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Venturelli Lab Develops Computational Model to Predict Butyrate Production by the Human Gut Microbiome

Researchers have developed the capability to predict and design the metabolic activities of microbial communities, which has broad implications for human health, agriculture and bioprocessing.

In a paper released May 31st in Nature Communications [link], Biochemistry Assistant Professor Ophelia Venturelli and Ryan Clark, formerly a postdoc in the Venturelli lab and now of Nimble Therapeutics, present a new computational model that predicts the community dynamics and production of the metabolite, butyrate, to explore a vast landscape of possible human gut communities. 

Photo of Prof Ophelia VenturelliOphelia Venturelli
Photo of Ryan ClarkRyan Clark

The human gut microbiome is highly complex due to myriad microbial interactions among community members and environmental factors such as pH and nutrients.

Researchers are interested in identifying what combinations of human gut species can perform certain desired metabolic functions. With this information, scientists could design communities with targeted outcomes.

For example, they could build communities to restore the gut microbiome to a healthy state following disturbance; enhance nutrient extraction from food; enhance nitrogen fixation for plants; or enhance the production of valuable compounds from renewable resources. 

“One of the challenges,” said Venturelli, “is that the number of possible communities increases exponentially with the number of possible organisms.”

That’s where the new model comes in.

In the study published in Nature Communications, researchers looked at butyrate, a fermentation end product produced by gut bacteria that has numerous health benefits. They used the computational model to explore the butyrate production landscape, and were able to accurately predict community assembly and butyrate production, and identify communities that have high butyrate production.

“Guided by our model,” said Venturelli, “we identified key ecological and molecular mechanisms shaping butyrate production in our system.”

This information provides insight into mechanisms that scientists can use to manipulate butyrate production in the human gut, which has potential effects on myriad health outcomes related to such diseases as colitis, diabetes, and colorectal cancer.

This successful deployment of the new model opens doors for scientists to guide the design of community metabolic activities.

“It also provides a framework for identifying significant interactions shaping these functions,” said Venturelli, “which will advance our ability to engineer the microbiome to our benefit.”

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