Unraveling gut microbiome evolution in mammals
How mammalian gut microbiomes evolve over long timescales remains equivocal: How conserved is their composition? What was the composition of ancestral mammalian microbiota? Do bacterial taxa covary in abundance over millions of years? What are the effects of current human-induced disturbances on microbiome evolution? Multivariate phylogenetic models are key to answering such questions, yet they are not directly applicable to microbiota data, which are usually characterized using 16S rRNA amplicon sequencing. In this presentation, I will present recent modeling advancements aimed at addressing these questions regarding gut microbiome evolution in mammals.
First, I will introduce a phylogenetic approach for modeling the fluctuations of bacterial relative abundances within gut microbiomes as mammals diversify. By applying this model to the gut microbiota of >200 mammal species, we find significant phylosymbiosis (the extent to which closely related mammal species harbor similar microbiota), that is not entirely explained by diet and geographic location. We also identify main shifts in microbiota composition during the evolution of mammals and infer an ancestral mammalian microbiota consistent with an insectivorous diet. Finally, we find remarkably consistent evolutionary covariations among bacterial orders within gut microbiomes. These findings suggest that other evolutionary-conserved physiological or immunological traits shape the variations of microbiota composition across mammals.
Second, we further investigate the impact of disturbances on the human gut microbiome. We observe that human gut microbiota is characterized by a widespread reduction in diversity compared with that of wild primate species. Among the bacterial strains lost in humans, phylogenetic models revealed that an important share corresponds to human-specific bacterial lineages that were transmitted within primate species for millions of years. In addition, we demonstrate that this loss of ancestral bacterial symbionts correlates with several immune disorders in industrialized human populations.
Overall, these findings indicate that, despite the substantial variability of present-day gut microbiota, some aspects of their composition are conserved over millions of years of mammalian evolutionary history. In the face of contemporary human-induced disturbances, gut microbiomes in industrialized populations exhibit a sharp decline in diversity, a phenomenon that notably correlates with human health.
Short bio
2014-2018: Student in Evolutionary biology at the Ecole normale supérieure (ENS).
2018-2021: PhD on the evolution of host-microbiota interactions between the ENS and the Muséum national d’Histoire Naturelle (MNHN) co-advised by Hélène Morlon, Marc-André Selosse et Florent Martos.
2021-2022: Postdoc at ENS.
2022-2024: Attaché temporaire d’enseignement et de recherche (ATER) in community ecology at ENS.
Laboratory of the speaker
Team Modeling Biodiversity, Institut de Biologie de l’ENS
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