Using long‐term experimental evolution to uncover the patterns and determinants of molecular evolution of an Escherichia coli natural isolate in the streptomycin‐treated mouse gut

Abstract

Though microbial ecology of the gut is now a major focus of interest, little is known about the molecular determinants of microbial adaptation in the gut. Experimental evolution coupled with whole genome sequencing can provide insights of the adaptive process. In vitro experiments have revealed some conserved patterns: intermediate convergence, epistatic interactions between beneficial mutations and mutations in global regulators. To test the relevance of these patterns and to identify the selective pressures acting in vivo, we have performed a long-term adaptation of an E. coli natural isolate, the streptomycin resistant strain 536, in the digestive tract of streptomycin treated mice. After a year of evolution, a clone from 15 replicates was sequenced. Consistently with in vitro observations, the identified mutations revealed a strong pattern of convergence at the mutation, gene, operon and functional levels. Yet, the rate of molecular evolution was lower than in in vitro and no mutations in global regulators were recovered. More specific targets were observed: the dgo operon, involved in the galactonate pathway that improved growth on Dgalactonate, and rluD and gidB, implicated in the maturation of the ribosomes, which mutations improved growth only in the presence of streptomycin. As in vitro, the non-random associations of mutations within the same pathways suggested a role of epistasis in shaping the adaptive landscape. Overall, we show that "evolve and sequence" approach coupled to an analysis of Data accessibilityThe date used to produce the figure 1, 4, 5 and 6 are accessible on the Dryad website : (http://datadryad.org) with the number doi: 10.5061/dryad.4g503 and in the table S1The date used to produce the figures 2 and 3 are presented in the convergence, when applied to a natural isolate, can be used to study adaptation in vivo and uncover the specific selective pressures of that environment.

Long‐term evolution of the natural isolate of Escherichia coli 536 in the mouse gut colonized after maternal transmission reveals convergence in the constitutive expression of the lactose operon

“…Among these, 73 were nonsynonymous including 3 stop mutations, 26 were synonymous, and 9 were intergenic. We observed an imbalance in favour of transitions for synonymous point mutations (19/26) as well as for nonsynonymous mutations (55/70) as previously reported (Lescat et al, ; Wielgoss et al, ) (Table ). Two large deletions (>30 bp) were observed as well as 18 small indels among which 10 lead to frameshifts, 3 were in frame, and 5 were intergenic.…”

“…After the period of breastfeeding, during which the colonization of offspring's gut by E. coli 536 occurred, thirty‐six 3‐week‐old female mice were distributed in 12 independent cages (3 mice per cage) per diet (seventy‐two mice in 24 independent cages in total) and followed during more than one year (Figure ). We considered that a lineage of E. coli 536 evolved in the three mice gut from the same cage as previously tested by Lescat et al ().…”

“…At each time point, for each cage, we sampled a colony isolated from the faeces of the mice with the highest E. coli density. Due to coprophagy, sampling one clone of one randomly selected mouse per cage is representative of the population of E. coli colonizing the three mice within a single cage (Lescat et al, ) (Figure ). These samples were then grown on liquid lysogeny broth (LB) O/N and thereafter called “isolate.” Finally, the 71 isolates obtained were labelled by the lineage (L) numbers from 1 to 24 and a suffix for the sampling day after inoculation (D).…”

“…Later, Barroso‐Batista et al using colonization of streptomycin‐treated mice by E. coli K‐12 MG1655 observed mutations in srlR gene encoding the repressor of the slr operon and several genes in the gat operon (Barroso‐Batista et al, ), whose operons are involved respectively in the metabolism of sorbitol and galactitol. Likewise, Lescat et al performed the colonization of streptomycin‐treated mice using a natural isolate of E. coli and observed convergence of mutation in the dgoRKAD operon responsible for the metabolism of galactonate (Lescat et al, ). These nearly constant observations reveal that (a) metabolism adjustments are highly selected in the gut and that consequently diet should have an impact, (b) these adjustments occur largely by change in the regulatory network, and (c) many of these changes involve gene inactivation that alters the regulatory structure of sugar metabolism.…”

Day-to-Day Dynamics of Commensal Escherichia coli in Zimbabwean Cows Evidence Temporal Fluctuations within a Host-Specific Population Structure

“…S1 in the supplemental material), it has been shown in mice that the establishment of a dominant clone within the gut took a few days (36,37), depending on its capacity to adapt its metabolism to the available carbon sources, which were mainly sugars (36,38). The adaptation of a clone to its environment is driven by a combination of periodic selection and clonal interference, which is the competition of clones carrying different beneficial mutations at the population level (37,39) and convergence and epistatic interactions at the genotype level (39,40). Furthermore, a high level of polymorphism in the ability of the E. coli species to use carbon sources (41, 42) could explain the diversity of the observed clones.…”