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Modeling Microbial Ecosystems, Part 1

April 08, 2014
12:30 PM - 01:30 PM
Goergen Hall, Room 101

Jack Gilbert

The understanding of Earth’s climate and ecology requires multi‐scale observations of the biosphere, of which microbial life are a major component. However, to acquire and process physical samples of soil, water and air that comprise the appropriate spatial and temporal resolution to capture the immense variation in microbial dynamics, would require a herculean effort and immense financial resources dwarfing even the most ambitious projects to date. To overcome this hurdle we created the Earth Microbiome Project, a crowd-sourced effort to acquire physical samples from researchers around the world that are, importantly, contextualized with physical, chemical and biological data detailing the environmental properties of that sample in the location and time it was acquired. The EMP leverages these existing efforts in a systematic analysis of microbial taxonomic and functional dynamics across a vast array of environmental gradients. The EMP uses the data standards format to capture the environmental gradients, location, time and sampling protocol information about every sample donated by our valued collaborators. Physical samples are then processed using a standardized DNA extraction, PCR, and shotgun sequencing protocol to generate comparable data regarding the microbial community structure and function in each sample. To date we have processed >20,000 samples, and have >20,000 in the process of being analyzed. One of the key goals of the EMP is to map the spatiotemporal variability of microbial communities to capture the changes in important processes that need to be appropriately expressed in models to provide reliable forecasts of ecosystem phenotype across our changing planet.

Dr Jack A Gilbert earned his Ph.D. from Nottingham University, UK in 2002, and received his postdoctoral training in Canada at Queens University. We subsequently returned to the UK in 2005 and worked for Plymouth Marine Laboratory at a senior scientist until his move to Argonne National Laboratory and the University of Chicago in 2010. Dr Gilbert is an Environmental Microbiologist at Argonne National Laboratory, Associate Professor in the Department of Ecology and Evolution at University of Chicago, and senior fellow of the Institute of Genomic and Systems Biology. Dr. Gilbert is currently applying next-generation sequencing technologies to microbial metagenomics and metatranscriptomics to test fundamental hypotheses in microbial ecology. He has authored >100 publications and book chapters on metagenomics and approaches to ecosystem ecology ( He has focused on analyzing microbial function and diversity, with a specific focus on nitrogen and phosphorus cycling, with an aim of predicting the metabolic output from a community. He is currently working on generating observational and mechanistic models of microbial communities associated with aquatic and terrestrial ecosystems. He is on the board of the Genomic Standards Consortium (, is an senior section editor for PLoS ONE and senior editor for the ISME Journal and Environmental Microbiology, and is PI for the Earth Microbiome Project (, Home Microbiome Project (, Gulf Microbial Modeling Project (, and Hospital Microbiome Project (

Host: Jack Werren

Category: Talks

  • Goergen Institute for Data Science
    University of Rochester
    Rochester, NY 14627

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