Whole species groups like Lactobacillus casei group not present in MetaPhlAn 3
I have tried to use MetaPhlAn with samples that have Bacillus subtilis and Lactobacillus casei but in the profile tables they are not present.
I have found this paper where they say that “multiple species included by the NCBI taxonomy into a ‘species-group’ are identified with unique markers for the whole species groups such as Lactobacillus casei group, Bacillus subtilis group…”
But when I run metaphlan with the database mpa_v30_CHOCOPhlAn_201901 this species groups arent shown and my relative abundances are computed with out this species…
How can I get a profile table with the relative abundances of these species groups?