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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.
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