for Journals by Title or ISSN
for Articles by Keywords
  Subjects -> BIOLOGY (Total: 2603 journals)
    - BIOCHEMISTRY (192 journals)
    - BIOENGINEERING (63 journals)
    - BIOLOGY (1322 journals)
    - BIOPHYSICS (42 journals)
    - BIOTECHNOLOGY (145 journals)
    - BOTANY (195 journals)
    - CYTOLOGY AND HISTOLOGY (24 journals)
    - ENTOMOLOGY (54 journals)
    - GENETICS (137 journals)
    - MICROBIOLOGY (210 journals)
    - MICROSCOPY (9 journals)
    - ORNITHOLOGY (23 journals)
    - PHYSIOLOGY (66 journals)
    - ZOOLOGY (121 journals)

BIOLOGY (1322 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: 164)
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: 15)
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: 3)
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: 253)
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: 23)
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: 52)
Evolution and Human Behavior     Hybrid Journal   (Followers: 9)
Evolutionary Applications     Open Access   (Followers: 3)
Evolutionary Bioinformatics     Open Access   (Followers: 14)
Evolutionary Biology     Hybrid Journal   (Followers: 16)
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: 7)
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)

  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  [2566 journals]   [SJR: 0.828]   [H-I: 39]
  • 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
  • Effect of Bdellovibrio bacteriovorus HD100 on multispecies oral
    • Abstract: Publication date: Available online 22 September 2014
      Author(s): Gitte Loozen , Nico Boon , Martine Pauwels , Vera Slomka , Esteban Rodrigues Herrero , Marc Quirynen , Wim Teughels
      The predation of Bdellovibrio bacteriovorus on different periodontal pathogens has already been described. However, it is necessary to consider the polymicrobial nature of periodontal disease. The current study explores the predation of Bdellovibrio on oral pathogens organized in multispecies communities. The effect of the predator was evaluated on in vitro six species communities with microbial culturing. Additionally, the effect on ex vivo subgingival plaque and saliva samples from periodontitis patients was assessed. In the latter experiment results were examined with microbial culturing, quantitative polymerase chain reaction (qPCR) and denaturing gradient gel electrophoresis (DGGE). The latter technique was used to get an overview of the whole mixed microbial population. Results showed that even in more complex models, B. bacteriovorus was still able to predate on F. nucleatum and A. actinomycetemcomitans. However predation on P. intermedia and P. gingivalis could not be validated in multispecies models. The effect of Bdellovibrio was not restricted to the target bacteria. Changes in the overall ecology of the different models were evident. It could be concluded that the efficiency of predation decreased when complexity of the models increased. However, B. bacteriovorus was able to attack two important oral pathogens, F. nucleatum, and A. actinomycetemcomitans, even when present in ex vivo clinical samples. These effects still have to be validated in in vivo models to see the impact of Bdellovibrio on the whole bacterial ecology.

      PubDate: 2014-09-23T23:48:12Z
  • Antimicrobial susceptibility patterns of Clostridium difficile strains
           belonging to different polymerase chain reaction ribotypes isolated in
           Poland in 2012
    • Abstract: Publication date: Available online 19 September 2014
      Author(s): Dominika Lachowicz , Hanna Pituch , Piotr Obuch-Woszczatyński
      In the beginning of 2012, a study was conducted to obtain an overview of Clostridium difficile infections (CDIs) in Polish hospitals. The collection of 83 toxigenic C. difficile isolates obtained from this hospital-based survey was used to identify antimicrobial susceptibility patterns. Among the C. difficile isolates analyzed, 48 (57.8%) belonged to PCR ribotype 027, 21 (25.3%) to its closely related PCR ribotype 176, and 14 (16.9%) to different PCR ribotypes. Seventy one (85.5%) isolates were resistant to erythromycin, whereas 23 (27.7%) had high-level clindamycin resistance, having minimum inhibitory concentrations (MICs) greater than 256 mg/L. All strains were ciprofloxacin resistant and 69 (83.1%) were moxifloxacin resistant. Seventy-three (87.9%) strains were imipenem resistant, but only 2 (2.4%) strains were resistant to tetracycline. All strains were sensitive to tigecycline. Metronidazole and vancomycin were generally effective against the C. difficile isolates, both having an MIC90 value of 0.75 mg/L. Isolates belonging to PCR ribotype 027 and the closely related PCR ribotype 176, showed higher resistance. All ribotype 027 and 176 C. difficile isolates demonstrated high-level resistance to erythromycin (MIC ≥ 256 mg/L), and 95,2% of ribotype 176 isolates were co-resistant to erythromycin and clindamycin. The MIC of moxifloxacin for this epidemic strain was very high (≥32 mg/L). Resistance to erythromycin, moxifloxacin, and rifampicin was observed in 15 (18%) of the isolates, all of which belonged to PCR ribotype 027. Multidrug resistance (MDR), defined as resistance at least to three classes of antimicrobial agents was observed in 85.5% (n=71) of toxigenic C. difficile strains.

