The genus Akkermansia is populated by a multitude of biological species with a wide distribution in the animal kingdom.

Background: The mucin-degrading bacterium Akkermansia muciniphila has attracted enormous interest for its beneficial effects on human health. However, growing evidence suggests that the Akkermansia genus is populated by several species that differ in phenotypic characteristics and association with human traits.

Results: We present the most comprehensive phylotaxonomic analysis of Akkermansia genomes in terms of sample size and host representation. By applying approaches based on average nucleotide identities and on the biological species concept, we show that the Akkermansia genus comprises at least 31 species, 13 of which can be detected in humans. The largest species diversity is contributed by non-human and non-mouse animals, and limited evidence of species-specificity is evident, with several Akkermansia species detected in phylogenetically distant animals. Analysis of accessory gene content among species also failed to reveal species-specific or diet-specific associations, but rather reflected genome size. Thus, A. muciniphila and A. ignis have, on average, small genomes and retain a part of genes that characterize either A. massiliensis or A. sp004167605/A. biwaensis. Finally, investigation of the population structure of A. muciniphila, the species that has been more intensely investigated due to its effects on human health, clearly distinguished two phylogroups corresponding to AmIa and AmIb. However, analysis of laboratory mouse-derived genomes revealed that additional populations, specific to these animals, exist. Such populations show limited evidence of admixture, suggesting bottleneck or competition effects.

Conclusions: Our data support the concept that the genetic diversity of Akkermansia should be taken into account in experimental settings. They also call for sequencing efforts to characterize the wider genetic diversity of Akkermansia bacteria.