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A Proposed Framework to Identify Dispensable and Essential Functions in Bifidobacteria: Case Study of Bifidobacterium breve UCC2003 as a Prototype of Its Genus

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Essential Genes and Genomes

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2377))

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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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Authors and Affiliations

  1. Department of Microbiology and Biochemistry of Dairy Products, Dairy Research Institute of Asturias (IPLA)-Spanish National Research Council (CSIC), Villaviciosa, Asturias, Spain

    Lorena Ruiz

  2. Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Asturias, Spain

    Lorena Ruiz

  3. School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland

    Francesca Bottacini & Douwe van Sinderen

  4. Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia

    Lucie Semenec & Amy Cain

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  1. Lorena Ruiz
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  2. Francesca Bottacini
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  3. Lucie Semenec
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  4. Amy Cain
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  5. Douwe van Sinderen
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Correspondence to Lorena Ruiz or Douwe van Sinderen .

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Editors and Affiliations

  1. Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA

    Ren Zhang

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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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  • DOI: https://doi.org/10.1007/978-1-0716-1720-5_15

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1719-9

  • Online ISBN: 978-1-0716-1720-5

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