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Mapping the dietary sources and preferences of gut bacteria

Joshua Rabinowitz

Ludwig Princeton Director Joshua Rabinowitz and his colleagues reported in a September issue of Cell their use of isotope tracing to map the nutrients consumed by bacteria in the mouse gut and their findings on the nutritional preferences of different types of bacteria in the microbiome. Tracing the incorporation of isotopes into bacteria-specific antigens, they found that fiber and protein are the main inputs that originate from the host diet. Major inputs generated by the host were found to be lactate, 3-hydroxybutyrate and urea, but not glucose or amino acids. Josh and his colleagues also mapped the nutrient preferences of different types of bacteria by tracing isotope incorporation into genus-specific proteins. For example, most genera in the phylum Firmicutes prefer dietary protein, while those belonging to Bacteroides have a predilection for dietary fiber. Changes in the relative diversity of microbiota that are induced by diet can be explained by the nutrient preferences of different microbes. Isotope tracing revealed that adding fiber to the host’s diet boosts the proportion of microbes that thrive on fiber, while a diet rich in protein similarly affects the proportion of those with a taste for protein. The study lays the foundations for understanding how diet controls the composition of the host microbiome, which is emerging as a significant determinant of responses to cancer immunotherapy.

Gut bacterial nutrient preferences quantified in vivo
Cell, 2022 September 7

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