Construction and characterization of a genome-scale ordered mutant collection of Bacteroides thetaiotaomicron

• Published in: BMC biology Vol. 20; no. 1; pp. 285 - 17
• Main Authors: Arjes, Heidi A, Sun, Jiawei, Liu, Hualan, Nguyen, Taylor H, Culver, Rebecca N, Celis, Arianna I, Walton, Sophie Jean, Vasquez, Kimberly S, Yu, Feiqiao Brian, Xue, Katherine S, Newton, Daniel, Zermeno, Ricardo, Weglarz, Meredith, Deutschbauer, Adam, Huang, Kerwyn Casey, Shiver, Anthony L
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 17.12.2022; BioMed Central; BMC
• Subjects: Anaerobic bacteria; Assembling; B. theta; Bacteroides thetaiotaomicron; Bacteroides thetaiotaomicron - genetics; Bar codes; BarSeq; Cell morphology; Cell size; Cytology; Datasets; DNA Transposable Elements; Flow cytometry; Gene Library; Genes; Genetic aspects; Genome, Bacterial; Genomes; Humans; Insertion; Intestinal microflora; Life Sciences & Biomedicine - Other Topics; Microbiome; Microbiota; Microbiota (Symbiotic organisms); Monoculture; Mutagenesis, Insertional; Mutants; Ordered library; Physiological aspects; RB-TnSeq; Scavenging; Thiamine; Transposon mutagenesis; Transposons; United States; B. theta; Ordered library; RB-TnSeq; Cell growth; Microbiota; Thiamine scavenging; Transposon mutagenesis; Sphingolipid synthesis; BarSeq; Cell morphology; Microbiome
• ISSN: 1741-7007; 1741-7007
• DOI: 10.1186/s12915-022-01481-2

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. 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. 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.