Researchers

Jennifer Auchtung

• ASSISTANT PROFESSOR, DEPARTMENT OF Food Science & Technology

The overall goal of research in the Auchtung lab is to understand how the gastrointestinal microbiome contributes to human health and to use this information to develop new microbiome-targeted therapies to treat disease. Currently, our work focuses on how antibiotics disrupt microbiome-mediated resistance to colonization by antibiotic-resistant pathogens. Our primary emphasis is the gastrointestinal pathogen Clostridium difficile, the leading cause of antibiotic-associated diarrhea and hospital-acquired infections. Our lab examines the impact that interpersonal variation in microbiome composition has on susceptibility to disease and response to potential therapeutics. We use two complimentary approaches to model interpersonal variation, human fecal minibioreactors and humanized microbiota mice.

Andy Benson

• Food for Health Presidential Chair and Director, Nebraska Food for Health Center
• Professor, Department of Food Science and Technology

Benson’s research group studies the complex sets of host and dietary factors that collectively influence composition and function of the gut microbiome. In collaboration with statisticians, computational biologists, and animal geneticists, Benson’s research program has focused on understanding how individual genetics can influence the microbiome and how dietary factors can modify the impact of host genetics, most likely through a direct impact of diet on the gut microbiome. Benson’s group is also spearheading the discovery component of the Nebraska Food for Health Center using complex trait analysis in crop plants to define components and molecules that can impact the gut microbiome of humans. Working closely with center members in plant genetics, statistics, and glycobiology, his team uses in vitro microbiomes in high-throughput screens of milled grains from large genetic resource populations of crop plants.

Siddappa Byrareddy

• Associate Professor, University of Nebraska Medical Center

The Byrareddy lab research activities include understanding of host-virus dynamics, pathogenesis and prevention strategies of Human/Simian Immunodeficiency viruses (HIV/SIV) and other infectious diseases in general using Non-Human Primate models. We recently showed that by blocking of α4β7 integrin, using an antibody against α4β7 (a gut homing molecule) provided sustain virological control in SIV macaque models, emphasizing an importance of gut hemostasis in controlling infection. Current research includes evaluating connection of microbiome-gut-brain axis to understand host immune homeostasis and developing therapeutics for gut-brain disorders. 

Edgar Cahoon

• Director, Plant Science Innovation
• George W. Holmes Professor of Biochemistry

The Cahoon lab conducts basic and applied research on plant lipid metabolism. The goals of our research are to enhance the nutritional and industrial value of crop plants and to probe the synthesis and function of bioactive lipids for nutritional biofortification and improved agronomic performance of crops.

Featured Publications

Iskandarov U, Silva JE, Kim HJ, Andersson M, Cahoon RE, Mockaitis K, Cahoon EB (2017) A specialized diacylglycerol acyltransferase contributes to the extreme medium-chain fatty acid content of Cuphea seed oil.  Plant Physiology 174:97-109.

Jennifer Clarke

• Director of the Quantitative Life Sciences Initiative
• Professor, Department of Statistics

Dr. Clarke's research interests encompass statistical methodology (with an emphasis on high dimensional and predictive methods), statistical computation, bioinformatics/computational biology, multi-type data analysis, data mining/machine learning, and bacterial genomics/metagenomics (gut function initiative). She is the director of the Quantitative Life Sciences Initiative.

Featured Publications

Clarke B, and Clarke J. Predictive Statistics, Cambridge University Press. A graduate level textbook on prediction in statistics. In production for publication in 2018.

Jonathan B. Clayton

• Assistant Professor, Department of Biology, University of Nebraska-Omaha
• Member, Callitrichid Research Center
• Member, GreenViet Biodiversity Conservation Center
• Founder, Primate Microbiome Project

The Clayton lab is studying host-microbiome interactions in humans and nonhuman primates. We are using nonhuman primates as a model for studying the effects of variations in dietary fiber and other dietary compounds, as well as lifestyle factors associated with modernized society, on the microbiome and metabolic health. Dr. Clayton received his Doctor of Veterinary Medicine (D.V.M.) and his Doctor of Philosophy (Ph.D.) in Comparative and Molecular Biosciences from the University of Minnesota. For his Ph.D. thesis research, he used nonhuman primates as a model system for studying the effects of emigration and lifestyle disruption on the human gut microbiome. During his Ph.D., Dr. Clayton founded the Primate Microbiome Project (PMP) with the intended purpose to develop a systematic map of variation in microbiome structure and function across all primates and to relate this to primate health, evolution, behavior, and conservation.

