Research Areas

Researchers across several Penn State colleges, departments, and centers are exploring microbiomes in soils, biocrusts, coral reefs, endangered amphibiansand geological settings, in both natural and man-made environments. This research also asks questions about how environmental microbiomes respond to changes in climate or ecology, and how these changes may be leveraged to improve key problems today in climate change, deforestation, and fire.

Researchers are trying to understand how microbiomes are linked to human health in all areas of the body. Many projects are working to understand which microbes are critical for disease initiation, treat metabolic disease with probiotics, and explore microbial transplantation as a solution to microbiome-associated diseases.

Integrative Analysis of Metabolic Phenotypes (IAMP)

The primary objective of the NIH T32 IAMP is to offer trainees specialized interdisciplinary training in the fundamental principles and cutting-edge tools for studying metabolism and shared host-microbiome metabolism. The IAMP program prepares trainees to work at the intersection of these disciplines, fostering future leaders in academia and industry who are pioneers in metabolic research. IAMP training aligns with the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) mission to advance medical research and training in diabetes, endocrine and metabolic diseases, digestive issues, nutrition, obesity, as well as kidney, urologic, and hematologic diseases to enhance health. Trainees are supported for two years as a part of their doctoral program.

Researchers in OHMC explore the microbial contributions to output and diseases of crops and livestock, discovering how microbiomes can be leveraged to improve food production, quality, and nutritional values in foods, as well as soil and plant health. Researchers are also exploring the effects of antibiotic resistance in food production and how integrating microbiomes into classical food science research may reduce foodborne illnesses.

The United States Department of Agriculture's National Institute of Food and Agriculture (USDA NIFA) awarded Penn State a five-year training grant to establish a first-of-its-kind graduate student pipeline centered on animal reproductive microbiomes. Led by the Center for Reproductive Biology and Health (CRBH) and the One Health Microbiome Center (OHMC), this initiative funds fellows researching how complex microbial communities interact with the reproductive tissues of livestock—such as cattle, pigs, and poultry—as well as insect pests. By preparing scientists to explore critical links between the microbiome, fertility, pregnancy, lactation, and disease vectors, the program aims to yield breakthroughs in sustainable animal agriculture, boost livestock production efficiency, and innovate pest control methods to suppress insect-borne diseases.

The Computational Analysis, Theory, and Statistics (CATS) focal area in OHMC serves as the vital analytical engine translating massive, complex genomic datasets into actionable insights across human, animal, and environmental health. By bridging computer science, statistics, and biology, CATS demystifies the "black box" of metagenomic data through the development of novel algorithms, free access to high-performance supercomputing, and expert consultations that ensure research is statistically rigorous from the start. Through hands-on bioinformatics boot camps and collaborative working groups, the initiative actively lowers barriers to entry for researchers, establishing the open-source infrastructure needed to drive the next generation of interdisciplinary microbiome discoveries. To see an overview of how the Center delivers interconnected capacities in computation, watch Supercharging Science with ROAR and KEGG.

The Microbiome Evolution theme at OHMC is dedicated to untangling the complex ecological, genomic, and evolutionary forces that shape microbial communities over time and space. Recognizing that microbiomes do not exist in isolation, researchers utilize advanced ecoevolutionary approaches, genomic epidemiology, mutualism modeling, and pioneering ancient DNA techniques—including in the Ancient Biomolecules Research Laboratory—to reconstruct how bacterial, viral, and fungal populations evolve alongside their human, animal, and plant hosts. By tracing these deep evolutionary histories, from ancient oral cavities to phylosymbiosis and modern agricultural plant-pathogen dynamics, the theme uncovers the fundamental biological rules governing microbial symbiosis. This evolutionary lens is vital to the center's "One Health" mission, providing the historical context and predictive power needed to understand how contemporary environmental shifts, diets, and medical practices drive microbial adaptations that ultimately impact global ecosystem resilience and human wellness.

The Microbiome Art (SciArt) efforts at the OHMC pioneeringly bridges the precision of science with the boundless creativity of art to explore the dynamic, invisible boundaries of our microbial world. Collaborating closely with Penn State’s College of Arts and Architecture and visiting bio-artists, this initiative leverages visual storytelling, interactive media, and living bio-materials to translate complex microbial systems into tangible, human-scale experiences. Cutting-edge collaborations span an extraordinary range of mediums—from "MycoKnit's" exploration of mycelium-fused textiles to create biodegradable, sustainable architectural structures, to interactive game installations like "CONTACT" that physically model bacterial community dynamics, and mixed-media sculptures examining the microbiological realities of artificial wombs. Through public exhibitions, hand-on agar sculpting workshops, and interdisciplinary residencies, the center's SciArt endeavors do more than just make research accessible; they challenge our concepts of individuality, inspire next-generation green designs, and cultivate a deeper, deeply human curiosity for the microscopic ecosystems that sustain us. To see an overview of sci-art efforts, watch Synergies in Art and Science.