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Formate cross-feeding and cooperative metabolic interactions revealed by transcriptomics in co-cultures of acetogenic and amylolytic human colonic bacteria.

Laverde Gomez JA, Mukhopadhya I, Duncan SH, Louis P, Shaw S, Collie-Duguid E, Crost E, Juge N, Flint HJ.

Environ Microbiol. 2019 Jan;21(1):259-271. doi: 10.1111/1462-2920.14454. Epub 2018 Nov 22.


Impact of carbohydrate substrate complexity on the diversity of the human colonic microbiota.

Chung WSF, Walker AW, Vermeiren J, Sheridan PO, Bosscher D, Garcia-Campayo V, Parkhill J, Flint HJ, Duncan SH.

FEMS Microbiol Ecol. 2019 Jan 1;95(1). doi: 10.1093/femsec/fiy201.


Alterations in the Abundance and Co-occurrence of Akkermansia muciniphila and Faecalibacterium prausnitzii in the Colonic Mucosa of Inflammatory Bowel Disease Subjects.

Lopez-Siles M, Enrich-Capó N, Aldeguer X, Sabat-Mir M, Duncan SH, Garcia-Gil LJ, Martinez-Medina M.

Front Cell Infect Microbiol. 2018 Sep 7;8:281. doi: 10.3389/fcimb.2018.00281. eCollection 2018.


Mutual Interaction of Phenolic Compounds and Microbiota: Metabolism of Complex Phenolic Apigenin-C- and Kaempferol-O-Derivatives by Human Fecal Samples.

Vollmer M, Esders S, Farquharson FM, Neugart S, Duncan SH, Schreiner M, Louis P, Maul R, Rohn S.

J Agric Food Chem. 2018 Jan 17;66(2):485-497. doi: 10.1021/acs.jafc.7b04842. Epub 2018 Jan 3.


Specific substrate-driven changes in human faecal microbiota composition contrast with functional redundancy in short-chain fatty acid production.

Reichardt N, Vollmer M, Holtrop G, Farquharson FM, Wefers D, Bunzel M, Duncan SH, Drew JE, Williams LM, Milligan G, Preston T, Morrison D, Flint HJ, Louis P.

ISME J. 2018 Feb;12(2):610-622. doi: 10.1038/ismej.2017.196. Epub 2017 Dec 1.


Sporulation capability and amylosome conservation among diverse human colonic and rumen isolates of the keystone starch-degrader Ruminococcus bromii.

Mukhopadhya I, Moraïs S, Laverde-Gomez J, Sheridan PO, Walker AW, Kelly W, Klieve AV, Ouwerkerk D, Duncan SH, Louis P, Koropatkin N, Cockburn D, Kibler R, Cooper PJ, Sandoval C, Crost E, Juge N, Bayer EA, Flint HJ.

Environ Microbiol. 2018 Jan;20(1):324-336. doi: 10.1111/1462-2920.14000. Epub 2017 Dec 7.


Prebiotic potential of pectin and pectic oligosaccharides to promote anti-inflammatory commensal bacteria in the human colon.

Chung WSF, Meijerink M, Zeuner B, Holck J, Louis P, Meyer AS, Wells JM, Flint HJ, Duncan SH.

FEMS Microbiol Ecol. 2017 Nov 1;93(11). doi: 10.1093/femsec/fix127.


Chlorogenic acid versus amaranth's caffeoylisocitric acid - Gut microbial degradation of caffeic acid derivatives.

Vollmer M, Schröter D, Esders S, Neugart S, Farquharson FM, Duncan SH, Schreiner M, Louis P, Maul R, Rohn S.

Food Res Int. 2017 Oct;100(Pt 3):375-384. doi: 10.1016/j.foodres.2017.06.013. Epub 2017 Jun 3.


Discovery of a novel lantibiotic nisin O from Blautia obeum A2-162, isolated from the human gastrointestinal tract.

Hatziioanou D, Gherghisan-Filip C, Saalbach G, Horn N, Wegmann U, Duncan SH, Flint HJ, Mayer MJ, Narbad A.