Tom Clemente

• Eugene W. Price Distinguished Professor of Biotechnology, Center for Plant Science and Innovation
• Professor, Department of Agronomy and Horticulture

The Clemente laboratory is a state-of the-art plant transformation facility that targets the introduction of genetic variation for novel input and output traits in the major commodity crops pertinent to the state of Nebraska, including maize, sorghum, soybean and wheat. The research expertise our program brings to the Nebraska Food for Health Center complements the Center’s transdisciplinary research activities by providing the wherewithal to optimize levels of identified macro and/or micro molecules in foods by genetic modification leading to value added seed traits.

Featured Publications

Peña, P.A,. T Quach, S. Sato, Z. Ge, N. Nersesian, T. Changa, I. Dweikat, M. Soundararajan, and T. E. Clemente. 2017. Expression of the maize Dof1 transcription factor in wheat and sorghum. Front. Plant Sci. 8:434. Doi: 10.3389/fpls.2017.00434

Samodha Fernando

• Associate Professor, Nutritional Biochemistry
• Nebraska Center for the Prevention of Obesity Diseases

Dr. Fernando's research interests are in understanding microbial structure-function relationships to improve human and animal nutrition. To this end, I am intersted in 1) understanding the role of the microbial food chain in methanogenesis and other metabolic disorders in ruminants; 2) developing new animal models to study structure-function relationships in the human microbiome; 3) understanding the influence of host-genotype, gut microbiota and environment towards pathogen colonization in humans and livestock; and 4) uncovering the gut virome in ruminants and non-ruminants.

Jeffrey A. French

• Varner Professor of Neuroscience and Psychology
• Director: Callitrichid Research Center, University of Nebraska at Omaha

Dr. French's research focuses on the neuroendocrine regulation of social behavior, stress, and cognition in marmosets, an important translational primate model for human behavior and mental health. The closest genetic relatives of humans (chimpanzees and gorillas) are primarily fruit and plant eaters, but marmoset feeding ecology, like the typical human diet, consists of an omnivorous diet of animal protein (~ 25% of food intake), fruits and leaves (25%), and complex carbohydrates (50%). The marmoset gut microbiome likely has diversity and complexity similar to the human the human microbiome. There is an intimate communication between the gut and the brain (via the enteric nervous system, immune signals, and metabolic and appetite-regulating hormones), and this communication is modulated in important ways by the gut microbiome.

Corrine Hanson

• M. Patricia and James. W. Leuschen Professor for Advancing Research in the Allied Health Professions, Medical Nutrition Education, University of Nebraska Medical Center

Dr. Corrine Hanson's career is dedicated to understanding effects of nutrition on the promotion of health and the development and progression of disease over the life course. Her work focuses primarily on two areas, specifically the role nutrition plays in lung health, and how nutrition during pregnancy impacts newborn outcomes and the development of disease later in life.

Robert Hutkins

• Khem Shahani Distinguished Professor of Food Science, Department of Food Science and Technology

The Hutkins lab studies bacteria important in human health and in fermented foods. The lab is particularly interested in understanding how diet and dietary food components influence the bacteria that reside in the gastrointestinal tract. The main goal is to understand and predict how diet-induced shifts in the microbiota ultimately influence human and animal health. Specifically, the lab is focused on prebiotic fibers and how these food components are selectively metabolized by member of the microbiota. We have developed a novel strategy for combining prebiotic fibers with selected strains of probiotic bacteria to enhance establishment of those organisms in the gastrointestinal tract. We also conduct clinical studies to assess the effects of prebiotic and probiotic interventions on gut barrier functions and other health outcomes. Dr.

David Hyten

• Haskins Professor in Plant Genetics and Associate Professor, Soybean Genetics/Genomics

The Hyten lab is focused on taking basic genetic and genomic discoveries in soybean and translating those discoveries into applied methods that can be used for the real-world improvement of soybean varieties. The program focuses specifically on improving agronomically important traits such as drought tolerance and response to water abundance.

As we experience climate change, making cultivars able to withstand drought and highly responsive to water abundance will be key to feeding the world. The Hyten lab is working towards understanding the underlying genetic diversity that leads to drought tolerance so that we can link genetic diversity to this agronomically important phenotype and understand how genetic diversity interacts across the diverse environments encountered across Nebraska and the rest of the United States.

