Dr. Jack A. Gilbert



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 as a senior scientist until his move to Argonne National Laboratory and the University of Chicago in 2010. Dr Gilbert is a Microbial Ecologist and Group Leader at Argonne National Laboratory, Associate Professor in the Department of Ecology and Evolution at University of Chicago, Senior Scientist at the Marine Biological Laboratory, Woods Hole, 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 more than peer reviewed 120 publications and book chapters on metagenomics and approaches to ecosystem ecology ( He has focused on analyzing microbial function and diversity, community assembly processes, and dynamic interactions between taxa, with an aim of predicting the metabolic output from a community. He is currently working on generating observational and mechanistic models of microbial communities in natural, urban, built and human ecosystems. He is on the board of the Genomic Standards Consortium (, is an 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 (, Hospital Microbiome Project (, and the Chicago River Microbiome Project.     


Sean M. Gibbons

(Ph.D Candidate)

I am currently a PhD candidate in the biophysical sciences program at the University of Chicago and a lead data analyst for the Earth Microbiome Project at Argonne National Laboratory. I studied French, cellular and molecular biology, microbiology, and chemistry at the University of Montana. After graduating from UM in 2008, I worked for a year as the lab manager for the UM Environmental and Industrial Microbiology Laboratory. I then went on to complete a Fulbright Graduate Fellowship at Uppsala University (Sweden), where I obtained an M.S. in microbiology in 2010. Upon returning to the U.S., I entered a research scientist position in the molecular ecology lab at MPG Operations, and taught an applied research course at Chief Dull Knife College from 2010-2011. In 2011, I joined the biophysical sciences program at UC, where I study molecular systems ecology. You can check out my peer-reviewed publications here.

 Kim M. Handley

(Post-Doctoral Research Associate)

I am an environmental microbiologist with a background in geochemistry, bacterial cultivation, and community genomics. I completed my PhD at the University of Manchester in the UK with Professor Jonathan Lloyd, where I studied microbial respiratory diversity and biogeochemical cycling in hydrothermal marine sediment. My postdoctoral training was undertaken at the University of California, Berkeley with Professor Jillian Banfield, during which time I studied microbial community interactions in the terrestrial subsurface utilizing community genomic and proteomics techniques paired with geochemical data and field experiments. Currently I hold a joint appointment with the Department of Ecology and Evolution at the University of Chicago and the Institute of Genomics and Systems Biology at Argonne National Laboratory where my research focuses on understanding the microbiology of both natural (e.g. oil-polluted sediments in the Gulf of Mexico) and built (e.g. environments. My research publication list is viewable via the following link (

Simon Lax

(Ph.D Candidate)

Simon Lax joined the lab in 2012 as a doctoral student in the Department of Ecology and Evolution at the University of Chicago. His work has focused primarily on the microbial ecology of the built environment, including the lab’s home and hospital microbiome projects.

Naseer Sangwan

(Post-Doctoral Research Associate)

I am a researcher active in the field of microbial community genomics with an emphasis on comparative population genomics of microbial gene-complements re-assembled across deeply sequenced metagenome datasets. I am currently a Post-doctoral Scholar at Argonne National Laboratory – Institute of Genomics and Systems Biology, where my research is focused to explore the microbial ecology of the Chicago Area Waterways system, using next generation sequencing techniques. Publications

Dr. Chris Marshall

(Post-Doctoral Research Associate)

I am a Director’s Postdoctoral Fellow at Argonne National Laboratory researching many aspects of applied and environmental microbiology. My background is in thermophilic and mesophilic extracellular electron transfer, anaerobic environmental microbiology, and bioelectrochemical systems. I am currently working on the commercial applications and environmental importance of extracellular electron transfer by microbes to and from insoluble electron acceptors and donors. Recently, my coworkers and I have developed electrosynthetic microbiomes generating high yields of fixed carbon products. I am now utilizing metagenomic and metatranscriptomic datasets in order to better understand this bioelectrochemical system and other microbial communities. My publications can be found here.