      PubDate: 2014-09-19T23:18:38Z
  • Biofilms of Clostridium species
    • Abstract: Publication date: Available online 19 September 2014
      Author(s): Véronique Pantaléon , Sylvie Bouttier , Anna Philibertine Soavelomandroso , Claire Janoir , Thomas Candela
      The biofilm is a microbial community embedded in a synthesized matrix and is the main bacterial way of life. A biofilm adheres on surfaces or is found on interfaces. It protects bacteria from the environment, toxic molecules and may have a role in virulence. Clostridium species are spread throughout both environments and hosts, but their biofilms have not been extensively described in comparison with other bacterial species. In this review we describe all biofilms formed by Clostridium species during both industrial processes and in mammals where biofilms may be formed either during infections or associated to microbiota in the gut. We have specifically focussed on Clostridium difficile and Clostridium perfringens biofilms, which have been studied in vitro. Regulatory processes including sporulation and germination highlight how these Clostridium species live in biofilms. Furthermore, biofilms may have a role in the survival and spreading of Clostridium species.

      PubDate: 2014-09-19T23:18:38Z
  • 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
  • Host recognition of Clostridium difficile and the innate immune response
    • Abstract: Publication date: Available online 16 September 2014
      Author(s): Carrie A. Cowardin , William A. Petri Jr.
      Clostridium difficile is a Gram-positive, spore forming bacillus and the most common cause of antibiotic-associated diarrhea in the United States. Clinical outcomes of C. difficile infection (CDI) range from asymptomatic colonization to pseudomembranous colitis, sepsis and death. Disease is primarily mediated by the action of the Rho-glucosylating toxins A and B, which induce potent pro-inflammatory signaling within the host. The role of this inflammatory response during infection is just beginning to be appreciated, with recent data suggesting inflammatory markers correlate closely with disease severity. In addition to the toxins, multiple innate immune signaling pathways have been implicated in establishing an inflammatory response during infection. In intoxication-based models of disease, inflammation typically enhances pathogenesis, while protection from infection seems to require some level of inflammatory response. Thus, the host immune response plays a key role in shaping the course of infection and a balanced inflammatory response which eradicates infection without damaging host tissues is likely required for successful resolution of disease.

      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
  • View from the front lines: An emergency medicine perspective on
           clostridial infections in injection drug users
    • Abstract: Publication date: Available online 16 September 2014
      Author(s): Richard Diego Gonzales y Tucker , Brad 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: 2014-09-19T23:18:38Z
  • 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
  • Analysis of Romanian Bacteroides isolates for antibiotic resistance levels
           and the corresponding antibiotic resistance genes
    • Abstract: Publication date: Available online 10 September 2014
      Author(s): Edit Székely , Zsuzsa Eitel , Szabolcs Molnár , Izabella Éva Szász , Doina Bilca , József Sóki
      As part of an ESCMID Study Group on Anaerobic Infections (ESGAI) project, a study was conducted to measure the antibiotic susceptibilities and corresponding gene contents of 53 B. fragilis group strains isolated in Romania. The antibiotic resistance data was comparable with the data found for other East-European countries. Here, no resistant isolate was found for imipenem, metronidazole and tigecycline. An increasing role of the cepA, cfxA and cfiA genes was observed in their corresponding antibiotic resistances. Moreover, no isolate was found that harbored the cfiA gene with a possible activating IS element. Clindamycin resistance was low, similarly to that the rate for the ermF gene. However, we did find some isolates with nimB, ermB, msrSA, linA, satG, tetX, tetM and bexA genes. This study was the first to provide antibiotic resistance data for clinical Bacteroides strains from Romania.

