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Harry J Flint - One of the best experts on this subject based on the ideXlab platform.
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Complete Genome Sequence of the Human Gut Symbiont Roseburia hominis
Genome announcements, 2015Co-Authors: Anthony J. Travis, Harry J Flint, Denise Kelly, Rustam AminovAbstract:Copyright © 2015 Travis et al. ACKNOWLEDGMENTS We thank Gillian Campbell, Pauline Young, Karen Garden, and Sylvia Duncan for contributing to this work, which was supported by Scottish Government RESAS (Rural and Environmental Sciences and Analytical Services).
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a representative of the dominant human colonic firmicutes Roseburia faecis m72 1 forms a novel bacteriocin like substance
Anaerobe, 2013Co-Authors: Diane Hatziioanou, Sylvia H. Duncan, Harry J Flint, Melinda J. Mayer, Arjan NarbadAbstract:During screening of human gut isolates in search of novel antimicrobials, the butyrate-producing strain Roseburia faecis M72/1 was found to produce an inhibitory substance active against Bacillus subtilis. Partial purification of the antimicrobial was achieved and activity found to be heat labile. Our findings suggest that R. faecis M72/1 produces a proteinaceous inhibitor whose production may be triggered by trypsin in the gastrointestinal tract.
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Correspondence
2013Co-Authors: Sylvia H. Duncan, Rustam I Aminov, Harry J Flint, Petra Louis, Karen P. Scott, Thaddeus B. StantonAbstract:Seven recently cultured bacterial isolates, although similar in their 16S rRNA gene sequences to Roseburia intestinalis L1-82 T (DSM 14610 T), were not sufficiently related for inclusion within existing species, forming three separate clusters in a 16S rRNA gene phylogenetic tree. The isolates, which were obtained from human stools, were Gram-variable or Gram-negative, strictly anaerobic, slightly curved rods; cells from all strains measured approximately 0?561?5–5?0 mm and were motile. Two strains belonging to one cluster (A2-181 and A2-183 T) were the only strains that were able to grow on glycerol and that failed to grow on any of the complex substrates tested (inulin, xylan and amylopectin). Strains belonging to a second cluster (represented by M6/1 and M72/1 T) differed from the other isolates in their ability to grow on sorbitol. Isolates belonging to a third cluster (L1-83 and A2-194 T) were the only strains that failed to grow on xylose and that gave good growth on inulin (strains M6/1 and M72/1 T gave weak growth). All strains were net acetate utilizers. The DNA G+C contents of representative Roseburia strains A2-183 T, A2-194 T, M72/1 T and R. intestinalis L1-82 T were 47?4, 41?4, 42?0 and 42?6 mol%, respectively. Based on 16S rRNA gene sequence similarity, three novel Roseburia species are proposed, with the names Roseburia hominis sp. nov. (type strain A2-183 T =DSM 16839 T =NCIMB 14029 T), Roseburi
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A representative of the dominant human colonic Firmicutes, Roseburia faecis M72/1, forms a novel bacteriocin-like substance.
Anaerobe, 2013Co-Authors: Diane Hatziioanou, Sylvia H. Duncan, Harry J Flint, Melinda J. Mayer, Arjan NarbadAbstract:During screening of human gut isolates in search of novel antimicrobials, the butyrate-producing strain Roseburia faecis M72/1 was found to produce an inhibitory substance active against Bacillus subtilis. Partial purification of the antimicrobial was achieved and activity found to be heat labile. Our findings suggest that R. faecis M72/1 produces a proteinaceous inhibitor whose production may be triggered by trypsin in the gastrointestinal tract.
