No species detected in RNA data

Microbial community profiling MetaPhlAn
1

Hi,

I’m trying to run metaphlan → humann (both version 3) with a mouse microbiome sample. I have RNA and DNA samples, and ran metaphlan (following kneaddata) on both, but only the DNA was able to detect any bacteria (all Unkown). I was wondering if this is likely because the RNA isn’t sequenced deep enough or if this is a typical problem associated with RNA given how metaphlan operates?

Also, since the DNA should have the same bacterial species / present, could the output from the DNA metaphlan run be used as a sort of reference for humann?

Thank you!

2

What do you mean by “DNA samples” and “RNA samples”? Is the DNA experiment whole genome sequencing or exome sequencing? Is the RNA experiment poly-A tail enrichment or total RNA extraction followed by ribosomal depletion? Some protocols are suited to sequencing bacteria but others are not. What tissue or fluid are you analysing?

3

Hi,

These were stool samples from mice.

DNA samples: extracted genomic DNA
RNA samples: total RNA extraction followed by DNA and ribosomal depletion