Mycobacteria taxonomy

Bacterial Taxonomy
1

Hi,

In 2018, Gupta et al proposed the reclassification of the genus Mycobacterium in to 4 new genera and emended Mycobacterium (Phylogenomics and Comparative Genomic Studies Robustly Support Division of the Genus Mycobacterium into an Emended Genus Mycobacterium and Four Novel Genera - PubMed).

This was controversial, to say the least, and the new names have not been universally adopted.

A recent analysis using GTDB data demonstrated that the Gupta taxonomy is incorrect https://(Toward Characterizing Environmental Sources of Non-tuberculous Mycobacteria (NTM) at the Species Level: A Tutorial Review of NTM Phylogeny and Phylogenetic Classification - PubMed).

The GTDB database continues to use the old names - is there a plan to incorporate the new names into the GTDB database? I know this is controversial - I’m interested in the perspectives of the GTDB creators.

Thank you!

Husain

2

Hi Husain,

Thank you for your question.

You are correct that the proposed reclassification by Gupta et al. (2018) has been controversial within the community. In GTDB, we initially adopted the five-genera classification in our earlier releases.

However, based on the phylogenomic evidence and our criteria for taxon circumscriptions (RED, monophyly, high support) and feedback from the community, we reverted this change in GTDB Release 95, i.e. returing to a single genus Mycobacterium. Splitting this genus according to Gupta et al. (2018) results in phylogenetically shallow and not well-supported groups in our trees.

Thanks for sharing the recent review and it aligns with the concerns that led to our decision to revert to the unified Mycobacterium. GTDB aims to provide a stable and phylogenetically robust taxonomy, and in cases where proposed classifications remain controversial or lack strong phylogenomic support, we prioritize taxonomic stability.

Hope this helps,

Best wishes,
Masha

3

Hi Masha,

Thanks for your quick response!

I should have read my message before posting - the GTDB taxonomy of Mycobacteria was correct (not incorrect) in the review I shared. Indeed there are three subsequent papers (since 2018) that show very similar taxonomy to what Gupta et al published.

What is the best way for me to calculate the RED and review previous versions and the supporting information around the taxonomy? Are some community feedback available for review?

Regards,

Husain