By running the “StrainPhlAn --print_clades_only” command, our target strains (s_Prevotella_bivia and s_Prevotella_oris ) only exist in 50% of our samples. The labeled samples were oral swab, and the fecal samples was not labeled. However, these strains are abundant in the macrogenomic species annotation provided by the company. Is this problem related to the depth of macrogenome sequencing of each sample? Our sequencing depth is 6 G per sample. What is the sequencing depth you usually choose for StrainPhlAn analysis?
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Thanks for getting in touch and sorry for the late reply, I just came back from the summer holidays. Both P. bivia and P. oris are not tipical members of the fecal microbiome, and when present in the gut, there are usually low abundant. While StrainPhlAn is not able to find them in your stool samples, it does not mean that they are not there (for this, you need to check the MetaPhlAn results). StrainPhlAn needs a depth of coverage of the target species ~1x to be able to reconstruct the marker genes and this is not always possible with low abundant taxa even at really high sequencing depth.