Tom Schmidt, Principal Investigator,

I was struck by the elegance of microbes during my first course in microbiology. The incredible diversity in the microbial world highlighted how unifying principles of thermodynamics and natural selection could explain patterns of physiological, ecological and evolutionary diversity. Along with a tremendously talented team of graduate and undergraduate students, post doctoral fellows and other collaborators, we continued to make discoveries to help illuminate fundamental principles that shape the world of microbes and consequently all of life.

Research in my laboratory is focused on the physiology and ecology of microbes. We routinely develop and apply nucleic acid-based methods to explore and understand patterns of diversity and function of microbial communities, and to guide cultivation efforts. Our research is currently focused on two environments: Microbial Communities in Soil, in particular bacteria that are involved in the flux of greenhouse gases, and microbes that constitute Mammalian Microbiomes.  As we develop a better appreciation for the relationship between the structure and function of these microbial communities, we are conducting research to uncover fundamental principles that explain patterns of distribution. A particular point of interest is testing the hypotheses that there is a tradeoff between growth rate and resource use efficiency.  Subtle changes in metabolism appear to poise microbes for a lifestyle of explosive growth or efficient conversion of resources into progeny, and in the spatially structured environments of soil and the gut mucosa, we are testing the hypothesis that efficiency confers a greater selective advantage than growth rate. These research projects have practical implications for the engineering of microbes and their maintenance in artificial and natural microbial communities.

Nielson Baxter, Postdoctoral Fellow,

I’m interested in how the gut microbiome can be manipulated to promote human health. My research focuses on how the addition of resistant starch to person’s diet impacts the structure and function of their gut microbiome, especially butyrate production. Butyrate is one of many metabolites produced by the microbiome that's important for maintaining human health. Modulating it's concentration may be useful for treating or preventing a variety of diseases.  I’ve also been given the opportunity to combine my research interests with my interest in undergraduate education as a co-instructor for the BIO173 Authentic Research Connection course, a microbiome-focused laboratory course in which undergraduates engage in and serve as subjects for microbiome research.

Matthew Hoostal, Post Doctoral Fellow,

My research examines how low concentrations of oxygen in the mucosa of the GI tract modulate bacterial communities in the gut. More specifically, the project investigates whether bacteria that utilize a high-affinity terminal oxidase for respiration have a fitness advantage relative to bacteria lacking the high-affinity oxidase. As such, this project evaluates microbial communities in the gut from both an ecological and evolutionary perspective. By providing an assessment of the relative importance of oxygen as a selective pressure in the gut, results from this work will have applications in the management of the human gut microbiome.

Brendan O'Neill, Graduate Student,

My research focuses on how cropping system diversity alters belowground ecosystem processes. At the Kellogg Biological Station LTER (Long Term Ecological Research) experiment, I monitor greenhouse gas flux, nutrient turnover potentials (primarily for carbon and nitrogen), and various measures of biological activity, such as soil enzyme activities. These processes are all a function of microbial processes I seek to quantify and describe using genomic analysis. A key question is whether managing for cropping system diversity fundamentally reshapes dominant ecosystem processes carried out by the microbial community. A goal of his work is to better understand key concepts in soil ecosystem function and, where possible, relate them to sustainable farming practices and provisioning of ecosystems services.

Kwi Kim, Research Technician,

The human gut has an incredible diversity of microbes, which interact in complex ways. The human gut microbiota is largely dominated by anaerobic bacteria and most of these bacteria still remain uncultured. The focus of my research is to mimic the gut ecosystem to cultivate novel anaerobic microbes using different growth factors, co-cultures and selective media methods.

Clegg Waldron, Adjunct Professor,

Since retiring in 2008 I have been volunteering in the lab of my collaborator and friend Tom Schmidt. I am particularly keen on introducing undergraduates to “real” discovery research so they can make better informed career choices. I also help George Garrity with a biotechnology course that emphasizes critical thinking and communication. It’s giving me an opportunity to improve my lectures into “active learning experiences”.

Most of my 26 years with Dow AgroSciences and its predecessors were spent in Discovery Research. I was initially a bench scientist but got increasingly involved in people management, strategy development and external collaborations. My research goals evolved as company needs changed: from genetically engineered crops to new target sites for agricultural chemicals to genes for insect resistance and natural products for pest and disease control. But the core technologies were always molecular genetics and microbiology. My final responsibility – natural products discovery – led to collaboration with Tom Schmidt and re-ignited my interest in novel approaches to culturing bacteria and in microbial ecology.

