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Arjes HA, Sun J, Liu H, Nguyen TH, Culver RN, Celis AI, Walton SJ, Vasquez KS, Yu FB, Xue KS, Newton D, Zermeno R, Weglarz M, Deutschbauer A, Huang KC, Shiver AL. Construction and characterization of a genome-scale ordered mutant collection of Bacteroides thetaiotaomicron. BMC Biol 2022; 20:285. [PMID: 36527020 PMCID: PMC9758874 DOI: 10.1186/s12915-022-01481-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 11/24/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Ordered transposon-insertion collections, in which specific transposon-insertion mutants are stored as monocultures in a genome-scale collection, represent a promising tool for genetic dissection of human gut microbiota members. However, publicly available collections are scarce and the construction methodology remains in early stages of development. RESULTS Here, we describe the assembly of a genome-scale ordered collection of transposon-insertion mutants in the model gut anaerobe Bacteroides thetaiotaomicron VPI-5482 that we created as a resource for the research community. We used flow cytometry to sort single cells from a pooled library, located mutants within this initial progenitor collection by applying a pooling strategy with barcode sequencing, and re-arrayed specific mutants to create a condensed collection with single-insertion strains covering >2500 genes. To demonstrate the potential of the condensed collection for phenotypic screening, we analyzed growth dynamics and cell morphology. We identified both growth defects and altered cell shape in mutants disrupting sphingolipid synthesis and thiamine scavenging. Finally, we analyzed the process of assembling the B. theta condensed collection to identify inefficiencies that limited coverage. We demonstrate as part of this analysis that the process of assembling an ordered collection can be accurately modeled using barcode sequencing data. CONCLUSION We expect that utilization of this ordered collection will accelerate research into B. theta physiology and that lessons learned while assembling the collection will inform future efforts to assemble ordered mutant collections for an increasing number of gut microbiota members.
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Affiliation(s)
- Heidi A. Arjes
- grid.168010.e0000000419368956Department of Bioengineering, Stanford University, Stanford, CA USA
| | - Jiawei Sun
- grid.168010.e0000000419368956Department of Bioengineering, Stanford University, Stanford, CA USA
| | - Hualan Liu
- grid.184769.50000 0001 2231 4551Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Taylor H. Nguyen
- grid.168010.e0000000419368956Department of Bioengineering, Stanford University, Stanford, CA USA
| | - Rebecca N. Culver
- grid.168010.e0000000419368956Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Arianna I. Celis
- grid.168010.e0000000419368956Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Sophie Jean Walton
- grid.168010.e0000000419368956Biophysics Training Program, Stanford University School of Medicine, Stanford, CA USA
| | - Kimberly S. Vasquez
- grid.168010.e0000000419368956Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Feiqiao Brian Yu
- grid.499295.a0000 0004 9234 0175Chan Zuckerberg Biohub, San Francisco, CA 94158 USA
| | - Katherine S. Xue
- grid.168010.e0000000419368956Department of Bioengineering, Stanford University, Stanford, CA USA ,grid.168010.e0000000419368956Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Daniel Newton
- grid.168010.e0000000419368956Department of Bioengineering, Stanford University, Stanford, CA USA
| | - Ricardo Zermeno
- grid.168010.e0000000419368956Stanford Shared FACS Facility, Center for Molecular and Genetic Medicine, Stanford University, Stanford, CA USA
| | - Meredith Weglarz
- grid.168010.e0000000419368956Stanford Shared FACS Facility, Center for Molecular and Genetic Medicine, Stanford University, Stanford, CA USA
| | - Adam Deutschbauer
- grid.184769.50000 0001 2231 4551Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA ,grid.47840.3f0000 0001 2181 7878Department of Plant and Microbial Biology, University of California, Berkeley, CA USA
| | - Kerwyn Casey Huang
- grid.168010.e0000000419368956Department of Bioengineering, Stanford University, Stanford, CA USA ,grid.168010.e0000000419368956Biophysics Training Program, Stanford University School of Medicine, Stanford, CA USA ,grid.168010.e0000000419368956Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305 USA ,grid.499295.a0000 0004 9234 0175Chan Zuckerberg Biohub, San Francisco, CA 94158 USA
| | - Anthony L. Shiver
- grid.168010.e0000000419368956Department of Bioengineering, Stanford University, Stanford, CA USA
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