In the same study, fungi OTUs are analyzed by species, bacteria OTUs by genus. This is what the data looks like, and we can not re-analysis it. Does that make scientific sense and common in microbiome study? Are there pitfalls we should be aware of when analyzing them？ Thank for your help!
Hi Wang,
Given your question I am going to make some assumptions.
1. These are marker gene amplification rather than shotgun sequencing based.
2. The maker genes were likely a (or a couple) 16s rRNA variable regions while the fungal identifications were made based on sequencing of the ITS region,
If I am wrong on these don't bother reading the rest. It is not unusual to have bacteria differentiated only to the genus level when using 16S rRNA variable regions. It does not mutate as quickly as the ITS region usually targeted in fungal studies and species level discrimination is not possible for many genera so the bacterial 16s rRNA sequences are often interpreted at the genus rat er than species level in many gene since the ITS region mutates faster and can more reliably discriminate down to the species level.
I hope this was helpful,
Frank
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