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Article: Formation of propionate and butyrate by the human colonic microbiota

Louis, Petra / Harry J. Flint

Environmental microbiology. 2017 Jan., v. 19, no. 1

2017

Abstract: The human gut microbiota ferments dietary nonâdigestible carbohydrates into shortâchain fatty acids (SCFA). These microbial products are utilized by the host and propionate and butyrate in particular exert a range of healthâpromoting functions. ... ...

Abstract	The human gut microbiota ferments dietary nonâdigestible carbohydrates into shortâchain fatty acids (SCFA). These microbial products are utilized by the host and propionate and butyrate in particular exert a range of healthâpromoting functions. Here an overview of the metabolic pathways utilized by gut microbes to produce these two SCFA from dietary carbohydrates and from amino acids resulting from protein breakdown is provided. This overview emphasizes the important role played by crossâfeeding of intermediary metabolites (in particular lactate, succinate and 1,2âpropanediol) between different gut bacteria. The ecophysiology, including growth requirements and responses to environmental factors, of major propionate and butyrate producing bacteria are discussed in relation to dietary modulation of these metabolites. A detailed understanding of SCFA metabolism by the gut microbiota is necessary to underpin effective strategies to optimize SCFA supply to the host.
Keywords	amino acids ; bacteria ; biochemical pathways ; butyrates ; carbohydrates ; dietary carbohydrate ; ecophysiology ; environmental factors ; health promotion ; humans ; intestinal microorganisms ; lactic acid ; metabolism ; metabolites ; propionic acid ; short chain fatty acids ; succinic acid
Language	English
Dates of publication	2017-01
Size	p. 29-41.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	REVIEW
ZDB-ID	2020213-1
ISSN	1462-2920 ; 1462-2912
ISSN (online)	1462-2920
ISSN	1462-2912
DOI	10.1111/1462-2920.13589
Database	NAL-Catalogue (AGRICOLA)

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Article: Phylogeny, culturing, and metagenomics of the human gut microbiota

Walker, Alan W / Harry J. Flint / Petra Louis / Sylvia H. Duncan

Trends in microbiology. 2014 May, v. 22, no. 5

2014

Abstract: The human intestinal tract is colonised by a complex community of microbes, which can have major impacts on host health. Recent research on the gut microbiota has largely been driven by the advent of modern sequence-based techniques, such as metagenomics. ...

Abstract	The human intestinal tract is colonised by a complex community of microbes, which can have major impacts on host health. Recent research on the gut microbiota has largely been driven by the advent of modern sequence-based techniques, such as metagenomics. Although these are powerful and valuable tools, they have limitations. Traditional culturing and phylogeny can mitigate some of these limitations, either by expanding reference databases or by assigning functionality to specific microbial lineages. As such, culture and phylogeny will continue to have crucially important roles in human microbiota research, and will be required for the development of novel therapeutics.
Keywords	databases ; humans ; intestinal microorganisms ; intestines ; metagenomics ; phylogeny ; therapeutics
Language	English
Dates of publication	2014-05
Size	p. 267-274.
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	1158963-2
ISSN	1878-4380 ; 0966-842X
ISSN (online)	1878-4380
ISSN	0966-842X
DOI	10.1016/j.tim.2014.03.001
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Faecalibacterium prausnitzii Strain HTF-F and Its Extracellular Polymeric Matrix Attenuate Clinical Parameters in DSS-Induced Colitis.

Oriana Rossi / M Tanweer Khan / Martin Schwarzer / Tomas Hudcovic / Dagmar Srutkova / Sylvia H Duncan / Ellen H Stolte / Hana Kozakova / Harry J Flint / Janneke N Samsom / Hermie J M Harmsen / Jerry M Wells

PLoS ONE, Vol 10, Iss 4, p e

2015 Volume 0123013

Abstract: A decrease in the abundance and biodiversity of intestinal bacteria within the Firmicutes phylum has been associated with inflammatory bowel disease (IBD). In particular, the anti-inflammatory bacterium Faecalibacterium prausnitzii, member of the ... ...

