MetaPhlan4 drastically underestimate the abundance of Bacillus_subtilis|t__SGB7788


I have used MetaPhlan 4.0.6 (database vOct22) to perform taxonomic profiling of the mock “ZymoBIOMICS Microbial Community DNA Standard D6306

I have noticed that the relative abundance of Bacillus subtilis is way below the theorical value mentionned by the manufacturer (0.98% vs 10.31%).

Here is the MetaPhlan4 output file:
MOCK_D6306_a_230121a.metaphlan4.tsv (32.7 KB)
mOTUs provides a estimated abundance much closer to what is expected:
MOCK_D6306_a_230121a.motus.tsv (717 Bytes)

Tell me if you need more information to investigate this.
I can send you the raw sequencing data if necessary.


Hi @fplaza
Please, have a look at the following post: Missing Bacillus species in Metaphlan3 - #5 by Thomas_Sewell

Thanks for the reply.
Would it be possible to merge multiple species (SGBXXXX_group) to accurately quantify the strain present in the Zymo mock community?

Hi @fplaza
It is something we will be working on for the next release!

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