Biology subjects

Frazao, N.

Publications and source records attributed to Frazao, N..

5 recordsLinked to original sources

bioRxiv2026

Pervasive bacterial and prophage hybridization during chronic gut inflammation

Inflammatory bowel diseases (IBD) are modulated by microbiota composition, host genetics, and environmental factors1. Humans and other mammals are colonized by multiple strains of Escherichia coli, a species that expands in abundance in IBD patients2. The state of chronic inflammation characteristic of IBD is expected to intensify selective pressures on the gut microbial community, leading to distinct adaptive trajectories among its constituents. Here we couple in vivo experimental evolution with short- and long-read sequencing to test this hypothesis at the level of mutation and horizontal gene transfer (HGT). By colonizing IL10KO mice, a model of IBD3, and healthy wild-type mice with two strains of E. coli, we show that the tempo and mode of evolution are strain-specific and strongly shaped by host inflammatory status. Unique mutations associate with host inflammatory status independently of microbiota composition, and rates of transfer are diagnostic of chronic inflammation. Extensive transduction events occur in the inflamed gut, giving rise to hybrid clones that form a new genetic lineage, one that becomes dominant in this disease context. The high levels of recombination between prophages uncovered here point to a critical role of HGT and viral evolution in IBD.

microbiology↗

bioRxiv2023

Massive lateral gene transfer under strain coexistence in the gut

Mammals are colonized by multiple strains of Escherichia coli, yet how such strain coexistence affects their tempo and mode of evolution is poorly understood. Here, by following the colonization of two phylogenetic distinct strains of E. coli in the mouse gut, we find a strain-specific mode of evolution and a remarkable level of gene transfer between strains. In the same host, despite accumulating mutations at the same rate, one strain evolves by diversifying selection and the other by directional selection, and a rich dynamics of bacteriophage and plasmid transfer is found. Our results provide support for an important role of lateral transduction in the mammalian gut.

evolutionary biology↗

bioRxiv2023

Shared evolutionary path in social microbiomes

Social networks can influence the ecology of gut bacteria, shaping the species composition of the gut microbiome in humans and other animals. Gut commensals evolve and can adapt at a rapid pace when colonizing healthy hosts. Here, we aimed at assessing the impact of host-to-host bacterial transmission on Escherichia coli evolution in the mammalian gut. Using an in vivo experimental evolution approach in mice, we found a transmission rate of 7% ({+/-}3% 2SE) of E. coli cells per day between hosts inhabiting the same household. Consistent with the predictions of a simple population genetics model of mutation-selection-migration, the level of shared events resulting from within host evolution is greatly enhanced in co-housed mice, showing that hosts undergoing the same diet and habit are not only expected to have similar microbiome species compositions but also similar microbiome evolutionary dynamics. Furthermore, we estimated the rate of mutation accumulation of E. coli to be 2.9x10-3 ({+/-}5x10-4 2SE) mutations/genome/generation, irrespective of the social context of the regime. Our results reveal the impact of bacterial migration across hosts in shaping the adaptive evolution of new strains colonizing gut microbiomes.

evolutionary biology↗

bioRxiv2022

Two modes of evolution shape bacterial strain diversity in the gut for thousands of generations

How and at what pace bacteria evolve when colonizing healthy hosts remains unclear. Here, by monitoring evolution for more than six thousand generations in the mouse gut, we show that the successful colonization of an invader Escherichia coli depends on the diversity of the existing microbiota and the presence of a closely related strain. Following colonization, two modes of evolution were observed: one in which diversifying selection leads to long-term coexistence of ecotypes and a second in which directional selection propels selective sweeps. These modes can be quantitatively distinguished by the statistics of mutation trajectories. In our experiments, diversifying selection was marked by the emergence of metabolic mutations, and directional selection by acquisition of prophages, which bring their own benefits and costs. In both modes, we observed parallel evolution, with mutation accumulation rates comparable to those typically observed in vitro on similar time scales. Our results show that gut environments can rapidly generate diversifying selection and ecotype formation.

evolutionary biology↗

bioRxiv2018

Sex overrides mutation in Escherichia coli colonizing the gut

Bacteria evolve by mutation accumulation in laboratory experiments, but the tempo and mode of evolution in natural environments are largely unknown. Here we show, by experimental evolution of E. coli in the mouse gut, that the ecology of the gut controls bacterial evolution. If a resident E. coli strain is present in the gut, an invading strain evolves by rapid horizontal gene transfer; this mode precedes and outweighs evolution by point mutations. An epidemic infection by two phages drives gene uptake and produces multiple co-existing lineages of phage-carrying (lysogenic) bacteria. A minimal dynamical model explains the temporal pattern of phage epidemics and their complex evolutionary outcome as generic effects of phage-mediated selection. We conclude that phages are an important eco-evolutionary driving force - they accelerate evolution and promote genetic diversity of bacteria.\n\nOne Sentence SummaryBacteriophages drive rapid evolution in the gut.

evolutionary biology↗