Organism

Peptostreptococcus describes a genus of commensal bacteria found in the human microbiome. Morphologically, they are anaerobic gram-positive cocci. Infections associated with these organisms are generally through to be opportunistic (wiki). While this group of organisms is numerically prevalent in the human microbiome, the diversity of organisms within this genus is not well described.

Map

A collection of 41 reference genomes were downloaded from the NCBI Genome database on December 17, 2021 as part of a general survey of bacteria with importance to human health.

Notes

Compared to many of the other maps in the collection, there are relatively fewer genomes available in NCBI which are annotated as Peptostreptococcus. Many of the genomes which are deposited with that label have been given relatively uninformative designations, such as “uncultured Peptostreptococcus species.”

My interest in showing this map was to demonstrate how pangenome maps can be used to understand the identity and relatedness of groups of organisms. In the map above we can clearly see a handful of groups of genomes which contain distinct groups of genes. By keeping an eye on where the named species fall within these clades we can make an informed guess as to the identity of the unnamed strains.

For example, the top-most clade contains a number of isolates named P. anaerobius, and all of the isolates with that name can be found within this clade. Based on that observation it would be reasonable to propose that the additional unnamed strains in this collection (e.g. MGYG-HGUT-00296) is a bona fide member of that species, even though is was not initially identified with this name.

As we continue to explore the biological complexity of the microbial world, it is my hope that pangenome analyses like this one will make it easier to classify and organize our collections of microbial genomes.