Supplemental data for: Longitudinal, multi-platform metagenomics yields a high-quality genomic catalog and guides an in vitro model for cheese communities

Microbiomes are intricately intertwined with human health, geochemical
cycles, and food production. While many microbiomes of interest are highly
complex and experimentally intractable, cheese rind microbiomes have
proven powerful model systems for the study of microbial interactions. To
provide a more comprehensive view of the genomic potential and temporal
dynamics of cheese rind communities, we combine longitudinal,
multi-platform metagenomics of three ripening washed-rind cheeses with
whole genome sequencing of community isolates. Sequencing-based approaches
revealed a highly reproducible microbial succession in each cheese,
co-existence of closely related Psychrobacter species, and
enabled the prediction of plasmid and phage diversity and their host
associations. Combined with culture-based approaches, we established a
genomic catalog and a paired 16-member in vitro washed
rind cheese system. The combination of multi-platform metagenomic
time-series data and an in vitro model provides a rich
resource for further investigation of cheese rind microbiomes both
computationally and experimentally.