University of Nebraska-Lincoln researchers have identified sorghum genes and traits — including seed color — that contribute to a healthy gut microbiome, and the ecosystem of microorganisms that live in GI tracts. This groundbreaking discovery paves the way for the identification of additional traits in sorghum and other crops that have the potential to improve human health, as well as for the emergence of new crop varieties developed with the health of the microbiome in mind.
The Nebraska Food Research for Health project focused on the traits and outcomes of sorghum seed, “Genetic analysis of seed traits in bicolor sorghum that affect the human gut microbiome,” It was recently published in Nature Communications. The principal investigator was Qinnan Yang, a postdoctoral researcher in the Department of Food Science and Technology. Other Husker scholars who contributed to the project were Andrew K. Benson, the corresponding author of the paper, and co-authors Mallory Van Huet, Nate Kurth, Scott E. Sattler, John Toye, Devin J. Rose, and James C. Schnabel.
Among their findings, the researchers identified segments on nine sorghum chromosomes where genetic differences lead to a significant impact on the microbiome’s fermentation activity. Scientists eventually found a significant association linking sorghum seed color, the presence of tannin in sorghum seeds, and effects on microorganisms: sorghum varieties with the functional genes Tan1 and Tan2 have dark-colored seeds and stimulate the growth of a range of microorganisms including Faecalibacterium and Roseburia and Christensennella.
Identifying the traits of the seeds that encourage the growth of the microbiome of these bacteria is medically important because they are linked to significant health benefits: reduced susceptibility to inflammatory bowel disease, as well as some metabolic diseases.
Husker’s research showed that light-colored seeds failed to encourage the production of such microbes.
“Now that we’ve shown that plant genes can control changes in the human gut microbiome, we can use our approach to examine hundreds or thousands of samples from different crops,” Yang said. “This makes it possible for plant breeding programs to take advantage of the natural genetic diversity in crops to breed new crop species that improve human health by promoting beneficial bacteria in the human gut.”
For this project, Food Center for Health researchers used a multi-stage laboratory technology that replicates the digestive and digestive activity of the human body by grinding selected samples of sorghum and placing the powder into test tubes for processing and analysis. Scientists faced a significant obstacle in advance, because the equipment in place for such a study is extensive and lacks the ability to process a large volume of samples in a rapid manner.
In this case, the Food Center for Health scientists needed to examine nearly 300 different lines of sorghum in time.
After extensive discussion and collaboration, including with industry, Center for Food for Health researchers have solved the problem by developing a micro-automated methodology they call Automated In Vitro Microbiome Assay (AiMS). At present, the Nebraska Institute of Agriculture and Natural Resources is the only academic institution in the world that uses this innovative technology to analyze seed/microbiome traits.
The Nature Communications paper is the first of many academic papers IANR Scientists prepare from their AiMS-enabled studies.
The concept of AiMS was nothing more than a dream six years ago. “Now, it has become a reality,” said Benson, director of the Center for Food for Health and the Presidential Chair of Food for Health in the Division of Food Science and Technology.
The AiMS methodology has many uses. With it, Husker scientists can screen a large set of genetic material for only a small group of people, or they can screen a large group of people for a small set of genetic traits. They can study the microbiome activity of healthy participants as well as participants with health challenges. They can study the metabolism of the intestines in humans and also in animals that are fed. Studies of seed traits can analyze the effects of the microbiome of any food crop.
“It’s really a powerful technology,” Benson said. “The sky is the limit for this.”
These steps forward represent the realization of the vision that has underpinned the Center for Food for Health since its inception, beginning with a set of preliminary papers by Benson and Robert Hotkins, Associate Professor of Food Science and Technology, drawn up in 2006 and 2007. DNA Sequencing technology was beginning to appear on the scientific horizon, they wrote, and the university needed to think strategically about how to use those new tools to make significant research contributions.
In subsequent years, IANR Faculty and administrators have pursued this vision through strategic discussions. the 2017 launch of the Food for Health Center and nutritional traits and microbiome research facilities on the Nebraska Innovation Campus; Major philanthropic and Husker investments in initiatives such as Gnotobiotic Mouse Facility and AiMS Technology; Ongoing collaboration across disciplines.
Benson said the Nature Communications paper is the beginning of a new phase of discovery at the Food Center for Health. The paper is “kind of on the front end. The joy now is to see how what we discover translates to the rest of the center. And the great thing is that we have collaborating researchers out there to do that. They are just waiting” for important follow-up projects and analysis.
All of these developments, Benson said, “go back to 2006 and 2007, when we said, ‘Gee, what if…’ Now, he said, ‘We’re here, actually trying to do it.'” “