Jacques Izard

• Clinical Research Director, Nebraska Food for Health Center
• Associate Professor, Department of Food Science & Technology

As the health status of the population is getting more complex, the Izard laboratory focuses on the interaction of our microbiome with diet and how this interaction impacts wellness. We use culture-dependent and -independent methods to understand the impact of the digestive tract bacteria in health and disease such as cancer.

Stephen Kachman

• Investigator, Nebraska Gateway to Nutrigenomics
• Professor and BORC Biostatistics Coordinator, Department of Statistics

Dr. Kachman's research is focused on the development and application of statistical methodology in the area of statistical genomics. Currently he is working on methodology on incorporating genomic information, primarily in the form of SNP genotypes, into national beef cattle evaluation (Matthew Spangler, Department of Animal Science). The statistical methodology development includes extensions based on generalized linear mixed models and Bayesian models. Other projects include genomics of swine reproduction (Daniel Ciobanu, Department of Animal Science, UNL), modeling of the host genetics influence of their gut microbial communities (Andrew Benson, Department of Food Science and Technology, UNL), genetic components of biological responses to stress (Lawrence Harshman, School of Biological Sciences, UNL), and statistical models for the evaluation of teachers and programs (Walter Stroup, Department of Statistics, UNL).

Tricia LeVan

• Director, Facility for Mutation of Methylation Analysis
• Associate Professor, Department of Epidemiology , University of Nebraska Medical Center

Dr. Levan's research interests include:  genomic medicine, genetic epidemiology, gene by environment interactions in COPD and asthma, functional genomic studies, and genetic and epigenetic influences of pathogen colonization in the lung.

Featured Publications

Boissy RJ, Romberger DJ, Roughead WA, Weissenburger-Moser L, Poole JA, LeVan TD. Shotgun pyrosequencing metagenomic analyses of dusts from swine confinement and grain facilities. PLoS One. 2014 Apr 18;9(4):e95578. doi:10.1371/journal.pone.0095578. eCollection 2014. PubMed PMID: 24748147; PubMed Central PMCID: PMC3991671.

Etsuko Moriyama

• Professor, School of Biological Sciences

Dr. Moryiama is interested in bioinformatics, molecular evolution, and molecular population genetics. Owing to many genome projects, almost infinite amount of molecular data is becoming available. They are filled with evolutionary footprints. Her interest revolves around mining such information from sequence data, reconstructing the evolutionary process of sequences, genes, and genomes, and applying knowledge we gain from these analyses for protein function prediction and gene mining.

Robert Norgren

• Professor, Department of Genetics, Cell Biology and Anatomy at the University of Nebraska Medical Center

The Norgren lab is focused on applying genomics to nonhuman primate models of human disease. The lab has developed a number of key resources necessary for nonhuman primate research including a Rhesus Macaque Genome Array (in collaboration with Affymetrix) for gene expression studies and a new rhesus macaque genome assembly and annotation which is widely used for NextGen sequencing studies with this species. In collaboration with the Byrareddy lab, we are looking at the interaction of the microbiome with rhesus macaques in health and disease. Rhesus macaques are important animal models for the study of vaccines and therapeutics for infectious diseases such as HIV.

Kurt Piepenbrink

• Assistant Professor, Department of Food Science and Technology

The goal of Dr. Piepenbrink’s research program is to elucidate the molecular mechanisms by which bacteria interact with their surroundings; this includes host cells, abiotic surfaces, extracellular structures and, in particular, other bacteria. Dr. Piepenbrink’s group is approaching the basic question of how bacteria self-assemble into communities by applying the lenses of structural biology and biophysics to microbial surface structures.

Amanda Ramer-Tait

• Harold and Esther Edgerton Associate Professor, Department of Food Science & Technology

Research interests in the Ramer-Tait laboratory center on the dynamic interactions between the mucosal immune system and intestinal microbial communities. Current research projects are aimed at understanding how host-microbial interactions in the gastrointestinal tract contribute to the pathogenesis of chronic, inflammatory diseases, including inflammatory bowel diseases and obesity. We are also intensively involved in research concerning the interactions among diet, the gut microbiota, and the immunological and metabolic health of the host. To study these complex relationships in vivo, we employ conventional flora, germ-free, and defined microbial community mouse model systems. We utilize approaches spanning the disciplines of cell biology, microbiology, and immunology to mechanistically interrogate the regulation of gastrointestinal homeostasis and inflammation.

