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Items: 1 to 50 of 161

1.

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 Feb 4. doi: 10.1038/s41564-018-0337-x. [Epub ahead of print]

PMID:
30718848
2.

Isolation of wheat bran-colonizing and metabolizing species from the human fecal microbiota.

De Paepe K, Verspreet J, Rezaei MN, Hidalgo Martinez S, Meysman F, Van de Walle D, Dewettinck K, Raes J, Courtin C, Van de Wiele T.

PeerJ. 2019 Jan 25;7:e6293. doi: 10.7717/peerj.6293. eCollection 2019.

3.

Metformin induces weight loss associated with gut microbiota alteration in non-diabetic obese women: a randomized double-blind clinical trial.

Ejtahed HS, Tito RY, Siadat SD, Hasani-Ranjbar S, Hoseini-Tavassol Z, Rymenans L, Verbeke K, Soroush AR, Raes J, Larijani B.

Eur J Endocrinol. 2018 Dec 1. pii: EJE-18-0826.R1. doi: 10.1530/EJE-18-0826. [Epub ahead of print]

PMID:
30540558
4.

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.

5.

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.

6.

Butyrate Producers as Potential Next-Generation Probiotics: Safety Assessment of the Administration of Butyricicoccus pullicaecorum to Healthy Volunteers.

Boesmans L, Valles-Colomer M, Wang J, Eeckhaut V, Falony G, Ducatelle R, Van Immerseel F, Raes J, Verbeke K.

mSystems. 2018 Nov 6;3(6). pii: e00094-18. doi: 10.1128/mSystems.00094-18. eCollection 2018 Nov-Dec.

7.

Integrated culturing, modeling and transcriptomics uncovers complex interactions and emergent behavior in a three-species synthetic gut community.

D'hoe K, Vet S, Faust K, Moens F, Falony G, Gonze D, Lloréns-Rico V, Gelens L, Danckaert J, De Vuyst L, Raes J.

Elife. 2018 Oct 16;7. pii: e37090. doi: 10.7554/eLife.37090.

8.

Author Correction: Regional variation limits applications of healthy gut microbiome reference ranges and disease models.

He Y, Wu W, Zheng HM, Li P, McDonald D, Sheng HF, Chen MX, Chen ZH, Ji GY, Zheng ZD, Mujagond P, Chen XJ, Rong ZH, Chen P, Lyu LY, Wang X, Wu CB, Yu N, Xu YJ, Yin J, Raes J, Knight R, Ma WJ, Zhou HW.

Nat Med. 2018 Dec;24(12):1940. doi: 10.1038/s41591-018-0219-z.

PMID:
30250144
9.

Linking gut microbiota, metabolic syndrome and economic status based on a population-level analysis.

He Y, Wu W, Wu S, Zheng HM, Li P, Sheng HF, Chen MX, Chen ZH, Ji GY, Zheng ZD, Mujagond P, Chen XJ, Rong ZH, Chen P, Lyu LY, Wang X, Xu JB, Wu CB, Yu N, Xu YJ, Yin J, Raes J, Ma WJ, Zhou HW.

Microbiome. 2018 Sep 24;6(1):172. doi: 10.1186/s40168-018-0557-6.

10.

Comparisons of gut microbiota profiles in wild-type and gelatinase B/matrix metalloproteinase-9-deficient mice in acute DSS-induced colitis.

de Bruyn M, Sabino J, Vandeputte D, Vermeire S, Raes J, Opdenakker G.

NPJ Biofilms Microbiomes. 2018 Sep 3;4:18. doi: 10.1038/s41522-018-0059-0. eCollection 2018.

11.

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. 2018 Aug 31. pii: gutjnl-2018-316106. doi: 10.1136/gutjnl-2018-316106. [Epub ahead of print]

12.

Regional variation limits applications of healthy gut microbiome reference ranges and disease models.

He Y, Wu W, Zheng HM, Li P, McDonald D, Sheng HF, Chen MX, Chen ZH, Ji GY, Zheng ZD, Mujagond P, Chen XJ, Rong ZH, Chen P, Lyu LY, Wang X, Wu CB, Yu N, Xu YJ, Yin J, Raes J, Knight R, Ma WJ, Zhou HW.

