Dr. Hutkins appears on NET radio--listen to his comments on raw cheese here.

Read our paper on Individuality of Gut Microbiota Composition in PNAS Early Edition.

The Gut Function Initiative was founded in 2006 by a group of microbiologists, nutritionists, and animal geneticists who came together to capture the technological and knowledge explosions in microbial ecology and the gut ecosystem.

The gut ecosystem of humans and monogastric animals is largely comprised of bacteria numerically ranging from 1,000,000 cells / milliliter in the upper portion of the small intestine to more than a trillion cells per gram in the large intestine. Collectively, these organisms are referred to as the “microbiota”. In humans and animals, the gut microbiota is dominated by species belonging to just five of the almost 100 known phyla in the bacterial kingdom. At the species level, however, the combination of taxa is extremely complex and the system likely features substantial taxonomic and functional redundancy. As a group, the microbiota behaves much like a metabolic organ, with multitudes of biochemical pathways that are generally lacking in the host. A mutualistic ecological relationship is believed to connect the host and the microbial community. Composition of the microbiota is generally conserved across members of the same host species. However, the conservation is most evident largely at higher taxonomic levels (family and above), which, again, points to functional redundancy as a possible built-in feature of the system. The conserved composition is very likely to be an important “trait” of a host because aberrations in composition of the microbiota are known to be associated with many diseases, including obesity, inflammatory bowel disease, and colonic cancers.

Given the rapidly growing body of knowledge about the gut ecosystem and the new tools of high-throughput DNA sequencing that allow analysis of complex ecosystems, the UNL Gut Initiative originated as a group of researchers with a common purpose to understand the relationship between the gut ecosystem and health and performance characteristics of humans and animals. Our ultimate goal is to translate our understanding into agricultural products that promote development and maintenance of healthy microbiota and which allow intervention in instances of disease. Complementing the health objectives, understanding how the gut microbiome is shaped in food animals will have significant impact on our ability to eliminate gut-borne zoonotic pathogens, which comprise the large proportion of foodborne pathogenic microorganisms. The initiative has three major research directions, each geared to synergistically contribute to our understanding of the gut ecosystem.

These objectives are:

1. To understand the microbial factors that influence the ability of species to colonize the GI tract
2. To understand host factors that shape the composition of the gut microbiome
3. To understand how dietary and other environemtnal factors shapes composition of the gut microbiome.

Members of the GFI collaborate on many highly interdisciplinary, large-scale research projects. These projects rely on the technical expertise of the GFI faculty and are supported by two very important core facilities: the Core for Applied Genomics and Ecology (CAGE) and the Germfree Mouse Facility (GMF). CAGE provides high throughput DNA sequencing capabilities that are used to analyze the composition of the complex GI microbiota. CAGE operates a Roche/454 pyrosequencer and maintains the bioinformatics pipelines to provide filtered data for GFI projects. CAGE operates as a self-funded core facility, but does provide its Next Gen sequencing services to researchers across the UNL and UNMC campuses at cost. GMF is a highly specialized facility for growing and maintaining mice under germ-free environments. This capability allows GFI researchers to specifically colonize these sterile animals with a single species of microorganism, allowing study of how a single organism interacts with the GI tract.