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Items: 35

1.

Supplementation with Akkermansia muciniphila in overweight and obese human volunteers: a proof-of-concept exploratory study.

Depommier C, Everard A, Druart C, Plovier H, Van Hul M, Vieira-Silva S, Falony G, Raes J, Maiter D, Delzenne NM, de Barsy M, Loumaye A, Hermans MP, Thissen JP, de Vos WM, Cani PD.

Nat Med. 2019 Jul;25(7):1096-1103. doi: 10.1038/s41591-019-0495-2. Epub 2019 Jul 1.

PMID:
31263284
2.

Quantitative microbiome profiling disentangles inflammation- and bile duct obstruction-associated microbiota alterations across PSC/IBD diagnoses.

Vieira-Silva S, Sabino J, Valles-Colomer M, Falony G, Kathagen G, Caenepeel C, Cleynen I, van der Merwe S, Vermeire S, Raes J.

Nat Microbiol. 2019 Jun 17. doi: 10.1038/s41564-019-0483-9. [Epub ahead of print]

PMID:
31209308
3.

The human microbiome in health and disease: hype or hope.

Falony G, Vandeputte D, Caenepeel C, Vieira-Silva S, Daryoush T, Vermeire S, Raes J.

Acta Clin Belg. 2019 Apr;74(2):53-64. doi: 10.1080/17843286.2019.1583782. Epub 2019 Feb 27.

PMID:
30810508
4.

The neuroactive potential of the human gut microbiota in quality of life and depression.

Valles-Colomer M, Falony G, Darzi Y, Tigchelaar EF, Wang J, Tito RY, Schiweck C, Kurilshikov A, Joossens M, Wijmenga C, Claes S, Van Oudenhove L, Zhernakova A, Vieira-Silva S, Raes J.

Nat Microbiol. 2019 Apr;4(4):623-632. doi: 10.1038/s41564-018-0337-x. Epub 2019 Feb 4.

PMID:
30718848
5.

Gut microbiota dynamics and uraemic toxins: one size does not fit all.

Joossens M, Faust K, Gryp T, Nguyen ATL, Wang J, Eloot S, Schepers E, Dhondt A, Pletinck A, Vieira-Silva S, Falony G, Vaneechoutte M, Vanholder R, Van Biesen W, Huys GRB, Raes J, Glorieux G.

Gut. 2018 Nov 21. pii: gutjnl-2018-317561. doi: 10.1136/gutjnl-2018-317561. [Epub ahead of print] No abstract available.

6.

A low-gluten diet induces changes in the intestinal microbiome of healthy Danish adults.

Hansen LBS, Roager HM, Søndertoft NB, Gøbel RJ, Kristensen M, Vallès-Colomer M, Vieira-Silva S, Ibrügger S, Lind MV, Mærkedahl RB, Bahl MI, Madsen ML, Havelund J, Falony G, Tetens I, Nielsen T, Allin KH, Frandsen HL, Hartmann B, Holst JJ, Sparholt MH, Holck J, Blennow A, Moll JM, Meyer AS, Hoppe C, Poulsen JH, Carvalho V, Sagnelli D, Dalgaard MD, Christensen AF, Lydolph MC, Ross AB, Villas-Bôas S, Brix S, Sicheritz-Pontén T, Buschard K, Linneberg A, Rumessen JJ, Ekstrøm CT, Ritz C, Kristiansen K, Nielsen HB, Vestergaard H, Færgeman NJ, Raes J, Frøkiær H, Hansen T, Lauritzen L, Gupta R, Licht TR, Pedersen O.

Nat Commun. 2018 Nov 13;9(1):4630. doi: 10.1038/s41467-018-07019-x.

7.

Population-level analysis of Blastocystis subtype prevalence and variation in the human gut microbiota.

Tito RY, Chaffron S, Caenepeel C, Lima-Mendez G, Wang J, Vieira-Silva S, Falony G, Hildebrand F, Darzi Y, Rymenans L, Verspecht C, Bork P, Vermeire S, Joossens M, Raes J.

Gut. 2019 Jul;68(7):1180-1189. doi: 10.1136/gutjnl-2018-316106. Epub 2018 Aug 31.

8.

