*2.1. Sauerkraut Preparation and Sampling Methods*

Sauerkraut for this study was sampled from a single 50 lb batch prepared for commercial sale during June 2017 in a facility located near Providence, Rhode Island. Cabbage was salted to a concentration of 2.25% before the addition of caraway seeds (<1% by weight). Ingredient samples were collected in triplicate during a normal production run; 0.5 g of each ingredient were placed into 1.5 mL Eppendorf tubes containing 500 µL of nuclease-free water. The batch of sauerkraut was sealed into airtight plastic drums for the fermentation period. Fermentation was conducted at approximately 21 ◦C. Successful fermentation was determined by a final pH below 3.6. Fermentation samples were collected in triplicate using Pasteur pipettes from the fermenting sauerkraut at Days 0, 2, 7, 10, and 14. Samples are not true biological replicates, since all triplicates came from the same batch of fermenting sauerkraut; this is a limitation of our study, and future studies should examine the consistency of microbiome dynamics between batches. Packaged, jarred sauerkraut from this producer was purchased from a commercial distributor and processed alongside fermentation samples for microbiome analysis of the finished product.

To sample the production environment, the production table, the industrial sink, and the floor of the production facility were swabbed in triplicate with flocked sterile swabs; these were then stored individually in Zymo Research DNA/RNA Shield Lysis Tubes (Zymo Research, Irvine, CA, USA; Cat: R1103). To sample the air in the facility, empty Petri dishes were left uncovered around the facility throughout the duration of the fermentation period. On Day 14, the Petri dishes were swabbed in the manner described above. After collection, all samples were immediately transported to the laboratory on ice and stored at −80 ◦C until processing.
