Microbiome Research

The Microbiome Research Group led by Mireia Valles-Colomer analyses the human body-associated microbial communities (microbiome) with computational methods to understand the role of the microbiome-host interaction in maintaining our health. Mireia is a tenure-track professor at the Medical and Life Sciences Department of the Universitat Pompeu Fabra, located at the PRBB.

Main research lines:

  • The neuroactivity of the gut microbiome

    Alterations in the composition of the gut microbiome have been associated with multiple neuropathologies. The members of the microbiome metabolise a myriad of neuroactive compounds, including GABA, serotonin, or dopamine which, through the microbiome-gut-brain axis, could influence mental health. We develop computational tools to profile the synthesis and degradation of such compounds in prokaryotic genomes and metagenomes, to better understand how alterations in the gut microbiome could be linked with mental health related conditions.

  • The social transmission of the microbiome

    Our microbiome is seeded during birth, and then shaped by transmission from proximate individuals. We use strain-level resolution metagenomics profiling to track microbiome transmission through social interaction, and how this shapes the microbiome in health and disease.

Highlighted publications

-Valles-Colomer M, Blanco-Miguez A, Manghi P, Asnicar F, Dubois L, Golzato D, Armanini F, Cumbo F, Huang KD, Manara S, Masetti G, Pinto F, Piperni E, Puncochar M, Ricci L, Zolfo M, Farrant O, Goncalves A, Selma-Royo M, Binetti AG, Becerra JE, Han B, Lusingu J, Amuasi J, Amoroso L, Visconti A, Steves CM, Falchi M, Filosi M, Tett A, Last A, Xu Q, Qin N, Qin H, May J, Eibach D, Corrias MV, Ponzoni M, Pasolli E, Spector TD, Domenici E, Collado MC, Segata N. The person-to-person transmission landscape of the gut and oral microbiomes. Nature 2023; 614(7946): 125-135.

-Valles-Colomer M, Bacigalupe R, Vieira-Silva S, Suzuki S, Darzi Y, Tito RY, Yamada T, Segata N, Raes J, Falony G. Variation and transmission of the human gut microbiota across multiple familial generations. Nature Microbiology 2022; 7(1): 87-96.

-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. The neuroactive potential of the human gut microbiota in quality of life and depression. Nature Microbiology 2019; 4(4): 623-632.


-Knowledge Generation Project (PID2022-139328OA-I00) from the Spanish Ministry of Science and Innovation

-La Caixa Incoming Junior Leader (fellowship 132107)

-Beatriz Galindo Junior fellowship (BG22/00172) from the Spanish Ministry of Universities

-EvoMG: Joint Program on Evolutionary Medical Genomics

The web page of the group is: https://www.upf.edu/web/microbiome

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