Analysis of Bacterial Communities Present on Fermented Foods: From Raw Sample to Analyzed Multi-Omics Data in Less than 48 Hours

In this pilot study, seven individuals contributed samples of their fermented foods and the surfaces coming into contact with those foods (i.e. fermentors, countertops, cutting boards, etc.). The same individuals also contributed samples collected from their own bodies, which are part of the American Gut Project (Qiita Study ID 10317). The purpose of this study was two-fold: first, we sought to identify and characterize the bacterial diversity associated fermented foods and how this diversity affects the microbiomes of the people in contact with those foods; second, this study was used as a platform for rapid response sample processing and analysis. Metabolomics analyses via mass spec were also performed on all samples.