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BIOLOGY (1323 journals)            First | 1 2 3 4 5 6 7 8 | Last

Ecoprint : An International Journal of Ecology     Open Access  
Ecoscience     Full-text available via subscription   (Followers: 2)
Educational Technology Research and Development     Partially Free   (Followers: 171)
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: 16)
el–Hayah     Open Access   (Followers: 1)
Embo Molecular Medicine     Open Access   (Followers: 3)
EMBO reports     Full-text available via subscription   (Followers: 16)
Emotion Review     Hybrid Journal   (Followers: 10)
Endocrine Connections     Open Access   (Followers: 4)
Engineering & Technology     Hybrid Journal   (Followers: 17)
Engineering Economist, The     Hybrid Journal   (Followers: 2)
Engineering in Life Sciences     Hybrid Journal   (Followers: 3)
Engineering Optimization     Hybrid Journal   (Followers: 6)
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: 268)
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: 4)
Ethology Ecology & Evolution     Hybrid Journal   (Followers: 10)
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: 24)
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: 55)
Evolution and Human Behavior     Hybrid Journal   (Followers: 10)
Evolutionary Applications     Open Access   (Followers: 3)
Evolutionary Bioinformatics     Open Access   (Followers: 14)
Evolutionary Biology     Hybrid Journal   (Followers: 17)
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: 4)
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: 8)
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: 3)
Frontiers in Evolutionary Neuroscience     Open Access   (Followers: 1)
Frontiers in Life Science     Hybrid Journal  
Frontiers in Marine Science     Open Access   (Followers: 1)
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: 5)
Fungal Biology Reviews     Full-text available via subscription   (Followers: 5)
Fungal Diversity     Hybrid Journal   (Followers: 2)
Fungal Ecology     Hybrid Journal   (Followers: 5)

  First | 1 2 3 4 5 6 7 8 | Last

Journal Cover Anaerobe
   Journal TOC RSS feeds Export to Zotero [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  [2570 journals]   [SJR: 0.828]   [H-I: 39]
  • Two cases of adult botulism caused by botulinum neurotoxin producing
           Clostridium baratii
    • Abstract: Publication date: Available online 18 October 2014
      Author(s): George E. Hannett , Joshua K. Schaffzin , Stephen W. Davis , Maureen P. Fage , Dianna Schoonmaker-Bopp , Nellie B. Dumas , Kimberlee A. Musser , Christina Egan
      Type F botulism occurs rarely in clinical cases. Two cases of type F botulism in elderly patients that were clustered in time and space are described. Clostridium baratii producing type F botulinum neurotoxin was isolated from both patients; molecular typing of these isolates revealed that they were unrelated strains.

      PubDate: 2014-10-21T02:28:57Z
  • The effect of moonlighting proteins on the adhesion and aggregation
           ability of Lactobacillus helveticus
    • Abstract: Publication date: Available online 13 October 2014
      Author(s): Adam Waśko , Magdalena Polak-Berecka , Roman Paduch , Krzysztof Jóźwiak
      The goal of this study was to identify moonlighting proteins in Lactobacillus helveticus that play an important role in adhesion and aggregation. The label-free method was used for identification and analysis of expression of cellular proteins. The analysis revealed the presence of eight moonlighting proteins in the cell envelope of Lb. helveticus. The tested strains mainly differed with respect to the presence of S-layer proteins and the level of expression of moonlighting proteins in Lb. helveticus strain T159. These surface proteins give the cell a hydrophobic character and play a role in specific interactions with intestinal epithelium cells and with other bacteria. In Lb. helveticus T159, the S-layer associated with moonlighting proteins (SLAPs) could act as adherence factors, which was evidenced by the high capability of adhesion, auto- and coaggregation. The hydrophobicity, adhesion and aggregation abilities provide biological activities in food products and they are regarded as an important criterion for probiotic selection.

      PubDate: 2014-10-16T02:07:52Z
  • Biosynthesis and cellular content of folate in bifidobacteria across host
           species with different diets
    • Abstract: Publication date: Available online 12 October 2014
      Author(s): Maria R. D'Aimmo , Monica Modesto , Paola Mattarelli , Bruno Biavati , Thomas Andlid
      Background Bifidobacteria, one of the most common bacteria of the intestinal tract, help establish balance in the gut microbiota and confer health benefits to the host. One beneficial property is folate biosynthesis, which is dependent on species and strains. It is unclear whether the diversity in folate biosynthesis is due to the adaptation of the bifidobacteria to the host diet or whether it is related to the phylogeny of the animal host. To date, folate production has been studied in the bifidobacteria of omnivorous, and a few herbivorous, non-primate hosts and humans, but not in carnivores, non-human primates and insects. In our study we screened folate content and composition in bifidobacteria isolated from carnivores (dog and cheetah), Hominoidea omnivorous non-human primates (chimpanzee and orangutan) and nectarivorous insects (honey bee). Results Bifidobacterium pseudolongum subsp. globosum, a species typically found in non-primates, was isolated from dog and cheetah, and B. adolescentis and B. dentium, species typically found in humans, were respectively obtained from orangutan and chimpanzee. Evidence of folate biosynthesis was found in bifidobacteria isolated from non-human primates, but not from the bifidobacteria of carnivores and honey-bee. On comparing species from different hosts, such as poultry and herbivorous/omnivorous non-primates, it would appear that folate production is characteristic of primate (human and non-human) bifidobacteria but not of non-primate. Isolates from orangutan and chimpanzee had a high total folate content, the mean values being 7792 μg/100 g dry matter (DM) for chimpanzee and 8368 μg/100 g DM for orangutan. The tetrahydrofolate (H4folate) and 5-methyl-tetrahydrofolate (5-CH3-H4folate) distribution varied in the bifidobacteria of the different animal species, but remained similar in the strains of the same species: B. dentium CHZ9 contained the least 5-CH3-H4folate (3749 μ/100 g DM), while B. adolescentis ORG10 contained the most (8210 μg/100 g DM). Conclusion Our data suggest a correlation between phylogenetic lineage and capacity of folate production by bifidobacteria, rather than with dietary type of the host.

