Looking at the Full Picture: Utilizing Topic Modeling to Determine Disease-Associated Microbiome Communities.

in health. Therefore, there is a need to develop tools to identify the communities of microbes making up the healthy and disease state microbiome. Here we applied topic modeling, a natural language processing tool, to identify microbial communities associated with relapsing-remitting MS (RRMS). Specifically, we show the advantage of topic modeling in identifying the bacterial community structure of RRMS patients, which includes previously reported bacteria linked to RRMS but also otherwise overlooked bacteria. These results reveal that integrating topic modeling with traditional approaches improves the understanding of the microbiome in RRMS and it could be employed with other diseases that are known to have an altered microbiome.