Danny is working with two mouse models: standard SPF mice as well as those harboring a complex wild “WildR” community. This model was described here: https://www.cell.com/fulltext/S0092-8674(17)31065-6. They have data demonstrating there are behavioral differences between mice colonized with SPF vs WildR microbiota, particularly relating to social behaviors. He is investigating the underlying mechanisms responsible, with a focus on the small molecule metabolites derived from the gut microbiome.
To that end, his goal is to integrate the metagenomics data generated here with a paired untargeted metabolomics dataset he already has, and predict relationships between specific microbial taxa/pathways/genes and metabolite features using mmvec. Let me know if we should discuss the format of this further or perhaps this is very standard for you.
The main comparison is between SPF and WildR animals (subcohort column) of both sexes.
Scripts are available both on OneDrive and this GitHub repository. Data, both input and results, are available exclusively on OneDrive