University of California, Davis

Beyond Nutrition: How UC Davis Research is Expanding the Boundaries of Human Health

A Focus on Forgotten Crops

UC Davis is partnering in a global plant-breeding consortium fighting malnutrition and poverty in Africa by improving the continent’s traditional crops.

The African Orphan Crop Consortium—conceived by Howard Shapiro, a senior fellow at UC Davis and the chief agricultural officer at Mars Inc.— is making great strides in its ambitious attempt to map and make public the genomes of 101 African food crops. 

These “orphan” crops are crucial to African livelihood and nutrition, but have been mostly ignored by science and agricultural companies because they are not traded internationally, like rice, corn, and wheat. The genomic data gathered on African orphan crops will help plant breeders select more quickly for traits that improve the nutritional content, productivity, and resilience of Africa’s most important food crops.

The consortium’s ultimate goal is to eradicate stunting, a condition caused by chronic malnutrition that affects 195 million children worldwide. In some countries in Africa, about 40 percent of children under 5 are stunted and never reach their full potential—physically, mentally, or economically.“I believe this project will succeed where others have failed because it focuses on crops that have evolved to grow here,” said Busiso Mavankeni, plant breeder with Zimbabwe’s Department of Research and Specialists Services and a recent graduate of the UC Davis Plant Breeding Academy in Africa, the educational arm of the consortium. “By improving these neglected crops, we help the children who eat them and the farmers who depend on them to support their families.”

At the UC Davis Plant Breeding Academy held in Nairobi, Kenya, Africa’s top breeders learn how to incorporate genomic information, statistics, and the latest breeding strategies into their programs.

Initially, the consortium planned to sequence the genome of about 16 African crops. “We were told in order to have any impact on nutrition we would need to improve at least 100 crops,” Shapiro said. “In the end, we went with 101 crops, including the Baobab tree, which can survive even the worst drought. You can eat its leaves, which are actually quite tasty.”

The group collaborates with researchers all over the world, and all of its sequence information will be posted to the Web and offered free to anyone on condition it not be patented.

“Because we share our information, we can build on each other’s research,” said Allen Van Deynze, professional researcher with the Department of Plant Sciences. “We hope to have five genomes out for public review within the next six months.”

Gut Ecology Matters

Eating nutritious food is important for good health, but it’s not the only ingredient. People benefit from good genes, for example, and access to health care, clean water, proper sanitation, and a healthy balance of bacteria in their gut.

Gut bacteria are the trillions of microbes that live in our intestines. They have co-evolved with mammals and greatly influence our health. We provide our community of intestinal bacteria—or gut microbiome—nutrients and a warm place to grow. In return, the microbiome helps us digest food, produces vitamins we can’t make, improves our immune system, and helps us harvest energy from our food.

In short, healthy bodies support hardy communities of microbes. But what comes first, the healthy body or the robust gut microbiome? New research is uncovering clues to cause and effect in nutrition, and the influence that our microbial comrades have on human health.

Microbes and Malnutrition

Professor Kathryn Dewey with the UC Davis Department of Nutrition was one of several co-authors of a study recently published in Science that shows microbes can influence an infant’s growth, rather than merely respond to that growth. Dewey worked with a team led by Jeffrey Gordon from the Washington University School of Medicine in St. Louis.

Malnourished children have underdeveloped gut microbiomes—their microbiological age lags behind their biological age. The team transplanted stool samples from underweight and normal weight Malawian infants into germ-free baby mice. The mice that received the microbes from the underweight infants gained less weight and developed weaker bones than those that received a healthy baby’s microbiome, even though they ate the exact same diet.

“It was stunning,” Dewey said. “The findings clearly indicate that the proper development of gut microbiota is important for normal growth.”

To further test microbial influence, researchers housed mice with healthy and immature microbiomes together in one cage. Their gut microbiomes mingle easily, because mice practice coprophagia (the eating of feces). Researchers discovered that the healthy communities of bacteria dominated the immature ones—invading and displacing them—so both sets of mice ended up with a healthy balance of bacteria.

