Hi,
I’m currently conducting a study on Mycobacterium ulcerans from skin lesions, with both culture and sequencing data. I’ve observed that, even with the latest MetaPhlAn4 database release, M. ulcerans is consistently misclassified as Mycobacterium marinum.
Would it be possible to address this classification issue in an upcoming database update?
Kind regards,
Thorsten
Hi @tthye
Are you referring to SGB15550? If so, the reason why it is reported as marinum is because the SGB is composed of 39 genomes which have average ANI below 95% of which 26 are M. marinum, 7 from M. ulcerans and the rest is other species; as a general rule we take the taxonomy of the most abundant genomes, but the alternative taxonomies are still reported in the profile.
Hi Claudia,
Yes—SGB15550 is exactly what I meant. Thank you for the clarification. Is there a way to adjust MetaPhlAn’s parameters or database settings to boost sensitivity for M. ulcerans so that it’s reported instead of M. marinum?
Best,
Thorsten