Microbiology. 2017 Sep;163(9):1292-1305. doi: 10.1099/mic.0.000515. Epub 2017 Aug 31.


Circulating and Tissue-Resident CD4+ T Cells With Reactivity to Intestinal Microbiota Are Abundant in Healthy Individuals and Function Is Altered During Inflammation.

Hegazy AN, West NR, Stubbington MJT, Wendt E, Suijker KIM, Datsi A, This S, Danne C, Campion S, Duncan SH, Owens BMJ, Uhlig HH, McMichael A; Oxford IBD Cohort Investigators, Bergthaler A, Teichmann SA, Keshav S, Powrie F.

Gastroenterology. 2017 Nov;153(5):1320-1337.e16. doi: 10.1053/j.gastro.2017.07.047. Epub 2017 Aug 4.


Oral treatment with Eubacterium hallii improves insulin sensitivity in db/db mice.

Udayappan S, Manneras-Holm L, Chaplin-Scott A, Belzer C, Herrema H, Dallinga-Thie GM, Duncan SH, Stroes ESG, Groen AK, Flint HJ, Backhed F, de Vos WM, Nieuwdorp M.

NPJ Biofilms Microbiomes. 2016 Jul 6;2:16009. doi: 10.1038/npjbiofilms.2016.9. eCollection 2016.


The impact of nutrition on intestinal bacterial communities.

Flint HJ, Duncan SH, Louis P.

Curr Opin Microbiol. 2017 Aug;38:59-65. doi: 10.1016/j.mib.2017.04.005. Epub 2017 May 6. Review.


Polysaccharide utilization loci and nutritional specialization in a dominant group of butyrate-producing human colonic Firmicutes.

O Sheridan P, Martin JC, Lawley TD, Browne HP, Harris HMB, Bernalier-Donadille A, Duncan SH, O'Toole PW, P Scott K, J Flint H.

Microb Genom. 2016 Feb 9;2(2):e000043. doi: 10.1099/mgen.0.000043. eCollection 2016 Feb.


Faecalibacterium prausnitzii: from microbiology to diagnostics and prognostics.

Lopez-Siles M, Duncan SH, Garcia-Gil LJ, Martinez-Medina M.

ISME J. 2017 Apr;11(4):841-852. doi: 10.1038/ismej.2016.176. Epub 2017 Jan 3. Review.


Lysozyme activity of the Ruminococcus champanellensis cellulosome.

Moraïs S, Cockburn DW, Ben-David Y, Koropatkin NM, Martens EC, Duncan SH, Flint HJ, Mizrahi I, Bayer EA.

Environ Microbiol. 2016 Dec;18(12):5112-5122. doi: 10.1111/1462-2920.13501. Epub 2016 Sep 7.


Availability and dose response of phytophenols from a wheat bran rich cereal product in healthy human volunteers.

Neacsu M, McMonagle J, Fletcher RJ, Hulshof T, Duncan SH, Scobbie L, Duncan GJ, Cantlay L, Horgan G, de Roos B, Duthie GG, Russell WR.

Mol Nutr Food Res. 2017 Mar;61(3). doi: 10.1002/mnfr.201600202. Epub 2017 Jan 25.


Objections to the proposed reclassification of Eubacterium rectale as Agathobacter rectalis.

Sheridan PO, Duncan SH, Walker AW, Scott KP, Louis P, Flint HJ.

Int J Syst Evol Microbiol. 2016 May;66(5):2106. doi: 10.1099/ijsem.0.000969. Epub 2016 Feb 24. No abstract available.


Modulation of the human gut microbiota by dietary fibres occurs at the species level.

Chung WS, Walker AW, Louis P, Parkhill J, Vermeiren J, Bosscher D, Duncan SH, Flint HJ.

BMC Biol. 2016 Jan 11;14:3. doi: 10.1186/s12915-015-0224-3.


Faecalibacterium prausnitzii A2-165 has a high capacity to induce IL-10 in human and murine dendritic cells and modulates T cell responses.