      PubDate: 2014-10-16T02:07:52Z
  • Antibiotic resistance patterns and PCR-ribotyping of Clostridium difficile
           strains isolated from swine and dogs in Italy
    • Abstract: Publication date: Available online 12 October 2014
      Author(s): Patrizia Spigaglia , Ilenia Drigo , Fabrizio Barbanti , Paola Mastrantonio , Luca Bano , Cosetta Bacchin , Cinzia Puiatti , Elena Tonon , Giacomo Berto , Fabrizio Agnoletti
      Recent studies suggest animals, in particular farm and companion animals, as possible reservoir for C. difficile human pathogenic strains. The aim of this study was to give a first characterization of C. difficile isolates from Italian swine and dogs. In total, 10 different PCR-ribotypes were identified among porcine strains and six among canine strains. The predominant type found among porcine strains was 078 (50%), whereas the most frequently detected among canine strains was the non-toxinogenic 010 (64%). Considering the CLSI breakpoints, 60% of porcine isolates was resistant to ERY, 35% to MXF, 15% to CLI, 5% to RIF, and none to MTZ or VAN. Among dogs, 51% of strains was resistant to CLI, 46% to ERY, 21% to MTZ and 5% to MXF or RIF, and none to VAN. Five porcine strains (10%) and 9 canine isolates (41%) were MDR. Interestingly, 8 MDR canine strains were higly resistant to MTZ, with MICs ≥ 32 mg/L. Considering the EUCAST cut-off for MTZ (MIC > 2 mg/L), 13 canine isolates and one porcine strain were found with reduced susceptibility to MTZ (MICs ranging from 3 to ≥256 mg/L). Swine and canine strains showing resistance or reduced susceptibility to MTZ belonged to PCR-ribotype 010 and 078. These PCR-ribotypes have been associated to reduced susceptibility to MTZ also in human, suggesting a potential risk for the emergence of C. difficile strains resistant to the current first-line antibiotic for CDI treatment. The agar incorporation method (AIM) was confirmed as the best method to detect C. difficile strains with this phenotype also after strains manipulations. The results obtained add further evidences about the possible role of animals as source of MDR C. difficile strains and reservoir of antibiotic resistance determinants.

      PubDate: 2014-10-16T02:07:52Z
  • Ruminococcus gnavus: An unusual pathogen in septic arthritis
    • Abstract: Publication date: Available online 13 October 2014
      Author(s): Marie Titécat , Frédéric Wallet , Marie-Hélène Vieillard , René J. Courcol , Caroline Loïez
      Ruminococcus gnavus is an anaerobic Gram positive coccus that can be found in the gastrointestinal tract of animals and humans. We report a case of septic arthritis caused by R. gnavus that was identified by mass spectrometry and confirmed by 16S rRNA sequencing.

      PubDate: 2014-10-16T02:07:52Z
  • Development of antimicrobial resistance in the normal anaerobic microbiota
           during one year after administration of clindamycin or ciprofloxacin
    • Abstract: Publication date: Available online 15 October 2014
      Author(s): Mamun-Ur Rashid , Andrej Weintraub , Carl Erik Nord
      Thirty healthy subjects (15 males and 15 females) were randomly assigned in three groups and clindamycin (150 mg qid) or ciprofloxacin (500 mg bid) or placebo was given for a 10-day period. Skin, nasal, saliva, faeces samples were collected at day -1, day 11, 1 month, 2 months, 4 months and 12 months post administration for microbiological analysis. Ciprofloxacin or clindamycin had no impact on the anaerobic skin microbiota and the proportions of antibiotic resistant anaerobic bacteria were similar as in the placebo group. Ciprofloxacin had impact on the P. acnes in the nasal microbiota that normalized after 1 month, however, ciprofloxacin-resistant P. acnes strains increased at month 2 and month 12. Clindamycin had no impact on the nasal microbiota. In the oropharyngeal microbiota, a higher proportion of ciprofloxacin resistant Veillonella was found, it lasting up to 12 months post dosing. In the clindamycin group, clindamycin-resistant Prevotella spp were found in increased proportions compared to placebo at various time points except month 4 in the saliva samples. The relative proportion of ciprofloxacin-resistant Bifidobacteria increased in the faecal samples on day 11, 1 month, 4 months and 12 months post dosing compared to placebo. The proportion of clindamycin-resistant Bacteroides spp increased at 1, 2, 4 and 12 months post dosing compared to placebo in the faecal samples. No C. difficile was recovered from any of the samples from any of the volunteers at any visit. The concentrations of ciprofloxacin or clindamycin in the faeces were higher than the MICs for most of the organisms present in the normal microbiota. No obvious correlation between the groups in resistant patterns for anaerobic bacteria was observed. In conclusion, based on the microbiological data of the microbiota as well as the results of the bioassays for ciprofloxacin and clindamycin concentrations in the faecal samples, oral administration of ciprofloxacin and clindamycin has an impact on the anaerobic microbiota and may have a long-term effect on the development and persistence of antibiotic-resistant anaerobes in the normal microbiota.

      PubDate: 2014-10-16T02:07:52Z
  • A case of imported Clostridium difficile PCR-ribotype 027 infection within
           the Czech Republic which has a high prevalence of Clostridium difficile
           ribotype 176
    • Abstract: Publication date: Available online 7 October 2014
      Author(s): Marcela Krutova , Otakar Nyc , Ed J. Kuijper , Lenka Geigerova , Jana Matejkova , Tamara Bergerova , Mardjan Arvand
      The first case of C. difficile RT027 infection in the Czech Republic (CZ) was identified. The patient had been hospitalised in Germany prior to moving to CZ. Multiple-Locus Variable number tandem repeat Analysis revealed a genetic relatedness between the patient´s isolate and RT027 isolate collected in the German hospital.

      PubDate: 2014-10-08T01:28:47Z
  • First Hungarian case of an infection caused by multidrug-resistant
           Bacteroides fragilis strain
    • Abstract: Publication date: Available online 5 October 2014
      Author(s): Dr. Edit Urbán , Zoltán Horváth , József Sóki , György Lázár
      We report a case caused by a multidrug-resistant (MDR) Bacteroides fragilis strain isolated from abdominal fluid of a male patient with complex underlying diseases. The patient had received antibiotics prior to the presented case. As far as we know, this case with a MDR B. fragilis is the first from Hungary, and Eastern-Europe, as well.

      PubDate: 2014-10-08T01:28:47Z
  • View from the front lines: An emergency medicine perspective on
           clostridial infections in injection drug users
    • Abstract: Publication date: December 2014
      Source:Anaerobe, Volume 30
      Author(s): Richard Diego Gonzales y Tucker , Bradley Frazee
      Injection drug use (IDU), specifically non-intravenous “skin-popping” of heroin, seems to provide optimal conditions for Clostridial infection and toxin production. IDU is therefore a major risk factor for wound botulism and Clostridial necrotizing soft tissue infections (NSTI) and continues to be linked to cases of tetanus. Case clusters of all 3 diseases have occurred among IDUs in Western U.S. and Europe. Medical personnel who care for the IDU population must be thoroughly familiar with the clinical presentation and management of these diseases. Wound botulism presents with bulbar symptoms and signs that are easily overlooked; rapid acquisition and administration of antitoxin can prevent neuromuscular respiratory failure. In addition to Clostridium perfringens, IDU-related NSTIs can be caused by Clostridium sordellii and Clostridium novyi, which may share a distinct clinical presentation. Early definitive NSTI management, which decreases mortality, requires a low index of suspicion on the part of emergency physicians and low threshold for surgical exploration and debridement on the part of the surgeon. Tetanus should be preventable in the IDU population through careful attention to vaccination status.

