Rxivist logo

Rxivist combines preprints from bioRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 57,506 bioRxiv papers from 264,779 authors.

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

By 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 Deutschbauer

Posted 09 Mar 2019
bioRxiv DOI: 10.1101/573055

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.

Download data

  • Downloaded 473 times
  • Download rankings, all-time:
    • Site-wide: 18,686 out of 57,506
    • In microbiology: 990 out of 4,580
  • Year to date:
    • Site-wide: 3,931 out of 57,506
  • Since beginning of last month:
    • Site-wide: 8,240 out of 57,506

Altmetric data

Downloads over time

Distribution of downloads per paper, site-wide

Sign up for the Rxivist weekly newsletter! (Click here for more details.)