Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

Large-scale chemical-genetics of the human gut bacterium Bacteroides thetaiotaomicron

Hualan Liu, Morgan N. Price, Hans K. Carlson, Yan Chen, Jayashree Ray, Anthony L. Shiver, Christopher J. Petzold, Kerwyn Casey Huang, Adam P. Arkin, Adam M. Deutschbauer
doi: https://doi.org/10.1101/573055
Hualan Liu
1Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Morgan N. Price
1Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Hans K. Carlson
1Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Yan Chen
2Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Jayashree Ray
1Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Anthony L. Shiver
3Department of Bioengineering, Stanford University, Stanford, CA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Christopher J. Petzold
2Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Kerwyn Casey Huang
3Department of Bioengineering, Stanford University, Stanford, CA, USA
4Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
5Chan Zuckerberg Biohub, San Francisco, CA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Adam P. Arkin
1Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
6Department of Bioengineering, University of California, Berkeley, CA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Adam M. Deutschbauer
1Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
7Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: AMDeutschbauer@lbl.gov
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Preview PDF
Loading

Abstract

The genomic catalogue of the human microbiota has expanded dramatically in recent years, and insights derived from human microbiota genomics has vast potential to generate treatments for human diseases. However, predictably harnessing the microbiota for beneficial outcomes is currently limited by our lack of understanding of the physiology of the constituent bacteria. For instance, the functions of most of their genes are not known. Here, we systematically measure mutant phenotypes for genes from the gut commensal Bacteroides thetaiotaomicron. Using a barcoded transposon mutant library, we measured the fitness of 4,055 B. thetaiotaomicron genes across 492 experiments, including growth on 45 carbon substrates and in the presence of 57 stress-inducing compounds. Our data is in strong agreement with previous studies, and more importantly also uncovers the biological roles of poorly annotated genes. We identified 497 genes with a specific phenotype in only one or a handful of conditions, thus enabling informed predictions of gene function for a subset of these genes. For example, we identified a glycoside hydrolase important for growth on type I rhamnogalacturonan, a DUF4861 protein for glycosaminoglycan utilization, a DUF1080 protein for disaccharide utilization, and a tripartite multidrug resistance system specifically important for bile salt tolerance. Our approach can be applied to other members of the human microbiota to experimentally characterize their genes.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
Back to top
PreviousNext
Posted March 09, 2019.
Download PDF

Supplementary Material

Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
Large-scale chemical-genetics of the human gut bacterium Bacteroides thetaiotaomicron
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Large-scale chemical-genetics of the human gut bacterium Bacteroides thetaiotaomicron
Hualan Liu, Morgan N. Price, Hans K. Carlson, Yan Chen, Jayashree Ray, Anthony L. Shiver, Christopher J. Petzold, Kerwyn Casey Huang, Adam P. Arkin, Adam M. Deutschbauer
bioRxiv 573055; doi: https://doi.org/10.1101/573055
Reddit logo Twitter logo Facebook logo LinkedIn logo Mendeley logo
Citation Tools
Large-scale chemical-genetics of the human gut bacterium Bacteroides thetaiotaomicron
Hualan Liu, Morgan N. Price, Hans K. Carlson, Yan Chen, Jayashree Ray, Anthony L. Shiver, Christopher J. Petzold, Kerwyn Casey Huang, Adam P. Arkin, Adam M. Deutschbauer
bioRxiv 573055; doi: https://doi.org/10.1101/573055

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Microbiology
Subject Areas
All Articles
  • Animal Behavior and Cognition (4654)
  • Biochemistry (10299)
  • Bioengineering (7614)
  • Bioinformatics (26189)
  • Biophysics (13446)
  • Cancer Biology (10620)
  • Cell Biology (15333)
  • Clinical Trials (138)
  • Developmental Biology (8452)
  • Ecology (12754)
  • Epidemiology (2067)
  • Evolutionary Biology (16763)
  • Genetics (11356)
  • Genomics (15400)
  • Immunology (10548)
  • Microbiology (25041)
  • Molecular Biology (10152)
  • Neuroscience (54096)
  • Paleontology (398)
  • Pathology (1655)
  • Pharmacology and Toxicology (2877)
  • Physiology (4314)
  • Plant Biology (9196)
  • Scientific Communication and Education (1579)
  • Synthetic Biology (2541)
  • Systems Biology (6752)
  • Zoology (1452)