Species delineation and clonal diversity in four Bifidobacterium species as revealed by multilocus sequencing |
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| Authors: | Alexis Delétoile Virginie Passet Julio Aires Isabelle Chambaud Marie-José Butel Tamara Smokvina Sylvain Brisse |
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| Institution: | 1. Institut Pasteur, Genotyping of Pathogens and Public Health (PF8), 28 rue du Dr Roux, F-75724 Paris Cedex, France;2. Paris Descartes University, Faculty of Pharmaceutical and Biological Sciences, EA4065 Paris, France;3. Danone Research, Centre Daniel Carasso, Palaiseau, France;1. Gazi University Faculty of Medicine Pediatric Infectious Diseases Unit, Ankara, Turkey;2. Ankara Hematology Oncology Children''s Training and Research Hospital, Ankara, Turkey;1. Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Skip Bertman Drive, SVM-3213, Baton Rouge, LA 70803, USA;2. Department of Science, Faculty of Science and Technology, Prince of Songkla University, Pattani 94000, Thailand;3. Department of Technology and Industry, Faculty of Science and Technology, Prince of Songkla University, Pattani 94000, Thailand;4. Rickettsial Zoonoses Branch, Mailstop G-13, Centers for Disease Control and Prevention, 1600 Clifton Rd., Atlanta, GA 30333, USA;1. Yakult Central Institute, 5-11 Izumi, Kunitachi, Tokyo 186-8650, Japan;2. Yakult Honsha European Research Center for Microbiology ESV, Technologiepark 4, 9052 Zwijnaarde, Belgium;3. Department of Agricultural Sciences, University of Bologna, Viale Fanin 42, 40127 Bologna, Italy;4. Lactic acid Bacteria and Mucosal Immunity Team, Institut Pasteur de Lille, Rue Prof. Calmette, F-59019 Lille Cedex, France;5. Center for Infection and Immunity of Lille, F-59019 Lille, France;6. Université Lille Nord de France, F-59019 Lille, France;7. CNRS, UMR 8204, F-59019 Lille, France;8. Department of Animal Science and Technology, National Taiwan University, No. 50, Lane 155, Sec 3, Keelung Rd., Taipei 10673, Taiwan, ROC;1. Department of Agricultural Sciences, University of Bologna, Italy;2. Natura Viva Garda Zoological Park S.r.l., Bussolengo, Verona, Italy;3. Institute of Earth Systems, Division of Rural Sciences & Food Systems, University of Malta, Msida, Malta |
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| Abstract: | The genus Bifidobacterium comprises several species that are important contributors to the gut microbiome, with some strains having beneficial health effects. Understanding the evolutionary emergence of advantageous biological properties requires knowledge of the genetic diversity and clonal structure of species. We sequenced seven housekeeping genes in 119 Bifidobacterium strains of Bifidobacterium animalis, Bifidobacterium bifidum, Bifidobacterium breve and Bifidobacterium longum. Phylogenetic analysis of concatenated sequences delineated sequence clusters that correspond to previously named taxa, and suggested that B. longum subsp. infantis is a nascent lineage emerging from within B. longum subsp. longum. Clear traces of recombination among distant bifidobacterial species indicate leaky species borders and warn against the practice of single gene-based identification. Multilocus sequence typing achieved precise strain genotyping, with discrimination indices above 99% in B. bifidum, B. breve and B. longum, providing a powerful tool for strain traceability, colonization dynamics and ecological studies. Frequent homologous recombination accelerates clonal diversification and may facilitate the transfer of biological properties among bifidobacterial strains. |
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