The goal of the Microbial Ecology and Theory of Animals Center in Systems Biology (META CSB) at the University of Oregon is to create the foundation for a new field of host-microbe Systems Biology. Our Center will innovate the tools, experimental approaches, best practices, analytical frameworks, and conceptual models required to describe how host-microbe systems organize, how hosts and microbes interact dynamically through space and time, and how these systems evolve. We will focus on the complex host associated microbial system of the vertebrate intestine and will study both sides of the interaction, characterizing the microbial communities as well as the host responses in toto with respect to their components, dynamics, and the evolutionary forces driving their interactions. We will use two fish models, zebrafish and stickleback, to perform well-controlled, manipulative experiments that mirror host-microbe interactions in humans. Our investigations will combine the theoretical rigor of community ecology and population biology with the experimental elegance of our gnotobiotic fish models, whose bacterial communities can be entirely defined. We will exploit innovations in sequencing technology and live imaging to create comprehensive large-scale datasets describing the membership and dynamics of host-associated microbial communities and corresponding host responses. We will innovate applications of sampling theory, spatial biodiversity theory, and probabilistic models to analyze our data and deduce system-level properties about host-microbe system assembly, dynamics, and evolution. The knowledge and approaches we develop for host-microbe Systems Biology will be directly applicable to studies of microbial communities associated with humans, such as the Human Microbiome Project, and will revolutionize the understanding of numerous diseases including inflammatory bowel diseases, diabetes, cancers, asthma, and autism. Our innovative and integrated approaches to scientific inquiry, education, and outreach will create a fertile training environment for a new and diverse generation of host-microbe System Biologists.

Public Health Relevance

Every human is an ecosystem inhabited by microbial communities that profoundly affect our health. The META CSB will pioneer systems-level studies of the assembly, dynamics, and evolution of host-microbe systems. Our discoveries and innovations will advance knowledge of human diseases with perturbed host associated microbial communities such as inflammatory bowel diseases, diabetes, cancers, and autism.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Specialized Center (P50)
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Special Emphasis Panel (ZGM1)
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Sledjeski, Darren D
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University of Oregon
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United States
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Burns, Adam R; Stephens, W Zac; Stagaman, Keaton et al. (2016) Contribution of neutral processes to the assembly of gut microbial communities in the zebrafish over host development. ISME J 10:655-64
Mason, Timothy; Snell, Kathy; Mittge, Erika et al. (2016) Strategies to Mitigate a Mycobacterium marinum Outbreak in a Zebrafish Research Facility. Zebrafish :
Wiles, Travis J; Jemielita, Matthew; Baker, Ryan P et al. (2016) Host Gut Motility Promotes Competitive Exclusion within a Model Intestinal Microbiota. PLoS Biol 14:e1002517
Hill, Jennifer Hampton; Franzosa, Eric A; Huttenhower, Curtis et al. (2016) A conserved bacterial protein induces pancreatic beta cell expansion during zebrafish development. Elife 5:
Milligan-Myhre, Kathryn; Small, Clayton M; Mittge, Erika K et al. (2016) Innate immune responses to gut microbiota differ between oceanic and freshwater threespine stickleback populations. Dis Model Mech 9:187-98
Zac Stephens, W; Burns, Adam R; Stagaman, Keaton et al. (2016) The composition of the zebrafish intestinal microbial community varies across development. ISME J 10:644-54
Preston, Jessica L; Royall, Ariel E; Randel, Melissa A et al. (2016) High-specificity detection of rare alleles with Paired-End Low Error Sequencing (PELE-Seq). BMC Genomics 17:464
Klein, Ann M; Bohannan, Brendan J M; Jaffe, Daniel A et al. (2016) Molecular Evidence for Metabolically Active Bacteria in the Atmosphere. Front Microbiol 7:772
Hammers, Matthew D; Taormina, Michael J; Cerda, Matthew M et al. (2015) A Bright Fluorescent Probe for H2S Enables Analyte-Responsive, 3D Imaging in Live Zebrafish Using Light Sheet Fluorescence Microscopy. J Am Chem Soc 137:10216-23
Stagaman, Keaton; Martinez, Emily S; Guillemin, Karen (2015) Immigrants in immunology: the benefits of lax borders. Trends Immunol 36:286-9

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