The Faculty


Stability of robust and well-defined microbial communities in fluid ecosystems


Ph.D., Marine Microbiology, University of Nottingham, UK.

Awards, Honors and Memberships

  • Member of the Society for General Microbiology
  • Member of the International Society for Microbial Ecology
  • Member of the American Society for Microbiology


Jack A. Gilbert is a microbial ecologist whose ongoing research is focused on exploring how microbial communities assemble themselves in natural and man-made environments. Jack’s interests include the use of ‘omics technologies (metagenomics, metatranscriptomics, metaproteomics, metametabolomics) and high-throughput sequencing to answer questions about microbial communities all over the world. He currently manages the Earth Microbiome Project, which is an ongoing effort to characterize the microbial diversity of our planet.

Jack also develops predictive models that help extrapolate our understanding of the microbial ecosystem function mediated by bacteria to the continental and global scale, and is spearheading an effort to include microbial ecosystem dynamics into global climate models. This is predicated on the understanding that microbes mediate the majority of the global CO2, NO, and CH4 cycles, and so by understanding how they do this we can better predict what the levels of these climate active gases will be in the future.

In addition to his duties at Argonne, Jack is also an Assistant Professor in the Department of Ecology and Evolution, and Department of Surgery at the University of Chicago, where he runs two externally funded initiatives. The Home Microbiome Project that is exploring how humans interact with the bacteria living in their homes; and the Hospital Microbiome Project that is examining how adding patients and staff into a hospital building effects the development of microbial communities and important pathogens.

Select Publications

  • Knight R, Jansson J, Field D, Fierer N, Desai N, Fuhrman J, Hugenholtz P, Meyer F, Stevens R, Bailey M, Gordon JI, Kowalchuk G, Gilbert JA. 2012. Designing Better Metagenomic Surveys: The role of experimental design and metadata capture in making useful metagenomic datasets for ecology and biotechnology. Nature Biotechnology. In press.
  • Larsen PE, Field D, Gilbert JA. 2012. Predicting bacterial community assemblages using an artificial neural network approach. Nature Methods. doi:10.1038/nmeth.1975
  • Larsen PE, Hamada Y, Gilbert JA. Modeling Microbial Communities. Journal of Biotechnology. In press
  • Gilbert JA, Meyer F. 2012. Modeling the Earth’s Microbiome: A real world deliverable for microbial ecology. ASM Microbe Magazine. 7 (2), 64
  • Gilbert JA, Steele J, Caporaso JG, Steinbruck L, Somerfield PJ, Reeder J, Temperton B, Huse S, Joint I, McHardy AC, Knight R, Fuhrman JA, Field D. 2012. Defining seasonal marine microbial community dynamics. ISME J. 6, 298-308.
  • Davies N, Field D, Meyer C, Gilbert JA. 2012. Sequencing data: A genomic network to monitor Earth. Nature. 481, 145.
  • Caporaso JG, Field D, Paszkiewicz K, Knight R, Gilbert JA. 2012. Evidence for a persistent microbial community in the Western English Channel. ISME J. 6, 1089–1093 doi:10.1038/ismej.2011.162.
  • Gilbert JA and Dupont C. 2011. Marine Metagenomics. Annual Review of Marine Science. Volume 3: 347-371.
  • Gilbert JA, O’Dor R, Vogel T. 2011. Survey studies are still vital to science. Nature. 469, 162.
  • Gilbert JA, Field D, Swift P, Thomas S, Cummings D, et al. (2010) The Taxonomic and Functional Diversity of Microbes at a Temperate Coastal Site: A ‘Multi-Omic’ Study of Seasonal and Diel Temporal Variation. PLoS ONE 5(11): e15545. doi:10.1371/journal.pone.0015545
  • Gilbert JA, Field D, Huang Y, Edwards R, Li W, et al. (2008) Detection of Large Numbers of Novel Sequences in the Metatranscriptomes of Complex Marine Microbial Communities. PLoS ONE 3(8): e3042. doi:10.1371/journal.pone.0003042