Our research focuses on understanding the function of microbial communities, in particular the human gastrointestinal microbiota, in health and disease.
We explore 1) the ecological variation and the resilience of the human gut microbiota in health, and 2) the contribution of abnormal microbiota composition (dysbiosis) to pathophysiology, notably in the clinical context of inflammatory, cardiometabolic and neuropsychiatric disorders.
Operating in a quantitative framework, we combine metagenomics, comparative genomics, evolutionary ecology and state of the art computational approaches to understand the role of microbial communities in human health. This includes predicting disease progression and treatment efficacy, in order to inform the design of new strategies for personalised medicine.
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Valles-Colomer M*, Bacigalupe R*, Vieira-Silva S*, Suzuki S, Darzi Y, Tito RY, Yamada T, Segata N, Raes J*, Falony G*. 2022. Variation and transmission of the human gut microbiota across multiple familial generations. Nat Microbiol, 7:87–96. * equal contribution
Lloréns-Rico V, Vieira-Silva S, Gonçalves PJ, Falony G*, Raes J*. 2021. Benchmarking microbiome transformations favors experimental quantitative approaches to address compositionality and sampling depth biases. Nat Commun, 12. * equal contribution
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, 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. * equal contribution
Vieira-Silva S*, Falony G*, Belda E*, Nielsen T, Aron-Wisnewsky J, Chakaroun R, Forslund SK, Assmann K, Valles-Colomer M, [MetaCardis Consortium: 90 authors], Stumvoll M, Vestergaard H, Zucker JD, Bork P, Pedersen O, Bäckhed F, Clément K, Raes J. 2020. Statin therapy is associated with lower prevalence of gut microbiota dysbiosis. Nature, 581: 310–315. * equal contribution
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 IBD/PSC diagnoses. Nat Microbiol, 4:1826–1831
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.
Falony G, Vieira-Silva S & Raes J. 2018. Richness and ecosystem development across faecal snapshots of the gut microbiota. Nat Microbiol 3, 526–528
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. * equal contribution § joint supervision
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. (2016) Species-function relationships shape ecological properties of the human gut microbiome. Nat Microbiol 1, 16088. * equal contribution
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, et al. (2016) Population-level analysis of gut microbiome variation. Science 352, 560–4. * equal contribution
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