A toolkit for transposon libraries and functional genomics in intestinal Bacteroidales

bioRxiv (Cold Spring Harbor Laboratory)

Abstract

Members of the order Bacteroidales include some of the most prevalent and abundant bacterial species in the healthy human gut microbiota. Yet, most of the functions encoded in their genomes remain poorly characterized, limiting our understanding of the different roles they play in the human gut microbiome. Towards addressing this gap, we developed tools and methods for genome-wide transposon mutagenesis in Bacteroidales, including broad-range transposon vectors with several antibiotic selection markers, a dual conjugation-cloning donor strain, and protocols for convenient library generation in liquid media. We then created saturated, barcoded, insertion mutant libraries in the type strains of three key representatives of the main genera within Bacteroidales: Bacteroides uniformis (ATCC 8492), Phocaeicola vulgatus (ATCC 8482) and Parabacteroides merdae (ATCC 43184). Based on the dense transposon insertion profiles and a workflow for comparing essentialomes across species, we identified 275 core essential genes shared across the three species, and 163 species-specific essential genes, some of which could be explained by functional redundancy and alternative metabolic pathways. We further identified essential non-protein coding elements and essential protein domains with known and unknown functions. Finally, using insertion directionality bias, we could map potential toxic modalities in the three genomes, including toxin-antitoxin pairs, mobile elements encoding toxic products and enzymes leading to toxic metabolic intermediates. Overall, the tools, workflows and genome-wide resources reported here expand the experimental repertoire for characterizing genes in key bacteria of the human gut microbiome, and pave the way for the establishment of similar genetic toolkits for other gut bacteria.

Authors 11

1. Carlos Geert Pieter Voogdt

   European Molecular Biology Laboratory · European Molecular Biology Laboratory

   Affiliation as printed

   Molecular Systems Biology unit, European Molecular Biology Laboratory, Heidelberg, Germany;

   Molecular Systems Biology unit, European Molecular Biology Laboratory, Heidelberg, Germany

2. Indra Roux

   University of Cambridge · MRC Toxicology Unit · Medical Research Council

   Affiliation as printed

   Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK;

   Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK

3. Nicolai Karcher

   European Molecular Biology Laboratory · European Molecular Biology Laboratory

   Affiliation as printed

   Molecular Systems Biology unit, European Molecular Biology Laboratory, Heidelberg, Germany;

   Molecular Systems Biology unit, European Molecular Biology Laboratory, Heidelberg, Germany

4. Afonso Martins Bravo

   European Molecular Biology Laboratory · European Molecular Biology Laboratory

   Affiliation as printed

   Molecular Systems Biology unit, European Molecular Biology Laboratory, Heidelberg, Germany;

   Molecular Systems Biology unit, European Molecular Biology Laboratory, Heidelberg, Germany

5. Lajos Kalmár

   University of Cambridge · MRC Toxicology Unit · Medical Research Council

   Affiliation as printed

   Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK;

   Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK

6. Vallo Varik

   University of Tartu

   Affiliation as printed

   Estonian Biofoundry, Institute of Bioengineering, University of Tartu, Tartu, Estonia;

   Estonian Biofoundry, Institute of Bioengineering, University of Tartu, Tartu, Estonia

7. Jacob Bobonis

   University of Vienna

   Affiliation as printed

   Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Austria.;

   Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Austria

8. Georg Zeller Aachen

   Leiden University · Leiden University Medical Center

   Affiliation as printed

   Leiden University Center for Infectious Diseases (LUCID), Leiden University Medical Center, Leiden, Netherlands;

   Leiden University Center for Infectious Diseases (LUCID), Leiden University Medical Center, Leiden, Netherlands

9. Michael Bruce Zimmermann

   European Molecular Biology Laboratory · European Molecular Biology Laboratory

   Affiliation as printed

   Molecular Systems Biology unit, European Molecular Biology Laboratory, Heidelberg, Germany;

   Molecular Systems Biology unit, European Molecular Biology Laboratory, Heidelberg, Germany

10. Kiran Raosaheb Patil

    University of Cambridge

    Affiliation as printed

    University of Cambridge, Cambridge, UK

11. Athanasios Typas corresponding

    European Molecular Biology Laboratory · European Molecular Biology Laboratory

    Affiliation as printed

    Molecular Systems Biology unit, European Molecular Biology Laboratory, Heidelberg, Germany;

    Molecular Systems Biology unit, European Molecular Biology Laboratory, Heidelberg, Germany