Collection and taxonomic annotation of Akkermansia sp. genomes

The Akkermansia genomic sequences used in this work were retrieved from four sources: (i) newly sequenced Akkermansia genomes from cultivated strains [43], (ii) publicly available isolated genomes from NCBI (downloaded as of March 2020) that were labeled as Akkermansia muciniphila or Akkermansia sp., (iii) metagenome-assembled genomes (MAGs) coming from a collection of metagenomes from human microbiome by Pasolli et al. [3], and (iv) 166,518 additional MAGs reconstructed from 9172 metagenomes (Additional file 1: Table S4) obtained with a validated assembly-based pipeline similarly to Pasolli et al. [3].

For the 166,518 additional MAGs reconstructed specifically for this work, the metagenomes were assembled using metaSPAdes [73] if paired-end metagenomes were available, and MEGAHIT [74] otherwise. In both cases, default parameters were used. Contigs longer than 1500 nucleotides were binned into MAGs using MetaBAT2 [75]. We assigned MAGs to previously defined species-level genome bins (SGB) (Pasolli et al. [3]) based on whole-genome nucleotide similarity estimation using Mash [76] and only MAGs falling in the SGBs belonging to the Akkermansiaceae family were further considered. We then quality controlled the MAGs and genomes using checkM (version 1.1.3) [42] and kept genomes estimated to be high-quality according to genomic completeness >90% and genomic contamination <5%.

The above procedure resulted in a total of 2420 Akkermansia genomes being considered in this work (http://segatalab.cibio.unitn.it/data/Akkermansia_Karcher_et_al.html): 188 isolate genomes from NCBI (119 labeled as Akkermansia muciniphila and 69 labeled as Akkermansia sp.), 2226 MAGs, and 6 novel genomes coming from strains isolated from the human gut. The 2420 genomes were assigned to a total of five candidate species which includes the already recognized Akkermansia muciniphila species and four additional SGBs: SGB9223, SGB9224, SGB9227, and SGB9228 as summarized in Table ​Table11.

Summary of the number of genomes per candidate species