      PubDate: 2014-10-08T01:28:47Z
  • Performance assessment of the BD MAX Cdiff assay in comparison to Xpert C.
           difficile assay in a setting with very low prevalence of toxigenic
           Clostridium difficile PCR ribotype 027
    • Abstract: Publication date: Available online 7 October 2014
      Author(s): Donald Chiang , Sally Ng , My-Van La , Roland Jureen , Raymond T.P. Lin , Jeanette W.P. Teo
      In a clinical setting with low prevalence of ‘epidemic’ PCR ribotype 027, the BD MAX Cdiff assay was found to be a suitable alternative to the Xpert C. difficile assay for the detection of toxigenic Clostridium difficile in samples which are reflex PCR tested after obtaining a discrepant immunoassay result. There was no significant difference between the sensitivities and specificities of both commercial molecular assays.

      PubDate: 2014-10-08T01:28:47Z
  • Study on bioactivity of cell-free filtrates from dairy propionibacteria
    • Abstract: Publication date: Available online 30 September 2014
      Author(s): Alfonso Filippone , Milena Sinigaglia , Clelia Altieri
      In this paper, the bioactivity of cell-free extracts obtained by dairy propionibacteria strains was investigated. Probiotic bifidobacteria and lactobacilli were used as microbial targets. The extracellular filtrates were added as ingredient (1% v/v) into the growth medium; the effect of cell-free filtrates was evaluated through viable count of microbial targets on appropriate media, monitoring the response of target microorganisms both in growth and death phase. The Gompertz equation was used to model the experimental data. Kinetics and time parameters were estimated in order to quantify the effectiveness of cell-free filtrates effect. To emphasize the results about the bioactivity of cell-free extract, supporting a complete picture of response, a new approach was developed: Probiotic Stability Time was calculated. This temporal parameter, defined as the time over that the cell load preserve a living value upper than 107 cfu ml-1, was very useful to evaluate the probiotic capability and effectiveness. A stimulant effect was registered on growth and a positive one was recordered on survival of both bifidobacteria and lactobacilli strains, and the results obtained suggest that a prebiotic activity by dairy propionibacteria cell-free filtrates could be supposed. The cell free filtrate obtained from P. freudenreichii subsp. shermanii was the most effective, in our experimental conditions. Although bifidobacteria were the most sensitive to the effect of cell-free filtrates, lactobacilli have been showed a similar probiotic stability time, showing an high sensitivity to the filtrates. This paper is the first report of a positive bioactivity by propionibacteria cell-free filtrates on lactobacilli.

      PubDate: 2014-10-03T00:51:24Z
  • The influence of Lactobacillus casei DN 114 001 on the activity of faecal
           enzymes and genotoxicity of faecal water in the presence of heterocyclic
           aromatic amines
    • Abstract: Publication date: Available online 30 September 2014
      Author(s): Adriana Nowak , Katarzyna Śliżewska , Janusz Błasiak , Zdzisława Libudzisz
      High activity of bacterial enzymes in human colon and genotoxicity of faecal water (FW) are biomarkers of the harmful action of microbiota. The aim of the present study was to assess the activity of β-glucuronidase and β-glucosidase and the genotoxicity of FW in vitro after incubation with 2-amino-3-methyl-3H-imidazo[4,5-f]quinoline (IQ) or 2-amino-1-methyl-6-phenyl-1H-imidazo [4,5-b]pyridine (PhIP) and probiotic Lb. casei DN 114 001 (Actimel). Our results indicate, that IQ and PhIP greatly increased the activity of faecal enzymes (it was up to four times higher, as measured by spectrophotometric methods) and the genotoxicity of FW (% DNA in the tail was up to 3.2 times higher, as evaluated by the comet assay on Caco-2 cells) in 15 individuals from three age-dependent groups (breast-fed children, adults aged 30-40 years, elderly aged 75-85 years). Lb. casei DN 114 001 decreased the activity of faecal enzymes and the genotoxicity of FW exposed to PhIP and IQ mostly to control values. The activity of faecal enzymes after incubation with IQ was reduced by 71.8% in the FW of children, 37.5% in adults and 64.2% in elderly (β-glucuronidase); as well as by 59.9% in children and 87.9% in elderly (β-glucosidase). For PhIP the reduction was by 59.0% in the FW of children, 50.0% in adults and 81.2% in elderly (β-glucuronidase) and by 20.2% in children, 20.7% in adults and 84.1% in elderly (β-glucosidase). Lb. casei DN 114 001 also decreased the genotoxicity of FW to the greatest extent in adults after incubation with IQ (by 65.4%) and PhIP (by 69.6%) and it was found to correlate positively with the decrease in faecal enzymes activity. In conclusion, Lb. casei DN 114 001 may exert the protective effects against genotoxic and possibly pro-carcinogenic effects of food processing-derived chemicals present in faecal water.

      PubDate: 2014-10-03T00:51:24Z
  • "Antibacterial activity of Pinus elliottii against anaerobic bacteria
           present in primary endodontic infections"
    • Abstract: Publication date: Available online 28 September 2014
      Author(s): Sandro Donizete Caetano da Silva , Maria Gorete Mendes de Souza , Miguel Jorge Oliveira Cardoso , Thais da Silva Moraes , Sérgio Ricardo Ambrósio , Rodrigo Cássio Sola Veneziani , Carlos Henrique G. Martins
      Endodontic infections have a polymicrobial nature, but anaerobic bacteria prevail among the infectious microbes. Considering that it is easy to eliminate planktonic bacteria, biofilm-forming bacteria still challenge clinicians during the fight against endodontic diseases. The chemical constituents of the oleoresin of Pinus elliottii, a plant belonging to the family Pinaceae, stand out in the search for biologically active compounds based on natural products with potential application in the treatment of endodontic infections. Indeed, plant oleoresins are an abundant natural source of diterpenes that display significant and well-defined biological activities as well as potential antimicrobial action. In this context, this study aimed to (1) evaluate the in vitro antibacterial activity of the oleoresin, fractions, and subfractions of P. elliottii as well as the action of dehydroabietic acid against 11 anaerobic bacteria that cause endodontic infection in both their planktonic and biofilm forms and (2) assess the in vitro antibiofilm activity of dehydroabietic acid against the same group of bacteria. The broth microdilution technique helped to determine the minimum inhibitory concentration (MIC) of the oleoresin and fractions. This same technique aided determination of the MIC values of nine subfractions of Fraction 1, the most active fraction. The MIC, minimum bactericidal concentration, and antibiofilm activity of dehydroabietic acid against the tested anaerobic bacteria were also examined. The oleoresin and fractions, especially fraction PE1, afforded promising MIC values, which ranged from 0.4 to 50 μg/mL. Concerning the nine evaluated subfractions, PE1.3 and PE1.4 furnished the most noteworthy MIC values, between 6.2 and 100 μg/mL. Dehydroabietic acid displayed antibacterial activity, with MIC values lying from 6.2 to 50 μg/mL, as well as bactericidal effect for all the investigated bacteria, except for P. nigrescens. Assessment of the antibiofilm activity revealed significant results - MICB50 lay between 7.8 and 62.5 μg/mL, and dehydroabietic acid prevented all the evaluated bacteria from forming a biofilm. Hence, the chemical constituents of P. elliottii are promising biomolecules to develop novel therapeutic strategies to fight against endodontic infections.

