Hi, we did shotgun metagenomics sequencing on mouse fecal samples and 2 mock community control samples which are a mixture of 20 known strains. We did quality control using Kneaddata v0.10.0 and we have over ~85% of reads retained after qc for each sample (we did trimming and decontamination to remove mouse host sequences).
Then we did taxonomy profiling using MetaPhlAn version 3.0.14 (19 Jan 2022).
The –unknown_estimation option was added when running Metaphlan to check the percentage of reads classified; however, all the mouse fecal samples had over 80% of unknown reads and the known reads were 100% classified to bacteria. The mock community control samples had only 2% of unknown reads.
I wonder is this normal for profiling mouse gut metagenome using Metaphlan? We sequenced quite deep for these samples and we were surprised to see that the majority of reads were unclassified.
Thank you so much for your help!