Proposal to unify Clostridium orbiscindens Winter et al. 1991 and Eubacterium plautii (Séguin 1928) Hofstad and Aasjord 1982, with description of Flavonifractor plautii gen. nov., comb. nov., and reassignment of Bacteroides capillosus to Pseudoflavonifractor capillosus gen. nov., comb. nov.

Carlier, Jean‐Philippe; Bedora-Faure, Marie; K'ouas, Guylène; Alauzet, Corentine; Mory, F.

doi:10.1099/ijs.0.016725-0

Cited by 109 publications

(73 citation statements)

References 30 publications

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“…Among these, the greatest proportion was composed of B. capillosus. B. capillosus is usually found in the intestinal tract of humans (40) and has the ability to ferment 1,3-1,4-␤-glucanase (27) and pectin (41). However, in recent reports, B. capillosus was reclassified using genotyping to Firmicutes and was found to be closely related to Clostridium or Ruminococcus (40,42,43).…”

Section: Figmentioning

confidence: 99%

FLX Pyrosequencing Analysis of the Effects of the Brown-Algal Fermentable Polysaccharides Alginate and Laminaran on Rat Cecal Microbiotas

Kuda

Yazaki

et al. 2013

Appl Environ Microbiol

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Edible brown algae are used as major food material in Far East Asian countries, particularly in South Korea and Japan. They contain fermentable dietary fibers, alginic acid (uronic acid polymer) and laminaran (␤-1,3-glucan), that are fermented into organic acids by intestinal bacteria. To clarify the effect of edible algae on the intestinal environment, the cecal microbiotas of rats fed diets containing no dietary fiber (control) or 2% (wt/wt) sodium alginate or laminaran for 2 weeks were analyzed using FLX amplicon pyrosequencing with bar-coded primers targeting the bacterial 16S rRNA gene. The most abundant phylum in all groups was Firmicutes. Specifically, Allobaculum was dominant in all diet groups. In addition, Bacteroides capillosus (37.1%) was abundant in the alginate group, while Clostridium ramosum (3.14%) and Parabacteroides distasonis (1.36%) were only detected in the laminaran group. Furthermore, rats fed alginate showed simplified microbiota phylotypes compared with others. With respect to cecal chemical compounds, laminaran increased cecal organic acid levels, particularly propionic acid. Alginate increased total cecal organic acids. Cecal putrefactive compounds, such as indole, H 2 S, and phenol, were decreased by both alginate and laminaran. These results indicate that edible brown algae can alter the intestinal environment, with fermentation by intestinal microbiota.

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Section: Figmentioning

confidence: 99%

FLX Pyrosequencing Analysis of the Effects of the Brown-Algal Fermentable Polysaccharides Alginate and Laminaran on Rat Cecal Microbiotas

Kuda

Yazaki

et al. 2013

Appl Environ Microbiol

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“…The CE concept was applied to other bacterial species such as Campylobacter sp. (Aho et al, 1992;Schoeni and Doyle, 1992), C. perfringens (Fukata et al, 1991;Hofacre et al, 2002), Listeria monocytogenes (Hume et al, 1998), and pathogenic E. coli (Stavric et (Carlier at al., 2010), and Bacteroides sp. have been included as a mixture prepared from defined bacteria (Impey et al, 1982).…”

Section: Discussionmentioning

confidence: 99%

Nurmi-type Culture Prepared using Culture Media without <sub>L</sub>-Cysteine Enhances <i>Salmonella </i>Exclusion in Hatched Layer Chicks