      PubDate: 2014-10-03T00:51:24Z
  • Probiotic characteristics of lactobacillus fermentum strains isolated from
           tulum cheese
    • Abstract: Publication date: Available online 28 September 2014
      Author(s): Şener Tulumoğlu , Halil İbrahim Kaya , Ömer Şimşek
      The aim of this study was to characterize the probiotic characteristics of L. fermentum strains isolated from Tulum cheese. Seven L. fermentum strains were selected among the isolated and identified lactobacillus strains due to their abundance. When the gastric condition was considered, L. fermentum LP3 and LP4 were able to tolerate pH 2.5 and 1% bile salt. All L. fermentum strains had similar enzymatic activity and antibiotic resistance pattern but the highest antagonistic effect was detected within LP3, LP4 and LP6. Cholesterol assimilation amount of L. fermentum strains ranged between 12.1-45.3% in MRS and 20.7-71.1% in MRS with bile. The highest cholesterol assimilation in MRS and MRS with bile was occurred by LP3 and LP4, respectively. L. fermentum LP2 adhered to caco-2 cells more than L. rhamnosus LGG where LP3, LP4 and LP5 adhered at similar level. In conclusion, L. fermentum LP3 and LP4 fulfilled sufficient criteria to be probiotics for use as a starter culture in the production of tulum cheese or other dairy products. Also this study indicated that some food-associated Lactobacillus strains non-predominant for gut biota have significant probiotic potential.

      PubDate: 2014-10-03T00:51:24Z
  • Carriage of Clostridium difficile in free-living South American coati
           (Nasua nasua) in Brazil
    • Abstract: Publication date: Available online 27 September 2014
      Author(s): Rodrigo Otávio Silveira Silva , Lara Ribeiro de Almeida , Carlos Augusto Oliveira Junior , Danielle Ferreira de Magalhães Soares , Pedro Lúcio Lithg Pereira , Maja Rupnik , Francisco Carlos Faria Lobato
      The objective of this study was to isolate and characterize Clostridium difficile strains in stool samples from a wild urban mammal, a South American coati (Nasua nasua) in Brazil. Forty-six free-living N. nasua were trapped, and stool samples were collected. C. difficile was isolated from three (6.5%) sampled animals, two strains were toxigenic (A+B+CDT−, PCR ribotype 014/020 and 106) and one was non toxigenic (A−B−CDT−, PCR ribotype 053). The present work confirms that ring-tailed coati (N. nasua) could harbor C. difficile strains, including those PCR ribotypes commonly reported in C. difficile infection in humans.

      PubDate: 2014-09-28T00:00:25Z
  • Azorean wild rabbits as reservoirs of antimicrobial resistant Escherichia
    • Abstract: Publication date: Available online 20 September 2014
      Author(s): Catarina Marinho , Gilberto Igrejas , Alexandre Gonçalves , Nuno Silva , Tiago Santos , Ricardo Monteiro , David Gonçalves , Tiago Rodrigues , Patrícia Poeta
      Antibiotic resistance in bacteria is an increasing problem that is not only constrained to the clinical setting but also to other environments that can lodge antibiotic resistant bacteria and therefore they may serve as reservoirs of genetic determinants of antibiotic resistance. One hundred and thirty-six faecal samples from European wild rabbits (Oryctolagus cuniculus algirus) were collected on São Jorge Island in Azores Archipelago, and analysed for Escherichia coli isolates. Seventy-seven isolates (56.6%) were recovered and studied for antimicrobial resistance, one isolate per positive sample. Thirteen (16.9%), 19 (24.7%), 25 (32.4%) and 20 (26%) isolates were ascribed to A, B1, B2 and D phylogenetic groups, respectively, by specific primer polymerase chain reaction. Different E. coli isolates were found to be resistant to ampicillin (16.9%), tetracycline (1.3%), streptomycin (42.9%), sulfamethoxazole-trimethoprim (1.3%), amikacin (1.3%), tobramycin (2.6%) and nalidixic acid (1.3%). Additionally, the bla TEM, tetA, strA/strB, aadA, sul1, intI, intI2 and qacEΔ+sul1 genes were found in most resistant isolates. This study showed that E. coli from the intestinal tract of wild rabbits from Azores Archipelago are resistant to widely prescribed antibiotics in medicine and they constitute a reservoir of antimicrobial resistant genes, which may play a significant role in the spread of antimicrobial resistance. Therefore, antibiotic resistant E. coli from Azorean wild rabbits may represent an ecological and public health problem.
      Graphical abstract image

      PubDate: 2014-09-23T23:48:12Z
  • Evaluation of MALDI-TOF mass spectrometry for identification of anaerobic
    • Abstract: Publication date: Available online 23 September 2014
      Author(s): M.J. Barba , A. Fernández , M. Oviaño , B. Fernández , D. Velasco , G. Bou
      In this study MALDI-TOF MS was evaluated in the identification of anaerobic bacteria comparing it with Rapid ID 32A system. Discrepancies were solved by 16S r-RNA gene sequencing. At the species level MALDI-TOF MS identified 94.82% and Rapid ID 32A 86.67%, showing the superiority of MALDI-TOF MS to conventional methods.

      PubDate: 2014-09-23T23:48:12Z
  • Clostridium perfringens epsilon toxin: The third most potent bacterial
           toxin known
    • Abstract: Publication date: Available online 16 September 2014
      Author(s): Guilherme Guerra Alves , Ricardo Andrez Machado de Ávila , Carlos Delfin Chávez-Olórtegui , Francisco Carlos Faria Lobato
      Epsilon toxin (ETX) is produced by Clostridium perfringens type B and D strains and causes enterotoxemia, a highly lethal disease with major impacts on the farming of domestic ruminants, particularly sheep. ETX belongs to the aerolysin-like pore-forming toxin family. Although ETX has striking similarities to other toxins in this family, ETX is often more potent, with an LD50 of 100 ng/kg in mice. Due to this high potency, ETX is considered as a potential bioterrorism agent and has been classified as a category B biological agent by the Centers for Disease Control and Prevention (CDC) of the United States. The protoxin is converted to an active toxin through proteolytic cleavage performed by specific proteases. ETX is absorbed and acts locally in the intestines then subsequently binds to and causes lesions in other organs, including the kidneys, lungs and brain. The importance of this toxin for veterinary medicine and its possible use as a biological weapon have drawn the attention of researchers and have led to a large number of studies investigating ETX. The aim of the present work is to review the existing knowledge on ETX from C. perfringens type B and D.

