A new study sheds light on the behavior of yeast cells in the gut, paving the way for new lines of yeast that more efficiently produce therapeutic drugs tailored to address specific diseases.

“Yeast is promising as a drug-delivery platform,” says Nathan Crook, corresponding author of the study and an associate professor of chemical and biomolecular engineering at North Carolina State University. “Previous work has shown that yeast cells can be modified to produce specific molecules in the gut, such as therapeutics that can reduce inflammation, help fight disease, and so on. However, while we know that yeasts can do this, we don’t know how the yeast cells are doing this. Which genes are turned off or on? What is the yeast eating? Is the yeast producing any other molecules that might be harmful?

“Our goal with this project was to measure gene expression of Saccharomyces boulardii (Sb) yeast cells in the gut. That information is critical if we want to engineer these cells to make them more efficient and effective drug-delivery vehicles.”

The researchers chose to work with Sb yeast because it is the only species of yeast that is already in use as a probiotic, but the biochemical processes of the species have not been well studied. For this study, the researchers used an off-the-shelf strain of Sb yeast that had not been genetically modified in any way.

The researchers introduced the Sb yeast cells into laboratory mice that were specially raised to be “germ-free,” meaning that they had no gut microbiome. The researchers then collected fecal and intestinal samples from the mice and used a novel combination of established sampling and analytical techniques to measure the RNA produced by the yeast cells as they passed through the guts of the mice. Because the mice were germ-free, there were no other microbial species in the gut producing RNA, making it easier to identify the RNA from the yeast cells.

“One of the key findings is that we’ve identified which genes in the Sb yeast are much more likely to be activated when in the gut as opposed to other environments. That tells us which sections of DNA are most responsive to the gut environment. And that is useful because we can then target these ‘promoter’ sections of DNA as on-switches that tell the yeast cell when to start producing therapeutic molecules. In other words, we’ve identified the best candidates for helping us ensure the yeast cell is producing medicine when we want it to, which makes it a much more efficient drug-delivery platform.”

The researchers also found that genes in the yeast associated with the production of potentially pathogenic behavior were not activated while in the gut.

“This isn’t surprising, given that Sb yeast is already used as a probiotic – which would be unlikely if it was causing intestinal problems. However, it’s good to establish this before moving forward with additional efforts to engineer Sb cells for drug delivery.”

Lastly, gene activation of the yeast cells in the gut suggests that the gut is not a nutrient-rich environment for the yeast. Specifically, the yeast cells were digesting more lipids than carbohydrates.

“This is not entirely surprising, but it’s important because if we want the yeast cells to essentially serve as factories that produce medicine on-site, then you need those cells to have energy to do their work efficiently. Our findings suggest it may be beneficial to modify the yeast cells so that they can make better use of the complex carbohydrates in the gut ecosystem.

“We’re optimistic about the potential of Saccharomyces boulardii for the development of new pharmaceuticals, and this work provides a roadmap for the most promising paths forward.”

The paper, “Transcriptomic Responses of Saccharomyces boulardii to the Germ-Free Mouse Gut,” is published open access in the journal BMC Genomics. Co-lead authors of the paper are Genan Wang, a postdoctoral researcher at NC State; and Deniz Durmusoglu, a former Ph.D. student and postdoctoral researcher at NC State.

The authors have filed patent applications and invention disclosures related to the engineering of probiotic yeast.

This work was done with support from the National Science Foundation, under grant 1934284; the Novo Nordisk Foundation, under grant NNF19SA0035474; and the National Institutes of Health, under grant 1DP2AT012795-01.