Jack Gilbert Lab

Jack Gilbert

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.

Selected publications

Shogan BD, et al. Intestinal anastomotic injury alters spatially defined microbiome composition and function
Microbiome. 2014 Sep 15. eCollection 2014.
PMID: 25250176

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.
PMID: 25249279

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.
PMID: 25197496

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.
PMID: 25177538

Lax S, et al. Longitudinal analysis of microbial interaction between humans and the indoor environment
Science. 2014 Aug 29. science.1254529.
PMID: 25170151

Kyrpides NC, et al. Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains
PLoS Biol. 2014 Aug 5. eCollection 2014 Aug.
PMID: 25093819

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]
PMID: 25072414

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.
PMID: 24995004

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]
PMID: 24958360

Winston ME, et al. Understanding cultivar-specificity and soil determinants of the cannabis microbiome
PLoS One. 2014 Jun 16. journal.pone.0099641. eCollection 2014.
PMID: 24932479

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.
PMID: 24451203

Lab Members


Melissa Dsouza

Melissa Dsouza

MBL-UChicago Postdoctoral Scholar
Gilbert Lab, Department of Ecology and Evolution
Sean Gibbons

Sean Gibbons

Dual-Advised Graduate Student; Resident Associate
Jack Gilbert and Maureen Coleman Laboratories
IGSB Argonne National Laboratory
Jack Gilbert

Jack Gilbert

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
(630) 252-7489
Kim M. Handley

Kim M. Handley

Postdoctoral Research Associate, Department of Ecology and Evolution
Gilbert Lab
Naseer Sangwan

Naseer Sangwan

Bio-Sciences Division Argonne National Laboratory
Post-Doctoral Research Associate
630 854 7656
Daniel Smith

Daniel Smith

Argonne, Postdoc,
Current Affiliation: Research Associate Alkek Center for Metagenomics and Microbiome Research
Previous Affiliation: Jack Gilbert
(630) 252-6257
Iratxe Zarraonaindia Martinez

Iratxe Zarraonaindia Martinez

Post-doctoral Researcher
Current Affiliation: Research Associate Genomics University of the Basque-Country, Spain
Previous Affiliation: Jack Gilbert Lab

Additional Lab Members

Sean Gibbons sgibbons@uchicago.edu
Simon Lax simonlax24@gmail.com
Jarrad Marcell jhampton-marcell@anl.gov
Angel Frazier frazierangel43@gmail.com
Tifani Anton tweshoo@gmail.com
kim handley kmhandley@uchicago.edu
Nicole Scott nicolescott1@gmail.com
Chris Marshall chris.w.marshall@gmail.com
Naseer Sangwan nikki1018sangwan@gmail.com
Cesar Cardona cesarcardona@uchicago.edu
Pamela Weisenhorn weise088@umn.edu


Start-up founded by IGSB faculty wins $250,000 Polsky Center award

BiomeSense, a startup developing biosensors that can detect particular kinds of bacteria in patients’ feces that could help improve the efficacy of clinical trials, won the University of Chicago’s Innovation Fund finals and an investment of up to $250,000 from the college.

Jack Gilbert Heading UChicago Startup that Aims to Predict Behavior of Trillions of Microorganisms

IGSB Faculty member Jack Gilbert co-founded Gusto Global to better understand microorganisms inside humans and harness them to treat disease.

Jack Gilbert weighs in on whether probiotics are truly good for you

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.

Jack Gilbert’s Ted Talk Why Getting Dirty is the New Clean

IGSB Faculty member Jack Gilbert covers "Why Getting Dirty is the New Clean" at TEDxNaperville. 

Jack Gilbert named in Science Brilliant 10.

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. 

Jack Gilbert is the Field Museum’s newest Research Associate

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.

Looking Closer at the Role of Microbiome

"...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.”

How Germs Might Shape the Future of Architecture

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 Recognized by Crain’s “40 Under 40”

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.

Research Papers