      PubDate: 2014-09-19T23:18:38Z
  • Comparing the identification of Clostridium spp. by two Matrix-Assisted
           Laser Desorption Ionization-Time of Flight (MALDI-TOF) mass spectrometry
           platforms to 16S rRNA PCR sequencing as a reference standard: A detailed
           analysis of age of culture and sample preparation
    • Abstract: Publication date: Available online 16 September 2014
      Author(s): Roy Chean , Despina Kotsanas , Michelle J. Francis , Enzo A. Palombo , Snehal R. Jadhav , Milena M. Awad , Dena Lyras , Tony M. Korman , Grant A. Jenkin
      We compared the identification of Clostridium species using mass spectrometry by two different Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) platforms (Bruker MS and Vitek MS) against 16S rRNA sequencing as the reference standard. We then examined the impact of different sample preparations and (on one of those platforms) age of bacterial colonial growth on the performance of the MALDI-TOF MS systems. We identified 10 different species amongst the 52 isolates by 16S rRNA sequencing, with Clostridium perfringens the most prevalent (n = 30). Spectrometric analysis using Vitek MS correctly speciated 47/52 (90.4%) isolates and was not affected by the sample preparation used. Performance of the Bruker MS was dependent on sample preparation with correct speciation obtained for 36 of 52 (69.2%) isolates tested using the Direct Transfer [DT] protocol, but all 52 (100%) isolates were correctly speciated using either an Extended Direct Transfer [EDT] or a Full Formic Extraction [EX] protocol. We then examined the effect of bacterial colonial growth age on the performance of Bruker MS and found substantial agreement in speciation using DT (Kappa = 0.62, 95% CI: 0.46–0.75), almost perfect agreement for EDT (Kappa = 0.94, 95% CI: 0.86–1.00) and exact agreement for EX (Kappa = 1.00) between different days.

      PubDate: 2014-09-19T23:18:38Z
  • Clostridium difficile-induced colitis in mice is independent of
    • Abstract: Publication date: Available online 16 September 2014
      Author(s): Bruno C. Trindade , Casey M. Theriot , Jhansi L. Leslie , Paul E. Carlson Jr. , Ingrid L. Bergin , Marc Peters-Golden , Vincent B. Young , David M. Aronoff
      Clostridium difficile is the major cause of antibiotic-associated diarrhea and pseudomembranous colitis in healthcare settings. However, the host factors involved in the intestinal inflammatory response and pathogenesis of C. difficile infection (CDI) are largely unknown. Here we investigated the role of leukotrienes (LTs), a group of pro-inflammatory lipid mediators, in CDI. Notably, the neutrophil chemoattractant LTB4, but not cysteinyl (cys) LTs, was induced in the intestine of C57BL/6 mice infected with either C. difficile strain VPI 10463 or strain 630. Genetic or pharmacological ablation of LT production did not ameliorate C. difficile colitis or clinical signs of disease in infected mice. Histological analysis demonstrated that intestinal neutrophilic inflammation, edema and tissue damage in mice during acute and severe CDI were not modulated in the absence of LTs. In addition, CDI induced a burst of cytokines in the intestine of infected mice in a LT-independent manner. Serum levels of anti-toxin A immunoglobulin (Ig) G levels were also not modulated by endogenous LTs. Collectively, our results do not support a role for LTs in modulating host susceptibility to CDI in mice.

      PubDate: 2014-09-19T23:18:38Z
  • Effect of prebiotics on the fecal microbiota of elderly volunteers after
           dietary supplementation of Bacillus coagulans GBI-30, 6086
    • Abstract: Publication date: Available online 16 September 2014
      Author(s): Edna P. Nyangale , Sean Farmer , David Keller , D. Chernof , Glenn R. Gibson
      In advancing age, gut populations of beneficial microbes, notably Bifidobacterium spp., show a marked decline. This contributes to an environment less capable of maintaining homoeostasis. This in vitro investigation studied the possible synergistic effects of probiotic supplementation in modulating the gut microbiota enabling prebiotic therapy to in elderly persons. Single stage batch culture anaerobic fermenters were used and inoculated with fecal microbiota obtained from volunteers after taking a 28 day treatment of Bacillus coagulans GBI-30, 6086 (GanedenBC30 (BC30)) or a placebo. The response to prebiotic supplements fructooligosaccharides (FOS) and galactooligosaccharides (GOS) in the fermenters was assessed. Bacterial enumeration was carried out using fluorescent in situ hybridisation and organic acids measured by gas chromatography. Baseline populations of Faecalibacterium prausnitzii, Clostridium lituseburense and Bacillus spp. were significantly higher in those having consumed BC30 compared to the placebo. Both prebiotics increased populations of several purportedly beneficial bacterial groups in both sets of volunteers. Samples from volunteers having ingested the BC30 also increased populations of C. lituseburense, Eubacterium rectale and F. prausnitzii more so than in persons who had consumed the placebo, this also resulted in significantly higher concentrations of butyrate, acetate and propionate. This shows that consumption of BC30 and subsequent use of prebiotics resulted in elevated populations of beneficial genres of bacteria as well as organic acid production.

      PubDate: 2014-09-19T23:18:38Z
  • Branched-chain alcohol formation from branched-chain amino acids by
           Thermoanaerobacter brockii and Thermoanaerobacter yonseiensis
    • Abstract: Publication date: Available online 16 September 2014
      Author(s): Sean Michael Scully , Johann Orlygsson
      Thermoanaerobacter species degrade branched-chain amino acids to a mixture of their corresponding branched-chain fatty acids and alcohols in the presence of thiosulfate; only acid formation occurred when Thermoanaerobacter strains were cultivated in co-culture with a hydrogenotrophic methanogen. Increased pH2 at high liquid–gas phase ratios increases the relative concentration of branched-chain alcohol.
      Graphical abstract image

