfringens. The resistance rates to tetracycline, doxycycline, chloramphenicol and erythromycin against C. difficile and C. perfringens isolates ranged from 2.05% to 8.16% and from 20% to 50%, respectively. Among all antimicrobial agents tested against C. difficile, percentages of resistance to quinolones ciprofloxacin, norfloxacin and nalidixic acid as well as to gentamicin and cefotaxime were the highest. Eight resistant phenotypes were defined for C. difficile isolates and eleven resistant phenotypes for C. perfringens isolates. Clindamycin/gentamicin/cefotaxime/ciprofloxacin/norfloxacin/nalidixic acid resistance was the most common phenotype for C. difficile (55.10% of isolates) while norfloxacin/nalidixic acid resistance was the most common phenotype for C. perfringens (20% of isolates).

      PubDate: 2014-06-06T14:44:06Z
  • Antifungal activity and identification of Lactobacilli, isolated from
           traditional dairy product “katak”
    • Abstract: Publication date: Available online 1 June 2014
      Author(s): Rositsa Tropcheva , Dilyana Nikolova , Yana Evstatieva , Svetla Danova
      Filamentous moulds are the main spoilage microorganisms, responsible for significant economic losses and several healthy risks in human food chain. The lactic acid bacteria (LAB), especially lactobacilli could be a natural antagonist of these dangerous organisms. In Bulgaria, a very limited data exists on the antifungal activity of LAB microbiota of fermented dairy products. In the present study, four active strains were isolated from traditional fermented curd/yogurt-like product “katak”, produced in Bulgaria from centuries. The new isolates KR3, KR4, KR51 and KR53 were identified by API 50 CH biochemical test and different molecular methods (species-specific PCR, RAPD-PCR and 16S rDNA sequence analysis) as Lactobacillus brevis. According to our knowledge, this is the first data on the molecular characterization of the Lactobacillus microbiota of “katak”. A broad spectrum of antifungal activity of the four L. brevis KR strains against test-cultures representatives of carcinogenic, toxigenic, deteriorative and allergenic fungi from the genera Aspergillus, Fusarium, Penicillium and Trichoderma was estimated. Strains L. brevis KR3, KR4 and KR51 completely suppress the growth of Penicillium claviforme, Aspergillus awamori and Aspergillus niger. With regard to Aspergillus flavus and Trichoderma viride, a lower and strain-specific inhibitory activity was observed. The antifungal activity of our new L. brevis isolates seems to be a promising advantage of these four strains, suggesting their potential applications in different food technologies as bio-preservative agents against moulds.

      PubDate: 2014-06-06T14:44:06Z
  • A combined metabolomic and phylogenetic study reveals putatively prebiotic
           effects of high molecular weight arabino-oligosaccharides when assessed by
           in vitro fermentation in bacterial communities derived from humans
    • Abstract: Publication date: Available online 4 June 2014
      Author(s): Karolina Sulek , Louise Kristine Vigsnaes , Line Rieck Schmidt , Jesper Holck , Henrik Lauritz Frandsen , Jørn Smedsgaard , Thomas Hjort Skov , Anne S. Meyer , Tine Rask Licht
      Prebiotic oligosaccharides are defined by their selective stimulation of growth and/or activity of bacteria in the digestive system in ways claimed to be beneficial for health. However, apart from the short chain fatty acids, little is known about bacterial metabolites created by fermentation of prebiotics, and the significance of the size of the oligosaccharides remains largely unstudied. By in vitro fermentations in human fecal microbial communities (derived from six different individuals), we studied the effects of high-mass (HA, >1 kDa), low-mass (LA, <1 kDa) and mixed (BA) sugar beet arabino-oligosaccharides (AOS) as carbohydrate sources. Fructo-oligosaccharides (FOS) were included as reference. The changes in bacterial communities and the metabolites produced in response to incubation with the different carbohydrates were analyzed by quantitative PCR (qPCR) and Liquid Chromatography–Mass Spectrometry (LC–MS), respectively. All tested carbohydrate sources resulted in a significant increase of Bifidobacterium spp. between 1.79 fold (HA) and 1.64 fold (FOS) in the microbial populations after fermentation, and LC–MS analysis suggested that the bifidobacteria contributed to decomposition of the arabino-oligosaccharide structures, most pronounced in the HA fraction, resulting in release of the essential amino acid phenylalanine. Abundance of Lactobacillus spp. correlated with the presence of a compound, most likely a flavonoid, indicating that lactobacilli contribute to release of such health-promoting substances from plant structures. Additionally, the combination of qPCR and LC–MS revealed a number of other putative interactions between intestinal microbes and the oligosaccharides, which contributes to the understanding of the mechanisms behind prebiotic impact on human health.

