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

Citation

Saak, Christina C. et al. (2022), Supplemental data for: Longitudinal, multi-platform metagenomics yields a high-quality genomic catalog and guides an in vitro model for cheese communities, Dryad, Dataset, https://doi.org/10.5061/dryad.bg79cnpd8

Abstract

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. 

Methods

A detailed methods description can be found in the corresponding manuscript "Longitudinal, multi-platform metagenomics yields a high-quality genomic catalog and guides an in vitro model for cheese communities".

Funding

National Institutes of Health, Award: DP2 AT010401

David and Lucile Packard Foundation, Award: 2016-65131

Pew Charitable Trusts, Award: Pew Scholar in Biomedical Sciences

Graduate Women in Science, Award: Nell Mondy Fellowship

Graduate Women in Science, Award: Elizabeth Weisburger Fellowship