Wednesday, April 27, 2011

Wanted: Sample collections for the Earth Microbiome Project (EMP); help make an open Field Guide to the Microbes

The Earth Microbiome Project (EMP) is "a systematic attempt to characterize the global microbial taxonomic and functional diversity".  A little more detail is provided on the project website:

The Earth Microbiome Project is a proposed massively multidisciplinary effort to analyze microbial communities across the globe. The general premise is to examine microbial communities from their own perspective. Hence we propose to characterize the Earth by environmental parameter space into different biomes and then explore these using samples currently available from researchers across the globe. We will analyze 200,000 samples from these communities using metagenomics, metatranscriptomics and amplicon sequencing 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 all information.
This project is certainly incredibly ambitious.  But hey, why not aim high?  The project is being coordinated by Jack Gilbert, Folker Meyer, and Rick Stevens from Argonne National Lab and the University of Chicago as well as Janet Jansson from Lawrence Berkeley National Lab and Rob Knight from U. Colorado Boulder. 

I note I am not unbiased here as I am one of the members of the EMP Steering Committee (others on the Committee include Jed Fuhrman, Janet Jansson, and Rob Knight).  

If you want to learn a bit more about the origins of the project, read this paper which is a report from a meeting where the idea came together as well as a follow up paper

Anyway, the reason I am writing this post is that the EMP is looking for collaborators and participants.  In particular we are hoping to line up lots of large sample collections that could be included in future analyses.  Currently a pilot project is being done on ~10,000 samples.  These will be characterized in a variety of ways including collection of metadata and also generation of sequence information for DNA from the samples (including both rDNA and metagenomic sequencing).  But the EMP wants more - much more.  So the EMP is recruiting anyone who either currently has, or could possibly collect, large collections of samples for microbial characterization along with rich contextual data about the samples.  The contextual data would ideally include as much information about the physical, chemical and biological parameters found at the time of sampling as possible. These parameters include, but are not limited to, nutrient concentrations, temperature, salinity, porosity, moisture content, time of day, latitude and longitude, depth below surface, elevation, pH, etc.

What types of samples are wanted?  Well, right now, just about anything could be useful.  Examples of things that could be useful include soil samples from a transect along the equator, filtered water from all lakes in Minnesota, deep sea sediment cores, filtered air from giant dust storms, microbial mats from hypersaline ponds, and so on.  The goal of the project is to develop and use massively high throughput methods to extract DNA and then generate sequence data from millions of samples.  There is of course a fund raising component and work is underway to secure funds to characterize the first collections.  Some corporations and institutes have already promised some support (e.g., Eppendorf and MoBio - see here). 

I note that the plans for the project are to be completely open in terms of data release.  Data that is generated will be released with no restrictions on use to everyone and anyone interested in utilizing it.

So if you have or might be able to collect some interesting samples and are interesting in participating in this open science initiative please contact to start this process rolling. We have already collated 55,000 from 30 PIs across the globe and this number is growing rapidly.

Be part of a revolution - open access data analysis to help define the microbial world which supports life on this planet. Plus, its better than working alone.

Note there is an upcoming meeting focusing on the EMP.  The meeting is in Shenzen June 13-15th.  This is a good place to have the meeting as the Beijing Genome Institute is a key partner in the EMP.

A final note this project is a key step in my dream - to have a field guide to the microbes.  It will not be all that is needed but it will be a good component. 

For some additional discussions of the EMP see:
And most importantly - sign up to provide samples


  1. Presumably these "microbes" are prokaryote-only? Or are protistan microbes finally not gonna be neglected this time? ;-)

  2. Nothing I am aware of in this project excluded eukaryotes ... and the hope is to deal with those virus things at some point too

  3. Oh and I note -I organized the first Protist Genomics workshop and have been pushing for more work on them for years ....

  4. Yaaay! Is this gonna be strictly genome-based, or are morphological contributions welcome too? (guess this makes a lot more sense for euks than prokes) I'm always bothered when there are only numbers and sequences and the actual organisms themselves are somewhat ignored... ;-)

    Soil viruses would be really cool. Imagine very little must be known about them; wouldn't be surprised if many more weird viral stories can be uncovered in soil protists and bacteria...

  5. well this project is focusing on sequencing but trying to partner with people getting good metadata

  6. great metadata would include cultured and morphology and experiments ...


Irresponsible reporting on "poop doping" from the Washington Post

UPDATE - see below - the author updated her article including some of my critiques. Went on a bit of a Twitter tirade last night. See mor...