      PubDate: 2014-06-06T14:44:06Z
  • Flux analysis of the human proximal colon using Anaerobic Digestion Model
    • Abstract: Publication date: Available online 28 May 2014
      Author(s): Anne Marieke Motelica-Wagenaar , Arjen Nauta , Ellen G.H.M. van den Heuvel , Robbert Kleerebezem
      The colon can be regarded as an anaerobic digestive compartment within the gastro intestinal tract (GIT). An in silico model simulating the fluxes in the human proximal colon was developed on basis of the anaerobic digestion model 1 (ADM1), which is traditionally used to model waste conversion to biogas. Model calibration was conducted using data from in vitro fermentation of the proximal colon (TIM-2), and, amongst others, supplemented with the bio kinetics of prebiotic galactooligosaccharides (GOS) fermentation. The impact of water and solutes absorption by the host was also included. Hydrolysis constants of carbohydrates and proteins were estimated based on total short chain fatty acids (SCFA) and ammonia production in vitro. Model validation was established using an independent dataset of a different in vitro model: an in vitro three-stage continuous culture system. The in silico model was shown to provide quantitative insight in the microbial community structure in terms of functional groups, and the substrate and product fluxes between these groups as well as the host, as a function of the substrate composition, pH and the solids residence time (SRT). The model confirms the experimental observation that methanogens are washed out at low pH or low SRT-values. The in silico model is proposed as useful tool in the design of experimental setups for in vitro experiments by giving insight in fermentation processes in the proximal human colon.

      PubDate: 2014-05-30T20:38:09Z
  • The relationship between bifidobacteria and allergic asthma and/or
           allergic dermatitis: A prospective study of 0-3 years-old children in
    • Abstract: Publication date: Available online 28 May 2014
      Author(s): Hatice Kubra Akay , Hrisi Bahar Tokman , Nevin Hatipoglu , Huseyin Hatipoglu , Rengin Siraneci , Mehmet Demirci , Baris Ata Borsa , Pelin Yuksel , Asiye Karakullukcu , Achille Aime Kangaba , Serhat Sirekbasan , Sibel Aka , Muzeyyen Mamal Torun , Bekir S. Kocazeybek
      Bifidobacteria are beneficial bacteria for humans. These bacteria are particularly effective at protecting against infectious diseases and modulating the immune response. It was shown that in newborns, the fecal distribution of the colonizing Bifidobacterium species influences the prevalence of allergic diseases. This study aimed to compare the faecal Bifidobacterium species of allergic children to those of healthy children to detect species level differences in faecal distribution. Stool samples were obtained from 99 children between 0 and 3 years of age whose clinical symptoms and laboratory reports were compatible with atopic dermatitis and allergic asthma. Samples were also obtained from 102 healthy children who were similar to the case group with respect to age and sex. Bifidobacteria were isolated by culture and identified at the genus level by API 20 A. In addition, 7 unique species-specific primers were used for the molecular characterization of bifidobacteria. The McNemar test was used for statistical analyses, and p < 0.05 was accepted as significant. Bifidobacterium longum was detected in 11 (11.1%) of the allergic children and in 31 (30.3%) of the healthy children. Statistical analysis revealed a significant difference in the prevalence of Bifidobacterium longum between these two groups (X2: 11.2, p< 0.001). However, no significant differences in the prevalence of other Bifidobacterium species were found between faecal samples from healthy and allergic children. (p> 0.05). The significant difference in the isolation of B. longum from our study groups suggests that this species favours the host by preventing the development of asthma and allergic dermatitis. Based on these results, we propose that the production of probiotics in accordance with country-specific Bifidobacterium species densities would improve public health. Thus, country-specific prospective case-control studies that collect broad data sets are needed.