Abstract	A decrease in the abundance and biodiversity of intestinal bacteria within the Firmicutes phylum has been associated with inflammatory bowel disease (IBD). In particular, the anti-inflammatory bacterium Faecalibacterium prausnitzii, member of the Firmicutes phylum and one of the most abundant species in healthy human colon, is underrepresented in the microbiota of IBD patients. The aim of this study was to investigate the immunomodulatory properties of F. prausnitzii strain A2-165, the biofilm forming strain HTF-F and the extracellular polymeric matrix (EPM) isolated from strain HTF-F. For this purpose, the immunomodulatory properties of the F. prausnitzii strains and the EPM were studied in vitro using human monocyte-derived dendritic cells. Then, the capacity of the F. prausnitzii strains and the EPM of HTF-F to suppress inflammation was assessed in vivo in the mouse dextran sodium sulphate (DSS) colitis model. The F. prausnitzii strains and the EPM had anti-inflammatory effects on the clinical parameters measured in the DSS model but with different efficacy. The immunomodulatory effects of the EPM were mediated through the TLR2-dependent modulation of IL-12 and IL-10 cytokine production in antigen presenting cells, suggesting that it contributes to the anti-inflammatory potency of F. prausnitzii HTF-F. The results show that F. prausnitzii HTF-F and its EPM may have a therapeutic use in IBD.
Keywords	Medicine ; R ; Science ; Q
Subject code	610
Language	English
Publishing date	2015-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Lysozyme activity of the Ruminococcus champanellensis cellulosome

MoraÃ¯s, Sarah / Darrell W. Cockburn / Yonit BenâDavid / Nicole M. Koropatkin / Eric C. Martens / Sylvia H. Duncan / Harry J. Flint / Itzhak Mizrahi / Edward A. Bayer

Environmental microbiology. 2016 Dec., v. 18, no. 12

2016

Abstract: Ruminococcus champanellensis is a keystone species in the human gut that produces an intricate cellulosome system of various architectures. A variety of cellulosomal enzymes have been identified, which exhibit a range of hydrolytic activities on ... ...

Abstract	Ruminococcus champanellensis is a keystone species in the human gut that produces an intricate cellulosome system of various architectures. A variety of cellulosomal enzymes have been identified, which exhibit a range of hydrolytic activities on lignocellulosic substrates. We describe herein a unique R. champanellensis scaffoldin, ScaK, which is expressed during growth on cellobiose and comprises a cohesin module and a family 25 glycoside hydrolase (GH25). The GH25 is nonâautolytic and exhibits lysozymeâmediated lytic activity against several bacterial species. Despite the narrow acidic pH curve, the enzyme is active along a temperature range from 2 to 85Â°C and is stable at very high temperatures for extended incubation periods. The ScaK cohesin was shown to bind selectively to the dockerin of a monovalent scaffoldin (ScaG), thus enabling formation of a cellâfree cellulosome, whereby ScaG interacts with a divalent scaffodin (ScaA) that bears the enzymes either directly or through additional monovalent scaffoldins (ScaC and ScaD). The ScaK cohesin also interacts with the dockerin of a protein comprising multiple Fn3 domains that can potentially promote adhesion to carbohydrates and the bacterial cell surface. A cellâfree cellulosomal GH25 lysozyme may provide a bacterial strategy to both hydrolyze lignocellulose and repel eventual food competitors and/or cheaters.
Keywords	Ruminococcus ; adhesion ; bacteria ; cellobiose ; cellulosome ; digestive system ; glycosides ; humans ; keystone species ; lignocellulose ; lysozyme ; pH ; temperature
Language	English
Dates of publication	2016-12
Size	p. 5112-5122.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	2020213-1
ISSN	1462-2920 ; 1462-2912
ISSN (online)	1462-2920
ISSN	1462-2912
DOI	10.1111/1462-2920.13501
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Gut microbiota signatures predict host and microbiota responses to dietary interventions in obese individuals.

Katri Korpela / Harry J Flint / Alexandra M Johnstone / Jenni Lappi / Kaisa Poutanen / Evelyne Dewulf / Nathalie Delzenne / Willem M de Vos / Anne Salonen

PLoS ONE, Vol 9, Iss 6, p e

2014 Volume 90702

Abstract: Background Interactions between the diet and intestinal microbiota play a role in health and disease, including obesity and related metabolic complications. There is great interest to use dietary means to manipulate the microbiota to promote health. ... ...

Abstract	Background Interactions between the diet and intestinal microbiota play a role in health and disease, including obesity and related metabolic complications. There is great interest to use dietary means to manipulate the microbiota to promote health. Currently, the impact of dietary change on the microbiota and the host metabolism is poorly predictable and highly individual. We propose that the responsiveness of the gut microbiota may depend on its composition, and associate with metabolic changes in the host. Methodology Our study involved three independent cohorts of obese adults (n = 78) from Belgium, Finland, and Britain, participating in different dietary interventions aiming to improve metabolic health. We used a phylogenetic microarray for comprehensive fecal microbiota analysis at baseline and after the intervention. Blood cholesterol, insulin and inflammation markers were analyzed as indicators of host response. The data were divided into four training set - test set pairs; each intervention acted both as a part of a training set and as an independent test set. We used linear models to predict the responsiveness of the microbiota and the host, and logistic regression to predict responder vs. non-responder status, or increase vs. decrease of the health parameters. Principal findings Our models, based on the abundance of several, mainly Firmicute species at baseline, predicted the responsiveness of the microbiota (AUC = 0.77-1; predicted vs. observed correlation = 0.67-0.88). Many of the predictive taxa showed a non-linear relationship with the responsiveness. The microbiota response associated with the change in serum cholesterol levels with an AUC of 0.96, highlighting the involvement of the intestinal microbiota in metabolic health. Conclusion This proof-of-principle study introduces the first potential microbial biomarkers for dietary responsiveness in obese individuals with impaired metabolic health, and reveals the potential of microbiota signatures for personalized nutrition.
Keywords	Medicine ; R ; Science ; Q
Subject code	796
Language	English
Publishing date	2014-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Rumen cellulosomics

