Nutrient Availability and Pathogen Clearance Impact Microbiome Composition in a Gnotobiotic Kimchi Model

We conducted a controlled study using gnotobiotic Napa cabbage media inoculated with E. coli and B. cereus, alongside a kimchi starter culture, under varying nutrient conditions. Bacterial growth was assessed in three media types: pure cabbage media, cabbage media supplemented with tryptic soy broth, and cabbage media buffered with Tris HCl. Colony-forming units were measured via serial dilution plating at multiple time points to track E. coli and B. cereus survival. Additionally, microbial composition was analyzed using long-read 16S amplicon sequencing V4 to V9 regions on an Oxford Nanopore Technologies MinION sequencer.