Rachel Bessire, Graduate Student,

I'm a Master's student in the School of Public Health studying Nutritional Sciences and Dietetics. After taking an introductory microbiology course, I decided to pursue a bachelor's degree in microbiology from the University of Washington in Seattle. I worked in a variety of labs before landing a position in the Schmidt lab as a graduate student instructor and lab assistant. In a USGS lab, I looked at the impact of estradiol and bisphenol A on early-life exposures in zebrafish and was also involved with the Human Microbiome Project at the Fred Hutch Cancer Research Center. Because the microbiome is recognized as an important component of gut health, I am passionate about translating microbiome research into nutritional practice. 

Brad Pingel, Graduate Student,

Steve Stoddard, Researcher,

Chris Wright, Graduate Student,

I love to study fungi, and am fascinated by the many ways our world is shaped by these functionally diverse microbes.  Fungi form essential, symbiotic partnerships with plans for maximal primary production, manufacture the biological glue that gives our soils structure, deconstruct complex, organic molecules in order to detoxify and recycle nutrients into our eco systems, and intercede at critical steps of our global biogeochemical cycles.  My studies have focused on how differing agricultural land-management practices shape the taxonomic and functional structure of lignolytic, decomposing fungal communities inhabiting those soils, with the goal of understanding how we may use this knowledge to help sustainably manage our agricultural ecosystems.

Byron Smith, Graduate Student,

Microbial ecology has entered a renaissance of exploration thanks in large part to the meta-omics techniques which us to survey the phylogenetic/functional/metabolic profiles of complex environmental communities.  While these "top-down" approaches are undoubtedly valuable components of our currents attempts to develop theoretical and predictive frameworks for microbial ecosystems, I am interested in combining metagenomics and metatranscriptomics with concomitant "bottom-up" studies of simplified and well defined ecologies.  My current work is diverse; one project take an experimental approach to examine the relative importance of various nitrogen compound metabolic pathways in a number of environments, especially agricultural soil.  Another project is exploring the role of spatial structure in the evolution of efficient growth strategies in microbes.

Alex Schmidt, Lab Manager,

I have been the lab manager for the Schmidt Lab since the winter of 2013 and have been with the Schmidt Lab since September, 2012.  I support the research of our lab members by maintaining our equipment and inventory.  I also perform data analysis of 16S targeted metagenomes and curate our human-associated microbial strain collection.


  • Ben Roller | | | Post Doctoral Fellow - Center for Adaptation to a Changing Environment, ETH Zürich
  • Kevin R Theis | |   | Assistant Professor - Department of Immunology & Microbiology, Wayne State University
  • Dishari Mukherjee | |  | Graduate Student, University of Michigan
  • Jessica Sieber | | 2014-2015 Post Doctoral Fellow | Postdoctoral Fellow - Andrews Lab, University of Minnesota-Duluth
  • Brian Gray | | 2013-2014 Post Doctoral Fellow | Assistant Professor of Biology, York College of Pennsylvania
  • Rachel Morris | | 2012-2013 Post Doctoral Fellow | Teaching Specialist, Biomedical Laboratory Diagnostics Program, Michigan State University
  • Dongjuan Dai | Postdoctoral Fellow 2011-2012 | Research Associate, Stanford University
  • Tracy Teal | Post Doctoral Fellow 2008-2012 | Assistant Professor, Microbiology and Molecular Genetics, Michigan State University
  • Bjorn Ostman | Postdoctoral Fellow 2010-2012 |  Post Doctoral Fellow, BEACON, MSU
  • Keara Towery | M.S. 2012 | Research Technician, Michigan State University
  • Zarraz May Ping Lee | Ph.D. 2011 | Post Doctoral Fellow, Arizona State University
  • Uri Levine | Ph.D. 2009, EPA Star Fellow | Post Doctoral Fellow, USDA
  • Dana Gerken | M.S. 2009 |  Research Technician, Auburn University
  • Stephanie Eichorst | Ph.D. 2007 | Research Scientist, University of Vienna
  • Kristin Huizinga | Ph.D. 2006 |  Research Scientist, Monsanto
  • Les Dethlefsen | Ph.D. 2004, EPA Star Fellow, DuVall Award |  Postdoctoral Fellow, Stanford University
  • Joel Klappenbach | Ph.D. 2001, Hugh Award |  Research Scientist, Merck
  • Daniel Buckley | Ph.D. 2000, Duvall Award | Associate Professor, Cornell University 
  • Bradley Stevenson | Ph.D. 2000, DuVall Award | Associate Professor, Oklahoma State University
  • Joel Hashimoto | M.S. 2000 |  Research Associate, Oregon Health and Sciences
  • Paul Lepp | Ph.D. 1997 | Associate Professor, Minot University