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Mycobacteria taxonomy and names
This is a brief explanation of the mycobacteria taxonomy
names reported by mykrobe when using the species tb.
There is no consensus as to the naming of mycobacteria genera and species.
In 2018 the taxonomy was emended [1], splitting the genus Mycobacterium into five separate genera. This is now the taxonomy used by the NCBI. It has been debated in the literature, see for example [2], [3], making the case for using the previous names instead of the emended ones.
Unfortunately, species names and tree topologies mean that there is no one-to-one correspondence between the "old" (pre-2018) and "new" names. This is a problem for mykrobe when calling species, since it cannot consistently call both taxonomies at the same time.
We use GTDB [4] to make the latest (panel 202309) species probes. GTDB uses "old" names, and has one or more genomes per species. Each of those genomes has a corresponding "new" taxon name. Usually these are the same, but not always. For example, GTDB had (at the time of writing) four Mycobacterium algericum genomes. Two of those have the "new" name Mycolicibacter algericus, and the other two had names Mycolicibacter sinensis and Mycobacterium novum.
Mykrobe panels pre-2023 (walker-2015, bradley-2015, 202001, 202010, 202206) all used the "old" names and taxonomy. Their species probes were made before 2018.
In September 2023, the mykrobe species probes were updated. The updated panel is called 202309. It uses GTDB as the primary source of metadata, genomes, genus/species names and taxonomy. The default names reported by mykrobe are those used by GTDB (and are essentially the "old" names).
You can also ask mykrobe to report the "new"/NCBI names.
However, since there is no direct lookup between old and
new names, the best we can do is given a species name,
report its matching NCBI names. Returning to the
example above using Mycobacterium algericum: if mykrobe
reports this species, then using the flag --ncbi_names
will result in this entry in the output:
"ncbi_names": {
"Mycolicibacter_sinensis": 1,
"Mycolicibacter_algericus": 2,
"Mycobacterium_novum": 1
}
[1] Gupta et al, Phylogenomics and comparative genomic studies robustly support division of the genus Mycobacterium into an emended genus Mycobacterium and four novel genera, Front Microbiol 2018, 9: 67, https://doi.org/10.3389/fmicb.2018.00067
[2] Tortoli et al, Same meat, different gravy: ignore the new names of mycobacteria, European Respiratory Journal 2019 54: 1900795; https://doi.org/10.1183/13993003.00795-2019
[3] Meehan et al, Reconstituting the genus Mycobacterium, Int J Syst Evol Microbiol., 2021; 71(9): 004922, https://doi.org/10.1099%2Fijsem.0.004922
[4] Parks et al, GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy, Nucleic Acids Research, Volume 50, Issue D1, 7 January 2022, Pages D785–D794, https://doi.org/10.1093/nar/gkab776