Fitness advantage of Bacteroides thetaiotaomicron capsular polysaccharide in the mouse gut depends on the resident microbiota
- ETH Zurich, Switzerland
- Max Planck Institute for Evolutionary Biology, Germany
- Weizmann Institute of Science, Israel
- University Hospital of Zurich, Switzerland
- University of Michigan-Ann Arbor, United States
- UPMC, CNRS, France
Abstract
Many microbiota-based therapeutics rely on our ability to introduce a microbe of choice into an already-colonized intestine. In this study, we used genetically barcoded Bacteroides thetaiotaomicron (B. theta) strains to quantify population bottlenecks experienced by a B. theta population during colonization of the mouse gut. As expected, this reveals an inverse relationship between microbiota complexity and the probability that an individual wildtype B. theta clone will colonize the gut. The polysaccharide capsule of B. theta is important for resistance against attacks from other bacteria, phage, and the host immune system, and correspondingly acapsular B. theta loses in competitive colonization against the wildtype strain. Surprisingly, the acapsular strain did not show a colonization defect in mice with a low-complexity microbiota, as we found that acapsular strains have an indistinguishable colonization probability to the wildtype strain on single-strain colonization. This discrepancy could be resolved by tracking in vivo growth dynamics of both strains: acapsular B .theta shows a longer lag-phase in the gut lumen as well as a slightly slower net growth rate. Therefore, as long as there is no niche competitor for the acapsular strain, this has only a small influence on colonization probability. However, the presence of a strong niche competitor (i.e., wildtype B. theta, SPF microbiota) rapidly excludes the acapsular strain during competitive colonization. Correspondingly, the acapsular strain shows a similarly low colonization probability in the context of a co-colonization with the wildtype strain or a complete microbiota. In summary, neutral tagging and detailed analysis of bacterial growth kinetics can therefore quantify the mechanisms of colonization resistance in differently-colonized animals.
Data availability
Relevant numerical source data for Figures and Supplementary is available in Source Data 1. Raw sequencing data accessed on ENA (https://www.ebi.ac.uk/ena/browser/home) under Project ID PRJEB57876 and PRJEB53981. Raw data and code used for generating all figures in this publication are made available in a curated data archive at ETH Zurich (https://www.research-collection.ethz.ch/) under the DOI 10.3929/ethz-b-000557179.
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Population dynamics of Bacteroides thetaiotaomicron during the early colonization of the murine gutEuropean Nucleotide Archive, PRJEB57876.
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Metabolic reconstitution by a gnotobiotic microbiota varies over the circadian cycleEuropean Nucleotide Archive, PRJEB53981.
Article and author information
Author details
Wolf-Dietrich Hardt
Funding
Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (NCCR Microbiome)
- Wolf-Dietrich Hardt
- Shinichi Sunagawa
- Emma Slack
Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (40B2-0_180953)
- Emma Slack
Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (310030_185128)
- Emma Slack
Gebert Rüf Stiftung (GR073_17)
- Claude Loverdo
- Emma Slack
Botnar Research Centre for Child Health, University of Basel (BRCCH_MIP)
- Shinichi Sunagawa
- Emma Slack
Agence Nationale de la Recherche (ANR-21-CE45-0015)
- Claude Loverdo
Agence Nationale de la Recherche (ANR-20-CE30-0001)
- Claude Loverdo
Centre National de la Recherche Scientifique (MITI CNRS AAP adaptation du vivant à son environnement)
- Claude Loverdo
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Ethics
Animal experimentation: All animal experiments were performed with approval from the Zürich Cantonal Authority under license number ZH120/19.
Copyright
© 2023, Hoces et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Fitness advantage of Bacteroides thetaiotaomicron capsular polysaccharide in the mouse gut depends on the resident microbiota
eLife 12:e81212.
https://doi.org/10.7554/eLife.81212
Further reading
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Glutamine synthetases (GS) are central enzymes essential for the nitrogen metabolism across all domains of life. Consequently, they have been extensively studied for more than half a century. Based on the ATP-dependent ammonium assimilation generating glutamine, GS expression and activity are strictly regulated in all organisms. In the methanogenic archaeon Methanosarcina mazei, it has been shown that the metabolite 2-oxoglutarate (2-OG) directly induces the GS activity. Besides, modulation of the activity by interaction with small proteins (GlnK1 and sP26) has been reported. Here, we show that the strong activation of M. mazei GS (GlnA1) by 2-OG is based on the 2-OG dependent dodecamer assembly of GlnA1 by using mass photometry (MP) and single particle cryo-electron microscopy (cryo-EM) analysis of purified strep-tagged GlnA1. The dodecamer assembly from dimers occurred without any detectable intermediate oligomeric state and was not affected in the presence of GlnK1. The 2.39 Å cryo-EM structure of the dodecameric complex in the presence of 12.5 mM 2-OG demonstrated that 2-OG is binding between two monomers. Thereby, 2-OG appears to induce the dodecameric assembly in a cooperative way. Furthermore, the active site is primed by an allosteric interaction cascade caused by 2-OG-binding towards an adaption of an open active state conformation. In the presence of additional glutamine, strong feedback inhibition of GS activity was observed. Since glutamine dependent disassembly of the dodecamer was excluded by MP, feedback inhibition most likely relies on the binding of glutamine to the catalytic site. Based on our findings, we propose that under nitrogen limitation the induction of M. mazei GS into a catalytically active dodecamer is not affected by GlnK1 and crucially depends on the presence of 2-OG.
