Abstract:
Recent genomic analyses have revealed that microbial communities are predominantly
composed of persistent, sequence-discrete species and intraspecies
units (genomovars), but themechanisms that create andmaintain these
units remain unclear. By analyzing closely-related isolate genomes from the
same or related samples and identifying recent recombination events using a
novel bioinformaticsmethodology,we showthat high ecological cohesiveness
coupled to frequent-enough and unbiased (i.e., not selection-driven) horizontal
gene flow, mediated by homologous recombination, often underlie
these diversity patterns. Ecological cohesiveness was inferred based on greater
similarity in temporal abundance patterns of genomes of the same vs. different
units, and recombination was shown to affect all sizable segments of the
genome (i.e., be genome-wide) and have two times or greater impact on
sequence evolution than point mutations. These results were observed in both
Salinibacter ruber, an environmental halophilic organism, and Escherichia coli,
themodel gut-associated organism and an opportunistic pathogen, indicating
that they may be more broadly applicable to the microbial world. Therefore,
our results represent a departure compared to previous models of microbial
speciation that invoke either ecology or recombination, but not necessarily
their synergistic effect, and answer an important question for microbiology:
what a species and a subspecies are.
Description:
CODE AVAILABILITY : Our main analysis workflow is available at: https://github.com/
rotheconrad/F100_Prok_Recombination. (https://doi.org/10.5281/
zenodo.13922077) and https://github.com/rotheconrad/Population-
Genome-Simulator (https://doi.org/10.5281/zenodo.13922083); and
for Supplementary analysis/figures, https://github.com/catbrink/
Explaining-ANI-gaps-Code-for-supplementary-figures.git.
DATA AVAILABILITY : Accession codes for the genomic sequence datasets analyzed in this study are provided in Supplementary Data 1. Other data are available in the main text or the Supplementary Information document.