      PubDate: 2014-09-11T22:23:48Z
  • Antimicrobial resistance among anaerobes isolated from clinical specimens
           in Kuwait hospitals: Comparative analysis of 11-year data
    • Abstract: Publication date: Available online 2 September 2014
      Author(s): Wafaa Jamal , Ghayda Al Hashem , Vincent O. Rotimi
      Our objective was to compare the antimicrobial resistance trends among clinically relevant anaerobes against 9 different antibiotics over two periods, 2008–2012 and 2002–2007. Antimicrobial susceptibility testing was performed by determining the MICs using E test method. The interpretation of results was according to the breakpoints recommended by the Clinical Laboratory and Standard Institute (CLSI) and European Committee on Antimicrobial Susceptibility Testing (EUCAST). A total of 2240 clinically significant isolates were collected between 2008 and 2012 in four teaching hospitals in Kuwait. The commonest isolates were Bacteroides fragilis (40.4%), Prevotella bivia (18.6%), Peptostreptococcus spp. (13.8%) and Bacteroides ovatus (11.1%). According to CLSI and EUCAST breakpoints used for the 2008–2012 and 2002–2007 isolates, high resistance rates to amoxicillin–clavulanic acid, clindamycin, penicillin and piperacillin were noted among the Gram-negative isolates. They ranged between 0 and 0–62.1 and 62.1%, and 0 and 0–59.1 and 62.1%, respectively against clindamycin, 0 and 0–34.5 and 45.3%, and 0 and 0–45 and 57.5%, respectively against piperacillin and 0 and 0–24.2 and 24.2%, and 0 and 0–23.1 and 30.6%, respectively against amoxicillin–clavulanic acid. The mean interpretative results by both CLSI and EUCAST during the 2008–2012 and 2002–2007 periods showed that the B. fragilis isolates were highly resistant to penicillin (100 vs 100%), clindamycin (43.7 vs 44.2%), piperacillin (35.8 vs 42.7%) and amoxicillin–clavulanic acid (13.2 vs 14%), respectively. When compared with 2002–2007, the CLSI, but not EUCAST, demonstrated statistically significant decreased resistance to clindamycin (P < 0.03). However, both interpretative criteria showed demonstrable statistically significant decrease in resistance rates to imipenem (P < 0.00097 vs P < 0.00074), meropenem (P < 0.000006 vs P < 0.0407) and piperacillin (P < 0.000017 vs P < 0.0461). Our data shows that there is a need for periodic monitoring of the susceptibility testing for anaerobic bacteria in the face of increasing resistance rates as well as to guide in the empirical therapy of anaerobic infections.

      PubDate: 2014-09-05T21:44:27Z
  • 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
  • Clostridium difficile infection in elderly nursing home residents
    • Abstract: Publication date: Available online 23 August 2014
      Author(s): C. Rodriguez , N. Korsak , B. Taminiau , V. Avesani , J. Van Broeck , M. Delmée , G. Daube
      Age-related changes in intestinal flora and host defences, the receipt of antibiotic treatment, and the presence of underlying diseases are some of the most common risk factors associated with Clostridium difficile infection. Therefore, retirement care facilities for elderly people have been pinpointed as frequent sources of contamination. There is only limited data regarding the presence and epidemiology of C. difficile in nursing homes, and this gap in the current literature emphasises the need to gain a better understanding of the situation in order to prevent the emergence of new outbreaks among this population group.

      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
  • Antibiotic susceptibility profiles of anaerobic pathogens in The
    • Abstract: Publication date: Available online 1 September 2014
      Author(s): A.C.M. Veloo , A.J. van Winkelhoff
      The antibiotic susceptibility profile of the Bacteroides fragilis group, gram-positive anaerobic cocci (GPAC), Fusobacterium spp., Prevotella spp., Veillonella spp. and Bilophila wadsworthia for amoxicillin, amoxicillin-clavulanic acid, clindamycin and metronidazole was determined. Human clinical isolates were isolated between 2011-2013 at the microbiological diagnostic laboratory of the University Medical Center Groningen, The Netherlands and subjected to MALDI-TOF MS identification and susceptibility testing using Etest for MIC determination. Differences in clindamycin susceptibility between species of the B. fragilis group and GPAC were observed, with Bacteroides ovatus and Peptoniphilus harei having the highest resistance rates. Compared to other European countries, in The Netherlands the MIC90 for clindamycin of fusobacteria is low. Metronidazole resistance was first encountered in the genus Prevotella in 2013, but not in species of GPAC as reported in Belgium and Bulgaria. The differences in clindamycin resistance between the different European countries and reports of metronidazole resistance within the genera Prevotella and GPAC warrant more extensive susceptibility studies on anaerobic pathogens.

      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
  • 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
  • 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
School of Mathematical and Computer Sciences
Heriot-Watt University
Edinburgh, EH14 4AS, UK
Tel: +00 44 (0)131 4513762
Fax: +00 44 (0)131 4513327
About JournalTOCs
News (blog, publications)
JournalTOCs on Twitter   JournalTOCs on Facebook

JournalTOCs © 2009-2014