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Using “omics” and integrated multi-omits approaches to guide probiotic selection to mitigate chytridiomycosis and other emerging infectious diseases
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
Community richness of amphibian skin bacteria correlates with bioclimate at the global scale
Animal-associated microbiomes are integral to host health, yet key biotic and abiotic factors that shape host-associated microbial communities at the global scale remain poorly understood. We investigated global patterns in amphibian skin bacterial communities, incorporating samples from 2,349 individuals representing 205 amphibian species across a broad biogeographic range. We analysed how biotic and abiotic factors correlate with skin microbial communities using multiple statistical approaches. Global amphibian skin bacterial richness was consistently correlated with temperature-associated factors. We found more diverse skin microbiomes in environments with colder winters and less stable thermal conditions compared with environments with warm winters and less annual temperature variation. We used bioinformatically predicted bacterial growth rates, dormancy genes and antibiotic synthesis genes, as well as inferred bacterial thermal growth optima to propose mechanistic hypotheses that may explain the observed patterns. We conclude that temporal and spatial characteristics of the host’s macro-environment mediate microbial diversity.National Science Foundation/[DEB-1146284]/NSF/Estados UnidosNational Science Foundation/[IOS-1121758]/NSF/Estados UnidosNational Science Foundation/[DEB-1310036]/NSF/Estados UnidosJohn Templeton Foundation/[]/JTF/Estados UnidosDeutsche Forschungsgemeinschaft/[]/DFG/AlemaniaDeutsche Forschungsgemeinschaft/[VE247/9-1]/DFG/AlemaniaCoordenação de Aperfeiçoamento de Pessoal de Nível Superior/[]/CAPES/BrasilFundação de Amparo à Pesquisa do Estado de São Paulo/[#2013/50741-7]/FAPESP/BrasilConselho Nacional de Desenvolvimento Científico e Tecnológico/[]/CNPq/BrasilSimons Foundation/[429440, WTW]//Estados UnidosDeutscher Akademischer Austauschdienst/[]/DAAD/AlemaniaUniversidad de Costa Rica/[801-B2-029]/UCR/Costa RicaMinisterio de Ciencia, Tecnología y Telecomunicaciones/[849-PINN-2015]/MICITT/Costa RicaNational Research Foundation of Korea/[2015R1D1A1A01057282]/NRF/Corea del SurUCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Básicas::Centro de Investigación en Biología Celular y Molecular (CIBCM)UCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Básicas::Centro de Investigación en Estructuras Microscópicas (CIEMIC