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Microbial communities in a dynamic in vitro model for the human ileum resemble the human ileal microbiota.

Stolaki M, Minekus M, Venema K, Lahti L, Smid EJ, Kleerebezem M, Zoetendal EG.

FEMS Microbiol Ecol. 2019 Aug 1;95(8). pii: fiz096. doi: 10.1093/femsec/fiz096.


Differences in Fecal Gut Microbiota, Short-Chain Fatty Acids and Bile Acids Link Colorectal Cancer Risk to Dietary Changes Associated with Urbanization Among Zimbabweans.

Katsidzira L, Ocvirk S, Wilson A, Li J, Mahachi CB, Soni D, DeLany J, Nicholson JK, Zoetendal EG, O'Keefe SJD.

Nutr Cancer. 2019 Apr 22:1-12. doi: 10.1080/01635581.2019.1602659. [Epub ahead of print]


Metabolic improvement in obese patients after duodenal-jejunal exclusion is associated with intestinal microbiota composition changes.

de Jonge C, Fuentes S, Zoetendal EG, Bouvy ND, Nelissen R, Buurman WA, Greve JW, de Vos WM, Rensen SS.

Int J Obes (Lond). 2019 Feb 14. doi: 10.1038/s41366-019-0336-x. [Epub ahead of print]


High throughput cultivation-based screening on porous aluminum oxide chips allows targeted isolation of antibiotic resistant human gut bacteria.

Versluis D, de J Bello González T, Zoetendal EG, Passel MWJV, Smidt H.

PLoS One. 2019 Jan 17;14(1):e0210970. doi: 10.1371/journal.pone.0210970. eCollection 2019.


Bacterial folate biosynthesis and colorectal cancer risk: more than just a gut feeling.

Kok DE, Steegenga WT, Smid EJ, Zoetendal EG, Ulrich CM, Kampman E.

Crit Rev Food Sci Nutr. 2018 Dec 3:1-13. doi: 10.1080/10408398.2018.1522499. [Epub ahead of print]


Gut Microbiota and Body Weight in School-Aged Children: The KOALA Birth Cohort Study.

Mbakwa CA, Hermes GDA, Penders J, Savelkoul PHM, Thijs C, Dagnelie PC, Mommers M, Zoetendal EG, Smidt H, Arts ICW.

Obesity (Silver Spring). 2018 Nov;26(11):1767-1776. doi: 10.1002/oby.22320. Epub 2018 Oct 8.


Age-dependent changes in GI physiology and microbiota: time to reconsider?

An R, Wilms E, Masclee AAM, Smidt H, Zoetendal EG, Jonkers D.

Gut. 2018 Dec;67(12):2213-2222. doi: 10.1136/gutjnl-2017-315542. Epub 2018 Sep 7. Review.


Short-Term Microbiota Manipulation and Forearm Substrate Metabolism in Obese Men: A Randomized, Double-Blind, Placebo-Controlled Trial.

Reijnders D, Goossens GH, Hermes GDA, Smidt H, Zoetendal EG, Blaak EE.

Obes Facts. 2018;11(4):318-326. doi: 10.1159/000492114. Epub 2018 Aug 9.


Effect of Vegan Fecal Microbiota Transplantation on Carnitine- and Choline-Derived Trimethylamine-N-Oxide Production and Vascular Inflammation in Patients With Metabolic Syndrome.

Smits LP, Kootte RS, Levin E, Prodan A, Fuentes S, Zoetendal EG, Wang Z, Levison BS, Cleophas MCP, Kemper EM, Dallinga-Thie GM, Groen AK, Joosten LAB, Netea MG, Stroes ESG, de Vos WM, Hazen SL, Nieuwdorp M.

J Am Heart Assoc. 2018 Mar 26;7(7). pii: e008342. doi: 10.1161/JAHA.117.008342.


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.


Endothelial dysfunction: what is the role of the microbiota?

Zoetendal EG, Smidt H.

Gut. 2018 Feb;67(2):201-202. doi: 10.1136/gutjnl-2017-314012. Epub 2017 Jun 28. No abstract available.


Differences in Microbiota Membership along the Gastrointestinal Tract of Piglets and Their Differential Alterations Following an Early-Life Antibiotic Intervention.

Mu C, Yang Y, Su Y, Zoetendal EG, Zhu W.

