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Gnotobiotic rainbow trout (Oncorhynchus mykiss) model reveals endogenous bacteria that protect against Flavobacterium columnare infection

View ORCID ProfileDavid Pérez-Pascual, Sol Vendrell-Fernández, Bianca Audrain, Joaquín Bernal-Bayard, Rafael Patiño-Navarrete, Vincent Petit, Dimitri Rigaudeau, View ORCID ProfileJean-Marc Ghigo
doi: https://doi.org/10.1101/2020.06.19.161471
David Pérez-Pascual
1Unité de Génétique des Biofilms, Institut Pasteur, UMR CNRS2001, Paris, France
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  • ORCID record for David Pérez-Pascual
  • For correspondence: jmghigo@pasteur.fr david.perezpascual@pasteur.fr
Sol Vendrell-Fernández
1Unité de Génétique des Biofilms, Institut Pasteur, UMR CNRS2001, Paris, France
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Bianca Audrain
1Unité de Génétique des Biofilms, Institut Pasteur, UMR CNRS2001, Paris, France
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Joaquín Bernal-Bayard
1Unité de Génétique des Biofilms, Institut Pasteur, UMR CNRS2001, Paris, France
5Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Apartado 1095, 41080 Sevilla, Spain
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Rafael Patiño-Navarrete
2Evolution and Ecology of Resistance to Antibiotics Unit, Institut Pasteur-APHP University Paris Sud, Paris, France
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Vincent Petit
3AQUALANDE, Gué de Bern, 40410 Pissos, France
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Dimitri Rigaudeau
4Unité Infectiologie Expérimentale Rongeurs et Poissons, INRAE, Université Paris-Saclay, 78350 Jouy-en-Josas, France
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Jean-Marc Ghigo
1Unité de Génétique des Biofilms, Institut Pasteur, UMR CNRS2001, Paris, France
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  • ORCID record for Jean-Marc Ghigo
  • For correspondence: jmghigo@pasteur.fr david.perezpascual@pasteur.fr
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ABSTRACT

The health and environmental risks associated with antibiotic use in aquaculture have promoted bacterial probiotics as an alternative approach to control fish infections in vulnerable larval and juvenile stages. However, evidence-based identification of probiotics is often hindered by the complexity of bacteria-host interactions and host variability in microbiologically uncontrolled conditions. While these difficulties can be partially resolved using gnotobiotic models harboring no or reduced microbiota, most host-microbe interaction studies are carried out in animal models with little relevance for fish farming. Here we studied host-microbiota-pathogen interactions in a germ-free and gnotobiotic model of rainbow trout (Oncorhynchus mykiss), one of the most widely cultured salmonids. We demonstrated that germ-free larvae raised in sterile conditions displayed no significant difference in growth after 35 days compared to conventionally-raised larvae, but were extremely sensitive to infection by Flavobacterium columnare, a common freshwater fish pathogen causing major economic losses worldwide. Furthermore, re-conventionalization with 11 culturable species from the conventional trout microbiota conferred resistance to F. columnare infection. Using mono-re-conventionalized germ-free trout, we identified that this protection is determined by a commensal Flavobacterium strain displaying antibacterial activity against F. columnare. Finally, we demonstrated that use of gnotobiotic trout is a suitable approach for the systematic identification of both endogenous and exogenous probiotic bacterial strains that may protect teleostean hosts against F. columnare and other pathogens. This study establishes a novel and ecologically-relevant gnotobiotic model that will improve the sustainability and health of aquaculture.

Competing Interest Statement

The authors of this manuscript have the following competing interests: a provisional patent application has been filed: bacterial strains for use as probiotics, compositions thereof, deposited strains and method to identify probiotic bacterial strains, by J.-M.G, D.P.-P. and J.B.-B. The other authors declare no conflict of interest in relation to the submitted work.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted June 20, 2020.
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Gnotobiotic rainbow trout (Oncorhynchus mykiss) model reveals endogenous bacteria that protect against Flavobacterium columnare infection
David Pérez-Pascual, Sol Vendrell-Fernández, Bianca Audrain, Joaquín Bernal-Bayard, Rafael Patiño-Navarrete, Vincent Petit, Dimitri Rigaudeau, Jean-Marc Ghigo
bioRxiv 2020.06.19.161471; doi: https://doi.org/10.1101/2020.06.19.161471
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Gnotobiotic rainbow trout (Oncorhynchus mykiss) model reveals endogenous bacteria that protect against Flavobacterium columnare infection
David Pérez-Pascual, Sol Vendrell-Fernández, Bianca Audrain, Joaquín Bernal-Bayard, Rafael Patiño-Navarrete, Vincent Petit, Dimitri Rigaudeau, Jean-Marc Ghigo
bioRxiv 2020.06.19.161471; doi: https://doi.org/10.1101/2020.06.19.161471

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