2024
Caenepeel C*, Falony G*, Machiels K, Verstockt B, Goncalves PJ, Ferrante M, Sabino J, Raes J, Vieira-Silva S and Vermeire S ( 2024 ) Dysbiosis and associated stool features improve prediction of response to biological therapy in inflammatory bowel disease. Gastroenterology , 166:483–495 (*indicates joint contribution) Link
2023
Andrikopoulos P#, Aron-Wisnewsky J#, Chakaroun R#, Myridakis A#, Forslund SK#, Nielsen T, Adriouch S, Holmes B, Chilloux J, Vieira-Silva S, Falony G, Salem JE, Andreelli F, Belda E, Kieswich J, Chechi K, Puig-Castellvi F, Chevalier M, Le Chatelier E, Olanipekun MT, Hoyles L, Alves R, Helft G, Isnard R, Køber L, Coelho LP, Rouault C, Gauguier D, Gøtze JP, Prifti E, Froguel P, MetaCardis Consortium, Zucker JD, Bäckhed F, Vestergaard H, Hansen T, Oppert JM, Blüher M, Nielsen J, Raes J, Bork P, Yaqoob MM, Stumvoll M, Pedersen O, Ehrlich SD, Clément K and Dumas ME ( 2023 ) Evidence of a causal and modifiable relationship between kidney function and circulating trimethylamine N-oxide. Nat Commun , 14:5843 (# indicates joint correspondence) Link
Devolder L, Pauwels A, Van Remoortel A, Falony G, Vieira-Silva S, Nagels G, De Keyser J, Raes J and D'Hooghe MB ( 2023 ) Gut microbiome composition is associated with long-term disability worsening in multiple sclerosis. Gut Microbes , 15:2180316 Link
Fan Y*, Støving RK*, Berreira Ibraim S*, Hyötyläinen T, Thirion F, Arora T, Lyu L, Stankevic E, Hansen TH, Déchelotte P, Sinioja T, Ragnarsdottir O, Pons N, Galleron N, Quinquis B, Levenez F, Roume H, Falony G, Vieira-Silva S, Raes J, Clausen L, Telléus GK, Bäckhed F, Oresic M, Ehrlich SD and Pedersen O ( 2023 ) The gut microbiota contributes to the pathogenesis of anorexia nervosa in humans and mice. Nat Microbiol , 8:787–802 (*indicates joint contribution) Link
Jansen D, Falony G, Vieira-Silva S, Simsek C, Marcelis T, Caenepeel C, Machiels K, Raes J, Vermeire S and Matthijnssens J ( 2023 ) Community types of the human gut virome are associated with endoscopic outcome in ulcerative colitis. J Crohns Colitis , 17:1504–1513 Link
Loreti S, Thiele K, De Brucker M, Olsen C, Centelles-Lodeiro J, Bourgain C, Waelput W, Tournaye H, Griesinger G, Raes J, Vieira-Silva S, Arck P, Blockeel C and Mackens S ( 2023 ) Oral dydrogesterone versus micronized vaginal progesterone for luteal phase support: a double-blind crossover study investigating pharmacokinetics and impact on the endometrium. Hum Reprod , https://doi.org/10.1093/humrep/dead256 Link
Poppe J, Vieira-Silva S, Raes J, Verbeke K* and Falony G* ( 2023 ) Systematic optimization of fermentation conditions for in vitro fermentations with fecal inocula. Front Microbiol , 14:1198903 (*indicates joint contribution) Link
2022
Belda E, Voland L, Tremaroli V, … Vieira-Silva S, … Bäckhed F, Raes J and Clément K (2022) Impairment of gut microbial biotin metabolism and host biotin status in severe obesity: effect of biotin and prebiotic supplementation on improved metabolism. Gut, 71:2463-2480 Link
Beller L, Deboutte W, Vieira-Silva S, Falony G, Tito RY, Rymenans L, Yinda CK, Vanmechelen B, Van Espen L, Jansen D, Shi C, Zeller M, Maes P, Faust K, Van Ranst M, Raes J and Matthijnssens J (2022) The virota and its transkingdom interactions in the healthy infant gut. Proc Natl Acad Sci USA, 119:e2114619119 Link
Fromentin S, Forslund SK, Chechi K,… Vieira-Silva S, … Dumas ME, Ehrlich SD and Pedersen O (2022) Microbiome and metabolome features of the cardiometabolic disease spectrum. Nat Med, 28:303–314 Link