et al. 2016

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To determine the influence of media composition on Salmonella exclusion of Nurmi-type cultures, two and four types of cultures in the first and second trial, respectively, were prepared from the cecal contents of conventional laying hens, and Salmonella exclusion was assessed in newly hatched chicks. In the first trial, modified Viande Levure (VL) broth or nutrient broth (NB) were used to prepare Nurmi-type cultures (N-VL and N-NB), which were administered to the newly hatched chicks. Twenty-four hours later, the chicks were challenged with Salmonella enterica Typhimurium EF85-9 (ST). ST recoveries (log 10 colony forming units/g of cecal contents) from the N-VL-, N-NB-, and control-treated groups 5 days after the challenge were 7.6±0.6, 0.9±1.9, and 7.7±0.4, respectively. The results suggested the influence of L-cysteine (Cys) present in the VL broth. Thus, we determined the effect of Cys in the second trial. We prepared two other cultures using VL broth without Cys (N-VL−Cys) and NB with Cys (NNB＋Cys). ST recoveries from the cecal contents of the N-VL-, N-VL−Cys-, and control-treated groups were 6.3± 0.9, 2.1±2.5, and 9.2±0.8, respectively. ST was not recovered from the N-NB-and N-NB＋Cys-treated groups. To identify bacteria with Salmonella exclusion activity, we isolated 41 bacterial strains from the ceca of N-NB-treated chicks without Salmonella challenge. Most isolates were identified as Enterococcus faecalis or E. mundtii based on 16S rRNA gene sequencing, and only four cultures excluded Salmonella. Therefore, VL broth containing Cys was not always required for preparing Nurmi-type cultures. The use of media prepared with Cys at the lowest possible concentration or without Cys would promote to enhance Salmonella exclusion from Nurmi-type cultures.

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“…The family level taxonomic assignment of ORFs containing cellulosome modules in the metasecretome was analysed based on the best BLASTP hit against the NCBI-NR database. For hits with a 40 bit-score threshold for cohesin and SLH module-containing ORFs, and a 35 bit-score threshold for dockerin-module containing ORFs, taxonomic family assignments of the host organism for the best BLAST hit were manually curated using recent bacterial classification proposals [56, 77–81]. …”

Section: Methodsmentioning

confidence: 99%

Metasecretome-selective phage display approach for mining the functional potential of a rumen microbial community

et al. 2014

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BackgroundIn silico, secretome proteins can be predicted from completely sequenced genomes using various available algorithms that identify membrane-targeting sequences. For metasecretome (collection of surface, secreted and transmembrane proteins from environmental microbial communities) this approach is impractical, considering that the metasecretome open reading frames (ORFs) comprise only 10% to 30% of total metagenome, and are poorly represented in the dataset due to overall low coverage of metagenomic gene pool, even in large-scale projects.ResultsBy combining secretome-selective phage display and next-generation sequencing, we focused the sequence analysis of complex rumen microbial community on the metasecretome component of the metagenome. This approach achieved high enrichment (29 fold) of secreted fibrolytic enzymes from the plant-adherent microbial community of the bovine rumen. In particular, we identified hundreds of heretofore rare modules belonging to cellulosomes, cell-surface complexes specialised for recognition and degradation of the plant fibre.ConclusionsAs a method, metasecretome phage display combined with next-generation sequencing has a power to sample the diversity of low-abundance surface and secreted proteins that would otherwise require exceptionally large metagenomic sequencing projects. As a resource, metasecretome display library backed by the dataset obtained by next-generation sequencing is ready for i) affinity selection by standard phage display methodology and ii) easy purification of displayed proteins as part of the virion for individual functional analysis.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-356) contains supplementary material, which is available to authorized users.

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Proposal to unify Clostridium orbiscindens Winter et al. 1991 and Eubacterium plautii (Séguin 1928) Hofstad and Aasjord 1982, with description of Flavonifractor plautii gen. nov., comb. nov., and reassignment of Bacteroides capillosus to Pseudoflavonifractor capillosus gen. nov., comb. nov.

Cited by 109 publications

References 30 publications

FLX Pyrosequencing Analysis of the Effects of the Brown-Algal Fermentable Polysaccharides Alginate and Laminaran on Rat Cecal Microbiotas

FLX Pyrosequencing Analysis of the Effects of the Brown-Algal Fermentable Polysaccharides Alginate and Laminaran on Rat Cecal Microbiotas

Nurmi-type Culture Prepared using Culture Media without <sub>L</sub>-Cysteine Enhances <i>Salmonella </i>Exclusion in Hatched Layer Chicks

Metasecretome-selective phage display approach for mining the functional potential of a rumen microbial community

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