Nat Med. 2018 Oct;24(10):1532-1535. doi: 10.1038/s41591-018-0164-x. Epub 2018 Aug 27. Erratum in: Nat Med. 2018 Sep 24;:.

PMID:
30150716
13.

Editorial overview: It's the ecology, stupid: microbiome research in the post-stamp collecting age.

Raes J.

Curr Opin Microbiol. 2018 Aug;44:iv-v. doi: 10.1016/j.mib.2018.07.008. Epub 2018 Aug 22. No abstract available.

PMID:
30145038
14.

Introducing insoluble wheat bran as a gut microbiota niche in an in vitro dynamic gut model stimulates propionate and butyrate production and induces colon region specific shifts in the luminal and mucosal microbial community.

De Paepe K, Verspreet J, Verbeke K, Raes J, Courtin CM, Van de Wiele T.

Environ Microbiol. 2018 Sep;20(9):3406-3426. doi: 10.1111/1462-2920.14381. Epub 2018 Sep 9.

PMID:
30126070
15.

Go with the flow or solitary confinement: a look inside the single-cell toolbox for isolation of rare and uncultured microbes.

Huys GR, Raes J.

Curr Opin Microbiol. 2018 Aug;44:1-8. doi: 10.1016/j.mib.2018.05.002. Epub 2018 Jun 13. Review.

PMID:
29908491
16.

Meta-analysis of human genome-microbiome association studies: the MiBioGen consortium initiative.

Wang J, Kurilshikov A, Radjabzadeh D, Turpin W, Croitoru K, Bonder MJ, Jackson MA, Medina-Gomez C, Frost F, Homuth G, Rühlemann M, Hughes D, Kim HN; MiBioGen Consortium Initiative, Spector TD, Bell JT, Steves CJ, Timpson N, Franke A, Wijmenga C, Meyer K, Kacprowski T, Franke L, Paterson AD, Raes J, Kraaij R, Zhernakova A.

Microbiome. 2018 Jun 8;6(1):101. doi: 10.1186/s40168-018-0479-3.

17.

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
18.

Menaquinone Content of Cheese.

Vermeer C, Raes J, van 't Hoofd C, Knapen MHJ, Xanthoulea S.

Nutrients. 2018 Apr 4;10(4). pii: E446. doi: 10.3390/nu10040446.

19.

The Human Gut Microbiome: From Association to Modulation.

Schmidt TSB, Raes J, Bork P.

Cell. 2018 Mar 8;172(6):1198-1215. doi: 10.1016/j.cell.2018.02.044. Review.

PMID:
29522742
20.

Publisher Correction: Enterotypes in the landscape of gut microbial community composition.

Costea PI, Hildebrand F, Arumugam M, Bäckhed F, Blaser MJ, Bushman FD, de Vos WM, Ehrlich SD, Fraser CM, Hattori M, Huttenhower C, Jeffery IB, Knights D, Lewis JD, Ley RE, Ochman H, O'Toole PW, Quince C, Relman DA, Shanahan F, Sunagawa S, Wang J, Weinstock GM, Wu GD, Zeller G, Zhao L, Raes J, Knight R, Bork P.

Nat Microbiol. 2018 Mar;3(3):388. doi: 10.1038/s41564-018-0114-x.

PMID:
29440750
21.

Impact of red and processed meat and fibre intake on treatment outcomes among patients with chronic inflammatory diseases: protocol for a prospective cohort study of prognostic factors and personalised medicine.

Christensen R, Heitmann BL, Andersen KW, Nielsen OH, Sørensen SB, Jawhara M, Bygum A, Hvid L, Grauslund J, Wied J, Glerup H, Fredberg U, Villadsen JA, Kjær SG, Fallingborg J, Moghadd SAGR, Knudsen T, Brodersen J, Frøjk J, Dahlerup JF, Bojesen AB, Sorensen GL, Thiel S, Færgeman NJ, Brandslund I, Bennike TB, Stensballe A, Schmidt EB, Franke A, Ellinghaus D, Rosenstiel P, Raes J, Boye M, Werner L, Nielsen CL, Munk HL, Nexøe AB, Ellingsen T, Holmskov U, Kjeldsen J, Andersen V.

