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

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

Journal

Cell reports
ISSN: 2211-1247
Titre abrégé: Cell Rep
Pays: United States
ID NLM: 101573691

Informations de publication

Date de publication:
22 Dec 2023
Historique:
received: 17 07 2023
revised: 22 10 2023
accepted: 14 11 2023
medline: 24 12 2023
pubmed: 24 12 2023
entrez: 24 12 2023
Statut: aheadofprint

Résumé

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.

Identifiants

DOI: 10.1016/j.celrep.2023.113519 PMID: 38142398
pubmed: 38142398
pii: S2211-1247(23)01531-0
doi: 10.1016/j.celrep.2023.113519
pii:
doi:

Types de publication

Journal Article Review

Langues

eng

Sous-ensembles de citation

IM

Pagination

113519

Informations de copyright

Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.

Déclaration de conflit d'intérêts

Declaration of interests The authors declare no competing interests.

Auteurs

Carlos Geert Pieter Voogdt (CGP)

Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Structural and Computational Biology Unit, EMBL, Heidelberg, Germany.

Surya Tripathi (S)

Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA.

Stefan Oliver Bassler (SO)

Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, Grabengasse 1, 69117 Heidelberg, Germany.

Saria A McKeithen-Mead (SA)

Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.

Emma R Guiberson (ER)

Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.

Alexandra Koumoutsi (A)

Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany.

Afonso Martins Bravo (AM)

Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland.

Cullen Buie (C)

Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

Michael Zimmermann (M)

Structural and Computational Biology Unit, EMBL, Heidelberg, Germany.

Justin L Sonnenburg (JL)

Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.

Athanasios Typas (A)

Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Structural and Computational Biology Unit, EMBL, Heidelberg, Germany. Electronic address: typas@embl.de.

Adam M Deutschbauer (AM)

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.

Anthony L Shiver (AL)

Department of Bioengineering, Stanford University, Stanford, CA 94305, USA. Electronic address: ashiver@stanford.edu.

Kerwyn Casey Huang (KC)

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.

Classifications MeSH