@article{204341,
  keywords = {methodology, metabolomics, proteomics, Mice, Diet, metabolism, nutrient, microbiome, isotope tracing, host-microbiome interactions},
  author = {Xianfeng Zeng and Xi Xing and Meera Gupta and Felix C. Keber and Jaime G. Lopez and Ying-Chiang J. Lee and Asael Roichman and Lin Wang and Michael D. Neinast and Mohamed S. Donia and Martin W{\"u}hr and Cholsoon Jang and Joshua D. Rabinowitz},
  title = {Gut bacterial nutrient preferences quantified in vivo},
  abstract = {<p>Summary Great progress has been made in understanding gut microbiomes{\textquoteright} 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.</p>
},
  year = {2022},
  journal = {Cell},
  volume = {185},
  pages = {3441-3456.e19},
  month = {07/2022},
  issn = {0092-8674},
  url = {https://www.sciencedirect.com/science/article/pii/S0092867422009230},
  doi = {10.1016/j.cell.2022.07.020},
  language = {eng},
}