Organism

Akkermansia muciniphila is a Gram negative, anaerobic, oval-shaped, mucin-degrading bacterium found in the human gut which has been studied in relation to a number of different important diseases (wiki). The probiotic industry has generated considerable interest in this organism, and academic research groups have identified a number of biological mechanisms by which it may influence human health.

Map

A collection of 246 reference genomes were downloaded from the NCBI Genome database on January 13, 2022 as part of a general survey of bacteria with importance to human health.

Notes

The genomes of A. muciniphila currently available in NCBI appear to fall into three distinct clades, each of which contains a considerable amount of unique genomic content. Based on the presence of a large number of genes which are shared across all three clades, I would personally characterize these groups as subspecies (rather than proposing that there are three distinct species). The image below shows the core genome along with each of the clade-specific regions.

In addition to these clade-specific genetic elements, we can also see a group of genetic elements which are each distributed across a smattering of isolates from all three clades. These are most likely horizontally-transferred elements which are able to move between lineages.

This map was interesting to me because it emphasizes how little we know about the organisms that are thought to influence human health. It’s possible that all three of these clades have an identical effect on host physiology, but I would be surprised if researchers didn’t end up uncovering important differences one day.