Jack Gilbert Lab
Argonne National Laboratory
9700 South Cass Avenue
Argonne, IL 60439
Phone: (630) 252-7489
About the Lab
My laboratory focuses on numerous key aspects of how bacteria assemble into distinct communities, the metabolic mechanisms that structure these assemblages, and whether these systems can be predictively modeled over time and space. We use next generation sequencing approaches to access phylogenetic and functional information embedded within the genes of bacteria that populate these communities. Our goal is to use this information to reconstruct community interactions, and ultimately to build statistical models of the microbial ecosystem. These models will help us visualize large-scale patterns, generate predictions of responses to changes in an environment, and to identify gaps in our sampling campaigns.
We are a very collaborative group. Currently, we are involved in the (1) Earth Microbiome Project, which is a systematic characterization of microbial life across the biomes of planet earth; (2) Home Microbiome Project, an ongoing study to determine the rate and direction of microbial interaction between people, their pets and their homes; (3) Chicago Waterways Metagenomic Initiative, which aims to map and model the dynamics of microbial metabolism in the Chicago River and surrounding canals; (4) The Gulf of Mexico Microbial Metabolic Modeling Initiative that will map and model the microbial dynamics of the Gulf of Mexico; (5) American Gut, which aims to characterize the microbial diversity of 20,000 humans over the next 2 years; (6) The Autism Microbiome Consortium, which is providing a nexus for research into the influence of microbial metabolism on the symptoms of Autism; (7) Microbial Assemblage Prediction, which involves developing microbial modeling tools capable of allowing global forecasting of microbial community structure and metabolic potential across planet earth.
Our group also leadS the Hospital Microbiome Project, which is characterizing the taxonomic composition of surface-, air-, water- and human associated microbial communities in the new Center for Care and Discovery hospital. The aim is to determine the influence of human population demographics on the directionality in which the microbial communities evolve and the rate of colonization by potential pathogens.
In addition to these core projects, we also have over 35 ongoing collaborations with researchers from around the world and right here in Chicago.
Shogan BD, et al. Intestinal anastomotic injury alters spatially defined microbiome composition and function
Microbiome. 2014 Sep 15. eCollection 2014.
Zaborin A, et al. Membership and Behavior of Ultra-Low-Diversity Pathogen Communities Present in the Gut of Humans during Prolonged Critical Illness
MBio. 2014 Sep 23. mBio.01361-14.
Hawley ER, et al. Metagenomic analysis of microbial consortium from natural crude oil that seeps into the marine ecosystem offshore Southern California
Stand Genomic Sci. 2014 Jan 2. eCollection 2014 Jun 15.
Rideout JR, et al. Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences
PeerJ. 2014 Aug 21. eCollection 2014.
Lax S, et al. Longitudinal analysis of microbial interaction between humans and the indoor environment
Science. 2014 Aug 29. science.1254529.
Kyrpides NC, et al. Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains
PLoS Biol. 2014 Aug 5. eCollection 2014 Aug.
Larsen PE, et al. Satellite remote sensing data can be used to model marine microbial metabolite turnover
ISME J. 2014 Jul 29. ismej.2014.107. [Epub ahead of print]
Parfrey LW, et al. Communities of microbial eukaryotes in the mammalian gut within the context of environmental eukaryotic diversity
Front Microbiol. 2014 Jun 19. fmicb.2014.00298. eCollection 2014.
Hawley ER, et al. Metagenomes from two microbial consortia associated with Santa Barbara seep oil
Mar Genomics. 2014 Jun 20. margen.2014.06.003. [Epub ahead of print]
Winston ME, et al. Understanding cultivar-specificity and soil determinants of the cannabis microbiome
PLoS One. 2014 Jun 16. journal.pone.0099641. eCollection 2014.
Mason OU, et al. Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill
ISME J. 2014 Jul. ismej.2013.254. Epub 2014 Jan 23.
MBL-UChicago Postdoctoral Scholar
Gilbert Lab, Department of Ecology and Evolution
Dual-Advised Graduate Student; Resident Associate
Jack Gilbert and Maureen Coleman Laboratories
IGSB Argonne National Laboratory
Argonne, Core Member, Fellow,
Microbial Ecologist, Group Leader in Biosciences Division, Argonne National Laboratories
Associate Professor (Part-Time), Department of Ecology & Evolution, The University of Chicago
Adjunct Senior Scientist at the Marine Biological Laboratory
Postdoctoral Research Associate, Department of Ecology and Evolution
Bio-Sciences Division Argonne National Laboratory
Post-Doctoral Research Associate
630 854 7656
Current Affiliation: Research Associate Alkek Center for Metagenomics and Microbiome Research
Previous Affiliation: Jack Gilbert
Current Affiliation: Research Associate Genomics University of the Basque-Country, Spain
Previous Affiliation: Jack Gilbert Lab
Additional Lab Members
Sean Gibbons firstname.lastname@example.org
Simon Lax email@example.com
Jarrad Marcell firstname.lastname@example.org
Angel Frazier email@example.com
Tifani Anton firstname.lastname@example.org
kim handley email@example.com
Nicole Scott firstname.lastname@example.org
Chris Marshall email@example.com
Naseer Sangwan firstname.lastname@example.org
Cesar Cardona email@example.com
Pamela Weisenhorn firstname.lastname@example.org
Watch UChicago’s Jack Gilbert and Julie Bubeck Wardenburg weigh in on whether probiotics are truly good for you in the latest video from Argonne’s Microbiome Project series here.