Le Roy T, Moens De Hase E, Van Hul M, Paquot A, Pelicaen R, Régnier M, Depommier C, Druart C, Everard A, Maiter D, Delzenne NM, Bindels LB, De Barsy M, Loumaye A, Hermans MP, Thissen JP, Vieira-Silva S, Falony G, Raes J, Muccioli GG and Cani PD (2022) Dysosmobacter welbionis is a newly isolated human commensal bacterium preventing diet-induced obesity and metabolic disorders in mice. Gut, 71:534–543 Link
Malan-Muller S, Valles-Colomer M, Foxx CL, Vieira-Silva S, van den Heuvel LL, Raes J, Seedat S, Lowry CA and Hemmings SMJ (2022) Exploring the relationship between the gut microbiome and mental health outcomes in a posttraumatic stress disorder cohort relative to trauma-exposed controls. Eur Neuropsychopharmacol, 56:24–38 Link
Steenackers N, Falony G, Augustijns P, Van der Schueren B, Vanuytsel T, Vieira-Silva S, Wauters L, Raes J and Matthys C (2022) Specific contributions of segmental transit times to gut microbiota composition. Gut, 71:1443–1444 Link
Suriano F, Vieira-Silva S, Falony G, de Wouters d’Oplinter A, Paone P, Delzenne NM, Everard A, Raes J, Van Hul M* and Cani PD* (2022) Fat and not sugar as the determining factor for gut microbiota changes, obesity and related metabolic disorders in mice. Am J Physiol Metab, 324:E85-E96 (*indicates joint contribution) Link
Valles-Colomer M, Bacigalupe R, Vieira-Silva S, Suzuki S, Darzi Y, Tito RY, Yamada T, Segata N, Raes J and Falony G (2022) Variation and transmission of the human gut microbiota across multiple familial generations. Nat Microbiol, 7:87–96 Link
2021
Beller L, Deboutte W, Falony G, Vieira-Silva S, Tito RY, Valles-Colomer M, Rymenans L, Jansen D, Van Espen L, Papadaki MI, Shi C, Yinda CK, Zeller M, Faust K, Van Ranst M, Raes J and Matthijnssens J (2021) Successional stages in infant gut microbiota maturation. MBio, 12:e0185721 Link
Brial F, Chilloux J, Nielsen T, Vieira-Silva S, Falony G, Andrikopoulos P, Olanipekun M, Hoyles L, Djouadi F, Neves AL, Rodriguez-Martinez A, Mouawad GI, Pons N, Forslund S, Le-Chatelier E, Le Lay A, Nicholson J, Hansen T, Hyötyläinen T, Clément K, Oresic M, Bork P, Ehrlich SD, Raes J, Pedersen OB, Gauguier D and Dumas ME (2021) Human and preclinical studies of the host-gut microbiome co-metabolite hippurate as a marker and mediator of metabolic health. Gut, 70:2105–2114 Link
Forslund SK, Chakaroun R, Zimmermann-Kogadeeva M, … Vieira-Silva S, … Clément K, Stumvoll M and Bork P (2021) Combinatorial, additive and dose-dependent drug–microbiome associations. Nature, 600:500–505 Link
Kurilshikov A, Medina-Gomez C, Bacigalupe R, … Vieira-Silva S,… Kraaij R, Raes J and Zhernakova A (2021) Large-scale association analyses identify host factors influencing human gut microbiome composition. Nat Genet, 53:156–165 Link
Lloréns-Rico V, Vieira-Silva S, Gonçalves PJ, Falony G and Raes J (2021) Benchmarking microbiome transformations favors experimental quantitative approaches to address compositionality and sampling depth biases. Nat Commun, 12:3562 Link
Steenackers N, Wauters L, Van der Schueren B, Augustijns P, Falony G, Koziolek M, Lannoo M, Mertens A, Meulemans A, Raes J, Vangoitsenhoven R, Vieira-Silva S, Weitschies W, Matthys C and Vanuytsel T (2021) Effect of obesity on gastrointestinal transit, pressure and pH using a wireless motility capsule. Eur J Pharm Biopharm, 167:1–8 Link
Suriano F, Vieira-Silva S, Falony G, Roumain M, Paquot A, Pelicaen R, Régnier M, Delzenne NM, Raes J, Muccioli GG, Van Hul M and Cani PD (2021) Novel insights into the genetically obese (ob/ob) and diabetic (db/db) mice: two sides of the same coin. Microbiome, 9:147 Link
2020
Caenepeel C, Sadat Seyed Tabib N, Vieira-Silva S and Vermeire S (2020) Review article: how the intestinal microbiota may reflect disease activity and influence therapeutic outcome in inflammatory bowel disease. Aliment Pharmacol Ther, 52:1453–1468 Link