Richness and ecosystem development across faecal snapshots of the gut microbiota.

Falony G, Vieira-Silva S, Raes J.

Nat Microbiol. 2018 May;3(5):526-528. doi: 10.1038/s41564-018-0143-5. No abstract available.

PMID:
29693658
9.

Prebiotic Wheat Bran Fractions Induce Specific Microbiota Changes.

D'hoe K, Conterno L, Fava F, Falony G, Vieira-Silva S, Vermeiren J, Tuohy K, Raes J.

Front Microbiol. 2018 Jan 24;9:31. doi: 10.3389/fmicb.2018.00031. eCollection 2018.

10.

Quantitative microbiome profiling links gut community variation to microbial load.

Vandeputte D, Kathagen G, D'hoe K, Vieira-Silva S, Valles-Colomer M, Sabino J, Wang J, Tito RY, De Commer L, Darzi Y, Vermeire S, Falony G, Raes J.

Nature. 2017 Nov 23;551(7681):507-511. doi: 10.1038/nature24460. Epub 2017 Nov 15.

PMID:
29143816
11.

Nlrp6- and ASC-Dependent Inflammasomes Do Not Shape the Commensal Gut Microbiota Composition.

Mamantopoulos M, Ronchi F, Van Hauwermeiren F, Vieira-Silva S, Yilmaz B, Martens L, Saeys Y, Drexler SK, Yazdi AS, Raes J, Lamkanfi M, McCoy KD, Wullaert A.

Immunity. 2017 Aug 15;47(2):339-348.e4. doi: 10.1016/j.immuni.2017.07.011. Epub 2017 Aug 8.

12.

Corrigendum: Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota.

Forslund K, Hildebrand F, Nielsen T, Falony G, Le Chatelier E, Sunagawa S, Prifti E, Vieira-Silva S, Gudmundsdottir V, Pedersen HK, Arumugam M, Kristiansen K, Voigt AY, Vestergaard H, Hercog R, Costea PI, Kultima JR, Li J, Jørgensen T, Levenez F, Dore J; MetaHIT consortium, Nielsen HB, Brunak S, Raes J, Hansen T, Wang J, Ehrlich SD, Bork P, Pedersen O.

Nature. 2017 May 3;545(7652):116. doi: 10.1038/nature22318. No abstract available.

PMID:
28470190
13.

Prebiotic inulin-type fructans induce specific changes in the human gut microbiota.

Vandeputte D, Falony G, Vieira-Silva S, Wang J, Sailer M, Theis S, Verbeke K, Raes J.

Gut. 2017 Nov;66(11):1968-1974. doi: 10.1136/gutjnl-2016-313271. Epub 2017 Feb 17.

14.

Water activity does not shape the microbiota in the human colon.

Vandeputte D, Falony G, D'hoe K, Vieira-Silva S, Raes J.

Gut. 2017 Oct;66(10):1865-1866. doi: 10.1136/gutjnl-2016-313530. Epub 2017 Jan 6. No abstract available.

15.

Heritable components of the human fecal microbiome are associated with visceral fat.

Beaumont M, Goodrich JK, Jackson MA, Yet I, Davenport ER, Vieira-Silva S, Debelius J, Pallister T, Mangino M, Raes J, Knight R, Clark AG, Ley RE, Spector TD, Bell JT.

Genome Biol. 2016 Sep 26;17(1):189.

16.

Species-function relationships shape ecological properties of the human gut microbiome.

Vieira-Silva S, Falony G, Darzi Y, Lima-Mendez G, Garcia Yunta R, Okuda S, Vandeputte D, Valles-Colomer M, Hildebrand F, Chaffron S, Raes J.

Nat Microbiol. 2016 Jun 13;1(8):16088. doi: 10.1038/nmicrobiol.2016.88.

PMID:
27573110
17.

Human gut microbes impact host serum metabolome and insulin sensitivity.

Pedersen HK, Gudmundsdottir V, Nielsen HB, Hyotylainen T, Nielsen T, Jensen BA, Forslund K, Hildebrand F, Prifti E, Falony G, Le Chatelier E, Levenez F, Doré J, Mattila I, Plichta DR, Pöhö P, Hellgren LI, Arumugam M, Sunagawa S, Vieira-Silva S, Jørgensen T, Holm JB, Trošt K; MetaHIT Consortium, Kristiansen K, Brix S, Raes J, Wang J, Hansen T, Bork P, Brunak S, Oresic M, Ehrlich SD, Pedersen O.