      PubDate: 2014-05-30T20:38:09Z
  • The influence of oral Veillonella species on biofilms formed by
           Streptococcus species
    • Abstract: Publication date: Available online 23 May 2014
      Author(s): Izumi Mashima , Futoshi Nakazawa
      Oral Veillonella, V. atypica, V. denticariosi, V. dispar, V. parvula, V. rogosae, and V. tobetsuensis are known as early colonizers in oral biofilm formation. To investigate the role of oral Veillonella, biofilms formed by the co-culture of Streptococcus gordonii, S. mutans, S. salivarius, or S. sanguinis, with oral Veillonella were examined at the species level. The amount of biofilm formed by S. mutans, S. gordonii, and S. salivarius in the presence of the six Veillonella species was greater than that formed in the control experiments, with the exception of S. mutans with V. dispar. In contrast, in the case of biofilm formation by S. sanguinis, the presence of Veillonella species reduced the amount of the biofilm, with the exception of V. parvula and V. dispar. The time-dependent changes in the amount of biofilm and the number of planktonic cells were grouped into four patterns over the 24 combinations. Only that of S. gordonii with V. tobetsuensis showed a unique pattern. These results indicate that the mode of action of this combination differed from that of the other combinations with respect to biofilm formation. It is possible that there may be several factors involved in the interaction between Streptococcus and Veillonella species.

      PubDate: 2014-05-24T12:53:22Z
  • Antagonistic mechanisms of synbiosis between Lactobacillus plantarum
           CIF17AN2 and green banana starch in the proximal colon model challenged
           with Salmonella Typhimurium
    • Abstract: Publication date: Available online 21 May 2014
      Author(s): Supansa Uraipan , Patrizia Brigidi , Tipparat Hongpattarakere
      Antagonistic mechanisms of Lactobacillus plantarum CIF17AN2 (an infant isolate), saba starch, and their synbiotic combination against Salmonella Typhimurium SA2093 were evaluated. The anti-Salmonella activity was investigated under the competitive niche of fecal microbiota using the simulated proximal colon model. The alterations of the dominant fecal microbiota and beneficial bacteria were also displayed using FISH and PCR-DGGE techniques. Lactobacillus plantarum CIF17AN2 exhibited anti-Salmonella mechanisms through secretion of antimicrobial compounds, adhesion ability and competitive adhesion to mucin and HT-29 cell line. However, the Salmonella inhibition was significantly reduced in the presence of human fecal microflora. The combination of saba starch with L. plantarum CIF17AN2 showed the greatest inhibition against Sal. Typhimurium SA2093 in the simulated colon model. The enhancement of anti-Salmonella activity due to the addition of saba starch corresponded to a significant decrease in pH and an increase of lactic acid and short chain fatty acids. According to PCR-DGGE analysis, L. plantarum CIF17AN2 was able to survive and effectively compete with fecal microflora. Saba starch supplement modified bifidobacterial profile but had a slight impact on the profile of lactic acid bacteria. This prebiotic approach alleviated the nutrient limitation in the proximal colon model leading to the selective stimulation of beneficial lactobacilli and bifidobacteria, hence the enhancement of anti-Salmonella activity.

      PubDate: 2014-05-24T12:53:22Z
  • Effect of Bifidobacterium animalis B/12 administration in healthy dogs
    • Abstract: Publication date: Available online 15 May 2014
      Author(s): Viola Strompfová , Monika Pogány Simonová , Soňa Gancarčíková , Dagmar Mudroňová , Jana Farbáková , Aladár Maďari , Andrea Lauková
      Bifidobacterium species constitute the most frequently used health-enhancing bacteria in functional foods or probiotic products, and most of their health benefits have been demonstrated in human or mice studies. However, knowledge of the effects of these bacteria in the canine organism is very limited. In this study, the canine-derived strain B. animalis B/12 (109 CFU) was tested for its effects on faecal microbiota, faecal characteristics, faecal organic acid concentrations, blood biochemistry, haematological and immunological parameters in healthy dogs (C-control, BA- B.animalis B/12 group, 10 dogs in each). The experiment lasted for 49 days with a 14-day treatment period (sample collection at days 0, 7, 14, 21, 28, and 49). A significantly higher population of lactic acid bacteria was detected (day 7) while the counts of coliform bacteria were lower in faeces of the BA group (days 14, 21, 28, 49) compared to control group C. Faecal concentrations of acetic (day 7, 21, 28, 49), acetoacetic (7-49) and valeric acid (14) were higher in contrast to formic acid (day 7-21), which was decreased after the treatment. In blood serum, significantly lower concentrations of triglyceride (day 14) and albumin (day 14, 28, 49) and significantly higher levels of alanine aminotrasferase (day 14) and alkaline phosphatase (day 14, 28) were observed in the BA dogs. The phagocytic activity of leukocytes (especially of neutrophils) was higher in dogs after 14-day consumption of B/12 strain (day 14). The results show that many of these effects could also still be recorded several weeks after the treatment period.