Front Microbiol. 2017 May 9;8:797. doi: 10.3389/fmicb.2017.00797. eCollection 2017.


Microbial shifts and signatures of long-term remission in ulcerative colitis after faecal microbiota transplantation.

Fuentes S, Rossen NG, van der Spek MJ, Hartman JH, Huuskonen L, Korpela K, Salojärvi J, Aalvink S, de Vos WM, D'Haens GR, Zoetendal EG, Ponsioen CY.

ISME J. 2017 Aug;11(8):1877-1889. doi: 10.1038/ismej.2017.44. Epub 2017 Apr 11.


Supplementation of Diet With Galacto-oligosaccharides Increases Bifidobacteria, but Not Insulin Sensitivity, in Obese Prediabetic Individuals.

Canfora EE, van der Beek CM, Hermes GDA, Goossens GH, Jocken JWE, Holst JJ, van Eijk HM, Venema K, Smidt H, Zoetendal EG, Dejong CHC, Lenaerts K, Blaak EE.

Gastroenterology. 2017 Jul;153(1):87-97.e3. doi: 10.1053/j.gastro.2017.03.051. Epub 2017 Apr 8.


Effects of Gut Microbiota Manipulation by Antibiotics on Host Metabolism in Obese Humans: A Randomized Double-Blind Placebo-Controlled Trial.

Reijnders D, Goossens GH, Hermes GD, Neis EP, van der Beek CM, Most J, Holst JJ, Lenaerts K, Kootte RS, Nieuwdorp M, Groen AK, Olde Damink SW, Boekschoten MV, Smidt H, Zoetendal EG, Dejong CH, Blaak EE.

Cell Metab. 2016 Aug 9;24(2):341. doi: 10.1016/j.cmet.2016.07.008. No abstract available.


NG-Tax, a highly accurate and validated pipeline for analysis of 16S rRNA amplicons from complex biomes.

Ramiro-Garcia J, Hermes GDA, Giatsis C, Sipkema D, Zoetendal EG, Schaap PJ, Smidt H.

Version 2. F1000Res. 2016 Jul 22 [revised 2018 Jan 1];5:1791. doi: 10.12688/f1000research.9227.2. eCollection 2016.


Effects of Gut Microbiota Manipulation by Antibiotics on Host Metabolism in Obese Humans: A Randomized Double-Blind Placebo-Controlled Trial.

Reijnders D, Goossens GH, Hermes GD, Neis EP, van der Beek CM, Most J, Holst JJ, Lenaerts K, Kootte RS, Nieuwdorp M, Groen AK, Olde Damink SW, Boekschoten MV, Smidt H, Zoetendal EG, Dejong CH, Blaak EE.

Cell Metab. 2016 Jul 12;24(1):63-74. doi: 10.1016/j.cmet.2016.06.016.


The Intestinal Microenvironment and Functional Gastrointestinal Disorders.

Barbara G, Feinle-Bisset C, Ghoshal UC, Quigley EM, Santos J, Vanner S, Vergnolle N, Zoetendal EG.

Gastroenterology. 2016 Feb 18. pii: S0016-5085(16)00219-5. doi: 10.1053/j.gastro.2016.02.028. [Epub ahead of print]


Age, introduction of solid feed and weaning are more important determinants of gut bacterial succession in piglets than breed and nursing mother as revealed by a reciprocal cross-fostering model.

Bian G, Ma S, Zhu Z, Su Y, Zoetendal EG, Mackie R, Liu J, Mu C, Huang R, Smidt H, Zhu W.

Environ Microbiol. 2016 May;18(5):1566-77. doi: 10.1111/1462-2920.13272. Epub 2016 Mar 21.


The gut microbiota and host health: a new clinical frontier.

Marchesi JR, Adams DH, Fava F, Hermes GD, Hirschfield GM, Hold G, Quraishi MN, Kinross J, Smidt H, Tuohy KM, Thomas LV, Zoetendal EG, Hart A.

Gut. 2016 Feb;65(2):330-9. doi: 10.1136/gutjnl-2015-309990. Epub 2015 Sep 2. Review.


Fecal Microbiota in Pediatric Inflammatory Bowel Disease and Its Relation to Inflammation.