Nature. 2016 Jul 21;535(7612):376-81. Epub 2016 Jul 13.

PMID:
27409811
18.

Primary sclerosing cholangitis is characterised by intestinal dysbiosis independent from IBD.

Sabino J, Vieira-Silva S, Machiels K, Joossens M, Falony G, Ballet V, Ferrante M, Van Assche G, Van der Merwe S, Vermeire S, Raes J.

Gut. 2016 Oct;65(10):1681-9. doi: 10.1136/gutjnl-2015-311004. Epub 2016 May 20.

19.

Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity.

Zhernakova A, Kurilshikov A, Bonder MJ, Tigchelaar EF, Schirmer M, Vatanen T, Mujagic Z, Vila AV, Falony G, Vieira-Silva S, Wang J, Imhann F, Brandsma E, Jankipersadsing SA, Joossens M, Cenit MC, Deelen P, Swertz MA; LifeLines cohort study, Weersma RK, Feskens EJ, Netea MG, Gevers D, Jonkers D, Franke L, Aulchenko YS, Huttenhower C, Raes J, Hofker MH, Xavier RJ, Wijmenga C, Fu J.

Science. 2016 Apr 29;352(6285):565-9. doi: 10.1126/science.aad3369. Epub 2016 Apr 28.

20.

Population-level analysis of gut microbiome variation.

Falony G, Joossens M, Vieira-Silva S, Wang J, Darzi Y, Faust K, Kurilshikov A, Bonder MJ, Valles-Colomer M, Vandeputte D, Tito RY, Chaffron S, Rymenans L, Verspecht C, De Sutter L, Lima-Mendez G, D'hoe K, Jonckheere K, Homola D, Garcia R, Tigchelaar EF, Eeckhaudt L, Fu J, Henckaerts L, Zhernakova A, Wijmenga C, Raes J.

Science. 2016 Apr 29;352(6285):560-4. doi: 10.1126/science.aad3503. Epub 2016 Apr 28.

21.

Faecal Metaproteomic Analysis Reveals a Personalized and Stable Functional Microbiome and Limited Effects of a Probiotic Intervention in Adults.

Kolmeder CA, Salojärvi J, Ritari J, de Been M, Raes J, Falony G, Vieira-Silva S, Kekkonen RA, Corthals GL, Palva A, Salonen A, de Vos WM.

PLoS One. 2016 Apr 12;11(4):e0153294. doi: 10.1371/journal.pone.0153294. eCollection 2016.

22.

Meta-omics in Inflammatory Bowel Disease Research: Applications, Challenges, and Guidelines.

Valles-Colomer M, Darzi Y, Vieira-Silva S, Falony G, Raes J, Joossens M.

J Crohns Colitis. 2016 Jun;10(6):735-46. doi: 10.1093/ecco-jcc/jjw024. Epub 2016 Jan 22. Review.

PMID:
26802086
23.

Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota.

Forslund K, Hildebrand F, Nielsen T, Falony G, Le Chatelier E, Sunagawa S, Prifti E, Vieira-Silva S, Gudmundsdottir V, Pedersen HK, Arumugam M, Kristiansen K, Voigt AY, Vestergaard H, Hercog R, Costea PI, Kultima JR, Li J, Jørgensen T, Levenez F, Dore J; MetaHIT consortium, Nielsen HB, Brunak S, Raes J, Hansen T, Wang J, Ehrlich SD, Bork P, Pedersen O.

Nature. 2015 Dec 10;528(7581):262-266. doi: 10.1038/nature15766. Epub 2015 Dec 2. Erratum in: Nature. 2017 May 3;545(7652):116.

24.

Towards biome-specific analysis of meta-omics data.

Darzi Y, Falony G, Vieira-Silva S, Raes J.

ISME J. 2016 May;10(5):1025-8. doi: 10.1038/ismej.2015.188. Epub 2015 Dec 1. No abstract available.

25.