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Pro-Inflammatory Flagellin Proteins of Prevalent Motile Commensal Bacteria Are Variably Abundant in the Intestinal Microbiome of Elderly Humans
PloS one, 2013Co-Authors: B. Anne Neville, Sylvia H. Duncan, Harry J Flint, Paul O. Sheridan, Hugh M. B. Harris, Simone Coughlan, Ian B. Jeffery, Marcus J. Claesson, R. Paul Ross, Karen P. ScottAbstract:Some Eubacterium and Roseburia species are among the most prevalent motile bacteria present in the intestinal microbiota of healthy adults. These flagellate species contribute “cell motility” category genes to the intestinal microbiome and flagellin proteins to the intestinal proteome. We reviewed and revised the annotation of motility genes in the genomes of six Eubacterium and Roseburia species that occur in the human intestinal microbiota and examined their respective locus organization by comparative genomics. Motility gene order was generally conserved across these loci. Five of these species harbored multiple genes for predicted flagellins. Flagellin proteins were isolated from R. inulinivorans strain A2-194 and from E. rectale strains A1-86 and M104/1. The amino-termini sequences of the R. inulinivorans and E. rectale A1-86 proteins were almost identical. These protein preparations stimulated secretion of interleukin-8 (IL-8) from human intestinal epithelial cell lines, suggesting that these flagellins were pro-inflammatory. Flagellins from the other four species were predicted to be pro-inflammatory on the basis of alignment to the consensus sequence of pro-inflammatory flagellins from the β- and γ- proteobacteria. Many fliC genes were deduced to be under the control of σ28. The relative abundance of the target Eubacterium and Roseburia species varied across shotgun metagenomes from 27 elderly individuals. Genes involved in the flagellum biogenesis pathways of these species were variably abundant in these metagenomes, suggesting that the current depth of coverage used for metagenomic sequencing (3.13–4.79 Gb total sequence in our study) insufficiently captures the functional diversity of genomes present at low (≤1%) relative abundance. E. rectale and R. inulinivorans thus appear to synthesize complex flagella composed of flagellin proteins that stimulate IL-8 production. A greater depth of sequencing, improved evenness of sequencing and improved metagenome assembly from short reads will be required to facilitate in silico analyses of complete complex biochemical pathways for low-abundance target species from shotgun metagenomes.
Sylvia H. Duncan - One of the best experts on this subject based on the ideXlab platform.
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Polysaccharide utilization loci and nutritional specialization in a dominant group of butyrate-producing human colonic Firmicutes
Microbial Genomics, 2016Co-Authors: Paul O. Sheridan, Sylvia H. Duncan, Jennifer C. Martin, Trevor D. Lawley, Hilary P. Browne, Hugh M. B. Harris, Annick Bernalier, Paul W. O'toole, Karen P. Scott, Harry J. FlintAbstract:Firmicutes and Bacteroidetes are the predominant bacterial phyla colonizing the healthy human large intestine. Whilst both ferment dietary fibre, genes responsible for this important activity have been analysed only in the Bacteroidetes , with very little known about the Firmicutes . This work investigates the carbohydrate-active enzymes (CAZymes) in a group of Firmicutes , Roseburia spp. and Eubacterium rectale , which play an important role in producing butyrate fr om dietary carbohydrates and in health maintenance. Genome sequences of 11 strains representing E. rectale and four Roseburia spp. were analysed for carbohydrate-active genes. Following assembly into a pan-genome, core, variable and uniqu e genes were identified. The 1840 CAZyme genes identified in the pan-genome were assigned to 538 orthologous groups, of which only 26 were present in all strains, indicating considerable inter- strain variability. This analysis was used to categorize the 11 strains into four carbohydrate utilization ecotypes (CUEs), which were shown to correspond to utilization of diffe rent carbohydrates for growth. Many glycoside hydrolase genes were found linked to genes encoding oligosaccharide transporters and regulatory elements in the genomes of Roseburia spp. and E. rectale ,forming distinct polysaccharide utilization loci (PULs). Whilst PULs are also a common feature in Bacteroidetes , key differences were noted in these Firmicutes , including the absence of close homologues of Bacteroides polysaccharide utilization genes, hence we refer to Gram-positive PULs (gpPULs). Most CAZyme genes in the Roseburia / E. rectale group are organized into gpPULs. Variation in gpPULs can explain the high degree of nutritional specialization at the species level within this group.
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a representative of the dominant human colonic firmicutes Roseburia faecis m72 1 forms a novel bacteriocin like substance
Anaerobe, 2013Co-Authors: Diane Hatziioanou, Sylvia H. Duncan, Harry J Flint, Melinda J. Mayer, Arjan NarbadAbstract:During screening of human gut isolates in search of novel antimicrobials, the butyrate-producing strain Roseburia faecis M72/1 was found to produce an inhibitory substance active against Bacillus subtilis. Partial purification of the antimicrobial was achieved and activity found to be heat labile. Our findings suggest that R. faecis M72/1 produces a proteinaceous inhibitor whose production may be triggered by trypsin in the gastrointestinal tract.
