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
Affiliations
Carlos Geert Pieter Voogdt
Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Structural and Computational Biology Unit, EMBL, Heidelberg, Germany
Surya Tripathi
Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
Stefan Oliver Bassler
Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, Grabengasse 1, 69117 Heidelberg, Germany
Saria A. McKeithen-Mead
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
Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
Alexandra Koumoutsi
Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
Afonso Martins Bravo
Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
Cullen Buie
Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
Michael Zimmermann
Structural and Computational Biology Unit, EMBL, Heidelberg, Germany
Justin L. Sonnenburg
Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
Athanasios Typas
Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Structural and Computational Biology Unit, EMBL, Heidelberg, Germany; Corresponding author
Adam M. Deutschbauer
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; Corresponding author
Anthony L. Shiver
Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Corresponding author
Kerwyn Casey Huang
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; Corresponding author
Summary: 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.
