Significance Diet is known to alter the gut microbiota composition by supplying nutrients that promote the expansion of particular microorganisms. However, we demonstrate that fructose, a common dietary additive in the Western world, decreases the abundance of a regulator of gut colonization in the human gut commensal Bacteroides thetaiotaomicron. Rendering the levels of this colonization factor refractory to silencing by fructose confers an advantage in mice fed a fructose-rich diet. We provide a singular example of the host diet controlling the amounts of a bacterial protein necessary for murine gut colonization by a beneficial gut commensal bacterium, but dispensable for growth on such dietary components.

Abstract The composition of the gut microbiota is largely determined by environmental factors including the host diet. Dietary components are believed to influence the composition of the gut microbiota by serving as nutrients to a subset of microbes, thereby favoring their expansion. However, we now report that dietary fructose and glucose, which are prevalent in the Western diet, specifically silence a protein that is necessary for gut colonization, but not for utilization of these sugars, by the human gut commensal Bacteroides thetaiotaomicron. Silencing by fructose and glucose requires the 5′ leader region of the mRNA specifying the protein, designated Roc for regulator of colonization. Incorporation of the roc leader mRNA in front of a heterologous gene was sufficient for fructose and glucose to turn off expression of the corresponding protein. An engineered strain refractory to Roc silencing by these sugars outcompeted wild-type B. thetaiotaomicron in mice fed a diet rich in glucose and sucrose (a disaccharide composed of glucose and fructose), but not in mice fed a complex polysaccharide-rich diet. Our findings underscore a role for dietary sugars that escape absorption by the host intestine and reach the microbiota: regulation of gut colonization by beneficial microbes independently of supplying nutrients to the microbiota.

The gut microbiota is critical to human health (1). The composition of the gut microbiota can be modified by diet (2⇓⇓⇓⇓⇓–8). For example, complex polysaccharides commonly referred to as dietary fiber remain undigested in the small intestine, reach the microbiota in the distal gut, and promote colonization by beneficial microbes associated with lean and healthy individuals (3, 4, 7, 9, 10). Accordingly, polysaccharide-rich diets favor expansion of those organisms that can take up and break down dietary fiber (7, 11⇓–13). Conversely, diets rich in simple sugars favor the expansion of organisms that utilize mucosal glycans because simple sugars are believed to be absorbed in the small intestine and, thus, are unavailable to the microbiota in the distal gut (12, 14).

The monosaccharide fructose can escape absorption in the small intestine and reach the microbiota in the distal gut (15, 16), where microbiota-derived products of fructose metabolism enter the host blood (15). Given the alarming increase in consumption of fructose and sucrose (a heterodimer of glucose and fructose) by Western populations (17, 18), we wondered how these simple sugars impact colonization by Bacteroides thetaiotaomicron, a member of the gut microbiota associated with lean and healthy individuals.

The BT3172 gene, herein named roc for “regulator of colonization,” is required for B. thetaiotaomicron colonization of germ-free mice fed a polysaccharide-rich diet (19). By contrast, the roc mutant exhibits no fitness defect in mice fed a simple sugar diet composed of glucose and sucrose (19). These findings suggested that Roc promotes gut colonization in a diet-dependent manner by mediating the utilization of a dietary component(s) present in the complex polysaccharide-rich diet but absent from the simple sugar chow. This is because Roc belongs to a class of proteins, designated hybrid two-component systems, that activate transcription of clustered polysaccharide utilization genes in response to a polysaccharide-derived ligand (19⇓⇓⇓⇓–24). Roc directly controls the adjacent polysaccharide utilization genes BT3173 and BT3174 (21), which likely facilitate the utilization of the Roc ligand. However, the mRNA abundance of BT3173 was less than twofold lower in the roc mutant than in the wild-type strain in bacteria collected from the ceca of mice fed a polysaccharide-rich diet (19). These results imply that the ceca of mice fed a polysaccharide-rich diet contain very low amounts of the Roc-activating ligand, the identity of which remains unknown. How, then, does diet control Roc’s ability to promote gut colonization by B. thetaiotaomicron?

We report that dietary glucose and sucrose silence Roc expression and that Roc is dispensable for utilization of glucose and sucrose-derived fructose. We establish that the mRNA leader preceding the roc-coding region is necessary and sufficient for Roc silencing by fructose and glucose. Furthermore, we engineered a strain that is refractory to silencing by these simple sugars and demonstrate that the engineered strain outcompetes wild-type B. thetaiotaomicron in mice fed glucose and sucrose. Our findings demonstrate how dietary simple sugars can suppress gut colonization in a commensal bacterium just by altering the levels of a colonization factor dispensable for the utilization of such sugars.

Materials and Methods Materials and methods including culturing conditions, strain construction, qPCR, Western blot analysis, mouse experiments, colony blotting, and sugar quantification are detailed in SI Appendix. Experiments using germ-free mice were approved by the Institutional Animal Care and Use Committee of Yale University.

Acknowledgments We thank Hubert Salvail, Bentley Lim, Liza-Marie Valle, and Diane Lazo for technical advice and support and Jennifer Aronson for comments on the manuscript. This research was supported with funds from Yale University and NIH Grant GM123798 (to E.A.G.).

Footnotes Author contributions: G.E.T., A.L.G., and E.A.G. designed research; G.E.T., W.H., N.D.S., V.R., and N.A.B. performed research; G.E.T. and W.H. contributed new reagents/analytic tools; G.E.T., W.H., N.D.S., V.R., and E.A.G. analyzed data; and G.E.T. and E.A.G. wrote the paper.

The authors declare no conflict of interest.

This article is a PNAS Direct Submission.

This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1813780115/-/DCSupplemental.