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Front Microbiol. 2016 Feb 2;7:68. doi: 10.3389/fmicb.2016.00068. eCollection 2016.

Using "Omics" and Integrated Multi-Omics Approaches to Guide Probiotic Selection to Mitigate Chytridiomycosis and Other Emerging Infectious Diseases.

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Department of Biology, James Madison University Harrisonburg, VA, USA.
Unit for Environmental Sciences and Management, North-West UniversityPotchefstroom, South Africa; Institute of Zoology, Zoological Society of LondonLondon, UK; School of Environment and Life Sciences, University of SalfordSalford, UK.
Center for Conservation and Evolutionary Genetics, Smithsonian Conservation Biology Institute, National Zoological Park Washington, DC, USA.
Department of Biological Sciences, Virginia Tech Blacksburg, VA, USA.
Zoological Institute, Technische Universität Braunschweig Braunschweig, Germany.
Rowland Institute, Harvard University Cambridge, MA, USA.
Institute of Zoology, Zoological Society of London London, UK.
Department of Ecology and Evolutionary Biology, University of Colorado Boulder, CO, USA.
Department of Zoology, Biodiversity Research Centre, University of British Columbia Vancouver, BC, Canada.
Department of Chemistry, Villanova University Villanova, PA, USA.
Department of Pathology, Microbiology and Immunology and Department of Pediatrics, Vanderbilt University School of Medicine, Department of Biological Sciences, Vanderbilt University Nashville, TN, USA.
Department of Chemical and Biological Engineering, University of Colorado at Boulder Boulder, CO, USA.
Department of Biology, University of Massachusetts Boston Boston, MA, USA.


Emerging infectious diseases in wildlife are responsible for massive population declines. In amphibians, chytridiomycosis caused by Batrachochytrium dendrobatidis, Bd, has severely affected many amphibian populations and species around the world. One promising management strategy is probiotic bioaugmentation of antifungal bacteria on amphibian skin. In vivo experimental trials using bioaugmentation strategies have had mixed results, and therefore a more informed strategy is needed to select successful probiotic candidates. Metagenomic, transcriptomic, and metabolomic methods, colloquially called "omics," are approaches that can better inform probiotic selection and optimize selection protocols. The integration of multiple omic data using bioinformatic and statistical tools and in silico models that link bacterial community structure with bacterial defensive function can allow the identification of species involved in pathogen inhibition. We recommend using 16S rRNA gene amplicon sequencing and methods such as indicator species analysis, the Kolmogorov-Smirnov Measure, and co-occurrence networks to identify bacteria that are associated with pathogen resistance in field surveys and experimental trials. In addition to 16S amplicon sequencing, we recommend approaches that give insight into symbiont function such as shotgun metagenomics, metatranscriptomics, or metabolomics to maximize the probability of finding effective probiotic candidates, which can then be isolated in culture and tested in persistence and clinical trials. An effective mitigation strategy to ameliorate chytridiomycosis and other emerging infectious diseases is necessary; the advancement of omic methods and the integration of multiple omic data provide a promising avenue toward conservation of imperiled species.


amphibians; emerging diseases; metabolomics; metagenomics; probiotics; transcriptomics

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