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Correspondence
2013Co-Authors: Sylvia H. Duncan, Rustam I Aminov, Harry J Flint, Petra Louis, Karen P. Scott, Thaddeus B. StantonAbstract:Seven recently cultured bacterial isolates, although similar in their 16S rRNA gene sequences to Roseburia intestinalis L1-82 T (DSM 14610 T), were not sufficiently related for inclusion within existing species, forming three separate clusters in a 16S rRNA gene phylogenetic tree. The isolates, which were obtained from human stools, were Gram-variable or Gram-negative, strictly anaerobic, slightly curved rods; cells from all strains measured approximately 0?561?5–5?0 mm and were motile. Two strains belonging to one cluster (A2-181 and A2-183 T) were the only strains that were able to grow on glycerol and that failed to grow on any of the complex substrates tested (inulin, xylan and amylopectin). Strains belonging to a second cluster (represented by M6/1 and M72/1 T) differed from the other isolates in their ability to grow on sorbitol. Isolates belonging to a third cluster (L1-83 and A2-194 T) were the only strains that failed to grow on xylose and that gave good growth on inulin (strains M6/1 and M72/1 T gave weak growth). All strains were net acetate utilizers. The DNA G+C contents of representative Roseburia strains A2-183 T, A2-194 T, M72/1 T and R. intestinalis L1-82 T were 47?4, 41?4, 42?0 and 42?6 mol%, respectively. Based on 16S rRNA gene sequence similarity, three novel Roseburia species are proposed, with the names Roseburia hominis sp. nov. (type strain A2-183 T =DSM 16839 T =NCIMB 14029 T), Roseburi
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A representative of the dominant human colonic Firmicutes, Roseburia faecis M72/1, forms a novel bacteriocin-like substance.
Anaerobe, 2013Co-Authors: Diane Hatziioanou, Sylvia H. Duncan, Harry J Flint, Melinda J. Mayer, Arjan NarbadAbstract:During screening of human gut isolates in search of novel antimicrobials, the butyrate-producing strain Roseburia faecis M72/1 was found to produce an inhibitory substance active against Bacillus subtilis. Partial purification of the antimicrobial was achieved and activity found to be heat labile. Our findings suggest that R. faecis M72/1 produces a proteinaceous inhibitor whose production may be triggered by trypsin in the gastrointestinal tract.
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Pro-Inflammatory Flagellin Proteins of Prevalent Motile Commensal Bacteria Are Variably Abundant in the Intestinal Microbiome of Elderly Humans
PloS one, 2013Co-Authors: B. Anne Neville, Sylvia H. Duncan, Harry J Flint, Paul O. Sheridan, Hugh M. B. Harris, Simone Coughlan, Ian B. Jeffery, Marcus J. Claesson, R. Paul Ross, Karen P. ScottAbstract:Some Eubacterium and Roseburia species are among the most prevalent motile bacteria present in the intestinal microbiota of healthy adults. These flagellate species contribute “cell motility” category genes to the intestinal microbiome and flagellin proteins to the intestinal proteome. We reviewed and revised the annotation of motility genes in the genomes of six Eubacterium and Roseburia species that occur in the human intestinal microbiota and examined their respective locus organization by comparative genomics. Motility gene order was generally conserved across these loci. Five of these species harbored multiple genes for predicted flagellins. Flagellin proteins were isolated from R. inulinivorans strain A2-194 and from E. rectale strains A1-86 and M104/1. The amino-termini sequences of the R. inulinivorans and E. rectale A1-86 proteins were almost identical. These protein preparations stimulated secretion of interleukin-8 (IL-8) from human intestinal epithelial cell lines, suggesting that these flagellins were pro-inflammatory. Flagellins from the other four species were predicted to be pro-inflammatory on the basis of alignment to the consensus sequence of pro-inflammatory flagellins from the β- and γ- proteobacteria. Many fliC genes were deduced to be under the control of σ28. The relative abundance of the target Eubacterium and Roseburia species varied across shotgun metagenomes from 27 elderly individuals. Genes involved in the flagellum biogenesis pathways of these species were variably abundant in these metagenomes, suggesting that the current depth of coverage used for metagenomic sequencing (3.13–4.79 Gb total sequence in our study) insufficiently captures the functional diversity of genomes present at low (≤1%) relative abundance. E. rectale and R. inulinivorans thus appear to synthesize complex flagella composed of flagellin proteins that stimulate IL-8 production. A greater depth of sequencing, improved evenness of sequencing and improved metagenome assembly from short reads will be required to facilitate in silico analyses of complete complex biochemical pathways for low-abundance target species from shotgun metagenomes.
Glenn R Gibson - One of the best experts on this subject based on the ideXlab platform.