      PubDate: 2014-09-19T23:18:38Z
  • Plasmid transformation of Weissella paramesenteroides DX by
    • Abstract: Publication date: Available online 6 September 2014
      Author(s): Maria Papagianni , Emmanuel M. Papamichael
      The present investigation sought to provide a reliable and highly efficient electrotransformation method for the lactic acid bacterium Weissella paramesenteroides DX. Experiments were carried out with the shuttle vectors pVS44 (2910 bps), pTRKH3 (7766 bps) and its derivative pTRKH3-1 (4855 bps). Several parameters, including the concentration of transforming plasmid DNA, plasmid size, electric field strength, age of the culture, cell density, and the pretreatment of cells with dl-threonine, lysozyme, and combined treatment with lithium acetate and dithiothreitol, were investigated and proved to influence the efficiency of transformation. Electrocompetence was found to peak in the early stationary phase (OD600 1.2). Other optimized conditions included: the concentration of 10 μg/ml transforming DNA, the cell density of 1010 cells/ml, a high-density electric field pulse of 2.5 kV, 25 μF and 200 Ω, pretreatment of cells with 40 mM dl-threonine and 2000 U/ml lysozyme, and yielded 3.5 × 104 transformants/μg DNA for pVS44 while 1.2 × 104 transformants/μg DNA for the large plasmid TRKH3. Compared to previously reported data, the obtained transformation efficiencies provided an 8.75-fold increase for pVS44 and ensured plasmid stability for 120 generations in non-selective medium.

      PubDate: 2014-09-11T22:23:48Z
  • Risk factors of Clostridium difficile infections among patients in a
           university hospital in Shanghai, China
    • Abstract: Publication date: Available online 8 September 2014
      Author(s): Haihui Huang , Shi Wu , Renjie Chen , Shaohua Xu , Hong Fang , Andrej Weintraub , Carl Erik Nord
      Clostridium difficile infection (CDI) is an increasing concern in China. However, the risk factors of CDI are rarely reported in the Chinese population. A prospective observational study was therefore conducted among patients with hospital-acquired C. difficile diarrhoea and the risk factors of CDI in a retrospective case-control study. The CDI patients were compared with the non-CDI diarrhoeal patients and those without diarrhoea, respectively. The recurrent CDI patients were compared with the corresponding non-recurrent CDI patients and those without diarrhoea, respectively. Overall, of the 240 patients with hospital-acquired diarrhoea 90 (37.5%) were diagnosed as CDI, and 12 (13.3%) of the 90 CDI patients experienced recurrence. Multivariate analysis indicated that renal disease, malignancy, hypoalbuminemia, prior antibiotic treatment, chemotherapy, nasogastric tube use, length of stay >14 days and intra-abdominal surgery, defined daily dose of antimicrobial agents ≥19, prior use of more than three antimicrobial agents, and use of carbapenems were independent risk factors for the first episode of CDI. Use of laxatives, the first- and second-generation narrow-spectrum cephalosporins or metronidazole was identified as protective factors. It is necessary to make testing of C. difficile available as a routine practice and control these risk factors in Chinese hospitals to avoid CDI outbreaks.

      PubDate: 2014-09-11T22:23:48Z
  • Dentilisin involvement in coaggregation between Treponema denticola and
           Tannerella forsythia
    • Abstract: Publication date: Available online 23 August 2014
      Author(s): Yumiko Sano , Kazuko Okamoto-Shibayama , Kimiko Tanaka , Rieko Ito , Seikou Shintani , Masashi Yakushiji , Kazuyuki Ishihara
      Periodontitis arises from a biofilm consisting of gram-negative anaerobic rods and spirochetes. Porphyromonas gingivalis, Treponema denticola, and Tannerella forsythia, termed the Red complex, have been co-isolated with high frequency from chronic periodontitis lesions, and these microorganisms are thought to be major pathogens of the disease. Coaggregation is an important strategy in the colonization of dental plaque biofilm by these bacteria. In the present study, we investigated the coaggregation of T. denticola strains with T. forsythia ATCC 43037 by use of visual grading or spectrophotometry. T. denticola ATCC 35405 coaggregated with T. forsythia, reaching a plateau at approximately 60 min. This coaggregation was inhibited by heat treatment of T. denticola ATCC 35405, but not of T. forsythia. Disaccharides such as sucrose, maltose, and lactose inhibited coaggregation by approximately 50%. The coaggregation reaction varied among T. denticola strains. There was somewhat less coaggregation between T. denticola ATCC 33520 and T. forsythia than between T. denticola ATCC 35405 and T. forsythia, although this difference was not statistically significant; T. denticola ATCC 33521 showed a trace level of coaggregation with T. forsythia. The magnitude of coaggregation among the three T. denticola strains was proportional to their dentilisin activities. Inactivation of dentilisin abolished coaggregation activity, but inactivation of the major outer sheath protein did not. In addition, phenylmethylsulfonyl fluoride did not affect coaggregation. These results indicate that dentilisin is involved indirectly in the coaggregation between T. denticola and T. forsythia, because its proteolytic activity is not required, possibly via ligand maturation.

      PubDate: 2014-09-01T21:10:28Z
  • Butyricicoccus pullicaecorum, a butyrate producer with probiotic
           potential, is intrinsically tolerant to stomach and small intestine
    • Abstract: Publication date: Available online 30 August 2014
      Author(s): Annelies Geirnaert , Alix Steyaert , Venessa Eeckhaut , Bo Debruyne , Jan B.A. Arends , Filip Van Immerseel , Nico Boon , Tom Van de Wiele
      Butyrate has several beneficial properties that are essential to maintain gastrointestinal health. Therefore butyrate-producing bacteria are seen as the next generation of probiotics. The butyrate-producing bacterium Butyricicoccus pullicaecorum (a clostridial cluster IV strain) is such a promising probiotic candidate for people suffering from inflammatory bowel disease. To exert its beneficial properties, it is crucial that B. pullicaecorum survives the harsh conditions of the upper gastrointestinal tract to arrive in the colon in a viable and metabolically active state. Before developing a stable formulation of B. pullicaecorum for oral administration, it is important to know its intrinsic acid and bile tolerance. We monitored the survival during and short chain fatty acid production after incubation in conditions simulating the stomach and small intestine using in vitro batch experiments. In case of acid conditions (pH 2 and pH 3), B. pullicaecorum was viable and active but not cultivable. Cultivability was restored during subsequent small intestine conditions. Importantly, bile and pancreatic juice had no lethal effect. Milk, as suspension medium, only had a protective effect on the cultivability during the first hour at pH 2. B. pullicaecorum was still metabolically active after upper gastrointestinal conditions and produced short chain fatty acids, but a shift from butyrate to acetate production was observed. Although the butyrate-producing anaerobe B. pullicaecorum showed good intrinsic acid and bile tolerance in terms of viability and metabolic activity, colonization efficiency and butyrate production under colon conditions is needed to further evaluate its probiotic potential.