Rossi O, van Berkel LA, Chain F, Tanweer Khan M, Taverne N, Sokol H, Duncan SH, Flint HJ, Harmsen HJ, Langella P, Samsom JN, Wells JM.

Sci Rep. 2016 Jan 4;6:18507. doi: 10.1038/srep18507.


Wheat bran promotes enrichment within the human colonic microbiota of butyrate-producing bacteria that release ferulic acid.

Duncan SH, Russell WR, Quartieri A, Rossi M, Parkhill J, Walker AW, Flint HJ.

Environ Microbiol. 2016 Jul;18(7):2214-25. doi: 10.1111/1462-2920.13158. Epub 2016 Jan 21.


Changes in the Abundance of Faecalibacterium prausnitzii Phylogroups I and II in the Intestinal Mucosa of Inflammatory Bowel Disease and Patients with Colorectal Cancer.

Lopez-Siles M, Martinez-Medina M, Surís-Valls R, Aldeguer X, Sabat-Mir M, Duncan SH, Flint HJ, Garcia-Gil LJ.

Inflamm Bowel Dis. 2016 Jan;22(1):28-41. doi: 10.1097/MIB.0000000000000590.


Enhanced butyrate formation by cross-feeding between Faecalibacterium prausnitzii and Bifidobacterium adolescentis.

Rios-Covian D, Gueimonde M, Duncan SH, Flint HJ, de los Reyes-Gavilan CG.

FEMS Microbiol Lett. 2015 Nov;362(21). pii: fnv176. doi: 10.1093/femsle/fnv176. Epub 2015 Sep 28.


Unique Organization of Extracellular Amylases into Amylosomes in the Resistant Starch-Utilizing Human Colonic Firmicutes Bacterium Ruminococcus bromii.

Ze X, Ben David Y, Laverde-Gomez JA, Dassa B, Sheridan PO, Duncan SH, Louis P, Henrissat B, Juge N, Koropatkin NM, Bayer EA, Flint HJ.

MBio. 2015 Sep 29;6(5):e01058-15. doi: 10.1128/mBio.01058-15.


Enzymatic profiling of cellulosomal enzymes from the human gut bacterium, Ruminococcus champanellensis, reveals a fine-tuned system for cohesin-dockerin recognition.

Moraïs S, Ben David Y, Bensoussan L, Duncan SH, Koropatkin NM, Martens EC, Flint HJ, Bayer EA.

Environ Microbiol. 2016 Feb;18(2):542-56. doi: 10.1111/1462-2920.13047. Epub 2015 Oct 14.


Mucosa-associated Faecalibacterium prausnitzii phylotype richness is reduced in patients with inflammatory bowel disease.

Lopez-Siles M, Martinez-Medina M, Abellà C, Busquets D, Sabat-Mir M, Duncan SH, Aldeguer X, Flint HJ, Garcia-Gil LJ.

Appl Environ Microbiol. 2015 Nov;81(21):7582-92. doi: 10.1128/AEM.02006-15. Epub 2015 Aug 21.


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

Rossi O, Khan MT, Schwarzer M, Hudcovic T, Srutkova D, Duncan SH, Stolte EH, Kozakova H, Flint HJ, Samsom JN, Harmsen HJ, Wells JM.

PLoS One. 2015 Apr 24;10(4):e0123013. doi: 10.1371/journal.pone.0123013. eCollection 2015.


Ruminococcal cellulosome systems from rumen to human.

Ben David Y, Dassa B, Borovok I, Lamed R, Koropatkin NM, Martens EC, White BA, Bernalier-Donadille A, Duncan SH, Flint HJ, Bayer EA, Moraïs S.

Environ Microbiol. 2015 Sep;17(9):3407-26. doi: 10.1111/1462-2920.12868. Epub 2015 May 7.


Links between diet, gut microbiota composition and gut metabolism.

Flint HJ, Duncan SH, Scott KP, Louis P.

Proc Nutr Soc. 2015 Feb;74(1):13-22. doi: 10.1017/S0029665114001463. Epub 2014 Sep 30.


