Gut bacterial nutrient preferences quantified in vivo

Xianfeng Zeng, Xi Xing, Meera Gupta, Felix C. Keber, Jaime G. Lopez, Ying Chiang J. Lee, Asael Roichman, Lin Wang, Michael D. Neinast, Mohamed S. Donia, Martin Wühr, Cholsoon Jang, Joshua D. Rabinowitz

Research output: Contribution to journalArticlepeer-review

57 Scopus citations


Great progress has been made in understanding gut microbiomes’ products and their effects on health and disease. Less attention, however, has been given to the inputs that gut bacteria consume. Here, we quantitatively examine inputs and outputs of the mouse gut microbiome, using isotope tracing. The main input to microbial carbohydrate fermentation is dietary fiber and to branched-chain fatty acids and aromatic metabolites is dietary protein. In addition, circulating host lactate, 3-hydroxybutyrate, and urea (but not glucose or amino acids) feed the gut microbiome. To determine the nutrient preferences across bacteria, we traced into genus-specific bacterial protein sequences. We found systematic differences in nutrient use: most genera in the phylum Firmicutes prefer dietary protein, Bacteroides dietary fiber, and Akkermansia circulating host lactate. Such preferences correlate with microbiome composition changes in response to dietary modifications. Thus, diet shapes the microbiome by promoting the growth of bacteria that preferentially use the ingested nutrients.

Original languageEnglish (US)
Pages (from-to)3441-3456.e19
Issue number18
StatePublished - Sep 1 2022

All Science Journal Classification (ASJC) codes

  • General Biochemistry, Genetics and Molecular Biology


  • diet
  • host-microbiome interactions
  • isotope tracing
  • metabolism
  • metabolomics
  • methodology
  • mice
  • microbiome
  • nutrient
  • proteomics


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