Bareket Dassa / Ilya Borovok / Vered Ruimy-Israeli / Raphael Lamed / Harry J Flint / Sylvia H Duncan / Bernard Henrissat / Pedro Coutinho / Mark Morrison / Pascale Mosoni / Carl J Yeoman / Bryan A White / Edward A Bayer

PLoS ONE, Vol 9, Iss 7, p e

divergent fiber-degrading strategies revealed by comparative genome-wide analysis of six ruminococcal strains.

2014 Volume 99221

Abstract: Background A complex community of microorganisms is responsible for efficient plant cell wall digestion by many herbivores, notably the ruminants. Understanding the different fibrolytic mechanisms utilized by these bacteria has been of great interest in ... ...

Abstract	Background A complex community of microorganisms is responsible for efficient plant cell wall digestion by many herbivores, notably the ruminants. Understanding the different fibrolytic mechanisms utilized by these bacteria has been of great interest in agricultural and technological fields, reinforced more recently by current efforts to convert cellulosic biomass to biofuels. Methodology/principal findings Here, we have used a bioinformatics-based approach to explore the cellulosome-related components of six genomes from two of the primary fiber-degrading bacteria in the rumen: Ruminococcus flavefaciens (strains FD-1, 007c and 17) and Ruminococcus albus (strains 7, 8 and SY3). The genomes of two of these strains are reported for the first time herein. The data reveal that the three R. flavefaciens strains encode for an elaborate reservoir of cohesin- and dockerin-containing proteins, whereas the three R. albus strains are cohesin-deficient and encode mainly dockerins and a unique family of cell-anchoring carbohydrate-binding modules (family 37). Conclusions/significance Our comparative genome-wide analysis pinpoints rare and novel strain-specific protein architectures and provides an exhaustive profile of their numerous lignocellulose-degrading enzymes. This work provides blueprints of the divergent cellulolytic systems in these two prominent fibrolytic rumen bacterial species, each of which reflects a distinct mechanistic model for efficient degradation of cellulosic biomass.
Keywords	Medicine ; R ; Science ; Q
Subject code	570
Language	English
Publishing date	2014-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Sporulation capability and amylosome conservation among diverse human colonic and rumen isolates of the keystone starchâdegrader Ruminococcus bromii

Mukhopadhya, Indrani / Sarah MoraÃ¯s / Jenny LaverdeâGomez / Paul O. Sheridan / Alan W. Walker / William Kelly / Athol V. Klieve / Diane Ouwerkerk / Sylvia H. Duncan / Petra Louis / Nicole Koropatkin / Darrell Cockburn / Ryan Kibler / Philip J. Cooper / Carlos Sandoval / Emmanuelle Crost / Nathalie Juge / Edward A. Bayer / Harry J. Flint

Environmental microbiology. 2018 Jan., v. 20, no. 1

2018

Abstract: Ruminococcus bromii is a dominant member of the human colonic microbiota that plays a âkeystoneâ role in degrading dietary resistant starch. Recent evidence from one strain has uncovered a unique cell surface âamylosomeâ complex that organizes ... ...

