Jack A Gilbert

Principal Investigator

Dr. Jack A. Gilbert earned his Ph.D. from Nottingham University, UK, in 2002 and received his postdoctoral training in Canada at Queens University. Subsequently, he returned to the UK in 2005  to work 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, as well as an Associate Professor in the Department of Ecology and Evolution at University of Chicago. Additionally, he is a 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 120 peer-reviewed publications and book chapters on metagenomics and approaches to ecosystem ecology, which can be found here. Primarily, his work focuses on analyzing microbial function and diversity, community assembly processes, and dynamic interactions between taxa with an aim of predicting the a community's metabolic output. Currently, he is working on generating observational and mechanistic models of microbial communities in natural, urban, built, and human ecosystems. He serves on the board of the Genomic Standards Consortium, contributes as a section editor for PLoS ONE, is a senior editor for the ISME Journal and Environmental Microbiology, and is the primary investigator for various research ventures, including the Earth Microbiome Project, the Home Microbiome Project, the Gulf Microbial Modeling Project, the Hospital Microbiome Project, and the Chicago River Microbiome Project.    

Melissa Dsouza

MBL-UChicago Postdoctoral Scholar

Melissa earned her B.Tech in Biotechnology (First Class Honors) from the University of Auckland, New Zealand, in 2010. Subsequently, she completed her PhD at the University of Auckland as a University of Auckland Doctoral Scholar in 2014. Her studies hoped to achieve a better understanding of the adaptations that allow bacteria their ability to grow and survive in the harsh, nutrient-depleted Antarctic soil environment. Currently, she is a joint Postdoctoral Fellow at the Marine Biological Laboratory, MA, and at the Department of Surgery, University of Chicago. Her current research focuses include investigating the ecology of microbial communities in a wide range of natural (e.g. forest soils, sediments) and built environments (e.g. Chicago Area Waterways Systems, Aquaponic and Hydroponic Systems, water purification membranes). Her publications can be found here

Beatriz Penalver Bernabe

Arnold O Beckman Postdoctoral Scholar

Beatriz holds a Chemical Engineering B.S. from the University of Murcia in Spain, a M.S. in Chemical Engineering from the University of Massachusetts, Amherst, and a Ph.D. in Chemical and Biological Engineering from Northwestern University in Chicago. Beatriz worked for several years as a Polymer Process Development Engineer with General Electric in her home country of Spain as well as within the United States. Beatriz is interested in understanding multicellular dynamic biologic complex systems in regenerative medicine. She is currently looking to apply her engineering and data science experience in understanding the complex relationships between mental health, endocrine system, and gut microbiome.

Naseer Sangwan

Postdoctoral Research Associate

Naseer is a Post-doctoral Scholar at Argonne National Laboratory – Institute of Genomics and Systems Biology, where his research is focused on exploring the microbial ecology of the Chicago Area Waterways system, using next generation sequencing techniques. He is 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. His publication can be found here.

 

 

Pamela Weisenhorn

Postdoctoral Research Associate

Pamela is a post-doctoral researcher at Argonne National Laboratory and is co-advised by Dr. Chris Henry. By trade, she is a microbial ecologist interested in the physiological and evolutionary constraints on bacterial utilization of resources, response to nutrients, and these two actions' influence biogeochemical cycling at the ecosystem level. She uses ‘omics and metabolic modeling to tease apart these complex constraints and community interactions. 

 

 

Holly Lutz

Postdoctoral Research Associate

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Dr. Lutz attained a PhD in Evolutionary Biology from Cornell University in 2016 and is currently a National Science Foundation Postdoctoral Fellow at the University of Chicago in conjunction with the Field Museum of Natural History. Through her initiation of the Bat Microbiome Project, she has begun studying the ecology and evolution of host-microbe interactions over a broad range of East African bat species. Additionally, her other projects include assessing the effects of habitat quality on ectoparasite and malaria prevalence in African bats and examining the influence of bat microbes on immunity and viral replication in mouse models. More information and a list of publications can be found on her website.

 

 

Jarrad Marcell-Hampton

Research Coordinator, UIC Ph.D. Candidate

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Jarrad is currently working in tandem with the University of Illinois at Chicago and Argonne National Lab to cultivate a comprehensive understanding of the methodology required to employ the use of micro biome data and samples to the forensic world. In understanding touch DNA and the various manners in which our microbiota interact with the environment surrounding us, the scientific community will be able to utilize such specific data to profile likely suspects and to match biological signatures once a suspect has been apprehended. Moreover, he continues to work on his PhD while coordinating various research projects throughout the labs.

