Randomly barcoded transposon mutant libraries for gut commensals II: Applying libraries for functional genetics

Carlos Geert Pieter Voogdt; Surya Tripathi; Stefan Oliver Bassler; Saria A McKeithen-Mead; Emma R Guiberson; Alexandra Koumoutsi; Afonso Martins Bravo; Cullen Buie; Michael Zimmermann; Justin L Sonnenburg; Athanasios Typas; Adam M Deutschbauer; Anthony L Shiver; Kerwyn Casey Huang

doi:10.1016/j.celrep.2023.113519

Randomly barcoded transposon mutant libraries for gut commensals II: Applying libraries for functional genetics

Cell Rep. 2024 Jan 23;43(1):113519. doi: 10.1016/j.celrep.2023.113519. Epub 2023 Dec 23.

Authors

Affiliations

¹ Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Structural and Computational Biology Unit, EMBL, Heidelberg, Germany.
² Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
³ Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, Grabengasse 1, 69117 Heidelberg, Germany.
⁴ Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.
⁵ Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.
⁶ Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany.
⁷ Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland.
⁸ Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
⁹ Structural and Computational Biology Unit, EMBL, Heidelberg, Germany.
¹⁰ Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
¹¹ Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Structural and Computational Biology Unit, EMBL, Heidelberg, Germany. Electronic address: typas@embl.de.
¹² Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. Electronic address: amdeutschbauer@lbl.gov.
¹³ Department of Bioengineering, Stanford University, Stanford, CA 94305, USA. Electronic address: ashiver@stanford.edu.
¹⁴ Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA. Electronic address: kchuang@stanford.edu.

PMID: 38142398
DOI: 10.1016/j.celrep.2023.113519

Abstract

The critical role of the intestinal microbiota in human health and disease is well recognized. Nevertheless, there are still large gaps in our understanding of the functions and mechanisms encoded in the genomes of most members of the gut microbiota. Genome-scale libraries of transposon mutants are a powerful tool to help us address this gap. Recent advances in barcoded transposon mutagenesis have dramatically lowered the cost of mutant fitness determination in hundreds of in vitro and in vivo experimental conditions. In an accompanying review, we discuss recent advances and caveats for the construction of pooled and arrayed barcoded transposon mutant libraries in human gut commensals. In this review, we discuss how these libraries can be used across a wide range of applications, the technical aspects involved, and expectations for such screens.

Keywords: CP: Microbiology; chemical genomics; genotype-phenotype mapping; gut microbiota; host-microbe interactions; transposon mutagenesis.

Publication types

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

MeSH terms

DNA Transposable Elements* / genetics
Gene Library
Humans
Mutagenesis, Insertional / genetics

Substances

DNA Transposable Elements

Grants and funding

RM1 GM135102/GM/NIGMS NIH HHS/United States