The research team identified five species of bacteria that colonized especially well and had a strong influence on the growth of their host, favoring the conversion of amino acids in their diet into flesh and muscle.

Testing Milk Compounds

There’s still much to learn, such as why the microbiome in malnourished infants stalls in the first place. Complex sugars in breast milk and in cow’s milk provide an important clue, according to a separate study involving Jeffrey Gordon from Washington University School of Medicine and David Mills, professor of food science and technology at UC Davis.

Previously, Mills and other UC Davis researchers have shown that breast milk is especially beneficial to human development because some of its complex sugars, or oligosaccharides, feed gut bacteria that boost a baby’s immunity. In a recent study reported in the journal Cell, Mills and others found that a specific type of these oligosaccharides called sialylated milk sugars are present at lower levels in the breast milk of mothers of malnourished children than in the breast milk of mothers of healthy children.

To explore that correlation, researchers transferred gut microbes from malnourished infants into germfree mice and piglets. They fed the mice and piglets a diet supplemented with oligosaccharides derived from cow’s milk, and their microbiomes improved. The bacteria in their guts became metabolically flexible, more able to switch to burning fat for energy when sugar isn’t available, something the microbiomes in undernourished mammals can’t do.

Breast milk contains many more of these important sugars than cow’s milk, but cow’s milk has the advantage of sheer volume. When the dairy industry makes cheese, the watery liquid that remains contains oligosaccharides. It is typically discarded as waste.

“There’s great value in that waste stream,” Mills said.

Industry partner Hilmar Cheese Company provided the oligosaccharides derived from cow’s milk for this study. Hilmar’s cheese-processing facility in Merced has the technical capacity and expertise to separate oligosaccharides from cheese-making waste streams. “This is a wonderful example of the dairy industry serving as a hands-on partner with UC Davis to make these high-end milk byproducts available for research,” Mills said.

It’s All Connected

What role does good nutrition play in the health and development of children? That’s the question Christine Stewart, a professor in the UC Davis Department of Nutrition, is helping address. She works with an international team on a project called “WASH Benefits,” measuring the combined impact of water quality, sanitation, hand-washing, and nutritional interventions during a child’s first years of life.

“We’re working with 5,500 families in Bangladesh and 8,000 families in Kenya,” Stewart said. “I’m looking at the nutritional aspects, providing education and nutrient-rich supplements to mothers to feed their infants.”

Poor nutrition and intestinal infection are closely connected. Malnourished children are more prone to infection.

“When children are fighting an infection, they aren’t hungry, their gut microbe balance is off, and they are not as able to absorb nutrients,” she added. “WASH Benefits is looking at all the interconnected pieces to determine what combination of interventions has the most impact and the best chance to succeed in improving child growth.”

“Nutritional security goes beyond providing access to nutritious food,” said Dewey, who has coordinated international research efforts to formulate and evaluate cost-effective supplements to pregnant and nursing women and their infants in impoverished nations. “Nutritional interventions must be coupled with comprehensive strategies for providing access to health care, adequate sanitation, clean water, and other factors that influence the ability to utilize nutrients for growth and development.”

Care For Your Bacteria

The jury is still out on what recent gut-bacteria research means for healthy adults, besides to keep eating your vegetables.

“And fruits and proteins and grains—as many different varieties as you can find, which isn’t easy in this day and age,” said Professor Carolyn Slupsky with the departments of nutrition, and food science and technology. “One of the many good things about the African Orphan Crop Consortium is it supports growing a wide variety of nutritious, traditional crops, which is good for humans and for the planet.

“The community of microbes inside our body is like the ecology of microbes in the ocean and soil and everywhere else on earth,” Slupsky continued. “Take care of your microbiome, and it will take care of you.”

Reprinted from University of California, Davis CA&ES Outlook Spring/ Summer 2016

Dr. Howard Shapiro
Busiso Mavankeni
Dr. Allen Van Deynze
Dr. Kathryn Dewey
Dr. Jeffrey Gordon
Dr. David Mills
Dr. Christine Stewart
Dr. Carolyn Slupsky
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