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

Enterococcus faecium is a major human opportunistic bacterial pathogen and a close relative of the recently established species Enterococcus lactis. As a species, commensal E. lactis remains relatively understudied, and its genetic connectivity with E. faecium is not thoroughly understood. Here, we introduce a large collection of whole-genome sequenced isolates comprising 894 E. faecium and 392 E. lactis 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 E. faecium; in particular, there is a radiation of E. faecium clades specialized to domesticated and pet animals among which E. lactis is uncommon. Of note, pangenome analyses reveal that E. lactis has significantly more allelic variation and lower recombination rates in core genes compared with E. faecium. These observations suggest that E. lactis represents a population that has occupied its ecological niche longer than E. faecium 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.