High proportion of unclassified taxa contributing to pathways and genes

Microbial community profiling HUMAnN
1

I am using humann 3.7 to analyze metatranscriptomes and in doing so I have noticed that the biggest contributors to each pathway from the taxonomy is “unclassified”. This is also true for individual genes. Is this common? Is there a way to “expand” the taxonomies included?

My samples are all from the mouse gut so they should be relatively well known. It looks like I get ~22 species contributing to pathways in total across the dataset.

Here is the commands that I am using:
for f in input_RNA/*fastq.gz;do humann --input $f --output humann_out_RNA --threads 20 --nucleotide-database /scratch/mirror/humann/3.7/chocophlan; done

humann_join_tables -i humann_out_RNA -o humann_pathabundance_RNA.tsv --file_name pathabundance

Anything that I should/could add?

Thanks!