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Items: 39

1.

Towards standards for human fecal sample processing in metagenomic studies.

Costea PI, Zeller G, Sunagawa S, Pelletier E, Alberti A, Levenez F, Tramontano M, Driessen M, Hercog R, Jung FE, Kultima JR, Hayward MR, Coelho LP, Allen-Vercoe E, Bertrand L, Blaut M, Brown JRM, Carton T, Cools-Portier S, Daigneault M, Derrien M, Druesne A, de Vos WM, Finlay BB, Flint HJ, Guarner F, Hattori M, Heilig H, Luna RA, van Hylckama Vlieg J, Junick J, Klymiuk I, Langella P, Le Chatelier E, Mai V, Manichanh C, Martin JC, Mery C, Morita H, O'Toole PW, Orvain C, Patil KR, Penders J, Persson S, Pons N, Popova M, Salonen A, Saulnier D, Scott KP, Singh B, Slezak K, Veiga P, Versalovic J, Zhao L, Zoetendal EG, Ehrlich SD, Dore J, Bork P.

Nat Biotechnol. 2017 Nov;35(11):1069-1076. doi: 10.1038/nbt.3960. Epub 2017 Oct 2.

PMID:
28967887
2.

16S sequencing and functional analysis of the fecal microbiome during treatment of newly diagnosed pediatric inflammatory bowel disease.

Ashton JJ, Colquhoun CM, Cleary DW, Coelho T, Haggarty R, Mulder I, Batra A, Afzal NA, Beattie RM, Scott KP, Ennis S.

Medicine (Baltimore). 2017 Jun;96(26):e7347. doi: 10.1097/MD.0000000000007347.

3.

Strain-Level Metagenomic Analysis of the Fermented Dairy Beverage Nunu Highlights Potential Food Safety Risks.

Walsh AM, Crispie F, Daari K, O'Sullivan O, Martin JC, Arthur CT, Claesson MJ, Scott KP, Cotter PD.

Appl Environ Microbiol. 2017 Aug 1;83(16). pii: e01144-17. doi: 10.1128/AEM.01144-17. Print 2017 Aug 15.

4.

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

Sheridan PO, Martin JC, Lawley TD, Browne HP, Harris HM, Bernalier-Donadille A, Duncan SH, O'Toole PW, Scott KP, Flint HJ.

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

5.

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.

PMID:
26916277
6.

First-Pass Meconium Samples from Healthy Term Vaginally-Delivered Neonates: An Analysis of the Microbiota.

Hansen R, Scott KP, Khan S, Martin JC, Berry SH, Stevenson M, Okpapi A, Munro MJ, Hold GL.

PLoS One. 2015 Jul 28;10(7):e0133320. doi: 10.1371/journal.pone.0133320. eCollection 2015.

7.

16S rRNA gene-based profiling of the human infant gut microbiota is strongly influenced by sample processing and PCR primer choice.

Walker AW, Martin JC, Scott P, Parkhill J, Flint HJ, Scott KP.

Microbiome. 2015 Jun 22;3:26. doi: 10.1186/s40168-015-0087-4. eCollection 2015.

8.

Manipulating the gut microbiota to maintain health and treat disease.

Scott KP, Antoine JM, Midtvedt T, van Hemert S.

Microb Ecol Health Dis. 2015 Feb 2;26:25877. doi: 10.3402/mehd.v26.25877. eCollection 2015.

9.

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.

PMID:
25268552
10.

Can prebiotics and probiotics improve therapeutic outcomes for undernourished individuals?

Sheridan PO, Bindels LB, Saulnier DM, Reid G, Nova E, Holmgren K, O'Toole PW, Bunn J, Delzenne N, Scott KP.

Gut Microbes. 2014 Jan-Feb;5(1):74-82. doi: 10.4161/gmic.27252. Epub 2013 Dec 16.

11.

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.

12.

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.

13.

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.

14.

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.

PMID:
23147033
15.

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.

PMID:
22945443
16.

Restoring specific lactobacilli levels decreases inflammation and muscle atrophy markers in an acute leukemia mouse model.

Bindels LB, Beck R, Schakman O, Martin JC, De Backer F, Sohet FM, Dewulf EM, Pachikian BD, Neyrinck AM, Thissen JP, Verrax J, Calderon PB, Pot B, Grangette C, Cani PD, Scott KP, Delzenne NM.

PLoS One. 2012;7(6):e37971. doi: 10.1371/journal.pone.0037971. Epub 2012 Jun 27.

17.

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.

18.

Evaluation of novel assays to assess the influence of different iron sources on the growth of Clostridium difficile.

Cernat RC, Scott KP.

Anaerobe. 2012 Jun;18(3):298-304. doi: 10.1016/j.anaerobe.2012.04.007. Epub 2012 Apr 25.

PMID:
22554901
19.

Optimization of a high-throughput CTAB-based protocol for the extraction of qPCR-grade DNA from rumen fluid, plant and bacterial pure cultures.

Minas K, McEwan NR, Newbold CJ, Scott KP.

FEMS Microbiol Lett. 2011 Dec;325(2):162-9. doi: 10.1111/j.1574-6968.2011.02424.x.

20.

Nutritional influences on the gut microbiota and the consequences for gastrointestinal health.

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

Biochem Soc Trans. 2011 Aug;39(4):1073-8. doi: 10.1042/BST0391073.

PMID:
21787350
21.

Substrate-driven gene expression in Roseburia inulinivorans: importance of inducible enzymes in the utilization of inulin and starch.

