Abstract
Functional genomics of bacteria commonly aims at establishing genotype-phenotype links in microorganisms of industrial, technological and biomedical relevance. In this regard, random transposon mutagenesis coupled to high-throughput next-generation sequencing approaches, termed transposon-insertion sequencing (TIS), has emerged as a robust, genome-wide alternative to perform functional genome analysis. Though these approaches have been used in a large number of studies involving pathogenic and clinically relevant bacteria, they have received little attention in the fields of commensal and potentially beneficial bacteria, including probiotic microorganisms. In this chapter, we describe the implementation of the TIS method Transposon-Directed Insertion Sequencing to describe the set of essential genes in a representative strain of a genus encompassing several commensal and potentially probiotic bacteria and discuss considerations when applying similar methodological approaches to other Bifidobacterium species/strains of interest.
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Acknowledgements
F.B. and D.v.S. are members of APC Microbiome Ireland, which is funded by Science Foundation Ireland (SFI) through the Irish Government’s National Development Plan (Grant Numbers SFI/12/RC/2273-P1 and SFI/12/RC/2273-P2). L.R. has received funding from the Spanish State Research Agency (RTI2018-095021-J-I00).
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Ruiz, L., Bottacini, F., Semenec, L., Cain, A., van Sinderen, D. (2022). A Proposed Framework to Identify Dispensable and Essential Functions in Bifidobacteria: Case Study of Bifidobacterium breve UCC2003 as a Prototype of Its Genus. In: Zhang, R. (eds) Essential Genes and Genomes. Methods in Molecular Biology, vol 2377. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1720-5_15
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