Almost all microbes unmapped or unintegrated - Rat Stool Samples

I am currently using Humann v3.8 to do some functional profiling on stool samples from rats. When I run humann on my samples using uniref90 I get around 50% unmapped and 50% unintegrated. When I rerun the samples with uniref50 I get around 30% unmapped and 70% unintegrated. I understand that not all bugs will get mapped or integrated but this feels very high to me. If you have any suggestions on how to get more to map/integrate it would be greatly appreciated. I will list some more details below:

-Python 3.7
-Quality control was performed at sequencing core
-Using Chocophlan v2019_v31

Thanks for any suggestions!

30% unmapped on UniRef50 is actually a very good rate! That is comparable to what we see for UniRef90 in the human gut. The unintegrated rate is a reflection of how well annotated these proteins are at the pathway level. This value tends to be high (even for the human gut) since most proteins are NOT annotated to a metabolic reaction, and therefore can’t be integrated into pathways.

This is very good news to hear. I will continue onward with the analysis then using the uniref50 results. Thank you for your answer and for all the hard work your lab does to enable high quality microbiome work!

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