Percorrer por autor "Seixas, Elsa"
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- Clonal interference and genomic repair during strain coexistence in the gutPublication . Frazão, Nelson; Seixas, Elsa; Mischler, Manolo; Moura-de-Sousa, Jorge; Barreto, Hugo C.; Gordo, IsabelHumans and other mammals are colonized by multiple strains of Escherichia coli, but the tempo and mode of evolution of different coexisting strains, between whom horizontal gene transfer (HGT) can occur, is poorly understood. Here, we follow in real time the evolution of two phylogenetic distinct strains of E. coli that co-colonize the mouse gut with different population sizes. We find qualitative differences in evolutionary dynamics between strains within the same host. In the strain with larger population size intense clonal interference occurs and polymorphism at a neutral marker locus is maintained, while in the strain with lower population size complete selective sweeps and loss of neutral marker polymorphism occurs. Strain coexistence is also accompanied by rich dynamics of HGT from one strain to the other. Strikingly, a rare HGT event could restore a previously lost genomic region in the recipient strain. Furthermore, we detect for the first time a case of phage piracy in the gut, where a putative phage satellite, lacking essential genes for their own replication, was likely mobilized by a helper phage to transfer between bacterial hosts. Our results show that HGT is a key mechanism underlying genetic exchanges and adaptive genomic repair in the mammalian gut.
- Evolution of Escherichia coli strains under competent or compromised adaptive immunityPublication . Ameline, Camille; Seixas, Elsa; Barreto, Hugo C.; Frazão, Nelson; Rodrigues, Miguel V.; Ventura, M. Rita; Lourenço, Marta; Gordo, IsabelEscherichia coli is a commensal of the intestine of most mammals, but also an important human pathogen. Within a healthy human its population structure is highly dynamic, where typically a dominant E. coli strain is accompanied by several low abundance satellite strains. However, the factors underlying E. coli strain dynamics and evolution within hosts are still poorly understood. Here, we colonised germ-free immune-competent (wild-type) or immune-compromised (Rag2KO) mice, with two phylogenetically distinct strains of E. coli, to determine if strain co-existence and within-strain evolution are shaped by the adaptive immune system. Irrespectively of the immune status of the mice one strain reaches a 100-fold larger abundance than the other. However, the abundance of the dominant strain is significantly higher in Rag2KO mice. Strains co-exist for thousands of generations and accumulate beneficial mutations in genes coding for different resource preferences. A higher rate of mutation accumulation in immune-compromised vs. immune-competent mice is observed and adaptative mutations specific to immune-competent mice are identified. Importantly, the presence of the adaptive immune system selects for mutations that increase stress resistance and the dynamics of such evolutionary events associates with the onset of an antibody response.