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in vitro fermentation of nutriose fb06 a wheat dextrin soluble fibre in a continuous culture human colonic model system
PLOS ONE, 2013Co-Authors: Mark R Hobden, Agustin Martinmorales, Laetitia Guerinderemaux, Daniel Wils, Adele Costabile, Gemma E Walton, Ian Rowland, Orla B Kennedy, Glenn R GibsonAbstract:Wheat dextrin soluble fibre may have metabolic and health benefits, potentially acting via mechanisms governed by the selective modulation of the human gut microbiota. Our aim was to examine the impact of wheat dextrin on the composition and metabolic activity of the gut microbiota. We used a validated in vitro three-stage continuous culture human colonic model (gut model) system comprised of vessels simulating anatomical regions of the human colon. To mimic human ingestion, 7 g of wheat dextrin (NUTRIOSE® FB06) was administered to three gut models, twice daily at 10.00 and 15.00, for a total of 18 days. Samples were collected and analysed for microbial composition and organic acid concentrations by 16S rRNA-based fluorescence in situ hybridisation and gas chromatography approaches, respectively. Wheat dextrin mediated a significant increase in total bacteria in vessels simulating the transverse and distal colon, and a significant increase in key butyrate-producing bacteria Clostridium cluster XIVa and Roseburia genus in all vessels of the gut model. The production of principal short-chain fatty acids, acetate, propionate and butyrate, which have been purported to have protective, trophic and metabolic host benefits, were increased. Specifically, wheat dextrin fermentation had a significant butyrogenic effect in all vessels of the gut model and significantly increased production of acetate (vessels 2 and 3) and propionate (vessel 3), simulating the transverse and distal regions of the human colon, respectively. In conclusion, wheat dextrin NUTRIOSE® FB06 is selectively fermented in vitro by Clostridium cluster XIVa and Roseburia genus and beneficially alters the metabolic profile of the human gut microbiota.
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in vitro fermentation of nutriose fb06 a wheat dextrin soluble fibre in a continuous culture human colonic model system
PLOS ONE, 2013Co-Authors: Mark R Hobden, Agustin Martinmorales, Laetitia Guerinderemaux, Daniel Wils, Adele Costabile, Gemma E Walton, Ian Rowland, Orla B Kennedy, Glenn R GibsonAbstract:Wheat dextrin soluble fibre may have metabolic and health benefits, potentially acting via mechanisms governed by the selective modulation of the human gut microbiota. Our aim was to examine the impact of wheat dextrin on the composition and metabolic activity of the gut microbiota. We used a validated in vitro three-stage continuous culture human colonic model (gut model) system comprised of vessels simulating anatomical regions of the human colon. To mimic human ingestion, 7 g of wheat dextrin (NUTRIOSE® FB06) was administered to three gut models, twice daily at 10.00 and 15.00, for a total of 18 days. Samples were collected and analysed for microbial composition and organic acid concentrations by 16S rRNA-based fluorescence in situ hybridisation and gas chromatography approaches, respectively. Wheat dextrin mediated a significant increase in total bacteria in vessels simulating the transverse and distal colon, and a significant increase in key butyrate-producing bacteria Clostridium cluster XIVa and Roseburia genus in all vessels of the gut model. The production of principal short-chain fatty acids, acetate, propionate and butyrate, which have been purported to have protective, trophic and metabolic host benefits, were increased. Specifically, wheat dextrin fermentation had a significant butyrogenic effect in all vessels of the gut model and significantly increased production of acetate (vessels 2 and 3) and propionate (vessel 3), simulating the transverse and distal regions of the human colon, respectively. In conclusion, wheat dextrin NUTRIOSE® FB06 is selectively fermented in vitro by Clostridium cluster XIVa and Roseburia genus and beneficially alters the metabolic profile of the human gut microbiota.
Christophe Chassard - One of the best experts on this subject based on the ideXlab platform.
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characterization of the xylan degrading microbial community from human faeces
FEMS Microbiology Ecology, 2007Co-Authors: Christophe Chassard, Vanessa Goumy, Marion Leclerc, Christophe Delhomme, Annick BernalierdonadilleAbstract:In humans, plant cell wall polysaccharides represent an important source of dietary fibres that are digested by gut microorganisms. Despite the extensive degradation of xylan in the colon, the population structure and the taxonomy of the predominant bacteria involved in degradation of this polysaccharide have not been extensively explored. The objective of our study was to characterize the xylanolytic microbial community from human faeces, using xylan from different botanic origins. The xylanolytic population was enumerated at high level in all faecal samples studied. The predominant xylanolytic organisms further isolated (20 strains) were assigned to Roseburia and Bacteroides species. Some Bacteroides isolates corresponded to the two newly described species Bacteroides intestinalis and Bacteroides dorei. Other isolates were closely related to Bacteroides sp. nov., a cellulolytic bacterium recently isolated from human faeces. The remaining Bacteroides strains could be considered to belong to a new species of this genus. Roseburia isolates could be assigned to the species Roseburia intestinalis. The xylanase activity of the Bacteroides and Roseburia isolates was found to be higher than that of other gut xylanolytic species previously identified. Our results provide new insights to the diversity and activity of the human gut xylanolytic community. Four new xylan-degrading Bacteroides species were identified and the xylanolytic capacity of R. intestinalis was further shown.