      PubDate: 2014-05-19T06:02:24Z
  • Probiotic potential and biotherapeutic effects of newly isolated vaginal
           Lactobacillus acidophilus 36YL strain on cancer cells
    • Abstract: Publication date: Available online 10 May 2014
      Author(s): Yousef Nami , Norhafizah Abdullah , Babak Haghshenas , Dayang Radiah , Rozita Rosli , Ahmad Yari Khosroushahi
      Lactobacillus acidophilus is categorized as a probiotic strain because of its beneficial effects in human health and prevention of disease transmission.This study is aimed to characterize the probiotic potential of L. acidophilus 36YL originally isolated from the vagina of healthy and fertile Iranian women. The L. acidophilus 36YL strain was identified using 16S rDNA gene sequencing and characterized by biochemical methodologies, such as antibiotics susceptibility, antimicrobial activity, and acid and bile resistance. The bioactivity of the secretion of this strain on four human cancer cell lines (AGS, HeLa, MCF-7, and HT-29) and one normal cell line (HUVEC) was evaluated by cytotoxicity assay and apoptosis analysis. This newly isolated strain was found to exhibit notable probiotic properties, such as admirable antibiotic susceptibility, good antimicrobial activity, and favorable resistance to acid and bile salt. The results of bioactivity assessment demonstrated acceptable anticancer effects on the four tested cancer cell lines and negligible side effects on the assayed normal cell line. Our findings revealed that the anticancer effect of L. acidophilus 36YL strain secretions depends on the induction of apoptosis in cancer cells. L. acidophilus 36YL strain is considered as a nutraceutical alternative or a topical medication with a potential therapeutic index because of the absence of cytotoxicity to normal cells, but effective toxicity to cancer cell lines.

      PubDate: 2014-05-14T03:51:14Z
  • In vitro effect of antibiotics on biofilm formation by B. fragilis group
           strains isolated from intestinal microbiota of dogs and their
           antimicrobial susceptibility
    • Abstract: Publication date: Available online 4 May 2014
      Author(s): Janice Oliveira Silva , Ana Catarina Martins Reis , Carlos Quesada-Gómez , Adriana Queiroz Pinheiro , Rosemary Souza Freire , Reinaldo Barreto Oriá , Cibele Barreto Mano de Carvalho
      The Bacteroides fragilis group strains colonize the intestinal tract of dogs as commensal bacteria. Nevertheless, they can be opportunistic pathogens responsible of significant morbidity and mortality rates in dogs, like in oral infections, abscesses and wound infections. The purpose of this study was to evaluate antimicrobial susceptibility in B. fragilis strains isolated from dogs intestinal microbiota and to evaluate the effect of subinhibitory concentrations of some antimicrobials on biofilm formation. A total of 30 B. fragilis group strains were tested for susceptibility to ten antimicrobial agents by broth microdilution method. Thirteen B. fragilis strains were tested for biofilm formation and the biofilm producer strains were chosen to evaluate the effect of subinhibitory concentrations of six antimicrobials on biofilm formation. The isolates were susceptible to amoxicillin-clavulanic acid, metronidazole, imipenem and chloramphenicol. Tetracycline and clindamycin were active against 50% and 33% of the strains, respectively. When biofilm-forming strains were grown in the presence of sub-MICs of imipenem and metronidazole, the inhibition of biofilm formation was observed. In contrast, enrofloxacin at ½ MIC caused a significant increase in biofilm formation in two of four strains examined. In conclusion, the B. fragilis group strains isolated were susceptible to most of the antimicrobials tested and the sub-MIC concentrations of imipenem, metronidazole and clindamycin were able to inhibit the biofilm formation.