      PubDate: 2014-09-01T21:10:28Z
  • Different effects of two newly-isolated probiotic Lactobacillus plantarum
           15HN and Lactococcus lactis subsp. Lactis 44Lac strains from traditional
           dairy products on cancer cell lines
    • Abstract: Publication date: Available online 27 August 2014
      Author(s): Babak Haghshenas , Norhafizah Abdullah , Yousef Nami , Dayang Radiah , Rozita Rosli , Ahmad Yari Khosroushahi
      Lactobacillus and Lactococcus strains isolated from food products can be introduced as probiotics because of their health-promoting characteristics and non-pathogenic nature. This study aims to perform the isolation, molecular identification, and probiotic characterization of Lactobacillus and Lactococcus strains from traditional Iranian dairy products. Primary probiotic assessments indicated high tolerance to low pH and high bile salt conditions, high anti-pathogenic activities, and susceptibility to high consumption antibiotics, thus proving that both strains possess probiotic potential. Cytotoxicity assessments were used to analyze the effects of the secreted metabolite on different cancer cell lines, including HT29, AGS, MCF-7, and HeLa, as well as a normal human cell line (HUVEC). Results showed acceptable cytotoxic properties for secreted metabolites (40 μg/ml dry weight) of Lactococcus lactis subsp. Lactis 44Lac. Such performance was similar to that of Taxol against all of the treated cancer cell lines; however, the strain exhibited no toxicity on the normal cell line. Cytotoxic assessments through flow cytometry and fluorescent microscopy demonstrated that apoptosis is the main cytotoxic mechanism for secreted metabolites of L. lactis subsp. Lactis 44Lac. By contrast, the effects of protease-treated metabolites on the AGS cell line verified the protein nature of anti-cancer metabolites. However, precise characterizations and in vitro/in vivo investigations on purified proteins should be conducted before these metabolites are introduced as potential anti-cancer therapeutics.

      PubDate: 2014-09-01T21:10:28Z
  • In vitro antibiotic susceptibility profile of Clostridium difficile
           excluding PCR ribotype 027 outbreak strain in Hungary
    • Abstract: Publication date: December 2014
      Source:Anaerobe, Volume 30
      Author(s): Gabriella Terhes , Akiko Maruyama , Krisztina Latkóczy , Lenke Szikra , Marianne Konkoly-Thege , Gyula Princz , Elisabeth Nagy , Edit Urbán
      Our study showed the antibiotic susceptibility profile of toxigenic Clostridium difficile isolated from nosocomial and community-acquired CDI between 2008 and 2010. MICs of 200 C. difficile strains were determined using E®test method in the case of erythromycin, clindamycin, moxifloxacin, rifampicin, and metronidazole. All strains were susceptible to metronidazole in the study period. Resistance rates to erythromycin, clindamycin and moxifloxacin were 31%, 29.5%, and 21.5%, respectively. In the case of rifampicin, the MIC range was quite wide, 11.5% of the tested strains proved to be highly resistant (MIC ≥32 μg/ml) to rifampicin. When we compared these results with our earlier findings from 2006 to 2007, only minor changes in susceptibility over the time-periods could be observed in the case of erythromycin, clindamycin, moxifloxacin, and rifampicin, but metronidazole susceptibility did not show changes.

      PubDate: 2014-09-01T21:10:28Z
  • First clinical and microbiological characterization of Clostridium
           difficile infection in a Croatian University Hospital
    • Abstract: Publication date: December 2014
      Source:Anaerobe, Volume 30
      Author(s): Anita Novak , Patrizia Spigaglia , Fabrizio Barbanti , Ivana Goic-Barisic , Marija Tonkic
      Clinical background and molecular epidemiology of Clostridium difficile infection (CDI) in the University Hospital Centre Split were investigated from January 2010 to December 2011. In total, 54 patients with first episode of CDI were consecutively included in the study based on the positive EIA test specific for A and B toxins. Demographic and clinical data were prospectively analyzed from medical records. CDI incidence rate was 0.6 per 10,000 patient-days. Thirty six cases (70.6%) were healthcare-associated, twelve cases (23.5%) were community-associated and three (5.9%) were indeterminate. Six patients (11.7%) had suffered one or more recurrences and 37 patients (72.5%) showed severe CDI. Prior therapy with third generation cephalosporin was significantly associated with severe CDI (P < 0.021). Fifty four toxigenic C. difficile strains were isolated and 50 of them were available for PCR-ribotyping. Sixteen different PCR-ribotypes were identified. The most prevalent were PCR-ribotype 001 (27.8%) and 014/020 (24.1%). Twenty three strains were resistant to at least one of the antibiotics tested. Among resistant strains, three (13.0%) – all PCR-ribotype 001 – were multi-resistant. Resistance to fluoroquinolones was significantly higher in strains that caused infection after previous use of fluoroquinolones (P = 0.04).

      PubDate: 2014-08-12T19:59:23Z
    • Abstract: Publication date: Available online 12 August 2014
      Author(s): Mutlu Keskin , Eija Könönen , Eva Söderling , Gülden Isik , Erhan Firatli , Veli Jukka Uitto , Ulvi Kahraman Gürsoy
      Human neutrophilic peptides (HNPs) constitute a class of host defense molecules, which contribute to the non-oxidative killing of bacteria and other microorganisms. Since the adaptability is crucial to bacterial survival in changing environments, it is of interest to know how Fusobacterium nucleatum, the major bridge organism connecting early and late colonizers in dental biofilms, defends itself against HNPs. This study aimed to examine the planktonic growth, membrane permeability, and biofilm formation characteristics as defense mechanisms of F. nucleatum against HNP-1. In all experiments, the type strain of F. nucleatum (ssp. nucleatum ATCC 25586) and two clinical strains (ssp. nucleatum AHN 9508 and ssp. polymorphum AHN 9910) were used. Planktonic growth (measured in colony forming units), capsular polysaccharide production (visualized by Ziehl-Neelsen stain), membrane permeability (demonstrated as N-phenyl-1-naphthylamine uptake), biofilm formation, and established biofilm development (measured as total mass and polysaccharide levels) were analyzed in the presence of 0 μg/ml (control), 1 μg/ml, 5 μg/ml, and 10 μg/ml of HNP-1. Planktonic growth of the strains AHN 9508 and ATCC 25586 were significantly (p<0.05) increased in the presence of HNP-1, while their membrane permeability decreased (p<0.005) in the planktonic form. HNP-1 decreased the biofilm formation of the strains ATCC 25586 and AHN 9910, whereas it increased the growth of the strain AHN 9508 in established biofilms. Capsule formation and polysaccharide production were not observed in any strain. We conclude that the inhibition of the membrane permeability and the increase in planktonic and established biofilm growth could act as bacterial defense mechanisms against neutrophilic defensins. In addition, this strain-dependent survival ability against HNP-1 may explain the variation in the virulence of different F. nucleatum strains.