Simon Lax

Ph.D. Candidate

Simon graduated from Columbia University in 2009 with a degree in environmental biology, where his thesis focused on deep subseafloor microbiology. He joined the Gilbert Lab in 2012 as a doctoral student in the Department of Ecology and Evolution at the University of Chicago. Primarily, his work focuses on the microbial ecology of the built environment, including the lab’s home and hospital microbiome projects. He went on to work as a research assistant in both cancer genetics and environmental microbiology research before returning to school. More information and a list of publications can be found on his website

 

Cesar Cardona

Ph.D. Candidate

Cesar is a Ph.D candidate from the Biophysical Sciences PhD Program at the University of Chicago, and a Student Researcher at Argonne National Labs. He works with Dr. Gilbert in Environmental Microbial Ecology and Dr Henry in Computational Microbial Metabolism labs. Cesar seeks to integrate Ecology and Biochemistry perspectives in characterizing microbial communities. In particular, seeking to combine metabolic modeling with co-occurrence and ecological networks theory to better understand stability and dynamics patterns in different microbial ecosystems. Interested in applications in built environments, bio-remediation, extreme environments and astrobiology. Prior undergraduate work in Computer Science at the Universidad Nacional de Colombia, Master’s degree in Computer Engineering at the University of Memphis, TN. He is a 2014 NSF GRFP fellow and 2016 NASA astrobiology summer school scholar. His publications can be seen in google scholar.

Alyson Yee

MD/Ph.D. Candidate

Alyson is an MD/PhD student at the University of Chicago Pritzker School of Medicine and the Committee on Microbiology. She graduated in 2012 from Tufts University with a B.S. in biology and French, then went on to work at the National Institutes of Health as a post-baccalaureate researcher for one year. Additionally, she was awarded a Fulbright grant to study the microbial ecology of cheese at the Institut National de la Recherche Agronomique in Rennes, France from 2013-2014. Alyson joined the Gilbert lab in October 2015 with the intent to explore how the early life microbiome contributes to human health, particularly in preterm infants. Her publications can be found here

 

Haitao Wang

Ph.D. Candidate

Haitao is currently a member of the lab as a visiting student to the University of Chicago. Primarily, his work centers around understanding the microbial ecology of urban greenspace soils, with the intent to reveal the impact of anthropological stresses, such as land utilizations and population changes, on the deep soil communities. He graduated from Sichuan Agricultural University in China in 2011 with a degree in Biology Science. He then went on to attend the Xiamen University in China for his MD study in microbiology. Since 2013, he has become a Ph.D. student in Xiamen University where his studies were mainly related with microbial ecology in the mangrove and urban soils of the area. His publications can be found here.

Thomas Kuntz

Ph.D. Candidate

Thomas decided to pursue a Ph.D. in Chemistry after graduating from Wesleyan University with a degree in Chemistry including an honor thesis on gas phase spectroscopy. He is keen to apply scientific concepts from across diverse fields to microbiome studies and is particularly interested in the connection between the gut microbiome and the neural networks of the brain, as he explores these interconnections through his current research experiments and endeavors. 

Elizabeth Ziegler

Graduate Student

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Elizabeth graduated from University of Texas at Dallas in 2015 with a B.S. in Biology and a minor in Public Health. While there, her undergraduate research project examined horizontal gene transfer and antiseptic-induced stress response in pathogenic Enterococcus species. Additionally, she spent time in Houston, TX, working with the Public Health Department’s West Nile surveillance team and spent a summer as a CDC Foundation fellow aiding in the design of training materials for the Stop Transmission of Polio (STOP) Program there. She is interested in the one health perspective as well as exploring the microbiome’s contribution to wildlife health and disease crossover in native species. 

 

Sophia Carryl

Graduate Student

Sophia graduated summa cum laude from CUNY Lehman College with a B.A. in Biology in 2015. There she investigated the effects of early environmental stressors on adult decision making in a lab colony of prairie voles (Microtus ochrogaster) with Dr. Maryam Bamshad for her honors thesis at Lehman College. Currently, she is a second year doctoral student in the Committee on Evolutionary Biology studying wildlife-microbe interactions in three populations of house sparrows (Passer domesticus). Her primary focus lies in discovering how differences in microbial communities due to environmental variations impact changes in the endocrine system, morphology, and behavior of house sparrows. Her end goal is to understand how microbes can influence fitness and shape the evolution of wildlife animals that are adapting to an increasingly urban world.

