Gut bacterial nutrient preferences quantified in vivo.

TitleGut bacterial nutrient preferences quantified in vivo.
Publication TypeJournal Article
Year of Publication2022
AuthorsZeng, X, Xing, X, Gupta, M, Keber, FC, Lopez, JG, Lee, Y-CJ, Roichman, A, Wang, L, Neinast, MD, Donia, MS, Wühr, M, Jang, C, Rabinowitz, JD
JournalCell
Volume185
Issue18
Pagination3441-3456.e19
Date Published2022/09/01
ISSN1097-4172
KeywordsAnimals, Bacteria, Diet, Dietary Fiber, Dietary Proteins, Gastrointestinal Microbiome, Lactates, Mice, Nutrients
Abstract

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.

DOI10.1016/j.cell.2022.07.020
Alternate JournalCell
PubMed ID36055202
PubMed Central IDPMC9450212
Grant ListDP1 DK113643 / DK / NIDDK NIH HHS / United States
R35 GM128813 / GM / NIGMS NIH HHS / United States
T32 CA257957 / CA / NCI NIH HHS / United States
T32 GM007388 / GM / NIGMS NIH HHS / United States