MetaPhlAn4 overestimates the abundance of Veillonella rogosae

Hi MetaPhlAn developers,

I am using MetaPhlan v. 4.0.6 (mpa_vOct22_CHOCOPhlAnSGB_202212 database) to perform taxonomic profiling of the mock community “ZymoBIOMICS Gut Microbiome Standard D6331”

The relative abundance I obtain for Veillonella rogosae is much higher than expected, 34% vs. 14%, and I am wondering what the issue can be.

I have provided the MetaPhlan4 output file:

Zymo_D6331.metaphlan4.txt (18.6 KB)

Let me know if you need further information and thank you for hopefully looking into this.

Best regards.

Hi @sarmol
This is a tricky scenario to assess. The difference with the expected relative abundance can be due to so many factors, even just the DNA extraction protocol. Are similar results reported with other profilers? Did you try other metaphlan versions?