Dr. Victor S. Pylro

(Post-Doctoral Research Associate)

Dr. Victor S. Pylro is a microbial ecologist holding experience on soil microbiology. He completed his Bachelor’s degree in Biological Sciences at Federal University of Ouro Preto/Brazil in 2008, and earned his Master’s and Ph.D. degrees (Agricultural Microbiology) from Viçosa Federal University/Brazil, with Sandwich Doctorate in Rothamsted Research/UK (Advisor: Dr. Penny R. Hirsch). He is one of the initiators of the Brazilian Microbiome Project (BMP –, a Brazilian Microbial Genomics Consortium and Database. At present, many microbial metagenomic projects underway in Brazil are widely known, and the main goal is to co-ordinate and standardize these, together with future projects. Dr. Victor Pylro is working closely to several Brazilian and International researchers and companies’ technicians, in order to standardize methods and protocols to be adopted by the BMP. Also, he is the coordinator of the Committee of Education and Extension of the National Institute of Science and Technology: Microbiome (recently proposed), concerned in the formation of human resources and the transfer of knowledge to society, by developing activities aimed at overcoming educational challenges in Brazil. Currently, he is a Post-doctoral at Argonne National Laboratory – Institute of Genomics and Systems Biology, where he is focusing his efforts to assemble the database and associated data analyses tools for the BMP.

Pamela Weisenhorn

(Post-Doctoral Research Associate)

I am a microbial ecologist interested in the physiological and evolutionary constraints on bacterial resource use and response to nutrients and how resource use and response influence biogeochemical cycling at the ecosystem level. I use ‘omics and metabolic modeling to tease apart these complex constraints and community interactions. I’m a post-doctoral researcher at Argonne National Laboratory and am co-advised by Dr. Chris Henry.


Cesar Cardona

(Ph.D Candidate)

First year student in the Biophysical Sciences PhD Program  at the University of Chicago, currently doing a rotation with Dr. Gilbert’s lab. Interested in bioremediation and environmental microbial ecology. Prior undergraduate work at the Universidad Nacional de Colombia and Master’s degree at the University of Memphis, TN.

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Tifani W. Eshoo

(Research Technician)

Before joining the Gilbert Lab as a Research Technician in 2013 Tifani worked for the IGSB Sequencing Core in several capacities from 2008-2012. Most recently she served as Laboratory Manager for the Core located at the University of Chicago. Before that she worked as a technician at the Argonne location operating the Illumina sequencing platform and processing microarrays. Prior to that she spent two years at Pennsylvania State University for graduate studies in the Axtell Lab helping develop a novel method to sequence degradation products of plant miRNAs. Beginning as an undergraduate she spent three years as a technician in the Amasino Lab, which studies the epigenetic controls of flowering in A. thaliana, at the University of Wisconsin-Madison. Publications



Past Lab Members



Iratxe zarraonaindia

(Post-Doctoral Research Associate)

Dr. Zarraonaindia is a PhD in Marine Population Genetics (October 2011) at the Genetics Department of the University of the Basque Country. During her PhD, Zarraonaindia developed traceability molecular tools to determine the geographic population origin of the European anchovy (Engraulis encrasicolus) and albacore (Thunnus alalunga) species. Zarraonaindia was given the “early career scientist” and “the best paper” award at the ICES Annual Science Conference (Bergen, 2012) for her work in fisheries genetics.Dr. Zarraonaindia achieved the first place on the selection for a postdoctoral grant offered by the Basque Government that included a 2 year stay with Dr. Jack A. Gilbert group at Argonne National Laboratory (2012-2014). During this period, she was involved in two main projects that used ‘omic approaches to 1) characterize the microbial community structure and host (plant) interactions in the Merlot grapevine, and 2) characterize the microbial community structure and functional potential in the Chicago Area Waterway System (CAWS) to determine sources of microbial pollution in this system.