      PubDate: 2014-05-09T06:25:21Z
  • Occurrence of Clostridium difficile PCR-ribotype 027 and it’s
           closely related PCR-ribotype 176 in hospitals in Poland in 2008-2010
    • Abstract: Publication date: Available online 2 May 2014
      Author(s): Piotr Obuch-Woszczatyński , Dominika Lachowicz , Anna Schneider , Anna Mól , Jolanta Pawłowska , Ewa Ożdżeńska-Milke , Piotr Pruszczyk , Dorota Wultańska , Grażyna Młynarczyk , Celine Harmanus , Ed J. Kuijper , Alex van Belkum , Hanna Pituch
      Since 2003, a rising incidence of Clostridium difficile infection (CDI) in North America and Europe has coincided with outbreaks of C. difficile PCR ribotype 027. This ribotype was not observed in Poland until 2008. In the period 2008–2010, outbreaks of antibiotic-associated diarrhoea occurred in three different hospitals in Poland. Of 30 C. difficile isolates available for microbiological characterisation, 17 (56%) were positive for binary toxin genes and belonged to PCR ribotype 027 (n = 7) and its closely related PCR ribotype 176 (n = 10). All 17 binary toxin–positive C. difficile strains demonstrated high-level resistance to fluoroquinolones (minimum inhibitory concentration (MIC) ≥ 32 mg/L), including ciprofloxacin, gatifloxacin, and moxifloxacin, as well as erythromycin and clindamycin (MIC ≥ 256 mg/L for both). Of 14 patients from whom clinical information was available, 50% had a severe form of CDI, defined by fever (>38.5°C), decreased kidney function, and high leukocyte count. We conclude that outbreaks of CDI associated with hypervirulent strains belonging to PCR ribotypes 027 and 176 occurred in hospitals in Poland. Further studies evaluating the clinical impact of type 176 are urgently needed.

      PubDate: 2014-05-04T07:20:37Z
  • Dynamics of microbial communities in untreated and autoclaved food waste
           anaerobic digesters
    • Abstract: Publication date: Available online 1 May 2014
      Author(s): Lucia Blasco , Minna Kahala , Elina Tampio , Satu Ervasti , Teija Paavola , Jukka Rintala , Vesa Joutsjoki
      This study describes the microbial community richness and dynamics of two semi-continuously stirred biogas reactors during a time-course study of 120 days. The reactors were fed with untreated and autoclaved (160°C, 6.2 bar) food waste. The microbial community was analyzed using a bacteria- and archaea-targeting 16S rRNA gene-based Terminal-Restriction Fragment Length Polymorphism (T-RFLP) approach. Compared with the archaeal community, the structures and functions of the bacterial community were found to be more complex and diverse. With the principal coordinates analysis it was possible to separate both microbial communities with 75 and 50% difference for bacteria and archaea, respectively, in the two reactors fed with the same waste but with different pretreatment. Despite the use of the same feeding material, anaerobic reactors showed a distinct community profile which could explain the differences in methane yield (2-17%). The community composition was highly dynamic for bacteria and archaea during the entire studied period. This study illustrates that microbial communities are dependent on feeding material and that correlations among specific bacterial and archaeal T-RFs can be established.

      PubDate: 2014-05-04T07:20:37Z
  • Potential of goat probiotic to bind mutagens
    • Abstract: Publication date: Available online 29 April 2014
      Author(s): Ana Lidia Apás , Silvia Nelina González , Mario Eduardo Arena
      The mutagen binding ability of the goat probiotics (Lactobacillus reuteri DDL 19, Lactobacillus alimentarius DDL 48, Enterococcus faecium DDE 39, and Bifidobacterium bifidum DDBA) was evaluated. The oral administration of these probiotics reduced fecal mutagens and intestinal cancer markers in goats. Secondly, the effects of probiotics against the mutagenesis induced by sodium azide (SA), and Benzopyrene (B[α]P) by performing the modified Ames test using Salmonella typhimurium TA 100 was investigated. The capacity to bind benzopyrene and the stability of the bacterial-mutagen complex was analyzed by HPLC. The dismutagenic potential against both mutagens was proportional to probiotic concentration. Results showed that probiotic antimutagenic capacity against SA was ranging from 13 to 78%. The mixture of four goat probiotics (MGP) displayed higher antimutagenic activity against SA than any individual strains at the same cell concentration. This study shows that the highest diminution of mutagenicity in presence of B[α]P (74%) was observed in presence of MGP. The antimutagenic activity of nearly all the individual probiotic and the MGP were in concordance with the B[α]P binding determined by HPLC. According to our results, the B[α]P binding to probiotic was irreversible still after being washed with DMSO solution. The stability of the toxic compounds-bacterial cell binding is a key consideration when probiotic antimutagenic property is evaluated. MGP exhibits the ability to bind and detoxify potent mutagens, and this property can be useful in supplemented foods for goats since it can lead to the removal of potent mutagens and protect and enhance ruminal health and hence food safety of consumers.