BMJ Open. 2018 Feb 8;8(2):e018166. doi: 10.1136/bmjopen-2017-018166.

22.

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.

23.

A global ocean atlas of eukaryotic genes.

Carradec Q, Pelletier E, Da Silva C, Alberti A, Seeleuthner Y, Blanc-Mathieu R, Lima-Mendez G, Rocha F, Tirichine L, Labadie K, Kirilovsky A, Bertrand A, Engelen S, Madoui MA, Méheust R, Poulain J, Romac S, Richter DJ, Yoshikawa G, Dimier C, Kandels-Lewis S, Picheral M, Searson S; Tara Oceans Coordinators, Jaillon O, Aury JM, Karsenti E, Sullivan MB, Sunagawa S, Bork P, Not F, Hingamp P, Raes J, Guidi L, Ogata H, de Vargas C, Iudicone D, Bowler C, Wincker P.

Nat Commun. 2018 Jan 25;9(1):373. doi: 10.1038/s41467-017-02342-1.

24.

Enterotypes in the landscape of gut microbial community composition.

Costea PI, Hildebrand F, Arumugam M, Bäckhed F, Blaser MJ, Bushman FD, de Vos WM, Ehrlich SD, Fraser CM, Hattori M, Huttenhower C, Jeffery IB, Knights D, Lewis JD, Ley RE, Ochman H, O'Toole PW, Quince C, Relman DA, Shanahan F, Sunagawa S, Wang J, Weinstock GM, Wu GD, Zeller G, Zhao L, Raes J, Knight R, Bork P.

Nat Microbiol. 2018 Jan;3(1):8-16. doi: 10.1038/s41564-017-0072-8. Epub 2017 Dec 18. Review. Erratum in: Nat Microbiol. 2018 Feb 13;:.

25.

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
26.

Microbiology: Crowdsourcing Earth's microbes.

Raes J.

Nature. 2017 Nov 1. doi: 10.1038/nature24756. [Epub ahead of print] No abstract available.

PMID:
29088699
27.

Low eukaryotic viral richness is associated with faecal microbiota transplantation success in patients with UC.

Conceição-Neto N, Deboutte W, Dierckx T, Machiels K, Wang J, Yinda KC, Maes P, Van Ranst M, Joossens M, Raes J, Vermeire S, Matthijnssens J.

Gut. 2018 Aug;67(8):1558-1559. doi: 10.1136/gutjnl-2017-315281. Epub 2017 Oct 24. No abstract available.

28.

Practical considerations for large-scale gut microbiome studies.

Vandeputte D, Tito RY, Vanleeuwen R, Falony G, Raes J.

FEMS Microbiol Rev. 2017 Aug 1;41(Supp_1):S154-S167. doi: 10.1093/femsre/fux027. Review.

PMID:
28830090
29.

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.

30.

The Gut Microbiome and Mental Health: Implications for Anxiety- and Trauma-Related Disorders.

Malan-Muller S, Valles-Colomer M, Raes J, Lowry CA, Seedat S, Hemmings SMJ.

OMICS. 2018 Feb;22(2):90-107. doi: 10.1089/omi.2017.0077. Epub 2017 Aug 2.

PMID:
28767318
31.

The resilience of the intestinal microbiota influences health and disease.

Sommer F, Anderson JM, Bharti R, Raes J, Rosenstiel P.

Nat Rev Microbiol. 2017 Oct;15(10):630-638. doi: 10.1038/nrmicro.2017.58. Epub 2017 Jun 19. Review.

PMID:
28626231
32.

A Proposal for a Study on Treatment Selection and Lifestyle Recommendations in Chronic Inflammatory Diseases: A Danish Multidisciplinary Collaboration on Prognostic Factors and Personalised Medicine.

Andersen V, Holmskov U, Sørensen SB, Jawhara M, Andersen KW, Bygum A, Hvid L, Grauslund J, Wied J, Glerup H, Fredberg U, Villadsen JA, Kjær SG, Fallingborg J, Moghadd SAGR, Knudsen T, Brodersen J, Frøjk J, Dahlerup JF, Nielsen OH, Christensen R, Bojesen AB, Sorensen GL, Thiel S, Færgeman NJ, Brandslund I, Stensballe A, Schmidt EB, Franke A, Ellinghaus D, Rosenstiel P, Raes J, Heitmann B, Boye M, Nielsen CL, Werner L, Kjeldsen J, Ellingsen T.