      PubDate: 2014-08-12T19:59:23Z
  • Longitudinal shifts in bacterial diversity and fermentation pattern in the
           rumen of steers grazing wheat pasture
    • Abstract: Publication date: December 2014
      Source:Anaerobe, Volume 30
      Author(s): D.W. Pitta , W.E. Pinchak , S. Dowd , K. Dorton , I. Yoon , B.R. Min , J.D. Fulford , T.A. Wickersham , D.P. Malinowski
      Grazing steers on winter wheat forage is routinely practiced in the Southern Great Plains of the US. Here, we investigated the dynamics in bacterial populations of both solid and liquid ruminal fractions of steers grazing on maturing wheat forage of changing nutritive quality. The relationship between bacterial diversity and fermentation parameters in the liquid fraction was also investigated. During the first 28 days, the wheat was in a vegetative phase with a relatively high crude protein content (CP; 21%), which led to the incidence of mild cases of frothy bloat among steers. Rumen samples were collected on days 14, 28, 56 and 76, separated into solid and liquid fractions and analyzed for bacterial diversity using 16S pyrotag technology. The predominant phyla identified were Bacteroidetes (59–77%) and Firmicutes (20–33%) across both ruminal fractions. Very few differences were observed in the rumen bacterial communities within solid and liquid fractions on day 14. However, by day 28, the relatively high CP content complemented a distinct bacterial and chemical composition of the rumen fluid that was characterized by a higher ratio (4:1) of Bacteroidetes:Firmicutes and a corresponding lower acetate:propionate (3:1) ratio. Further, a greater accumulation of biofilm (mucopolysaccharide complex) on day 28 was strongly associated with the abundance of Firmicutes lineages such as Clostridium, Ruminococcus, Oscillospira and Moryella (P < 0.05) in the fiber fraction. Such changes were diminished as the CP concentration declined over the course of the study. The abundance of Firmicutes was noticeable by 76 d in both fractions which signifies the development of a core microbiome associated with digestion of a more recalcitrant fiber in the mature wheat. This study demonstrates dynamics in the rumen microbiome and their association with fermentation activity in the rumen of steers during the vegetative (bloat-prone) and reproductive stages of wheat forage.

      PubDate: 2014-08-12T19:59:23Z
  • In vitro evaluation of the probiotic and functional potential of
           Lactobacillus strains isolated from fermented food and human intestine
    • Abstract: Publication date: December 2014
      Source:Anaerobe, Volume 30
      Author(s): Dayong Ren , Chang Li , Yanqing Qin , Ronglan Yin , Shouwen Du , Fei Ye , Cunxia Liu , Hongfeng Liu , Maopeng Wang , Yi Li , Yang Sun , Xiao Li , Mingyao Tian , Ningyi Jin
      This study aims to evaluate the functional and probiotic characteristics of eight indigenous Lactobacillus strains in vitro. The selected lactobacilli include strains of Lactobacillus casei subsp. casei, Lactobacillus salivarius subsp. salicinius, Lactobacillus fermentum, Lactobacillus plantarum, Lactobacillus delbrueckii subsp. lactis, Lactobacillus delbrueckii subsp. bulgaricus, and Lactobacillus rhamnosus. All strains tolerated both pH 2 for 3 h and 1% bile salt for 24 h. The strains CICC 23174 and CGMCC 1.557 were the most adhesive strains producing the highest quantity of EPS. Although a wide variation in the ability of the eight strains to deplete cholesterol and nitrite, antagonize pathogens, scavenge free radical, and stimulate innate immune response were observed, the strains CICC 23174 and CGMCC 1.557 showed the widest range of these useful traits. Taken together, the strains CICC 23174 and CGMCC 1.557 exhibited the best probiotic properties with the potential for use in the production of probiotic fermented foods.

      PubDate: 2014-08-07T19:47:41Z
  • Corticosteroid use is associated with a reduced incidence of Clostridium
           difficile-associated diarrhea: A retrospective cohort study
    • Abstract: Publication date: Available online 7 August 2014
      Author(s): Amy L. Wojciechowski , Ganapathi I. Parameswaran , Arun Mattappallil , Kari A. Mergenhagen
      The impact of corticosteroid use on the incidence of Clostridium difficile-associated diarrhea (CDAD) was examined retrospectively in 532 patients receiving antibiotic treatment for respiratory infections. As determined by logistic regression, corticosteroids were associated with a decreased incidence of CDAD (Odds Ratio 0.12, 95% Confidence Interval 0.006-0.95).

      PubDate: 2014-08-07T19:47:41Z
  • Vancomycin-resistant Clostridium innocuum bacteremia following oral
           vancomycin for Clostridium difficile infection
    • Abstract: Publication date: Available online 4 August 2014
      Author(s): Yuan-Pin Hung , Hsiao-Ju Lin , Chi-Jung Wu , Po-Lin Chen , Jen-Chieh Lee , Hsiao-Chieh Liu , Yi-Hui Wu , Fang Hao Yeh , Pei-Jane Tsai , Wen-Chien Ko
      An 85 year-old male initially admitted for septic shock due to urinary tract infection experienced Clostridium difficile-associated diarrhea during hospitalization and was treated by oral vancomycin. His clinical course was complicated by cytomegalovirus colitis and then vancomycin-resistant C. innocuum bacteremia, which was cured by uneventfully parenteral piperacillin-tazobactam therapy.

      PubDate: 2014-08-07T19:47:41Z
  • Peptoniphilus rhinitidis sp. nov., isolated from specimens of chronic
    • Abstract: Publication date: Available online 2 August 2014
      Author(s): Min Young Jung , Jae Hoon Cho , Yeseul Sin , Jayoung Paek , In-Soon Park , Joong-Su Kim , Wongyong Kim , Jin Yeul Ma , Soo-Je Park , Young-Hyo Chang
      Chronic rhinosinusitis (CRS) is an inflammatory disorder of the nasal cavity and paranasal sinus related to bacterial infection. A previous study suggested that a specific bacterial group may have an important role in the course of CRS. In this study, bacteria isolated from CRS patients were characterized. A total of 15 strains were identified as Gram-positive anaerobic cocci (GPAC), which were able to utilize peptone as a sole carbon source. Sequencing of the 16S ribosomal RNA gene revealed that the isolates were closely related to members of the genus Peptoniphilus (>97% similarity) within the Clostridiales Family XI. Incertae Sedis. Genotypic and phenotypic characterization suggests that these isolates represent a novel species of the genus Peptoniphilus associated with CRS. The type strain of Peptoniphilus rhinitidis is 1-13T (= KCTC 5985T = JCM 17448T).

      PubDate: 2014-08-03T19:33:18Z
  • 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
  • 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
  • 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
  • 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
  • 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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