Browsing by Author "Becker, Matthew H."
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- Community Structure and Function of Amphibian Skin Microbes: An Experiment with Bullfrogs Exposed to a Chytrid FungusWalke, Jenifer B.; Becker, Matthew H.; Loftus, Stephen C.; House, Leanna L.; Teotonio, Thais L.; Minbiole, Kevin P. C.; Belden, Lisa K. (PLOS, 2015-10-07)The vertebrate microbiome contributes to disease resistance, but few experiments have examined the link between microbiome community structure and disease resistance functions. Chytridiomycosis, a major cause of amphibian population declines, is a skin disease caused by the fungus, Batrachochytrium dendrobatidis (Bd). In a factorial experiment, bullfrog skin microbiota was reduced with antibiotics, augmented with an anti-Bd bacterial isolate (Janthinobacterium lividum), or unmanipulated, and individuals were then either exposed or not exposed to Bd. We found that the microbial community structure of individual frogs prior to Bd exposure influenced Bd infection intensity one week following exposure, which, in turn, was negatively correlated with proportional growth during the experiment. Microbial community structure and function differed among unmanipulated, antibiotic-treated, and augmented frogs only when frogs were exposed to Bd. Bd is a selective force on microbial community structure and function, and beneficial states of microbial community structure may serve to limit the impacts of infection.
- Culture Media and Individual Hosts Affect the Recovery of Culturable Bacterial Diversity from Amphibian SkinMedina, Daniel; Walke, Jenifer B.; Gajewski, Zachary J.; Becker, Matthew H.; Swartwout, Meredith C.; Belden, Lisa K. (Frontiers, 2017-08-24)One current challenge in microbial ecology is elucidating the functional roles of the large diversity of free-living and host-associated bacteria identified by culture-independent molecular methods. Importantly, the characterization of this immense bacterial diversity will likely require merging data from culture-independent approaches with work on bacterial isolates in culture. Amphibian skin bacterial communities have become a recent focus of work in host-associated microbial systems due to the potential role of these skin bacteria in host defense against the pathogenic fungus Batrachochytrium dendrobatidis (Bd), which is associated with global amphibian population declines and extinctions. As there is evidence that some skin bacteria may inhibit growth of Bd and prevent infection in some cases, there is interest in using these bacteria as probiotic therapy for conservation of at-risk amphibians. In this study, we used skin swabs from American toads Onaxyrus americanus) to: (1) assess the diversity and community structure of culturable amphibian skin bacteria grown on high and low nutrient culture media. (2) determine which culture media recover the highest proportion of the total skin bacterial community of individual toads relative to culture-independent data, and (3) assess whether the plated communities from the distinct media types vary in their ability to inhibit Bd growth in in-vitro assays. Overall, we found that culture media with low nutrient concentrations facilitated the growth of more diverse bacterial taxa and grew distinct communities relative to media with higher nutrient concentrations. Use of low nutrient media also resulted in culturing proportionally more of the bacterial diversity on individual toads relative to the overall community defined using culture-independent methods. However, while there were differences in diversity among media types, the variation among individual hosts was greater than variation among media types, suggesting that swabbing more individuals in a population is the best way to maximize culture collections, regardless of media type. Lastly, the function of the plated communities against Bd did not vary across culture media type or between high and low nutrient media. These results inform current efforts for developing a probiotic-based approach for amphibian conservation and help to ensure that culture collections are capturing the majority of the important diversity in these systems.
- Cutaneous Bacteria of the Redback Salamander Prevent Morbidity Associated with a Lethal DiseaseBecker, Matthew H.; Harris, Reid N. (PLOS, 2010-06-04)Chytridiomycosis, caused by the fungal pathogen Batrachochytrium dendrobatidis (Bd), is an infectious disease that causes population declines of many amphibians. Cutaneous bacteria isolated from redback salamanders, Plethodon cinereus, and mountain yellow-legged frogs, Rana muscosa, inhibit the growth of Bd in vitro. In this study, the bacterial community present on the skin of P. cinereus individuals was investigated to determine if it provides protection to salamanders from the lethal and sub-lethal effects of chytridiomycosis. When the cutaneous bacterial community was reduced prior to Bd exposure, salamanders experienced a significantly greater decrease in body mass, which is a symptom of the disease, when compared to infected individuals with a normal bacterial community. In addition, a greater proportion of infected individuals with a reduced bacterial community experienced limb-lifting, a behavior seen only in infected individuals. Overall, these results demonstrate that the cutaneous bacterial community of P. cinereus provides protection to the salamander from Bd and that alteration of this community can change disease resistance. Therefore, symbiotic microbes associated with this species appear to be an important component of its innate skin defenses.
- Dimension Reduction for Multinomial Models Via a Kolmogorov-Smirnov Measure (KSM)Loftus, Stephen C.; House, Leanna L.; Hughey, Myra C.; Walke, Jenifer B.; Becker, Matthew H.; Belden, Lisa K. (Virginia Tech, 2015)Due to advances in technology and data collection techniques, the number of measurements often exceeds the number of samples in ecological datasets. As such, standard models that attempt to assess the relationship between variables and a response are inapplicable and require a reduction in the number of dimensions to be estimable. Several filtering methods exist to accomplish this, including Indicator Species Analyses and Sure Information Screening, but these techniques often have questionable asymptotic properties or are not readily applicable to data with multinomial responses. As such, we propose and validate a new metric called the Kolmogorov-Smirnov Measure (KSM) to be used for filtering variables. In the paper, we develop the KSM, investigate its asymptotic properties, and compare it to group equalized Indicator Species Values through simulation studies and application to a well-known biological dataset.