Scott KP, Martin JC, Chassard C, Clerget M, Potrykus J, Campbell G, Mayer CD, Young P, Rucklidge G, Ramsay AG, Flint HJ.

Proc Natl Acad Sci U S A. 2011 Mar 15;108 Suppl 1:4672-9. doi: 10.1073/pnas.1000091107. Epub 2010 Aug 2.

22.

Distribution of tetracycline and erythromycin resistance genes among human oral and fecal metagenomic DNA.

Seville LA, Patterson AJ, Scott KP, Mullany P, Quail MA, Parkhill J, Ready D, Wilson M, Spratt D, Roberts AP.

Microb Drug Resist. 2009 Sep;15(3):159-66. doi: 10.1089/mdr.2009.0916.

PMID:
19728772
23.

Tetracycline resistome of the organic pig gut.

Kazimierczak KA, Scott KP, Kelly D, Aminov RI.

Appl Environ Microbiol. 2009 Mar;75(6):1717-22. doi: 10.1128/AEM.02206-08. Epub 2009 Jan 23.

24.

Assessment of metabolic diversity within the intestinal microbiota from healthy humans using combined molecular and cultural approaches.

Chassard C, Scott KP, Marquet P, Martin JC, Del'homme C, Dapoigny M, Flint HJ, Bernalier-Donadille A.

FEMS Microbiol Ecol. 2008 Dec;66(3):496-504. doi: 10.1111/j.1574-6941.2008.00595.x. Epub 2008 Sep 22.

25.

A new tetracycline efflux gene, tet(40), is located in tandem with tet(O/32/O) in a human gut firmicute bacterium and in metagenomic library clones.

Kazimierczak KA, Rincon MT, Patterson AJ, Martin JC, Young P, Flint HJ, Scott KP.

Antimicrob Agents Chemother. 2008 Nov;52(11):4001-9. doi: 10.1128/AAC.00308-08. Epub 2008 Sep 8.

26.

Transfer of conjugative elements from rumen and human Firmicutes bacteria to Roseburia inulinivorans.

Scott KP, Martin JC, Mrazek J, Flint HJ.

Appl Environ Microbiol. 2008 Jun;74(12):3915-7. doi: 10.1128/AEM.02807-07. Epub 2008 May 2.

27.

Antibiotics and resistance genes: influencing the microbial ecosystem in the gut.

Kazimierczak KA, Scott KP.

Adv Appl Microbiol. 2007;62:269-92. Review. No abstract available.

PMID:
17869608
28.

Interactions and competition within the microbial community of the human colon: links between diet and health.

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

Environ Microbiol. 2007 May;9(5):1101-11. Review.

PMID:
17472627
29.

Distribution of specific tetracycline and erythromycin resistance genes in environmental samples assessed by macroarray detection.

Patterson AJ, Colangeli R, Spigaglia P, Scott KP.

Environ Microbiol. 2007 Mar;9(3):703-15.

PMID:
17298370
30.

Tetracycline susceptibility of the ingested Lactobacillus acidophilus LaCH-5 and Bifidobacterium animalis subsp. lactis Bb-12 strains during antibiotic/probiotic intervention.

Saarela M, Maukonen J, von Wright A, Vilpponen-Salmela T, Patterson AJ, Scott KP, Hämynen H, Mättö J.

Int J Antimicrob Agents. 2007 Mar;29(3):271-80. Epub 2007 Jan 5.

PMID:
17207972
31.

Mosaic tetracycline resistance genes are widespread in human and animal fecal samples.

Patterson AJ, Rincon MT, Flint HJ, Scott KP.

Antimicrob Agents Chemother. 2007 Mar;51(3):1115-8. Epub 2006 Dec 18.

32.

Cell-associated alpha-amylases of butyrate-producing Firmicute bacteria from the human colon.

Ramsay AG, Scott KP, Martin JC, Rincon MT, Flint HJ.

Microbiology. 2006 Nov;152(Pt 11):3281-90.

PMID:
17074899
33.

Proposal of Roseburia faecis sp. nov., Roseburia hominis sp. nov. and Roseburia inulinivorans sp. nov., based on isolates from human faeces.

Duncan SH, Aminov RI, Scott KP, Louis P, Stanton TB, Flint HJ.

Int J Syst Evol Microbiol. 2006 Oct;56(Pt 10):2437-41.

PMID:
17012576
34.

Comparative analysis of sequences flanking tet(W) resistance genes in multiple species of gut bacteria.

Kazimierczak KA, Flint HJ, Scott KP.

Antimicrob Agents Chemother. 2006 Aug;50(8):2632-9.

35.
36.

Hybrid tet genes and tet gene nomenclature: request for opinion.

Stanton TB, Humphrey SB, Scott KP, Flint HJ.

Antimicrob Agents Chemother. 2005 Mar;49(3):1265-6. No abstract available.

38.

Characterization of XYN10B, a modular xylanase from the ruminal protozoan Polyplastron multivesiculatum, with a family 22 carbohydrate-binding module that binds to cellulose.

Devillard E, Bera-Maillet C, Flint HJ, Scott KP, Newbold CJ, Wallace RJ, Jouany JP, Forano E.

Biochem J. 2003 Jul 15;373(Pt 2):495-503.

39.

Effects of alternative dietary substrates on competition between human colonic bacteria in an anaerobic fermentor system.

Duncan SH, Scott KP, Ramsay AG, Harmsen HJ, Welling GW, Stewart CS, Flint HJ.

Appl Environ Microbiol. 2003 Feb;69(2):1136-42.

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