Inference of association with the gut microbiota in stool, swab and mucosal tissue samples

In this study, we collected matched stool, rectal swab and mucosal tissue samples from 240 study participants at two time points, which resulted in 1,397 shotgun metagenomes. We estimated the biospecimen type variation of both metagenome taxonomy and functional pathways. We also assessed whether the associations between taxa/pathways and age, sex, body mass index (BMI), non-steroidal anti-inflammatory drugs (NSAIDs) use and antibiotics use were consistent across the different sample types.