Evolution of a Dominant Natural Isolate of Escherichia coli in the Human Gut over the Course of a Year Suggests a Neutral Evolution with Reduced Effective Population Size

Abstract

and evolution experiments on revealed several principles of bacterial adaptation. However, few data are available in the literature describing the behavior of in its natural environment. We attempted here to study the evolution in the human gut of a commensal dominant clone ED1a belonging to B2 phylogroup, through a longitudinal genomic study. We sequenced 24 isolates sampled at three different time points within a healthy individual over almost a year. We computed amutation rate of 6.90x10 per base per year of the chromosome for ED1a in healthy human gut. We observed a very limited genomic diversity, and could not detect any evidence of selection contrary to what is observed in experimental evolution over similar length of time. We therefore suggest that ED1a being well adapted to the healthy human gut evolves mostly neutrally with a low effective population size (N ≈ 500 - 1700). In this study we follow the genomic fate of a dominant clone of in the human gut of a healthy individual over about a year. We could compute a low annual mutation rate that supports a low diversity and we could not retrieve any clear signature of selection. These observations support a neutral evolution of in the human gut, compatible with a very limited effective population size that deviates drastically with the observations made previously in experimental evolution.

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

“…The neutral mutation rate we estimated was about 5 × 10 −7 mutations per base per year with no statistically significant difference between the two applied diets. This rate is in the range of the ones estimated previously (a) in Richard Lenski's long-term evolution experiment (~2 × 10 −7 ) (Wielgoss et al, 2013) and (b) the mutation rate of a strain evolving in a household (Reeves et al, 2011) or the mutation rate of a dominant strain evolving in human gut (6.9 × 10 -7 ) (Ghalayini et al, 2018) or the synonymous mutation rate of the same strain evolving in the streptomycin-treated mice gut (6.4 × 10 −7 , 95% CI: 5.0 × 10 −7 -7.3 × 10 −7 estimated assuming the same mutational biases as the one observed here; Lescat et al, 2017).…”

“…We also removed mutations when they were too close from one another, by discarding variations that were <51 bp apart. These clustered mutations are indeed usually caused by reads erroneously mapped, and previous analyses showed that they are typically found in proghagic regions (Ghalayini et al, 2018). Those mobile regions are repeated in the genome but do not have 100% identity generating trouble in the mapping process, as they are still close enough from one another to be erroneously mapped.…”

“…Basically, the expected number of nonsynonymous of type i was computed as n iexpected = N i s i /S i . K a /K s was then defined as the ratio of observed to expected mutations: (Ghalayini et al, 2018;Lescat et al, 2017).…”

“…To identify the molecular bases involved in E. coli adaptation, experimental evolutions in controlled conditions coupled with wholegenome sequencing have been very successful (Barroso-Batista et al, 2014;Ghalayini et al, 2018;Lescat et al, 2017;Tenaillon et al, 2016). Over the last years, numerous in vitro experiments allowed us to decipher the main rules of bacterial adaptation.…”

Evolutionary dynamics of bacteria in the gut microbiome within and across hosts

“…Fortunately, two concurrent studies have also documented short-term evolution of gut bacteria within healthy human hosts using an isolate-based approach [86,87]. Each study focused on a single bacterial species, E. coli in Ref.…”