      PubDate: 2014-04-29T06:44:24Z
  • Towards molecular biomarkers for biogas production from
           lignocellulose-rich substrates
    • Abstract: Publication date: Available online 28 April 2014
      Author(s): Michael Lebuhn , Angelika Hanreich , Michael Klocke , Andreas Schlüter , Christoph Bauer , Carmen Marín Pérez
      Biogas production from lignocellulose-rich agricultural residues is gaining increasingly importance in sustainable energy production. Hydrolysis/acidogenesis (H/A) of lignocellulose as the initial rate limiting step deserves particular optimization. A mixture of straw/hay was methanized applying two-phase digester systems with an initial H/A reactor and a one-stage system at different, meso- and thermophilic temperatures. H/A was intensified with increasing pH-values and increasing temperature. H/A fermenters, however, were prone to switch to methanogenic systems at these conditions. Substrate turnover was accelerated in the bi-phasic process but did not reach the methanation efficiency of the single-stage digestion. There was no indication that 2 different cellulolytic inocula could establish in the given process. Bacterial communities were analyzed applying conventional amplicon clone sequencing targeting the hypervariable 16S rRNA gene region V6 – V8 and by metagenome analyses applying direct DNA pyrosequencing without a PCR step. Corresponding results suggested that PCR did not introduce a bias but offered better phylogenetic resolution. Certain Clostridium IV and Prevotella members were most abundant in the H/A system operated at 38°C, certain Clostridium III and Lachnospiraceae bacteria in the 45°C, and certain Clostridium IV and Thermohydrogenium/Thermoanaerobacterium members in the 55°C H/A system. Clostridium III representatives, Lachnospiraceae and Thermotogae dominated in the thermophilic single-stage system, in which also a higher portion of known syntrophic acetate oxidizers was found. Specific (RT-)qPCR systems were designed and applied for the most significant and abundant populations to assess their activity in the different digestion systems. The RT-qPCR results agreed with the DNA based community profiles obtained at the different temperatures. Up to 1012 16S rRNA copies * mL-1 were determined in H/A fermenters with prevalence of rRNA of a Ruminococcaceae subgroup. Besides, Thermohydrogenium/Thermoanaerobacterium rRNA prevailed at thermophilic and Prevotellaceae rRNA at mesophilic conditions. The developed (RT)-qPCR systems can be used as biomarkers to optimize biogas production from straw/hay and possibly other lignocellulosic substrates.

      PubDate: 2014-04-29T06:44:24Z
  • Anti stress proteins produced by Bacteroides thetaiotaomicron after
           nutrient starvation
    • Abstract: Publication date: Available online 28 April 2014
      Author(s): Anne-Cécile Hochart-Behra , Hervé Drobecq , Mélissa Tourret , Luc Dubreuil , Josette Behra-Miellet
      Bacteroides thetaiotaomicron may be one of the most adaptable intestinal bacteria due to its complex genome. Known to be an opportunistic pathogenic anaerobe, B. thetaiotaomicron has recently been described as a symbiont with anti-inflammatory properties. In this study, peptide mass finger printing technique was used to identify the stress proteins (maybe anti stress proteins for the host) extracted from B. thetataiotaomicron grown under nutrient starvation (without heme, blood or bile) prior to be placed in an aerobic solution containing a mild non-ionic detergent derived from cholic acid. We focus here on proteins related to stress, knowing that superoxide dismutase was previously identified in the extract. In parallel, the morphology of the bacterial cells was observed using electronic microscopy before and after the extraction process. The effective antioxidant effect of the extract was evaluated in vitro against hydrogen peroxide. This work highlights the B. thetaiotaomicron ability to produce a large amount of stress proteins and to remain viable during the extraction. Budding vesicles were observed on its cell wall. The extraction process did not exceed 20 h in order to preserve the bacterial viability that decreased significantly after 24 h in preliminary studies. In our experimental conditions, an inhibitory effect of the extract was found against hydrogen peroxide. Animal models of inflammation will later check in vivo if this extract of anti stress proteins is able to counter the respiratory burst beginning an inflammation process.
      Graphical abstract image