Modelling the emergent dynamics and major metabolites of the human colonic microbiota.

Kettle H, Louis P, Holtrop G, Duncan SH, Flint HJ.

Environ Microbiol. 2015 May;17(5):1615-30. doi: 10.1111/1462-2920.12599. Epub 2014 Oct 7.


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

Dassa B, Borovok I, Ruimy-Israeli V, Lamed R, Flint HJ, Duncan SH, Henrissat B, Coutinho P, Morrison M, Mosoni P, Yeoman CJ, White BA, Bayer EA.

PLoS One. 2014 Jul 3;9(7):e99221. doi: 10.1371/journal.pone.0099221. eCollection 2014.


Impact of diet and individual variation on intestinal microbiota composition and fermentation products in obese men.

Salonen A, Lahti L, Salojärvi J, Holtrop G, Korpela K, Duncan SH, Date P, Farquharson F, Johnstone AM, Lobley GE, Louis P, Flint HJ, de Vos WM.

ISME J. 2014 Nov;8(11):2218-30. doi: 10.1038/ismej.2014.63. Epub 2014 Apr 24.


Mucosa-associated Faecalibacterium prausnitzii and Escherichia coli co-abundance can distinguish Irritable Bowel Syndrome and Inflammatory Bowel Disease phenotypes.

Lopez-Siles M, Martinez-Medina M, Busquets D, Sabat-Mir M, Duncan SH, Flint HJ, Aldeguer X, Garcia-Gil LJ.

Int J Med Microbiol. 2014 May;304(3-4):464-75. doi: 10.1016/j.ijmm.2014.02.009. Epub 2014 Feb 21.


Phylogeny, culturing, and metagenomics of the human gut microbiota.

Walker AW, Duncan SH, Louis P, Flint HJ.

Trends Microbiol. 2014 May;22(5):267-74. doi: 10.1016/j.tim.2014.03.001. Epub 2014 Mar 31. Review.


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

Kennedy NA, Walker AW, Berry SH, Duncan SH, Farquarson FM, Louis P, Thomson JM; UK IBD Genetics Consortium, Satsangi J, Flint HJ, Parkhill J, Lees CW, Hold GL.

PLoS One. 2014 Feb 24;9(2):e88982. doi: 10.1371/journal.pone.0088982. eCollection 2014.


Functional genomics reveals that Clostridium difficile Spo0A coordinates sporulation, virulence and metabolism.

Pettit LJ, Browne HP, Yu L, Smits WK, Fagan RP, Barquist L, Martin MJ, Goulding D, Duncan SH, Flint HJ, Dougan G, Choudhary JS, Lawley TD.

BMC Genomics. 2014 Feb 25;15:160. doi: 10.1186/1471-2164-15-160.


Phylogenetic distribution of three pathways for propionate production within the human gut microbiota.

Reichardt N, Duncan SH, Young P, Belenguer A, McWilliam Leitch C, Scott KP, Flint HJ, Louis P.

ISME J. 2014 Jun;8(6):1323-35. doi: 10.1038/ismej.2014.14. Epub 2014 Feb 20. Erratum in: ISME J. 2014 Jun;8(6):1352.


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

Neville BA, Sheridan PO, Harris HM, Coughlan S, Flint HJ, Duncan SH, Jeffery IB, Claesson MJ, Ross RP, Scott KP, O'Toole PW.

PLoS One. 2013 Jul 23;8(7):e68919. doi: 10.1371/journal.pone.0068919. Print 2013.


Complete genome of a new Firmicutes species belonging to the dominant human colonic microbiota ('Ruminococcus bicirculans') reveals two chromosomes and a selective capacity to utilize plant glucans.

Wegmann U, Louis P, Goesmann A, Henrissat B, Duncan SH, Flint HJ.

Environ Microbiol. 2014 Sep;16(9):2879-90. doi: 10.1111/1462-2920.12217. Epub 2013 Aug 6.


A representative of the dominant human colonic Firmicutes, Roseburia faecis M72/1, forms a novel bacteriocin-like substance.

