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Earth Microbiome Project

Earth Microbiome Project

Earth Microbiome Project is a project to analyze the global microbial community.

The Earth Microbiome Project (EMP) is an effort to characterize all microbial life on earth. EMP uses DNA sequencing and mass spectrometry of crowd-sourced samples to look for patterns in microbial ecology across the biomes and habitats. The 16S rRNA gene is sequenced as it is a genetic marker for specific bacteria and archaea. The 16S rRNA sequences serve as “barcodes” to identify types of bacteria.

The EMP was founded in 2010 as a crowd-sourced effort to analyze all microbial communities. The Earth Microbiome Project was founded in 2010 by Rob Knight (UC San Diego), Jack Gilbert (University of Chicago, Argonne National Laboratory), Rick Stevens (Argonne National Laboratory, University of Chicago) and Janet Jansson (Pacific Northwest National Laboratory). The Earth Microbiome Project is co-led by researchers at University of California San Diego, Pacific Northwest National Laboratory, University of Chicago and Argonne National Laboratory, University of Chicago and Argonne National Laboratory.

EMP's goal is to analyze 200,000 samples 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. The purpose of the Earth Microbiome Project is to advance scientific understanding of microbes and their relationships with their environments, including plants, animals and humans. The resulting database also has applications in forensic science, since the relative quantities of microbes living in a sample can identify what kind of environment it came from.

As of 2017 the project had collected more than 27,000 samples from diverse environments around the world and analysed the microbiomes of each sample. These results were published in Nature with more than 300 co-authors from more than 160 institutions around the world. As of December 2018, EMP was not currently accepting new samples for the project. EMP datasets are open to the public for download at or

Data collected form the Earth Microbiome Project have been used in studies on the skin of whales, dolphins, seals, fish, birds, bats, cats, rats, rattlesnakes and Komodo dragons. Earth Microbiome data has been used in studies on drinking water, ocean communities, oil spills, primate gut health, gut microbes in ant digestion, the effects of soil microbes on wine, how obesity affects the smelling of wine aromas and how the human microbiome changes over time and changes the spaces we live in.


November 1, 2017
A communal catalogue reveals Earth's multiscale microbial diversity

A meta-analysis of microbial community samples collected by researchers for the Earth Microbiome Project.


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