 

Neil Gottel

Lab Manager

Neil is the lab manager for the Gilbert Lab. Prior to joining University of Chicago, he worked at Oak Ridge National Lab in Tennessee. As a student, he attended the University of Illinois in Urbana Champaign and the University of Texas in Austin. As a researcher, he maintains interests in both microbial ecology and synthetic biology projects throughout the lab. 

Lauren Cralle

Research Technician

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Lauren is a recent graduate from the University of California, Los Angeles. She graduated in June 2016 with a B.S. in Psychobiology and has been working with the Gilbert Lab since August 2016 with a joint appointment between the University of Chicago and Argonne National Laboratory. Her interests in the microbiome began with studies of the gut-brain axis as it relates to neurodegenerative diseases but has since expanded to include ecological impacts of microbial communities and human microbiome experiments. Her future projects aim to explore more of the human-microbe interactions as it relates to addiction treatment and mental health. 

 

Miles Richardson

Undergraduate Researcher

Miles is an undergraduate student at the University of Chicago, majoring in Biological Sciences with a specialization in microbiology and a second major in Music. While working with Simon Lax on the Hospital Microbiome Project, Miles focused on identifying the core microbiome characteristics of hospital surfaces and determining the directional flow of microbes between the patient and the surrounding environment during hospital stays. Currently, Miles is working on the Dorm Microbiome Project to explore the various microbial facets of an undergraduate residence hall and to look at the patterns of movement of skin-associated microbiota in a huge mixed-living situation.

Leron Perez

Undergraduate Researcher

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Leron is an undergraduate student at the University of Chicago, majoring in Molecular Engineering. He is currently working on community metabolic modelling in coordination with Dr. Pamela Weisenhorn at Argonne National Lab. Additionally, he is interested in applying systems biology and biophysics to remedy today's societal issues and influence global change.

 

 

 

Wyatt Arnold

Undergraduate Researcher

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Wyatt is an undergraduate student at the University of Chicago, double majoring in Biology and Environmental Science. Under the guidance of Neil and Jack, he is exploring the interface between the field of ceramics and biology, adopting a biogeochemical lens to look at the microbial and chemical interactions within clay. His current work underscores his interest in exposing more of the biological mechanisms behind what is seemingly industrial processes. He is hoping to understand how microbiome activity, which may alter the function and rheology of clays and glazes, could impact the ceramic trade. 

 

Alexandra Sjaarda

Undergraduate Researcher

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Ali Sjaarda is an undergraduate student at the University of Chicago who is interested in human host-microbiome interactions, especially as it related to the gut-brain axis. Currently, she is working on a project exploring the associations between the human microbiome and depression in pregnancy and in new mothers.

 

Former members

Sean M. Gibbons

Ph.D. Candidate

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Sean holds a PhD from the biophysical sciences program at the University of Chicago. He is a lead data analyst for the Earth Microbiome Project at Argonne National Laboratory. He studied French, cellular and molecular biology, microbiology, and chemistry at the University of Montana. After graduating from UM in 2008, he worked for a year as the lab manager for the UM Environmental and Industrial Microbiology Laboratory. He then went on to complete a Fulbright Graduate Fellowship at Uppsala University (Sweden), where he obtained an M.S. in microbiology in 2010. Upon returning to the U.S., he 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, he joined the biophysical sciences program at UC, where he studies molecular systems ecology. You can check out his peer-reviewed publications here. Currently he holds a postdoctoral position at Eric Alm lab at MIT.

Kim M. Handley

Postdoctoral Research Associate

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Kim is an environmental microbiologist with a background in geochemistry, bacterial cultivation, and community genomics. She completed her PhD at the University of Manchester in the UK with Professor Jonathan Lloyd, where she studied microbial respiratory diversity and biogeochemical cycling in hydrothermal marine sediment. Her postdoctoral training was undertaken at the University of California, Berkeley with Professor Jillian Banfield, during which time she studied microbial community interactions in the terrestrial subsurface utilizing community genomic and proteomics techniques paired with geochemical data and field experiments. Currently, she holds 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 her research focuses on understanding the microbiology of both natural (e.g. oil-polluted sediments in the Gulf of Mexico) and built (e.g. http://hospitalmicrobiome.com/) environments. Her research publication list is viewable here.

Victor S. Pylro

Postdoctoral Research Associate

Victor 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.