The Earth Microbiome Project is a systematic attempt to characterize global microbial taxonomic and functional diversity for the benefit of the planet and humankind.

The Earth Microbiome Project (EMP) is a massively collaborative effort to characterize microbial life on this planet. We use DNA sequencing and mass spectrometry of crowd-sourced samples to understand patterns in microbial ecology across the biomes and habitats of our planet. The EMP is a comprehensive example of open science, leveraging a collaborative network of 500+ investigators, supporting pre-publication data sharing, and crowdsourcing data analysis to enable universal principles to be explored. The standardized collection, curation, and analysis are enabling a robust interpretation of ecological trends.

The Vision: Constructing the Microbial Map for Planet Earth

The EMP was founded in 2010 as a massive crowd-sourced effort to analyze microbial communities across the globe. The general premise was to examine microbial communities from their own perspective. Hence we proposed to characterize the Earth by environmental parameter space into different biomes and then explore these using samples drawn from researchers across the globe. We set out to analyze 200,000 samples from these communities using amplicon sequencing, metagenomics, and metabolomics to produce a global Gene Atlas describing protein space, environmental metabolic models for each biome, approximately 500,000 reconstructed microbial genomes, a global metabolic model, and a data-analysis portal for visualization of processed information.

Data and Code

To explore and download the EMP datasets, please go to qiita.microbio.me/emp (individual studies) or ftp.microbio.me/emp (combined studies). Code is available at github.com/biocore/emp.

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Citing the EMP

If you are publishing data generated by the EMP, please feel free to include any members of the EMP team who have made a significant contribution to the work as co-authors, although this is not a requirement. The only requirements are these:

  1. Add the following text to the methods and acknowledgements: “Sample processing, sequencing, and core amplicon data analysis were performed by the Earth Microbiome Project (www.earthmicrobiome.org), and all amplicon sequence data and metadata have been made public through the EMP data portal (qiita.microbio.me/emp).”
  2. The current official citation for the EMP is the 2017 meta-analysis; please cite this paper when referencing the EMP in your article:
    • Thompson, L. R., Sanders, J. G., McDonald, D., Amir, A., …, Jansson, J. K., Gilbert, J. A., Knight, R., & The Earth Microbiome Project Consortium. (2017). A communal catalogue reveals Earth’s multiscale microbial diversity. Nature. doi:10.1038/nature24621.
  3. Additionally, you may cite the 2014 project update and the 2010 meeting report from the project’s founding:
    • Gilbert, J. A., Jansson, J. K., & Knight, R. (2014). The Earth Microbiome Project: successes and aspirations. BMC Biology, 12(1). doi:10.1186/s12915-014-0069-1.
    • Gilbert, J. A., Meyer, F., Antonopoulos, D., Balaji, P., Brown, C. T., Brown, C. T., …, Stevens, R. (2010). Meeting Report: The Terabase Metagenomics Workshop and the Vision of an Earth Microbiome Project. Standards in Genomic Sciences, 3(3), 243–248. doi:10.4056/sigs.1433550.

Funding

The EMP has received support from the John Templeton Foundation (Grant ID 44000, Convergent Evolution of the Vertebrate Microbiome), the W. M. Keck Foundation (DT061413), Argonne National Laboratory (U.S. Dept. of Energy Contract DE-AC02-06CH11357), the Australian Research Council, the Tula Foundation, and the Samuel Lawrence Foundation.

We thank MO BIO Laboratories, Luca Technologies, Eppendorf, Boreal Genomics, Illumina, Roche, and Integrated DNA Technologies for in-kind support at various phases of the project.