We study microbiome functions and their regulation to understand interactions with the host in health and disease.

The goal of our group is to understand which functions are being performed by the microorganisms in the gut microbiota and how they are regulated, to rationally develop targeted strategies to modulate the activity of our inner microbes.

Microorganisms, and in particular, bacteria, have a large functional plasticity to adapt to changes in their environment and survive. However, this functional plasticity is poorly understood in the context of complex ecosystems such as the gut microbiota. Our group will study what is the natural transcriptional variation in human gut bacteria, which host-related factors (such as diet or different diseases) alter this gene expression and what are the regulatory mechanisms underlying these changes. We will then harness this knowledge to develop novel strategies to modulate the activity of the gut microbiota in disorders where this functionality is altered.

To achieve our goals, we will use a Systems Biology approach that combines experimental work, using in vitro and in vivo models of the gut microbial communities, with multiomic profiling and computational data analysis and integration.


Get to know us better


Research Staff

The people who make it all possible

Verónica Llorens Rico

Cristina Marti Ibáñez

Ana Rosa Marquez Blesa


Our scientific contributions

Single-cell approaches in human microbiome research.
Lloréns-Rico V, Simcock JA, Huys GRB and Raes J
CELL, 2022 Jul,  DOI:  10.1016/j.cell.2022.06.040,  Vol. 185,  pag. 2725-2738

Clinical practices underlie COVID-19 patient respiratory microbiome composition and its interactions with the host.
Lloréns-Rico V, Gregory AC, Van Weyenbergh J, Jansen S, Van Buyten T, Qian J, Braz M, Menezes SM, Van Mol P, Vanderbeke L, Dooms C, Gunst J, Hermans G, Meersseman P, CONTAGIOUS collaborators, Wauters E, Neyts J, Lambrechts D, Wauters J and Raes J
Nature Communications, 2021 Oct,  DOI:  10.1038/s41467-021-26500-8,  Vol. 12,  pag. 6243-6243

Benchmarking microbiome transformations favors experimental quantitative approaches to address compositionality and sampling depth biases.
Lloréns-Rico V, Vieira-Silva S, Gonçalves PJ, Falony G and Raes J
Nature Communications, 2021 Jun,  DOI:  10.1038/s41467-021-23821-6,  Vol. 12,  pag. 3562-3562

Tracking humans and microbes.
Lloréns-Rico V and Raes J
NATURE, 2019 May,  DOI:  10.1038/d41586-019-01591-y,  Vol. 569,  pag. 632-633

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 and Raes J
eLife, 2018 Oct,  DOI:  10.7554/eLife.37090,  Vol. 7,  pag. 


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