Recurrent Reverse Evolution Maintains Polymorphism after Strong Bottlenecks in Commensal Gut Bacteria

Abstract

The evolution of new strains within the gut ecosystem is poorly understood. We used a natural but controlled system to follow the emergence of intraspecies diversity of commensal Escherichia coli, during three rounds of adaptation to the mouse gut (∼1,300 generations). We previously showed that, in the first round, a strongly beneficial phenotype (loss-of-function for galactitol consumption; gat-negative) spread to >90% frequency in all colonized mice. Here, we show that this loss-of-function is repeatedly reversed when a gat-negative clone colonizes new mice. The regain of function occurs via compensatory mutation and reversion, the latter leaving no trace of past adaptation. We further show that loss-of-function adaptive mutants reevolve, after colonization with an evolved gat-positive clone. Thus, even under strong bottlenecks a regime of strong-mutation-strong-selection dominates adaptation. Coupling experiments and modeling, we establish that reverse evolution recurrently generates two coexisting phenotypes within the microbiota that can or not consume galactitol (gat-positive and gat-negative, respectively). Although the abundance of the dominant strain, the gat-negative, depends on the microbiota composition, gat-positive abundance is independent of the microbiota composition and can be precisely manipulated by supplementing the diet with galactitol. These results show that a specific diet is able to change the abundance of specific strains. Importantly, we find polymorphism for these phenotypes in indigenous Enterobacteria of mice and man. Our results demonstrate that natural selection can greatly overwhelm genetic drift at structuring the strain diversity of gut commensals and that competition for limiting resources may be a key mechanism for maintaining polymorphism in the gut.

Host-Specific Adaptive Diversification of Crohn’s Disease-Associated Adherent-Invasive Escherichia coli

“…Two additional metabolic repressors were inactivated by IS elements in multiple isolates, including the tryptophan operon repressor and the galactitol utilization repressor, gatR, which controls galactitol consumption. This pathway is under selection in the mouse gut to maintain a polymorphic population of galactitol-positive and galactitol-negative populations (Sousa et al, 2017). In all 12 of the WGS isolates, we found evidence of at least two mutations predicted to affect regulatory proteins, consistent with the importance of regulatory evolution in bacterial pathoadaptation (Osborne et al, 2009).…”

Low Mutational Load Allows for High Mutation Rate Variation in Gut Commensal Bacteria

“…Such adaptive mutations are expected if galactonate and fructoselysine are present in the gut as limiting resources for E. coli . This form of adaptation has been previously shown to occur for the case of galactitol [73].…”

“…Another mechanism for reducing the effects of deleterious mutations is revealed by the nature of the adaptive mutations. As previously observed, adaptation of E. coli to the mouse gut involved mutations linked to carbohydrate metabolism, which were under negative frequency-dependent selection, likely created by niche segregation of the different mutants [35,73]. This segregation may reduce competition between lineages and therefore buffer the effect of deleterious mutations.…”

Directional selection limits ecological diversification and promotes ecological tinkering during the competition for substitutable resources

“…To analyze this process, we note that successful invasion events will occur as an inhomogeneous poisson process with rate λ(t) ∼ N U α f * argmax(Xi) |∆X|, where f * (t) and ∆X(t) are again determined by the diffusion model in Eq. (10). This leads to a characteristic invasion timescale…”

“…In the simplest cases, the population splits into a pair of lineages, or ecotypes, that stably coexist with each other due to frequency-dependent selection, leading to a breakdown of competitive exclusion (5,6,8,9,10). But evolution does not cease after ecological diversification occurs.…”