Species constitute the fundamental units of taxonomy and an ideal species definition would embody groups of genetically cohesive organisms reflecting their shared history, traits, and ecology. In contrast to animals and plants, where genetic cohesion can essentially be characterized by sexual compatibility and population structure, building a biologically relevant species definition remains a challenging endeavor in prokaryotes. Indeed, the structure, ecology, and dynamics of microbial populations are still largely enigmatic, and many aspects of prokaryotic genomics deviate from sexual organisms. In this chapter, I present the main concepts and operational definitions commonly used to designate microbial species. I further emphasize how these different concepts accommodate the idiosyncrasies of prokaryotic genomics, in particular, the existence of a core- and a pangenome. Although prokaryote genomics is undoubtedly different from animals and plants, there is growing evidence that gene flow—similar to sexual reproduction—plays a significant role in shaping the genomic cohesiveness of microbial populations, suggesting that, to some extent, a species definition based on the Biological Species Concept is applicable to prokaryotes. Building a satisfying species definition remains to be accomplished, but the integration of genomic data, ecology, and bioinformatics tools has expanded our comprehension of prokaryotic populations and their dynamics.
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