Hatziioanou D, Mayer MJ, Duncan SH, Flint HJ, Narbad A.

Anaerobe. 2013 Oct;23:5-8. doi: 10.1016/j.anaerobe.2013.07.006. Epub 2013 Aug 1.


Prebiotic stimulation of human colonic butyrate-producing bacteria and bifidobacteria, in vitro.

Scott KP, Martin JC, Duncan SH, Flint HJ.

FEMS Microbiol Ecol. 2014 Jan;87(1):30-40. doi: 10.1111/1574-6941.12186. Epub 2013 Aug 28.


Expression of cellulosome components and type IV pili within the extracellular proteome of Ruminococcus flavefaciens 007.

Vodovnik M, Duncan SH, Reid MD, Cantlay L, Turner K, Parkhill J, Lamed R, Yeoman CJ, Miller ME, White BA, Bayer EA, Marinšek-Logar R, Flint HJ.

PLoS One. 2013 Jun 4;8(6):e65333. doi: 10.1371/journal.pone.0065333. Print 2013.


Some are more equal than others: the role of "keystone" species in the degradation of recalcitrant substrates.

Ze X, Le Mougen F, Duncan SH, Louis P, Flint HJ.

Gut Microbes. 2013 May-Jun;4(3):236-40. doi: 10.4161/gmic.23998. Epub 2013 Apr 2. Review.


Probiotics and prebiotics and health in ageing populations.

Duncan SH, Flint HJ.

Maturitas. 2013 May;75(1):44-50. doi: 10.1016/j.maturitas.2013.02.004. Epub 2013 Mar 11. Review.


Major phenylpropanoid-derived metabolites in the human gut can arise from microbial fermentation of protein.

Russell WR, Duncan SH, Scobbie L, Duncan G, Cantlay L, Calder AG, Anderson SE, Flint HJ.

Mol Nutr Food Res. 2013 Mar;57(3):523-35. doi: 10.1002/mnfr.201200594. Epub 2013 Jan 24.


The gut microbial metabolome: modulation of cancer risk in obese individuals.

Russell WR, Duncan SH, Flint HJ.

Proc Nutr Soc. 2013 Feb;72(1):178-88. doi: 10.1017/S0029665112002881. Epub 2012 Nov 23. Review.


The influence of diet on the gut microbiota.

Scott KP, Gratz SW, Sheridan PO, Flint HJ, Duncan SH.

Pharmacol Res. 2013 Mar;69(1):52-60. doi: 10.1016/j.phrs.2012.10.020. Epub 2012 Nov 9. Review.


Targeted restoration of the intestinal microbiota with a simple, defined bacteriotherapy resolves relapsing Clostridium difficile disease in mice.

Lawley TD, Clare S, Walker AW, Stares MD, Connor TR, Raisen C, Goulding D, Rad R, Schreiber F, Brandt C, Deakin LJ, Pickard DJ, Duncan SH, Flint HJ, Clark TG, Parkhill J, Dougan G.

PLoS Pathog. 2012;8(10):e1002995. doi: 10.1371/journal.ppat.1002995. Epub 2012 Oct 25.


Anaerostipes hadrus comb. nov., a dominant species within the human colonic microbiota; reclassification of Eubacterium hadrum Moore et al. 1976.

Allen-Vercoe E, Daigneault M, White A, Panaccione R, Duncan SH, Flint HJ, O'Neal L, Lawson PA.

Anaerobe. 2012 Oct;18(5):523-9. doi: 10.1016/j.anaerobe.2012.09.002. Epub 2012 Sep 11.


The role of the gut microbiota in nutrition and health.

Flint HJ, Scott KP, Louis P, Duncan SH.

Nat Rev Gastroenterol Hepatol. 2012 Sep 4;9(10):577-89. doi: 10.1038/nrgastro.2012.156. eCollection 2012 Oct. Review.


Microbial degradation of complex carbohydrates in the gut.

Flint HJ, Scott KP, Duncan SH, Louis P, Forano E.

Gut Microbes. 2012 Jul-Aug;3(4):289-306. Epub 2012 May 10. Review.

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