Enterococcus lactis is ecologically and genetically distinct from the major opportunistic pathogen Enterococcus faecium

<i>Enterococcus faecium</i> is a major human opportunistic bacterial pathogen and a close relative of the recently established species <i>Enterococcus lactis</i>. As a species, commensal <i>E. lactis</i> remains relatively understudied, and its genetic connectivity with <i>E. faecium</i> is not thoroughly understood. Here, we introduce a large collection of whole-genome sequenced isolates comprising 894 <i>E. faecium</i> and 392 <i>E. lactis</i> genomes. Using these genomes to complement publicly available data, we studied the genome content and the evolutionary relationship between these species. A wider range of host species was observed in <i>E. faecium</i>; in particular, there is a radiation of <i>E. faecium</i> clades specialized to domesticated and pet animals among which <i>E. lactis</i> is uncommon. Of note, pangenome analyses reveal that <i>E. lactis</i> has significantly more allelic variation and lower recombination rates in core genes compared with <i>E. faecium</i>. These observations suggest that <i>E. lactis</i> represents a population that has occupied its ecological niche longer than <i>E. faecium</i> has. This study enhances understanding of the evolutionary histories of these species and highlights the importance of sampling and studying closely related commensal bacteria in addition to clinically relevant opportunistic pathogens.