García-Velasco JA, Budding D, Campe H, Malfertheiner SF, Hamamah S, Santjohanser C, Schuppe-Koistinen I, Nielsen HS, Vieira-Silva S and Laven J (2020) The reproductive microbiome – clinical practice recommendations for fertility specialists. Reprod Biomed Online, 41:443–453 Link
Hughes DA, Bacigalupe R, Wang J, Rühlemann MC, Tito RY, Falony G, Joossens M, Vieira-Silva S, Henckaerts L, Rymenans L, Verspecht C, Ring S, Franke A, Wade KH, Timpson NJ and Raes J (2020) Genome-wide associations of human gut microbiome variation and implications for causal inference analyses. Nat Microbiol, 5:1079–1087 Link
Madin JS, Nielsen DA, Brbic M, Corkrey R, Danko D, Edwards K, Engqvist MKM, Fierer N, Geoghegan JL, Gillings M, Kyrpides NC, Litchman E, Mason CE, Moore L, Nielsen SL, Paulsen IT, Price ND, Reddy TBK, Richards MA, Rocha EPC, Schmidt TM, Shaaban H, Shukla M, Supek F, Tetu SG, Vieira-Silva S, Wattam AR, Westfall DA and Westoby M (2020) A synthesis of bacterial and archaeal phenotypic trait data. Sci Data, 7:170 Link
Molinaro A, Bel Lassen P, Henricsson M, … Vieira-Silva S, … Aron-Wisnewsky J, Clément K and Bäckhed F (2020) Imidazole propionate is increased in diabetes and associated with dietary patterns and altered microbial ecology. Nat Commun, 11:5881 Link
Vieira-Silva S, Falony G, Belda E, … Bäckhed F, Clément K and Raes J (2020) Statin therapy is associated with lower prevalence of gut microbiota dysbiosis. Nature, 581:310–315 Link
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 and Cani PD (2019) Supplementation with Akkermansia muciniphila in overweight and obese human volunteers: a proof-of-concept exploratory study. Nat Med, 25:1096–1103 Link
2019
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 and Glorieux G (2019) Gut microbiota dynamics and uraemic toxins: one size does not fit all. Gut, 68:2257–2260 Link
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 and Raes J (2019) Population-level analysis of Blastocystis subtype prevalence and variation in the human gut microbiota. Gut, 68:1180–1189 Link
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 and Raes J (2019) The neuroactive potential of the human gut microbiota in quality of life and depression. Nat Microbiol, 4:623–632 Link
Vieira-Silva S, Sabino J, Valles-Colomer M, Falony G, Kathagen G, Caenepeel C, Cleynen I, van der Merwe S, Vermeire S and Raes J (2019) Quantitative microbiome profiling disentangles inflammation- and bile duct obstruction-associated microbiota alterations across PSC/IBD diagnoses. Nat Microbiol, 4:1826–1831 Link
2018
D’hoe K, Conterno L, Fava F, Falony G, Vieira-Silva S, Vermeiren J, Tuohy K and Raes J (2018) Prebiotic wheat bran fractions induce specific microbiota changes. Front Microbiol, 9:31 Link
Falony G, Vieira-Silva S and Raes J (2018) Richness and ecosystem development across faecal snapshots of the gut microbiota. Nat Microbiol, 3:526–528 Link
2017
Vandeputte D, Falony G, D’Hoe K, Vieira-Silva S and Raes J (2017) Water activity does not shape the microbiota in the human colon. Gut, 66:1865–1866 Link
Vandeputte D, Falony G, Vieira-Silva S, Wang J, Sailer M, Theis S, Verbeke K and Raes J (2017) Prebiotic inulin-type fructans induce specific changes in the human gut microbiota. Gut, 66:1968–1974 Link
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 and Raes J (2017) Quantitative microbiome profiling links gut community variation to microbial load. Nature, 551:507–511 Link
2016
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 and Bell JT (2016) Heritable components of the human fecal microbiome are associated with visceral fat. Genome Biol, 17:189 Link
Darzi Y, Falony G, Vieira-Silva S and Raes J (2016) Towards biome-specific analysis of meta-omics data. ISME J, 10:1025–1028 Link
