MetaPhlan4 drastically underestimate the abundance of Bacillus_subtilis|t__SGB7788

Microbial community profiling MetaPhlAn
1

Hello,

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.

Best,
Florian

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2

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

3

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?

4

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

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5

Hello!
I am just following up on this topic. I have just used the latest release of Metaphlan 4.1.1. and this issue of not being able to detected Bacillus subtilis from the Zymo mock community is still present. Is this still something you are hoping to address?

Thanks!

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6

Any update on this? Please check my related post

7

Hi,
in the latest database release (vJan25) we see an improvement in detection of Bacillus subtilis subsp. spizizenii under SGB7791_group in the ZymoBIOMICS Microbial Community Standard, which is around 9-10% now in the community (depending on different sequencing depth we had).

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