fig1

Figure 1. Phylogenetic analysis of Akkermansia genomes and evidence of speciation among seven major phylogroups. (A) ANI based on whole-genome comparisons, as calculated using pyANI in Anvi’o. The heatmap displays levels of ANI similarity between pairwise comparisons and grouping is set at a 95% similarity threshold. Red denotes a pairwise ANI of 95% or above. Major phylogroups are highlighted and labeled to maintain consistency with previous publications^[19-22]. Note the presence of the new AmV and AmVI phylogroups; (B) Comparison of average ANI between Akkermansia phylogroups. Differences in average ANI below 95% were used to denote new species among phylogroups and an average ANI between 95% and 98% was defined to assign new sub-phylogroups within those new species (dotted lines on each subplot); (C) Phylogenetic analysis of core Akkermansia proteins. The predicted amino acid sequences encoded by single-copy Akkermansia genes were aligned and concatenated using anvi-get-sequences-for-gene-clusters. anvi-gen-phylogenomic-tree was used to generate a phylogenomic tree with FastTree. A. glycaniphila was used as an outgroup, and individual strains are highlighted by the proposed species and subspecies. Numbers denote main branch lengths; (D) Comparison of average (red line) genome sizes of high-quality complete genomes of representative members of Akkermansia phylogroups; (E) Phylogenetic grouping of full-length 16S rRNA Akkermansia sequences is consistent with genomic ANI comparisons. Full-length 16S rRNA gene sequences were extracted from genome sequences within Anvi’o. Clustal Omega was used to perform the alignment of those sequences, and the resulting phylogenetic tree was used for visualization. A. glycaniphila was used as an outgroup, and individual strains have been highlighted by phylogroup. ANI: Average nucleotide identity.