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 and Raes J (2016) Population-level analysis of gut microbiome variation.Science, 352:560–564 Link
Kolmeder CA, Salojärvi J, Ritari J, De Been M, Raes J, Falony G, Vieira-Silva S, Kekkonen RA, Corthals GL, Palva A, Salonen A and De Vos WM (2016) Faecal metaproteomic analysis reveals a personalized and stable functional microbiome and limited effects of a probiotic intervention in adults. PLOS One, 11:e0153294 Link
Pedersen HK, Gudmundsdottir V, Nielsen HB, Hyotylainen T, Nielsen T, Jensen BAH, 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, Kristiansen K, Brix S, Raes J, Wang J, Hansen T, Bork P, Brunak S, Oresic M, Ehrlich SD and Pedersen O (2016) Human gut microbes impact host serum metabolome and insulin sensitivity. Nature, 535:376–381 Link
Valles-Colomer M, Darzi Y, Vieira-Silva S, Falony G, Raes J and Joossens M (2016) Meta-omics in inflammatory bowel disease research: Applications, challenges, and guidelines. J Crohn’s Colitis, 10:735–746 Link
Vandeputte D, Falony G, Vieira-Silva S, Tito RY, Joossens M and Raes J (2016) Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates. Gut, 65:57–62 Link
Vieira-Silva S, Falony G, Darzi Y, Lima-Mendez G, Garcia Yunta R, Okuda S, Vandeputte D, Valles-Colomer M, Hildebrand F, Chaffron S and Raes J (2016) Species-function relationships shape ecological properties of the human gut microbiome. Nat Microbiol, 1:16088 Link
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, Weersma RK, Feskens EJM, Netea MG, Gevers D, Jonkers D, Franke L, Aulchenko YS, Huttenhower C, Raes J, Hofker MH, Xavier RJ, Wijmenga C and Fu J (2016) Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity. Science, 352:565–569 Link
2015
Falony G, Vieira-Silva S and Raes J (2015) Microbiology meets big data: the case of gut microbiota-derived trimethylamine. Annu Rev Microbiol, 69:305–321 Link
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 H, Nielsen HB, Brunak S, Raes J, Hansen T, Wang J, Ehrlich SD, Bork P and Pedersen O (2015) Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota.Nature, 528:262–266 Link
Nguyen TLA, Vieira-Silva S, Liston A and Raes J (2015) How informative is the mouse for human gut microbiota research?DMM Dis Model Mech, 8:1–16 Link
Sunagawa S, Coelho LP, Chaffron S, … Vieira-Silva S, … Raes J, Acinas SG and Bork P (2015) Structure and function of the global ocean microbiome. Science, 348:1261359 Link
2014
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 and Van Loo G (2014) A20 controls intestinal homeostasis through cell-specific activities. Nat Commun, 5:5103 Link
2012
Gama JA, Abby SS, Vieira-Silva S, Dionisio F and Rocha EPC (2012) Immune subversion and quorum-sensing shape the variation in infectious dose among bacterial pathogens. PLOS Pathog, 8:e1002503 Link
2011
Goulao LF, Vieira-Silva S and Jackson PA (2011) Association of hemicellulose- and pectin-modifying gene expression with Eucalyptus globulus secondary growth. Plant Physiol Biochem, 49:873–881 Link
Vieira-Silva S, Touchon M, Abby SS and Rocha EPC (2011) Investment in rapid growth shapes the evolutionary rates of essential proteins. Proc Natl Acad Sci USA, 108:20030–20035 Link
2010
Vieira-Silva S and Rocha EPC (2010) The systemic imprint of growth and its uses in ecological (meta)genomics. PLOS Genet, 6:e1000808 Link
Vieira-Silva S, Touchon M and Rocha EPC (2010) No evidence for elemental-based streamlining of prokaryotic genomes.Trends Ecol Evol, 25:319–321 Link
2008
Vieira-Silva S and Rocha EPC (2008) An assessment of the impacts of molecular oxygen on the evolution of proteomes. Mol Biol Evol, 25:1931–1942 Link