Hello, I submitted some assembled metagenome sequences to IMG (https://img.jgi.doe.gov/) for functional annotation. These are environmental samples that were cultured and enriched for certain groups of bacteria/archaea, and each sample enrichment received one treatment and one control. Each sample went through whole genome shotgun sequencing, and I assembled and QC'd the reads.
I'm trying to see if the microbes in the treatment group have any genes involved in organic acid metabolism (or any pathways related to organic acid metabolism) that differ between the microbes in the control group. Through IMG, I'm able to see a long list of genes and proteins for each sample (and their COG, Pfam, etc categories). I'm not sure how to present this data in a meaningful way other than have a long list of genes that differ between the two, and my manager wants to have this functional annotation in a publication figure at some point. Could someone point me to any resources that might help with this? I'm not sure how to make sense of the data. I found a KEGG category page in IMG that tells me what genes in my sample encode for enzymes involved in butanoate metabolism and propanoate metabolism, but I would like to find genes involved in all types of organic acid metabolism, and I'm not sure if it'd be meaningful to just say "sample #1 has 1 more of a gene that codes for acetyl-CoA synthetase compared to sample #2" since there are so many different genes and proteins between the samples.
