March 14, 2023
Research Highlight

Surveying Earth’s Diverse Microbial Communities and their Metabolite Profiles

A multi-omics analysis provides the framework for gaining insights into the structure and function of microbial communities across multiple habitats on a planetary scale

An image of the world

An image of the world with various land use.

(Photo by Louis Reed | Unsplash)

The Science                                

Most studies on microbial communities focus on a single ecosystem and do not allow for comparison across multiple habitats. To understand and compare microbes on a planetary scale, this integrative approach included metabolomic and metagenomic data and utilized coordinated protocols and standardized metadata curation.

The Earth Microbiome Project (EMP) was founded in 2010 to characterize global taxonomic and functional diversity and to understand patterns in microbial ecology across biomes and habitats of the planet. As part of the second phase of the EMP, also known as EMP500, this study generated data for 880 environmental samples from 19 major environments.

Microbial communities produce diverse metabolites in different environments. This study found 52,496 unique molecular structures across all samples with 6588 of those being classified as putative, microbially related metabolites. Particular metabolites were found to be significantly enriched in certain environments. Machine learning was used to identify specific metabolites or microbial taxa or microbial functional products (enzymes) that are predictive of certain habitats. Analyses of metabolite-microbe co-occurrence were then combined with differential abundance data to reveal strong patterns of metabolite-microbe turnover across environments.

The Impact

This research provides insight into the microbial taxa and metabolites within diverse habitats across Earth. It provides a framework for leveraging multi-omics data to address important questions in microbial community ecology. By providing standardized laboratory protocols and computational workflows, and making this dataset publicly available, this study will serve as an important resource for continued collaborative investigations.

The meta-analysis identified specific metabolites, microbial taxa, and microbial enzymes as particularly important for distinguishing environments. This suggests that features can be useful for detecting certain environmental states and environmental change, or in predicting the diversity of other features.


This study advances the understanding of microbial community dynamics and functional diversity, providing a standardized workflow and protocols that can be used to assess microbial communities across multiple environments, allowing us to explore diversity at extraordinary scale.

PNNL Contact

Janet Jansson, Pacific Northwest National Laboratory,


Metabolomics analyses at Pacific Northwest National Laboratory (PNNL) were supported by the Laboratory Directed Research and Development program via the Microbiomes in Transition Initiative and performed in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the US Office of Biological and Environmental Research and located at PNNL. PNNL is a multiprogram national laboratory operated by Battelle for the Department of Energy (DOE) under contract DE-AC05-76RLO 1830.

Published: March 14, 2023

Shaffer, J.P., Nothias, LF., Thompson, L.R. et al. Standardized multi-omics of Earth’s microbiomes reveals microbial and metabolite diversity. Nat Microbiol 7, 2128–2150 (2022).