Kolho KL, Korpela K, Jaakkola T, Pichai MV, Zoetendal EG, Salonen A, de Vos WM.

Am J Gastroenterol. 2015 Jun;110(6):921-30. doi: 10.1038/ajg.2015.149. Epub 2015 May 19.


Fecal microbiota transplantation as novel therapy in gastroenterology: A systematic review.

Rossen NG, MacDonald JK, de Vries EM, D'Haens GR, de Vos WM, Zoetendal EG, Ponsioen CY.

World J Gastroenterol. 2015 May 7;21(17):5359-71. doi: 10.3748/wjg.v21.i17.5359. Review.


Fat, fibre and cancer risk in African Americans and rural Africans.

O'Keefe SJ, Li JV, Lahti L, Ou J, Carbonero F, Mohammed K, Posma JM, Kinross J, Wahl E, Ruder E, Vipperla K, Naidoo V, Mtshali L, Tims S, Puylaert PG, DeLany J, Krasinskas A, Benefiel AC, Kaseb HO, Newton K, Nicholson JK, de Vos WM, Gaskins HR, Zoetendal EG.

Nat Commun. 2015 Apr 28;6:6342. doi: 10.1038/ncomms7342.


Findings From a Randomized Controlled Trial of Fecal Transplantation for Patients With Ulcerative Colitis.

Rossen NG, Fuentes S, van der Spek MJ, Tijssen JG, Hartman JH, Duflou A, Löwenberg M, van den Brink GR, Mathus-Vliegen EM, de Vos WM, Zoetendal EG, D'Haens GR, Ponsioen CY.

Gastroenterology. 2015 Jul;149(1):110-118.e4. doi: 10.1053/j.gastro.2015.03.045. Epub 2015 Mar 30.


The mucosa-associated microbiota of PSC patients is characterized by low diversity and low abundance of uncultured Clostridiales II.

Rossen NG, Fuentes S, Boonstra K, D'Haens GR, Heilig HG, Zoetendal EG, de Vos WM, Ponsioen CY.

J Crohns Colitis. 2015 Apr;9(4):342-8. doi: 10.1093/ecco-jcc/jju023. Epub 2014 Dec 28.


Immunomodulatory properties of Streptococcus and Veillonella isolates from the human small intestine microbiota.

van den Bogert B, Meijerink M, Zoetendal EG, Wells JM, Kleerebezem M.

PLoS One. 2014 Dec 5;9(12):e114277. doi: 10.1371/journal.pone.0114277. eCollection 2014.


Molecular ecological tools to decipher the role of our microbial mass in obesity.

Hermes GD, Zoetendal EG, Smidt H.

Benef Microbes. 2015 Mar;6(1):61-81. doi: 10.3920/BM2014.0016. Review.


Reset of a critically disturbed microbial ecosystem: faecal transplant in recurrent Clostridium difficile infection.

Fuentes S, van Nood E, Tims S, Heikamp-de Jong I, ter Braak CJ, Keller JJ, Zoetendal EG, de Vos WM.

ISME J. 2014 Aug;8(8):1621-33. doi: 10.1038/ismej.2014.13. Epub 2014 Feb 27.


Effect of diet on the intestinal microbiota and its activity.

Zoetendal EG, de Vos WM.

Curr Opin Gastroenterol. 2014 Mar;30(2):189-95. doi: 10.1097/MOG.0000000000000048. Review.


Comparative genomics analysis of Streptococcus isolates from the human small intestine reveals their adaptation to a highly dynamic ecosystem.

Van den Bogert B, Boekhorst J, Herrmann R, Smid EJ, Zoetendal EG, Kleerebezem M.

PLoS One. 2013 Dec 30;8(12):e83418. doi: 10.1371/journal.pone.0083418. eCollection 2013.


Microbiome analysis of stool samples from African Americans with colon polyps.

Brim H, Yooseph S, Zoetendal EG, Lee E, Torralbo M, Laiyemo AO, Shokrani B, Nelson K, Ashktorab H.

PLoS One. 2013 Dec 20;8(12):e81352. doi: 10.1371/journal.pone.0081352. eCollection 2013.


Draft Genome Sequence of Enterococcus sp. Strain HSIEG1, Isolated from the Human Small Intestine.

van den Bogert B, Boekhorst J, Smid EJ, Zoetendal EG, Kleerebezem M.

