*2.2. DNA Extraction, 16S Library Preparation, and Sequencing*

The sauerkraut, environmental, and ingredient samples were processed using the ZymoBIOMICS DNA Microprep Kit (Zymo Research, Irvine, CA, USA; Cat: D4305) according to the manufacturer's instructions in order to extract DNA. Using the Earth Microbiome Project 16S Illumina Amplicon Protocol, we targeted the V4 hypervariable region of the bacterial 16S rRNA gene using an 806Rb reverse primer (GGACTACCAGGGTATCTAATCC) and a barcoded 515F forward primer (CAGCAGCCGCGGTAAT) [15–19]. PCR amplicons were generated using Phusion High-Fidelity polymerase (New England BioLabs, Ipswich, MA, USA) under the following conditions: 98 ◦C for 3 minutes, followed by 35 cycles of 98 ◦C for 45 s, 50 ◦C for 60 s, and 72 ◦C for 90 s, and ending with a final elongation at 72 ◦C for 10 minutes.

PCR amplicon concentrations were analyzed using the Qubit 3.0 Fluorometer and the dsDNA-HS kit (Thermo Fisher Scientific, Waltham, MA, USA) according to the manufacturer's instructions. Equal amounts of amplicons from each sample were pooled, concentrated, and gel purified using the Machery-Nagel NucleoSpin Gel and PCR Clean-Up kit (Machery-Nagel, Düren, Germany, Cat: 740609) according to the manufacturer's instructions. The pooled samples were submitted to the Rhode Island Genomics and Sequencing Center at the University of Rhode Island (Kingston, RI, USA) for quality control and sequencing. Amplicons were paired-end sequenced (2 × 250 bp) on an Illumina MiSeq platform using a 500-cycle kit with standard protocols.
