Using “Omics” and Integrated Multi-Omics 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

Ex situ diet influences the bacterial community associated with the skin of red-eyed tree frogs (Agalychnis callidryas)

Amphibians support symbiotic bacterial communities on their skin that protect against a range of infectious pathogens, including the amphibian chytrid fungus. The conditions under which amphibians are maintained in captivity (e.g. diet, substrate, enrichment) in ex situ conservation programmes may affect the composition of the bacterial community. In addition, ex situ amphibian populations may support different bacterial communities in comparison to in situ populations of the same species. This could have implications for the suitability of populations intended for reintroduction, as well as the success of probiotic bacterial inoculations intended to provide amphibians with a bacterial community that resists invasion by the chytrid fungus. We aimed to investigate the effect of a carotenoid-enriched diet on the culturable bacterial community associated with captive red-eyed tree frogs (Agalychnis callidryas) and make comparisons to bacteria isolated from a wild population from the Chiquibul Rainforest in Belize. We successfully showed carotenoid availability influences the overall community composition, species richness and abundance of the bacterial community associated with the skin of captive frogs, with A. callidryas fed a carotenoid-enriched diet supporting a greater species richness and abundance of bacteria than those fed a carotenoid-free diet. Our results suggest that availability of carotenoids in the diet of captive frogs is likely to be beneficial for the bacterial community associated with the skin. We also found wild A. callidryas hosted more than double the number of different bacterial species than captive frogs with very little commonality between species. This suggests frogs in captivity may support a reduced and diverged bacterial community in comparison to wild populations of the same species, which could have particular relevance for ex situ conservation projects

Search for resonant production of second-generation sleptons with same-sign dimuon events in proton-proton collisions at root s=13 TeV

A search is presented for resonant production of second-generation sleptons ( μ˜L , ν˜μ ) via the R-parity-violating coupling λ′211 to quarks, in events with two same-sign muons and at least two jets in the final state. The smuon (muon sneutrino) is expected to decay into a muon and a neutralino (chargino), which will then decay into a second muon and at least two jets. The analysis is based on the 2016 data set of proton-proton collisions at s√=13TeV recorded with the CMS detector at the LHC, corresponding to an integrated luminosity of 35.9 fb−1 . No significant deviation is observed with respect to standard model expectations. Upper limits on cross sections, ranging from 0.24 to 730 fb , are derived in the context of two simplified models representing the dominant signal contributions leading to a same-sign muon pair. The cross section limits are translated into coupling limits for a modified constrained minimal supersymmetric model with λ′211 as the only nonzero R-parity violating coupling. The results significantly extend restrictions of the parameter space compared with previous searches for similar models

A Bacillus thuringiensis kurstaki

Amphibians are in global decline, and anthropogenic activities are known leading causes of their demise. Thus the interaction between agriculture and amphibian health has been examined for decades. Many facets of amphibian physiology and ecology place them at high risk among the nontarget organisms affected by agricultural byproducts. Research has shown that many chemicals and fertilizers affect amphibian growth, reproduction, and survival. The impacts differ based on the type of agricultural byproduct (e.g., chemical pesticide or nutrient-heavy fertilizer) and amphibian species, but the effects are usually negative. However, minimal research exists on how organic biopesticides interact with amphibian populations. Biopesticides utilize insecticidal bacteria as the active ingredient in lieu of synthetic chemicals. The inert ingredients present in biopesticide commercial products are considered safe to nontarget organisms. The present study tested the impacts of a commercial biopesticide on the survival of amphibian embryos and larvae. We found that expected environmental concentrations of the microbial biopesticide Monterrey B.t. did not significantly reduce survival in embryos or larvae. However, the higher doses used to assess threshold toxicity levels caused significant mortality. Our data suggest that biopesticides are not directly harmful to amphibian embryos or larvae in concentrations regularly applied for pest control. Environ Toxicol Chem 2019;39:155–161. © 2019 SETAC

Susceptibility to disease varies with ontogeny and immunocompetence in a threatened amphibian

Ontogenetic changes in disease susceptibility have been demonstrated in many vertebrate taxa, as immature immune systems and limited prior exposure to pathogens can place less developed juveniles at a greater disease risk. By causing the disease chytridiomycosis, <i>Batrachochytrium dendrobatidis (Bd)</i> infection has led to the decline of many amphibian species. Despite increasing knowledge on how Bd varies in its effects among species, little is known on the interaction between susceptibility and development within host species. We compared the ontogenetic susceptibility of post-metamorphic green and golden bell frogs <i>Litoria aurea</i> to chytridiomycosis by simultaneously measuring three host-pathogen responses as indicators of the development of the fungus—infection load, survival rate, and host immunocompetence—following <i>Bd</i> exposure in three life stages (recently metamorphosed juveniles, subadults, adults) over 95 days. Frogs exposed to <i>Bd</i> as recently metamorphosed juveniles acquired higher infection loads and experienced lower immune function and lower survivorship than subadults and adults, indicating an ontogenetic decline in chytridiomycosis susceptibility. By corresponding with an intrinsic developmental maturation in immunocompetence seen in uninfected frogs, we suggest these developmental changes in host susceptibility in <i>L. aurea</i> may be immune mediated. Consequently, the physiological relationship between ontogeny and immunity may affect host population structure and demography through variation in life stage survival, and understanding this can shape management targets for effective amphibian conservation