      PubDate: 2014-04-29T06:44:24Z
  • 8th International Symposium on Anaerobic Microbiology (ISAM 8): No oxygen
           - still vigorous Innsbruck, Austria, June 12-15, 2013
    • Abstract: Publication date: Available online 29 April 2014
      Author(s): Heribert Insam , Sabine Marie Podmirseg , Andreas Otto Wagner , Jiri Simunek

      PubDate: 2014-04-29T06:44:24Z
  • Reactor performance of a 750 m3 anaerobic digestion plant: Varied
           substrate input conditions impacting methanogenic community
    • Abstract: Publication date: Available online 13 April 2014
      Author(s): Andreas Otto Wagner , Cornelia Malin , Philipp Lins , Gudrun Gstraunthaler , Paul Illmer
      A 750 m3 anaerobic digester was studied over a half year period including a shift from good reactor performance to a reduced one. Various abiotic parameters like volatile fatty acids (VFA) (formic-, acetic-, propionic-, (iso-)butyric-, (iso-)valeric-, lactic acid), total C, total N, NH4 -N, and total proteins, as well as the organic matter content and dry mass were determined. In addition several process parameters such as temperature, pH, retention time and input of substrate and the concentrations of CH4, H2, CO2 and H2S within the reactor were monitored continuously. The present study aimed at the investigation of the abundance of acetogens and total cell numbers and the microbial methanogenic community as derived from PCR-dHPLC analysis in order to put it into context with the determined abiotic parameters. An influence of substrate quantity on the efficiency of the anaerobic digestion process was found as well as a shift from a hydrogenotrophic in times of good reactor performance towards an acetoclastic dominated methanogenic community in times of reduced reactor performance. After the change in substrate conditions it took the methano-archaeal community about 5–6 weeks to be affected but then changes occurred quickly.

      PubDate: 2014-04-18T16:03:31Z
  • Process diagnosis using methanogenic Archaea in maize-fed, trace element
           depleted fermenters
    • Abstract: Publication date: Available online 18 April 2014
      Author(s): Bernhard Munk , Michael Lebuhn
      A mesophilic maize-fed pilot-scale fermenter was severely acidified due to trace element (TE) deficiency. Mainly cobalt (0.07 mg * kg-1 fresh mass (FM)), selenium (0.007 mg * kg-1 FM) and sodium (13 mg * kg-1 FM) were depleted. From this inoculum, three lab-scale flow-through fermenters were operated to analyse micronutrient deficiencies and population dynamics in more detail. One fermenter was supplemented with selenium, one with cobalt, and one served as control. After starvation and recovery of the fermenters, the organic loading rate (OLR) was increased. In parallel, the concentration (Real-Time PCR) of methanogens and their population composition (amplicon sequencing) was determined at the DNA and mRNA level. The parameters Metabolic Quotient (MQ) and cDNA/DNA were calculated to assess the activity of the methanogens. The control without TE supplementation acidified first at an OLR of 4.0 kg volatile solids (VS) * m-3 * d-1 while the singular addition of selenium and of cobalt positively influenced the fermenter stability up to an OLR of 4.5 or 5.0 kg VS * m-3 * d-1, respectively. In the stable process, the methanogenic populations were dominated by probably residual hydrogenotrophic Methanoculleus sp. (DNA-level), but representatives of versatile Methanosarcina sp. were most active (cDNA-level). When the TE supplemented fermenters began to acidify, Methanosarcina spp. were dominant in the whole (DNA-level) and the active (cDNA-level) community. The acidified control fermenter was dominated by Methanobacteriaceae genus IV. Until acidification, the concentration of methanogens increased with higher OLRs. The MQ indicated stress metabolism approximately one month before the TVA/TIC ratio reached a critical level of 0.7, demonstrating its suitability as early warning parameter of process acidification. The development of the cDNA/DNA ratio also reflected the increasing methanogenic activity with higher OLRs. Highest cDNA/DNA values (ca. 2) were obtained at metabolic strain of the methanogens, at the onset of acidification.

      PubDate: 2014-04-18T16:03:31Z
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