Genome Announc. 2013 Dec 12;1(6). pii: e01013-13. doi: 10.1128/genomeA.01013-13.


Transient inflammatory-like state and microbial dysbiosis are pivotal in establishment of mucosal homeostasis during colonisation of germ-free mice.

El Aidy S, Derrien M, Aardema R, Hooiveld G, Richards SE, Dane A, Dekker J, Vreeken R, Levenez F, Doré J, Zoetendal EG, van Baarlen P, Kleerebezem M.

Benef Microbes. 2014 Mar;5(1):67-77. doi: 10.3920/BM2013.0018.


Impact of oral vancomycin on gut microbiota, bile acid metabolism, and insulin sensitivity.

Vrieze A, Out C, Fuentes S, Jonker L, Reuling I, Kootte RS, van Nood E, Holleman F, Knaapen M, Romijn JA, Soeters MR, Blaak EE, Dallinga-Thie GM, Reijnders D, Ackermans MT, Serlie MJ, Knop FK, Holst JJ, van der Ley C, Kema IP, Zoetendal EG, de Vos WM, Hoekstra JB, Stroes ES, Groen AK, Nieuwdorp M.

J Hepatol. 2014 Apr;60(4):824-31. doi: 10.1016/j.jhep.2013.11.034. Epub 2013 Dec 6.


Draft Genome Sequence of Veillonella parvula HSIVP1, Isolated from the Human Small Intestine.

van den Bogert B, Boekhorst J, Smid EJ, Zoetendal EG, Kleerebezem M.

Genome Announc. 2013 Dec 5;1(6). pii: e00977-13. doi: 10.1128/genomeA.00977-13.


Richness of human gut microbiome correlates with metabolic markers.

Le Chatelier E, Nielsen T, Qin J, Prifti E, Hildebrand F, Falony G, Almeida M, Arumugam M, Batto JM, Kennedy S, Leonard P, Li J, Burgdorf K, Grarup N, Jørgensen T, Brandslund I, Nielsen HB, Juncker AS, Bertalan M, Levenez F, Pons N, Rasmussen S, Sunagawa S, Tap J, Tims S, Zoetendal EG, Brunak S, Clément K, Doré J, Kleerebezem M, Kristiansen K, Renault P, Sicheritz-Ponten T, de Vos WM, Zucker JD, Raes J, Hansen T; MetaHIT consortium, Bork P, Wang J, Ehrlich SD, Pedersen O.

Nature. 2013 Aug 29;500(7464):541-6. doi: 10.1038/nature12506.


A comprehensive metatranscriptome analysis pipeline and its validation using human small intestine microbiota datasets.

Leimena MM, Ramiro-Garcia J, Davids M, van den Bogert B, Smidt H, Smid EJ, Boekhorst J, Zoetendal EG, Schaap PJ, Kleerebezem M.

BMC Genomics. 2013 Aug 2;14:530. doi: 10.1186/1471-2164-14-530.


Diet, microbiota, and microbial metabolites in colon cancer risk in rural Africans and African Americans.

Ou J, Carbonero F, Zoetendal EG, DeLany JP, Wang M, Newton K, Gaskins HR, O'Keefe SJ.

Am J Clin Nutr. 2013 Jul;98(1):111-20. doi: 10.3945/ajcn.112.056689. Epub 2013 May 29.


Diversity of human small intestinal Streptococcus and Veillonella populations.

van den Bogert B, Erkus O, Boekhorst J, de Goffau M, Smid EJ, Zoetendal EG, Kleerebezem M.

FEMS Microbiol Ecol. 2013 Aug;85(2):376-88. doi: 10.1111/1574-6941.12127. Epub 2013 Apr 25.


Human intestinal microbiota composition is associated with local and systemic inflammation in obesity.

Verdam FJ, Fuentes S, de Jonge C, Zoetendal EG, Erbil R, Greve JW, Buurman WA, de Vos WM, Rensen SS.

Obesity (Silver Spring). 2013 Dec;21(12):E607-15. doi: 10.1002/oby.20466. Epub 2013 Jun 22.


Obesity, non-alcoholic fatty liver disease, and atherothrombosis: a role for the intestinal microbiota?

Knaapen M, Kootte RS, Zoetendal EG, de Vos WM, Dallinga-Thie GM, Levi M, Stroes ES, Nieuwdorp M.

