January 25, 2023
Journal Article

Standardized Multi-omics of Earth’s Microbiomes reveals microbial and metabolite diversity


As our understanding of the structure and diversity of the microbial world grows, interpreting its function is of critical interest for understanding and managing the many systems microbes influence. Despite advances in sequencing, lack of standardization challenges comparisons among studies that could provide insight into the structure and function of microbial communities across multiple habitats on a planetary scale. Technical variation among distinct studies without proper standardization of approaches prevents robust meta-analysis. Here, we present a multi-omics, meta-analysis of a novel, diverse set of microbial community samples collected for the Earth Microbiome Project. We include amplicon (16S, 18S, ITS) and shotgun metagenomic sequence data, and untargeted metabolomics data (tandem liquid chromatography mass spectrometry and gas chromatography mass spectrometry (LC-MS/MS, GC-MS)), centering our description on relationships and co-occurrences of microbially-related metabolites and microbial taxa across environments. Standardized protocols and analytical methods for characterizing microbial communities, including assessment of molecular diversity using untargeted metabolomics, facilitate identification of shared microbial and metabolite features, permitting us to explore diversity at an extraordinary scale. In addition to a reference database for metagenomic and metabolomic data, we provide a framework for incorporating additional studies, enabling the expansion of existing knowledge in the form of a community resource that will become more valuable with time. To provide examples of applying this database, we outline important ecological questions that can be addressed, and test the hypotheses that every microbe and metabolite is everywhere, but the environment selects. Our results show that metabolite diversity exhibits turnover and nestedness related to both microbial communities and the environment. The relative abundances of microbially-related metabolites vary and co-occur with specific microbial consortia in a habitat-specific manner, and highlight the power of certain chemistry – in particular terpenoids – in distinguishing Earth’s environments.

Published: January 25, 2023


Shaffer J.P., L. Nothias, L.R. Thompson, J.G. Sanders, R.A. Salido, S.P. Couvillion, and A. Brejnrod, et al. 2022. Standardized Multi-omics of Earth’s Microbiomes reveals microbial and metabolite diversity. Nature Microbiology 7, no. 12:2128–2150. PNNL-SA-174662. doi:10.1038/s41564-022-01266-x

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