Every year, Popular Science honors the 10 brightest young minds that are reshaping science and the world.
IGSB’s Jack Gilbert was named in the top 10, highlighting his work profiling microbiomes, for his energy and enthusiasm as well as his love for Ice Cream.
IGSB’s Jack Gilbert is the Field Museum’s newest Research Associate. This appointment is the latest collaboration between the Field museum and IGSB. Over the past 4 years Jack has been developing research collaborations with scientists at the Field museum to study the microbiome of Ants and Birds.
"...In fact, it’s beneficial. It helps train your immune system.” Your body wants it there, needs it there, has evolved to live with it. “It’s a natural part of your gut’s flora, your ecosystem.”
Do building materials affect how bacteria behave? That’s what Jack Gilbert, an environmental microbiologist at the University of Chicago, is investigating. He examines the metabolism of specific microbes under different indoor conditions. He’ll spray bacteria onto a variety of materials, such as steel, wood, and copper, looking for changes in their growth and proliferation, and he’ll adjust certain environmental variables, such as temperature and humidity—things humans like to control.
IGSB Core Member Jack Gilbert was honored by Crain’s Chicago Business as a proven leader in his field. Previous winners before their 40th birthday include Barack Obama, Nate Silver, and Kevin White.
- (Meta)genomic insights into the pathogenome of Cellulosimicrobium cellulans
- Athletic equipment microbiota are shaped by interactions with human skin
- Beyond the genome: community-level analysis of the microbial world
- Collagen degradation and MMP9 activation by Enterococcus faecalis contribute to intestinal anastomot
- Communities of microbial eukaryotes in the mammalian gut within the context of environmental eukaryo
- Comparative genomic analysis of nine Sphingobium strains: insights into their evolution
- Current developments in arbuscular mycorrhizal fungi research and its role in salinity stress allevi
- Distinct microbial communities associated with buried soils in the Siberian tundra.
- Disturbed subsurface microbial communities follow equivalent trajectories
- Does the brain listen to the gut?
- Evidence for a persistent microbial seed bank throughout the global ocean
- Forensic analysis of the microbiome of phones and shoes
- Genomics in marine monitoring: New opportunities for assessing marine health status
- Hospital-associated microbiota and implications for nosocomial infections
- Human and environmental impacts on river sediment microbial communities.
- Investigating the Impact of Storage Conditions on Microbial Community Composition in Soil Samples
- Key metabolic pathways involved in xenobiotic biotransformation and stress responses revealed
- Life in a World without Microbes
- Lifestyle evolution in cyanobacterial symbionts of sponges
- Metagenome Sequencing of Prokaryotic Microbiota Collected from Byron Glacier, Alaska
- Metagenomes from two microbial consortia associated with Santa Barbara seep oil
- Metagenomes from two microbial consortia associated with Santa Barbara seep oil.
- Metagenomics - a guide from sampling to data analysis
- Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill.
- Microbial terroir for wine grapes.
- Our interface with the built environment: immunity and the indoor microbiota
- Our unique microbial identity
- Potential contribution of anammox to nitrogen loss from paddy soils in Southern China
- Reconstructing the microbial diversity and function of pre-agricultural tallgrass prairie soils
- Satellite remote sensing data can be used to model marine microbial metabolite turnover
- Spatial and temporal variations in indoor environmental conditions, human occupancy, and operational
- Studying the microbiology of the indoor environment
- The Gut of Geographically Disparate Ciona intestinalis Harbors a Core Microbiota.
- The complete genome sequence for putative H₂- and S-oxidizer Candidatus Sulfuricurvum sp., assembled
- The microbe-mediated mechanisms affecting topsoil carbon stock in Tibetan grasslands
- The microbial nitrogen cycling potential is impacted by polyaromatic hydrocarbon pollution
- The ocean sampling day consortium
- The role of the commensal microbiota in the regulation of tolerance to dietary allergens
- The soil microbiome influences grapevine-associated microbiota
- Toward effective probiotics for autism and other neurodevelopmental disorders.
- Towards large-cohort comparative studies to define the factors influencing the gut microbial communi
- Understanding cultivar-specificity and soil determinants of the cannabis microbiome.
- Using corticosteroids to reshape the gut microbiome: implications for inflammatory bowel diseases