Molecular map points the way to better food choices

‘Gut health’ is a growing buzzword among foodies and dieticians alike – and for good reason. The trillions of microbes and bacteria that live in our gut are involved in countless aspects of health and disease.

Scientists at the Yale Mbiotic Sciences Institute have taken an important step toward evidence-driven personalized nutrition, tailored to individual gut health needs.

Andrew Goodman’s laboratory has generated the first systematic map showing how the molecules in certain foods interact with our unique gut bacteria. Their findings are published in the news Cell.

Building on previous research into drugs and gut bacteria, the scientists wanted to understand why different people react differently to the same foods.

“We know that diet is a huge part of our health and shapes our microbiome,” explains Elizabeth Culp, a former postdoctoral researcher in the Goodman Lab and first author of the study.

While a large body of work has described the effects of ‘macronutrients’ such as fiber on our gut microbiomes, surprisingly little is known about how other small molecule components in food cause health problems.

“Aside from anecdotal examples in the scientific literature, there is scant evidence about what dietary changes people can make to help them manage risk factors for diseases such as diabetes or cancer,” Culp said.

“It’s possible that this is because our microbiomes respond differently to the same molecules present in food.”

The scientists designed a systematic map of the interactions between small molecules in our food and various bacteria in the intestines.

The work is among the first to describe the specific microbial genes responsible for the metabolic transformation of food compounds and the mechanisms for how food compounds change our microbiomes.

Using liquid chromatography-mass spectrometry at the Yale West Campus Analytical Core, the scientists combined different molecules with gut bacteria to create growth models and maps for about 150 “xenobiotic” food compounds. Sequencing at the Yale Center for Genome Analysis allowed the team to measure the rate of change in the composition of human intestinal communities.

“We were surprised by the degree of variability,” says Goodman, CNH Long Professor and chair of Mbiotic Pathogenesis, and director of the Mbiotic Sciences Institute (MSI).

“The same nutrient could dramatically reshape the gut microbial communities of some individuals, while having virtually no impact on the microbiomes of other people,”

The molecular map provides a mechanism to explain these variable responses between different people, showing how a nutrient affects the growth of gut microbes and how that compound is metabolically altered by the microbial community.

Predicting how an individual will respond to a particular food – and ultimately how it will affect their health – remains difficult. But the findings provide a basis for understanding how metabolic responses vary between people and how these differences determine the growth of “good” or “bad” bacteria in our gut.

“If we can figure out the specific microbial genes that determine how a microbiome responds to a molecule in our food, and how these genes differ between the microbiomes of different people, correlations with diseases such as cancer, diabetes or gastrointestinal infections could become meaningful.” , concludes Culp, who is currently a scientist at Empress Therapeutics in Boston.

“This is the first step toward creating customized nutritional recommendations as part of personalized nutrition strategies.”