Matinée scientifique santé numérique au cours de laquelle nous accueillerons deux brillants scientifiques, Rayan Chikhi (http://rayan.chikhi.name/) et Florence Bansept (http://web.evolbio.mpg.de/~bansept/).
Rayan Chikhi : Sequence bioinformatics at large scale: petabase-scale sequence alignment catalyses viral discovery
Abstract: Petabytes of valuable sequencing data reside in public repositories, doubling in size every two years. They contain a wealth of genetic information about viruses that would help us monitor spillovers and anticipate future pandemics. We recently developed a bioinformatics cloud infrastructure, named Serratus, to perform petabase-scale sequence alignment. With it we analyzed all available RNA-seq samples (5.7 million samples, 10 petabytes) and discovered 10x more RNA viruses than previously known, including a new family of coronaviruses (Edgar et al, Nature, 2022). In this talk, I will present the computational infrastructure and some of the biological analyses.
Florence Bansept : Evolution in biphasic life cycles
Abstract: Microbial communities extend the host functional repertoire, thus making the host and its associated microbes a functional unit. We are only beginning to decipher how host and microbe fitnesses are intertwined: while it is now clear that the microbiota has a vast potential to affect the host physiology, less focus has been put to the microbial perspective, i.e. to understand what benefit or cost can microbes retrieve from their interaction with their host. In contrast to the common hypotheses of strong and continued coevolution proposed to explain the emergence of such elaborate symbioses, we focus here on the steps that can lead a microbial population to transition from a free-living life-style to an association with a host. In particular, we aim at understanding what selection pressures apply to microbes following a biphasic life cycle, in which they can regularly transit in and outside a host.
We study three simple models of such biphasic life cycles. In the first model, we study a homogeneous microbial population transiting between a host and its environment and perform a sensitivity analysis to show the existence of two different regimes: one where the effect of migration from the environment to the host dominates, and a second where the within-host replication rate matters most. The second model is an SI-inspired compartmental model, which accounts for the habitats’ dynamics. We show that microbial propagation across habitats depends on the product of the transmissibilities, which we propose as a new holistic measure of microbial fitness - bearing similitudes with the R0 of epidemiology. In the third model, we combine microbial population and habitats dynamics and derive predictions that are consistent with experimental observations of an increased ability to form biofilms in bacteria evolved in biphasic conditions with C. elegans.