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H2 and acetate transfers during xylan fermentation between a butyrate-producing xylanolytic species and hydrogenotrophic microorganisms from the human gut.
FEMS microbiology letters, 2006Co-Authors: Christophe Chassard, Annick Bernalier-donadilleAbstract:The aim of this work was to investigate in vitro interrelationships during xylan fermentation between an H2 and butyrate-producing xylanolytic species recently isolated in our laboratory from human faeces and identified as Roseburia intestinalis and the H2-utilizing acetogen Ruminococcus hydrogenotrophicus or the methanogen Methanobrevibacter smithii. H2 transfer between M. smithii or Ru. hydrogenotrophicus and the xylanolytic species was evidenced, confirming the great potential of these H2-consuming microorganisms to reutilize fermentative H2 during fibre fermentation in the gut. In addition, acetate transfer was demonstrated between the xylanolytic Roseburia sp. and the acetogenic species, both metabolites transfers leading to butyric fermentation of oat xylan without production of H2.
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H-2 and acetate transfers during xylan fermentation between a butyrate-producing xylanolytic species and hydrogenotrophic microorganisms from the human gut
FEMS Microbiology Letters, 2006Co-Authors: Christophe Chassard, Annick Bernalier-donadilleAbstract:The aim of this work was to investigate in vitro interrelationships during xylan fermentation between an H-2 and butyrate-producing xylanolytic species recently isolated in our laboratory from human faeces and identified as Roseburia intestinalis and the H-2-utilizing acetogen Ruminococcus hydrogenotrophicus or the methanogen Methanobrevibacter smithii. H-2 transfer between M. smithii or Ru. hydrogenotrophicus and the xylanolytic species was evidenced, confirming the great potential of these H-2-consuming microorganisms to reutilize fermentative H2 during fibre fermentation in the gut. In addition, acetate transfer was demonstrated between the xylanolytic Roseburia sp. and the acetogenic species, both metabolites transfers leading to butyric fermentation of oat xylan without production of H-2.
Annick Bernalier-donadille - One of the best experts on this subject based on the ideXlab platform.
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H2 and acetate transfers during xylan fermentation between a butyrate-producing xylanolytic species and hydrogenotrophic microorganisms from the human gut.
FEMS microbiology letters, 2006Co-Authors: Christophe Chassard, Annick Bernalier-donadilleAbstract:The aim of this work was to investigate in vitro interrelationships during xylan fermentation between an H2 and butyrate-producing xylanolytic species recently isolated in our laboratory from human faeces and identified as Roseburia intestinalis and the H2-utilizing acetogen Ruminococcus hydrogenotrophicus or the methanogen Methanobrevibacter smithii. H2 transfer between M. smithii or Ru. hydrogenotrophicus and the xylanolytic species was evidenced, confirming the great potential of these H2-consuming microorganisms to reutilize fermentative H2 during fibre fermentation in the gut. In addition, acetate transfer was demonstrated between the xylanolytic Roseburia sp. and the acetogenic species, both metabolites transfers leading to butyric fermentation of oat xylan without production of H2.
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H-2 and acetate transfers during xylan fermentation between a butyrate-producing xylanolytic species and hydrogenotrophic microorganisms from the human gut
FEMS Microbiology Letters, 2006Co-Authors: Christophe Chassard, Annick Bernalier-donadilleAbstract:The aim of this work was to investigate in vitro interrelationships during xylan fermentation between an H-2 and butyrate-producing xylanolytic species recently isolated in our laboratory from human faeces and identified as Roseburia intestinalis and the H-2-utilizing acetogen Ruminococcus hydrogenotrophicus or the methanogen Methanobrevibacter smithii. H-2 transfer between M. smithii or Ru. hydrogenotrophicus and the xylanolytic species was evidenced, confirming the great potential of these H-2-consuming microorganisms to reutilize fermentative H2 during fibre fermentation in the gut. In addition, acetate transfer was demonstrated between the xylanolytic Roseburia sp. and the acetogenic species, both metabolites transfers leading to butyric fermentation of oat xylan without production of H-2.
