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

Abstract

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.

Probiotic treatment restores protection against lethal fungal infection lost during amphibian captivity

“…For many species of conservation concern, captive assurance colonies are needed to preserve biological diversity until natural environments become more suitable [27], or new conservation tools are developed that can mitigate the effects of pathogens [28,29,30]. The results of this study underscore the importance of the microbiome in the health of amphibians and inform how we can improve captive rearing programmes [26].…”

Probiotic roles ofLactobacillussp. in swine: insights from gut microbiota

“…Similar to findings in other mammalian host niches, the inconsistent observations in swine may be due to ineffective selection of probiotic candidates based on limited knowledge of microbial diversity and ecological interactions within the swine gut (Rebollar et al . ). Given the ubiquity of lactobacilli in the host's external and internal environment, identification of autochthonous and allochthonous species is essential.…”

“…Protocol was adapted from Rebollar et al . () in amphibians. (a) Lactobacilli detected in various regions of the pig gastrointestinal tract as quantified using culture‐dependent methods.…”

Integration of multi-omics data for integrative gene regulatory network inference

“…Biological systems involve a sequence of complex interactions in multiple biological processes such as genetic, epigenetic, and transcriptional regulation (Kristensen, 2014; Higdon, 2015; Rebollar, 2016; Cisek et al, 2015). Specifically, gene expression is a product of sequential interactions of single nucleotide polymorphism (SNP), copy number variation (CNV), histone modifications, transcription factor, DNA methylation, other genes in relevant pathways, and many other factors (Aure et al, 2013; Wagner et al, 2014; Kang et al, 2015; Kim et al, 2015; Kang et al, 2016).…”