Heather Rasmussen

• ASSOCIATE PROFESSOR, DEPARTMENT OF NUTRITION AND HEALTH SCIENCES
• DIRECTOR, DIETETIC INTERNSHIP

Devin Rose

• Associate Professor, Departments of Agronomy and Horticulture and Food Science & Technology

The Rose lab applies our expertise in cereal chemistry with an emphasis on carbohydrates and nutrition to determine the importance of whole grains and dietary fibers in the diet. We believe that part of the key to unlocking the benefits of whole grains and dietary fibers lies in understanding how these materials interact with the bacteria in our gastrointestinal tract. To this end, we have developed and use several in vitro approaches to evaluate gut-health-promoting properties of dietary constituents. We also conduct in vivo feeding trials in humans and mice to how assess changes in gut bacteria are associated with health outcomes (reduction in inflammation, fasting blood glucose, etc.). Through these efforts we aim to introduce grains and dietary fibers with established health benefits that are mediated through their interactions with the gut microbiome.

Featured Publications

James Schnable

• Center for Plant Science and Innovation
• Quantitative Life Sciences Initiative
• Assistant Professor, Department of Agronomy and Horticulture

Dr. James Schnable's research group at the University of Nebraska–Lincoln works on developing new methods to combine information from corn, sorghum, and related orphan crops and wild species to identify genetic changes that alter crop traits important to farmers and food traits important to consumers. Working closely with computer scientists, statisticians, engineers, and applied plant breeders his research group develops new quantitative genetic and high throughput phenotyping techniques to analyze novel types of data, including high throughput RGB and hyperspectral imagery collected from plants on a daily basis and parallel genome wide association studies in corn, sorghum and foxtail millet. As part of the Nebraska Food for Health Center, he is working to identify genes in corn and sorghum that alter the biochemical composition of these foods and produce different perturbations of the human gut microbiome when consumed.

Hyun-Seob Song

• Associate Professor, Departments of Biological Systems Engineering and Food Science and Technology

The Song research group focuses on 1) developing model-data integration methods for understanding fundamental mechanisms of interspecies interactions in microbial communities and 2) applying ecological principles for microbiome engineering. The primary goal of human microbiome research in his group is to develop predictive community models for unraveling the relationships among perturbations, composition and functional activities in microbial communities (in particular, in the gut microbiota), and health and disease. For this purpose, they use a suite of complementary in silico tools for synergistic integration, including data-driven computational analysis (such as network inference and machine learning) and physics-based microbial modeling (such as metabolic network reconstruction, agent-based modeling, and cybernetic modeling).

Harkamal Walia

• Associate Professor, Department of Agronomy and Horticulture
• Robert B. Daugherty Water for Food Institute Fellow

Unfavorable environmental conditions such as drought, high temperature stress, salinity, and flooding result in heavy crop yield losses in the U.S. and worldwide. These stressful conditions are increasingly associated with a shift in agriculture to marginal lands, inherent uncertainty associated with extreme precipitation events and spikes in temperatures especially during yield sensitive developmental stages of crops. Dr. Walia’s research interest is in understanding how plants adapt to these environmental stresses. I am particularly interested in the physiological and genetic characterization of crop responses to drought, heat and salt stress.

Yanbin Yin

• ASSOCIATE PROFESSOR, DEPARTMENT OF Food Science & Technology

The Yin lab’s research falls into the Genomics and Bioinformatics Data Sciences. In relation to food for health research, our lab has been studying carbohydrate active enzymes (CAZymes) and CAZyme gene clusters (CGCs, also known as polysaccharide utilization loci or PULs) in both plants and microbes. We develop new computational models and informatics tools (e.g., dbCAN) that help automatically identify CAZymes and CGCs in the gut microbiome that can build, modify, and break down various complex carbohydrates. We are also interested in data mining gut microbial and viral microbiome for other important genetic elements (e.g., orphan genes, horizontally transferred genes, anti-CRISPR genes) to enhance their biotechnological and biomedical applications and understand genome biology/evolution.

Computational tools that are developed in the Yin lab include:

dbCAN: http://bcb.unl.edu/dbCAN2