You, me, and the EMP (Earth Microbiome Project)

In this guest post, Dr. Dorota Porazinska of the University of Colorado introduces the Earth Microbiome Project (EMP), an initiative to understand microbial communities, their diversity and function at the global scale, and explains how researchers can help the EMP as part of their own research projects. Communities like Plants-Soils-Ecosystems provide great environments for connecting like-minded researchers and encouraging collaboration – if you’re interested, read on, and get in touch! Now, over to Dorota:

The EMP was initiated in 2010 to understand patterns in microbial communities across different spatial, temporal and evolutionary scales, to understand the functional basis for these patterns, and to provide a portal for the analysis and visualization of the data. The EMP has primarily generated data from amplicon sequencing of Bacteria and Archaea to date, although expansion to other taxa including eukaryotes and viruses, and other forms of data generation including metagenomics, metatranscriptomics, and metabolomics, is anticipated in future.

emp-logo

The EMP is a massively collaborative project. Individual projects are stand-alone, hypotheses-driven studies contributed by PIs from around the world. The EMP has generated 16S rRNA profiles for >30,000 samples representing >40 ecological biomes, including oceans, sediments, rivers, lakes, human, plant- and animal-associated ecosystems. Soils constitute ~10% of these samples, and although many project contributions to date have been from agricultural sites from the North American meridian, the EMP results to date confirm our expectations of these ecosystems: high diversity, many novel taxa, and limited community overlap among biomes and geographic locations.

emp-wordle

The success of the EMP depends on your participation.

If you join the EMP, we will:

  • Extract DNA and sequence 16S rRNA amplicons free of charge using standardized protocols
  • Archive the data and make it publically available
  • Perform initial analysis of the sequencing data (quality-filtering, OTU-clustering, taxonomy assignment, and beta diversity analyses integrated with a vast database of other studies)

To join the EMP, we ask that you submit:

  • A one-paragraph proposal that describes your study, focusing on what the samples are and what spatial, temporal or evolutionary questions your sample set addresses in the microbial world
  • Information about each sample (“sample metadata”) that must be provided in standardized format (the EMP will assist with this) prior to sample receipt

For detailed information about goals and protocols, please visit the EMP website. Note the EMP data release policy, which is that all data are made freely available to the community upon sequencing.

For specific questions about submission of the proposal and the mandatory metadata, please email: dorota dot porazinska at colorado dot edu

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2 thoughts on “You, me, and the EMP (Earth Microbiome Project)

  1. Relena Ribbons (@relenaribbons)

    It is very cool to see data such as those being collected and processed by EMP, being made publicly available. Open access microbial data!
    It sounds like a really great way to ensure scientists can have access to high-quality data without necessarily spending the time, energy, and resources to go out and collect new data, when previously collected data would suffice to address their research questions. As I read through the Getting Involved pear (http://www.earthmicrobiome.org/getting-involved/) I wondered about data sharing policies and publication. Does the no strings attached use of data policy mean that your data can be used without any need for citation and attribution to the folks who originally collected the data? Looks like a very cool endeavor!

    Reply
  2. War War Min

    May i introduce myself. I am Dr. War War Min, Lecturer of Zoology Department at Yangon University,Myanmar. I got Ph.D in 2009 concern with Isopods that species live in Mangrove of Myanmar coastal region. So i want to study concern with soil and ecology of plants.

    Reply

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