On the road to genomically defining bacterial intra-species units

Over almost three decades, average nucleotide identity (ANI) analysis has been instrumental in operationally defining species in bacteria. However, barely any attention has been paid to soundly defining intra-species units employing ANI analyses until recently. Notably, some very recent publications are good steps forward in that direction. The level of granularity provided by these intra-species units will be relevant to understanding the eco-evolutionary dynamics and transmission of bacterial lineages and mobile genetic elements, antibiotic resistance, and virulence genes. These intra-species units will undoubtedly advance the genomic epidemiology of many bacterial pathogens. In the coming years, we anticipate that many studies will implement ANI-based definitions of different intra-species units, such as strains or sequence types, for many different bacterial species.