Clin Microbiol Infect. 2013 Apr;19(4):331-7. doi: 10.1111/1469-0691.12170. Epub 2013 Mar 2. Review.


Duodenal infusion of donor feces for recurrent Clostridium difficile.

van Nood E, Vrieze A, Nieuwdorp M, Fuentes S, Zoetendal EG, de Vos WM, Visser CE, Kuijper EJ, Bartelsman JF, Tijssen JG, Speelman P, Dijkgraaf MG, Keller JJ.

N Engl J Med. 2013 Jan 31;368(5):407-15. doi: 10.1056/NEJMoa1205037. Epub 2013 Jan 16.


Long-term monitoring of the human intestinal microbiota composition.

Rajilić-Stojanović M, Heilig HG, Tims S, Zoetendal EG, de Vos WM.

Environ Microbiol. 2012 Oct 15. doi: 10.1111/1462-2920.12023. [Epub ahead of print]


Microbiota conservation and BMI signatures in adult monozygotic twins.

Tims S, Derom C, Jonkers DM, Vlietinck R, Saris WH, Kleerebezem M, de Vos WM, Zoetendal EG.

ISME J. 2013 Apr;7(4):707-17. doi: 10.1038/ismej.2012.146. Epub 2012 Nov 29.


Gut bacteria-host metabolic interplay during conventionalisation of the mouse germfree colon.

El Aidy S, Derrien M, Merrifield CA, Levenez F, Doré J, Boekschoten MV, Dekker J, Holmes E, Zoetendal EG, van Baarlen P, Claus SP, Kleerebezem M.

ISME J. 2013 Apr;7(4):743-55. doi: 10.1038/ismej.2012.142. Epub 2012 Nov 22.


Effect of galactooligosaccharides and Bifidobacterium animalis Bb-12 on growth of Lactobacillus amylovorus DSM 16698, microbial community structure, and metabolite production in an in vitro colonic model set up with human or pig microbiota.

Martinez RC, Cardarelli HR, Borst W, Albrecht S, Schols H, Gutiérrez OP, Maathuis AJ, de Melo Franco BD, De Martinis EC, Zoetendal EG, Venema K, Saad SM, Smidt H.

FEMS Microbiol Ecol. 2013 Apr;84(1):110-23. doi: 10.1111/1574-6941.12041. Epub 2012 Dec 17.


Intestinal microbiota in functional bowel disorders: a Rome foundation report.

Simrén M, Barbara G, Flint HJ, Spiegel BM, Spiller RC, Vanner S, Verdu EF, Whorwell PJ, Zoetendal EG; Rome Foundation Committee.

Gut. 2013 Jan;62(1):159-76. doi: 10.1136/gutjnl-2012-302167. Epub 2012 Jun 22.


Transfer of intestinal microbiota from lean donors increases insulin sensitivity in individuals with metabolic syndrome.

Vrieze A, Van Nood E, Holleman F, Salojärvi J, Kootte RS, Bartelsman JF, Dallinga-Thie GM, Ackermans MT, Serlie MJ, Oozeer R, Derrien M, Druesne A, Van Hylckama Vlieg JE, Bloks VW, Groen AK, Heilig HG, Zoetendal EG, Stroes ES, de Vos WM, Hoekstra JB, Nieuwdorp M.

Gastroenterology. 2012 Oct;143(4):913-6.e7. doi: 10.1053/j.gastro.2012.06.031. Epub 2012 Jun 20. Erratum in: Gastroenterology. 2013 Jan;144(1):250.


Comparative analysis of Lactobacillus plantarum WCFS1 transcriptomes by using DNA microarray and next-generation sequencing technologies.

Leimena MM, Wels M, Bongers RS, Smid EJ, Zoetendal EG, Kleerebezem M.

Appl Environ Microbiol. 2012 Jun;78(12):4141-8. doi: 10.1128/AEM.00470-12. Epub 2012 Apr 6.


The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates.

Zoetendal EG, Raes J, van den Bogert B, Arumugam M, Booijink CC, Troost FJ, Bork P, Wels M, de Vos WM, Kleerebezem M.

ISME J. 2012 Jul;6(7):1415-26. doi: 10.1038/ismej.2011.212. Epub 2012 Jan 19.

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