I have been using SILVA v138 for assigning taxonomy to mouse gut microbiota. I was wondering if there is reference database specific for mouse gut microbiota?
It looks there are a couple of papers about references databases specifically for mouse gut microbiota. Exposing new taxonomic variation with inflammation — a murine model-specific genome database for gut microbiome researchers | Microbiome | Full Text
and https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6920994/. However, none of these are implemented in QIIME2 currently.
To give a little unsolicited advice, I try to avoid using databases that are created for only one specific environment because they can be overly bias towards that environment, and may stop you from finding unique/rare/unexpected microbes in your samples. I like to use a combination approach! I like using a broad classifier(gg, SILVA, etc) and then use taxonomic weights to help the classifier identify what might be more reasonable for the given environment. For example, if the classifier thinks that two taxonomic annotations are equally likely. It will chose the taxonomic annotation that is more likely to appear in your environment based on your taxonomic weights. This is possible using q2-Clawback! Here is the tutorial for clawback: Using q2-clawback to assemble taxonomic weights
Hope that helps!