Functional genetics of human gut commensal Bacteroides thetaiotaomicron reveals metabolic requirements for growth across environments

Cell Rep. 2021 Mar 2;34(9):108789. doi: 10.1016/j.celrep.2021.108789.

Abstract

Harnessing the microbiota for beneficial outcomes is limited by our poor understanding of the constituent bacteria, as the functions of most of their genes are unknown. Here, we measure the growth of a barcoded transposon mutant library of the gut commensal Bacteroides thetaiotaomicron on 48 carbon sources, in the presence of 56 stress-inducing compounds, and during mono-colonization of gnotobiotic mice. We identify 516 genes with a specific phenotype under only one or a few conditions, enabling informed predictions of gene function. For example, we identify a glycoside hydrolase important for growth on type I rhamnogalacturonan, a DUF4861 protein for glycosaminoglycan utilization, a 3-keto-glucoside hydrolase for disaccharide utilization, and a tripartite multidrug resistance system specifically for bile salt tolerance. Furthermore, we show that B. thetaiotaomicron uses alternative enzymes for synthesizing nitrogen-containing metabolic precursors based on ammonium availability and that these enzymes are used differentially in vivo in a diet-dependent manner.

Keywords: Bacteroides thetaiotaomicron; bile salts; polysaccharide utilization; random barcode transposon-site sequencing.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Adaptation, Physiological
  • Ammonium Compounds / metabolism
  • Animals
  • Anti-Bacterial Agents / metabolism
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism
  • Bacteroides thetaiotaomicron / drug effects
  • Bacteroides thetaiotaomicron / enzymology
  • Bacteroides thetaiotaomicron / genetics*
  • Bacteroides thetaiotaomicron / growth & development
  • Bile Acids and Salts / metabolism
  • Databases, Genetic
  • Diet*
  • Disaccharides / metabolism
  • Drug Resistance, Bacterial / genetics
  • Energy Metabolism / genetics*
  • Gastrointestinal Microbiome / drug effects
  • Gastrointestinal Microbiome / genetics*
  • Gene Expression Regulation, Bacterial
  • Glycoside Hydrolases / genetics
  • Glycoside Hydrolases / metabolism
  • Humans
  • Intestines / microbiology*
  • Male
  • Membrane Transport Proteins / genetics
  • Membrane Transport Proteins / metabolism
  • Mice
  • Mice, Inbred C57BL
  • Mutation
  • Substrate Specificity
  • Tripartite Motif Proteins / genetics
  • Tripartite Motif Proteins / metabolism

Substances

  • Ammonium Compounds
  • Anti-Bacterial Agents
  • Bacterial Proteins
  • Bile Acids and Salts
  • Disaccharides
  • Membrane Transport Proteins
  • Tripartite Motif Proteins
  • Glycoside Hydrolases