Nutrients. 2017 May 15;9(5). pii: E499. doi: 10.3390/nu9050499.

33.

Multi-stability and the origin of microbial community types.

Gonze D, Lahti L, Raes J, Faust K.

ISME J. 2017 Oct;11(10):2159-2166. doi: 10.1038/ismej.2017.60. Epub 2017 May 5.

34.

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
35.

From reads to operational taxonomic units: an ensemble processing pipeline for MiSeq amplicon sequencing data.

Mysara M, Njima M, Leys N, Raes J, Monsieurs P.

Gigascience. 2017 Feb 1;6(2):1-10. doi: 10.1093/gigascience/giw017.

36.

Reconciliation between operational taxonomic units and species boundaries.

Mysara M, Vandamme P, Props R, Kerckhof FM, Leys N, Boon N, Raes J, Monsieurs P.

FEMS Microbiol Ecol. 2017 Apr 1;93(4). doi: 10.1093/femsec/fix029.

37.

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.

38.

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.

39.

Fire modifies the phylogenetic structure of soil bacterial co-occurrence networks.

Pérez-Valera E, Goberna M, Faust K, Raes J, García C, Verdú M.

Environ Microbiol. 2017 Jan;19(1):317-327. doi: 10.1111/1462-2920.13609. Epub 2017 Jan 18.

PMID:
27871135
40.

CoNet app: inference of biological association networks using Cytoscape.

Faust K, Raes J.

Version 2. F1000Res. 2016 Jun 27 [revised 2016 Jan 1];5:1519. eCollection 2016.

41.

The Probiotic Butyricicoccus pullicaecorum Reduces Feed Conversion and Protects from Potentially Harmful Intestinal Microorganisms and Necrotic Enteritis in Broilers.

Eeckhaut V, Wang J, Van Parys A, Haesebrouck F, Joossens M, Falony G, Raes J, Ducatelle R, Van Immerseel F.

Front Microbiol. 2016 Sep 21;7:1416. eCollection 2016.

42.

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.

43.

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
44.

Assessment of faecal microbial transfer in irritable bowel syndrome with severe bloating.

Holvoet T, Joossens M, Wang J, Boelens J, Verhasselt B, Laukens D, van Vlierberghe H, Hindryckx P, De Vos M, De Looze D, Raes J.

Gut. 2017 May;66(5):980-982. doi: 10.1136/gutjnl-2016-312513. Epub 2016 Aug 10. No abstract available.

45.

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
46.

The Genomic Sequence of the Oral Pathobiont Strain NI1060 Reveals Unique Strategies for Bacterial Competition and Pathogenicity.

Darzi Y, Jiao Y, Hasegawa M, Moon H, Núñez G, Inohara N, Raes J.

PLoS One. 2016 Jul 13;11(7):e0158866. doi: 10.1371/journal.pone.0158866. eCollection 2016.

47.

Brief Report: Dialister as a Microbial Marker of Disease Activity in Spondyloarthritis.

Tito RY, Cypers H, Joossens M, Varkas G, Van Praet L, Glorieus E, Van den Bosch F, De Vos M, Raes J, Elewaut D.

Arthritis Rheumatol. 2017 Jan;69(1):114-121. doi: 10.1002/art.39802. Epub 2016 Dec 1.

48.

Species-sorting and mass-transfer paradigms control managed natural metacommunities.

Günther S, Faust K, Schumann J, Harms H, Raes J, Müller S.

Environ Microbiol. 2016 Dec;18(12):4862-4877. doi: 10.1111/1462-2920.13402. Epub 2016 Jul 8.

PMID:
27338005
49.

Host-microbe interaction: Rules of the game for microbiota.

Faust K, Raes J.

Nature. 2016 Jun 9;534(7606):182-3. doi: 10.1038/534182a. No abstract available.

PMID:
27279206
50.

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.

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