Microbiology Meets Big Data: The Case of Gut Microbiota-Derived Trimethylamine.

Falony G, Vieira-Silva S, Raes J.

Annu Rev Microbiol. 2015;69:305-21. doi: 10.1146/annurev-micro-091014-104422. Epub 2015 Aug 13. Review.

PMID:
26274026
26.

Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates.

Vandeputte D, Falony G, Vieira-Silva S, Tito RY, Joossens M, Raes J.

Gut. 2016 Jan;65(1):57-62. doi: 10.1136/gutjnl-2015-309618. Epub 2015 Jun 11.

27.

Ocean plankton. Structure and function of the global ocean microbiome.

Sunagawa S, Coelho LP, Chaffron S, Kultima JR, Labadie K, Salazar G, Djahanschiri B, Zeller G, Mende DR, Alberti A, Cornejo-Castillo FM, Costea PI, Cruaud C, d'Ovidio F, Engelen S, Ferrera I, Gasol JM, Guidi L, Hildebrand F, Kokoszka F, Lepoivre C, Lima-Mendez G, Poulain J, Poulos BT, Royo-Llonch M, Sarmento H, Vieira-Silva S, Dimier C, Picheral M, Searson S, Kandels-Lewis S; Tara Oceans coordinators, Bowler C, de Vargas C, Gorsky G, Grimsley N, Hingamp P, Iudicone D, Jaillon O, Not F, Ogata H, Pesant S, Speich S, Stemmann L, Sullivan MB, Weissenbach J, Wincker P, Karsenti E, Raes J, Acinas SG, Bork P.

Science. 2015 May 22;348(6237):1261359. doi: 10.1126/science.1261359.

28.

How informative is the mouse for human gut microbiota research?

Nguyen TL, Vieira-Silva S, Liston A, Raes J.

Dis Model Mech. 2015 Jan;8(1):1-16. doi: 10.1242/dmm.017400. Review.

29.

A20 controls intestinal homeostasis through cell-specific activities.

Vereecke L, Vieira-Silva S, Billiet T, van Es JH, Mc Guire C, Slowicka K, Sze M, van den Born M, De Hertogh G, Clevers H, Raes J, Rutgeerts P, Vermeire S, Beyaert R, van Loo G.

Nat Commun. 2014 Sep 30;5:5103. doi: 10.1038/ncomms6103.

PMID:
25267258
30.

Immune subversion and quorum-sensing shape the variation in infectious dose among bacterial pathogens.

Gama JA, Abby SS, Vieira-Silva S, Dionisio F, Rocha EP.

PLoS Pathog. 2012 Feb;8(2):e1002503. doi: 10.1371/journal.ppat.1002503. Epub 2012 Feb 2.

31.

Investment in rapid growth shapes the evolutionary rates of essential proteins.

Vieira-Silva S, Touchon M, Abby SS, Rocha EP.

Proc Natl Acad Sci U S A. 2011 Dec 13;108(50):20030-5. doi: 10.1073/pnas.1110972108. Epub 2011 Nov 30.

32.

Association of hemicellulose- and pectin-modifying gene expression with Eucalyptus globulus secondary growth.

Goulao LF, Vieira-Silva S, Jackson PA.

Plant Physiol Biochem. 2011 Aug;49(8):873-81. doi: 10.1016/j.plaphy.2011.02.020. Epub 2011 Mar 3.

PMID:
21429757
33.

No evidence for elemental-based streamlining of prokaryotic genomes.

Vieira-Silva S, Touchon M, Rocha EP.

Trends Ecol Evol. 2010 Jun;25(6):319-20; author reply 320-1. doi: 10.1016/j.tree.2010.03.001. Epub 2010 Apr 8. No abstract available.

PMID:
20381897
34.

The systemic imprint of growth and its uses in ecological (meta)genomics.

Vieira-Silva S, Rocha EP.

PLoS Genet. 2010 Jan 15;6(1):e1000808. doi: 10.1371/journal.pgen.1000808.

35.

An assessment of the impacts of molecular oxygen on the evolution of proteomes.

Vieira-Silva S, Rocha EP.

Mol Biol Evol. 2008 Sep;25(9):1931-42. doi: 10.1093/molbev/msn142. Epub 2008 Jun 25.

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