Abstract	Ruminococcus bromii is a dominant member of the human colonic microbiota that plays a âkeystoneâ role in degrading dietary resistant starch. Recent evidence from one strain has uncovered a unique cell surface âamylosomeâ complex that organizes starchâdegrading enzymes. New genome analysis presented here reveals further features of this complex and shows remarkable conservation of amylosome components between human colonic strains from three different continents and a R. bromii strain from the rumen of Australian cattle. These R. bromii strains encode a narrow spectrum of carbohydrate active enzymes (CAZymes) that reflect extreme specialization in starch utilization. Starch hydrolysis products are taken up mainly as oligosaccharides, with only one strain able to grow on glucose. The human strains, but not the rumen strain, also possess transporters that allow growth on galactose and fructose. R. bromii strains possess a full complement of sporulation and spore germination genes and we demonstrate the ability to form spores that survive exposure to air. Spore formation is likely to be a critical factor in the ecology of this nutritionally highly specialized bacterium, which was previously regarded as ânonâsporingâ, helping to explain its widespread occurrence in the gut microbiota through the ability to transmit between hosts.
Keywords	Ruminococcus bromii ; air ; bacteria ; cattle ; ecology ; enzymes ; fructose ; galactose ; genes ; glucose ; hosts ; humans ; hydrolysis ; intestinal microorganisms ; oligosaccharides ; resistant starch ; rumen ; sequence analysis ; spore germination ; spores ; sporulation ; transporters
Language	English
Dates of publication	2018-01
Size	p. 324-336.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	2020213-1
ISSN	1462-2920 ; 1462-2912
ISSN (online)	1462-2920
ISSN	1462-2912
DOI	10.1111/1462-2920.14000
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: The impact of different DNA extraction kits and laboratories upon the assessment of human gut microbiota composition by 16S rRNA gene sequencing.

Nicholas A Kennedy / Alan W Walker / Susan H Berry / Sylvia H Duncan / Freda M Farquarson / Petra Louis / John M Thomson / UK IBD Genetics Consortium / Jack Satsangi / Harry J Flint / Julian Parkhill / Charlie W Lees / Georgina L Hold

PLoS ONE, Vol 9, Iss 2, p e

2014 Volume 88982

Abstract: Introduction Determining bacterial community structure in fecal samples through DNA sequencing is an important facet of intestinal health research. The impact of different commercially available DNA extraction kits upon bacterial community structures has ...

Abstract	Introduction Determining bacterial community structure in fecal samples through DNA sequencing is an important facet of intestinal health research. The impact of different commercially available DNA extraction kits upon bacterial community structures has received relatively little attention. The aim of this study was to analyze bacterial communities in volunteer and inflammatory bowel disease (IBD) patient fecal samples extracted using widely used DNA extraction kits in established gastrointestinal research laboratories. Methods Fecal samples from two healthy volunteers (H3 and H4) and two relapsing IBD patients (I1 and I2) were investigated. DNA extraction was undertaken using MoBio Powersoil and MP Biomedicals FastDNA SPIN Kit for Soil DNA extraction kits. PCR amplification for pyrosequencing of bacterial 16S rRNA genes was performed in both laboratories on all samples. Hierarchical clustering of sequencing data was done using the Yue and Clayton similarity coefficient. Results DNA extracted using the FastDNA kit and the MoBio kit gave median DNA concentrations of 475 (interquartile range 228-561) and 22 (IQR 9-36) ng/µL respectively (p<0.0001). Hierarchical clustering of sequence data by Yue and Clayton coefficient revealed four clusters. Samples from individuals H3 and I2 clustered by patient; however, samples from patient I1 extracted with the MoBio kit clustered with samples from patient H4 rather than the other I1 samples. Linear modelling on relative abundance of common bacterial families revealed significant differences between kits; samples extracted with MoBio Powersoil showed significantly increased Bacteroidaceae, Ruminococcaceae and Porphyromonadaceae, and lower Enterobacteriaceae, Lachnospiraceae, Clostridiaceae, and Erysipelotrichaceae (p<0.05). Conclusion This study demonstrates significant differences in DNA yield and bacterial DNA composition when comparing DNA extracted from the same fecal sample with different extraction kits. This highlights the importance of ensuring that samples in ...
Keywords	Medicine ; R ; Science ; Q
Subject code	612
Language	English
Publishing date	2014-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Pro-inflammatory flagellin proteins of prevalent motile commensal bacteria are variably abundant in the intestinal microbiome of elderly humans.

B Anne Neville / Paul O Sheridan / Hugh M B Harris / Simone Coughlan / Harry J Flint / Sylvia H Duncan / Ian B Jeffery / Marcus J Claesson / R Paul Ross / Karen P Scott / Paul W O'Toole

PLoS ONE, Vol 8, Iss 7, p e

2013 Volume 68919

Abstract: 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 ... ...

Abstract	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 σ(28). 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 ...
Keywords	Medicine ; R ; Science ; Q
Subject code	590
Language	English
Publishing date	2013-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Correction

Maša Vodovnik / Sylvia H. Duncan / Martin D. Reid / Louise Cantlay / Keith Turner / Julian Parkhill / Raphael Lamed / Carl J. Yeoman / Margret E. Berg. Miller / Bryan A. White / Edward A. Bayer / Romana Marinšek-Logar / Harry J. Flint

PLoS ONE, Vol 8, Iss

Expression of Cellulosome Components and Type IV Pili within the Extracellular Proteome of 007.

2013 Volume 12

Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2013-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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