- Panamanian frog species host unique skin bacterial communitiesBelden, Lisa K.; Hughey, Myra C.; Rebollar, Eria A.; Umile, Thomas P.; Loftus, Stephen C.; Burzynski, Elizabeth A.; Minbiole, Kevin P. C.; House, Leanna L.; Jensen, Roderick V.; Becker, Matthew H.; Walke, Jenifer B.; Medina, Daniel; Ibanez, Roberto; Harris, Reid N. (Frontiers, 2015-10-27)Vertebrates, including amphibians, host diverse symbiotic microbes that contribute to host disease resistance. Globally, and especially in montane tropical systems, many amphibian species are threatened by a chytrid fungus, Batrachochytrium dendrobatidis (Bd), that causes a lethal skin disease. Bd therefore may be a strong selective agent on the diversity and function of the microbial communities inhabiting amphibian skin. In Panama, amphibian population declines and the spread of Bd have been tracked. In 2012, we completed a field survey in Panama to examine frog skin microbiota in the context of Bd infection. We focused on three frog species and collected two skin swabs per frog from a total of 136 frogs across four sites that varied from west to east in the time since Bd arrival. One swab was used to assess bacterial community structure using 16S rRNA amplicon sequencing and to determine Bd infection status, and one was used to assess metabolite diversity, as the bacterial production of anti fungal metabolites is an important disease resistance function. The skin microbiota of the three Panamanian frog species differed in OTU (operational taxonomic unit, bacterial species) community composition and metabolite profiles, although the pattern was less strong for the metabolites. Comparisons between frog skin bacterial communities from Panama and the US suggest broad similarities at the phylum level, but key differences at lower taxonomic levels. In our field survey in Panama, across all four sites, only 35 individuals (similar to 26%) were Bd infected. There was no clustering of OTUs or metabolite profiles based on Bd infection status and no clear pattern of west east changes in OTUs or metabolite profiles across the four sites. Overall, our field survey data suggest that different bacterial communities might be producing broadly similar sets of metabolites across frog hosts and sites. Community structure and function may not be as tightly coupled in these skin symbiont microbial systems as it is in many macro systems.
- The Role of Symbiotic Bacteria in Disease Resistance and Conservation of the Critically Endangered Panamanian Golden FrogBecker, Matthew H. (Virginia Tech, 2014-08-27)Amphibian populations have undergone unprecedented declines in recent decades. Many of these declines are due to the spread of the cutaneous fungal pathogen Batrachochytrium dendrobatidis (Bd), which causes the disease chytridiomycosis. The Panamanian golden frog (Atelopus zeteki) has not been seen in the wild since Bd spread through western Panama. In response to initial declines, golden frogs were collected from wild populations and placed in captive colonies with the goal of future reintroductions. An understanding of this species' natural defense mechanisms against Bd is needed for reintroduction to be successful. Previous studies indicate that cutaneous bacteria are an important defense mechanism for some amphibians and applying antifungal bacteria to the skin of Bd-susceptible amphibians (probiotic therapy) can prevent chytridiomycosis. Therefore, the goals of my dissertation were to characterize the bacterial community of A. zeteki and determine if probiotic therapy could be used to prevent chytridiomycosis in this species. I initially characterized the bacterial community of wild and captive golden frogs using samples collected prior to the initial declines and after approximately eight years in captivity. I found that the community structure of the microbiota was significantly different between wild and captive frogs; however, the offspring of the original captive frogs still shared 70% of their microbial community with wild frogs. Then, I characterized the Bd-inhibitory properties of 484 bacteria isolated from 11 species of free-living Panamanian amphibians. I found a large proportion of bacteria (75.2%) had the ability to inhibit Bd and this trait was widely distributed among bacterial taxa, although there was also significant variation within bacterial genera in their ability to inhibit Bd growth. I then experimentally tested the ability of four of these isolates to prevent chytridiomycosis in captive golden frogs. None of them successfully prevented infection; however, there were several frogs that cleared infection and this was correlated with composition of the bacteria initially present on their skin. Overall these results demonstrate that the structure of microbial communities of A. zeteki are important to host health and building on this might provide the best hope for reintroducing this iconic species back to its native habitat.
- Using "Omics" and Integrated Multi-Omics Approaches to Guide Probiotic Selection to Mitigate Chytridiomycosis and Other Emerging Infectious DiseasesRebollar, Eria A.; Antwis, Rachael E.; Becker, Matthew H.; Belden, Lisa K.; Bletz, Molly C.; Brucker, Robert M.; Harrison, Xavier A.; Hughey, Myra C.; Kueneman, Jordan G.; Loudon, Andrew H.; McKenzie, Valerie; Medina, Daniel; Minbiole, Kevin P. C.; Rollins-Smith, Louise A.; Walke, Jenifer B.; Weiss, Sophie; Woodhams, Douglas C.; Harris, Reid N. (Frontiers, 2016-02-02)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.