scholarly journals The Fungicide Chlorothalonil Changes the Amphibian Skin Microbiome: A Potential Factor Disrupting a Host Disease-Protective Trait

2021 ◽  
Vol 1 (1) ◽  
pp. 26-37
Author(s):  
Randall R. Jiménez ◽  
Gilbert Alvarado ◽  
Clemens Ruepert ◽  
Erick Ballestero ◽  
Simone Sommer
Keyword(s):  
Batrachochytrium Dendrobatidis ◽  
Bacterial Community Composition ◽  
Model Organism ◽  
Amplicon Sequencing ◽  
Anthropogenic Factors ◽  
Skin Microbiome ◽  
Amphibian Skin ◽  
16S Rrna Amplicon Sequencing ◽  
Potential Factor ◽  
Inhibitory Bacteria

The skin microbiome is an important part of amphibian immune defenses and protects against pathogens such as the chytrid fungus Batrachochytrium dendrobatidis (Bd), which causes the skin disease chytridiomycosis. Alteration of the microbiome by anthropogenic factors, like pesticides, can impact this protective trait, disrupting its functionality. Chlorothalonil is a widely used fungicide that has been recognized as having an impact on amphibians, but so far, no studies have investigated its effects on amphibian microbial communities. In the present study, we used the amphibian Lithobates vibicarius from the montane forest of Costa Rica, which now appears to persist despite ongoing Bd-exposure, as an experimental model organism. We used 16S rRNA amplicon sequencing to investigate the effect of chlorothalonil on tadpoles’ skin microbiome. We found that exposure to chlorothalonil changes bacterial community composition, with more significant changes at a higher concentration. We also found that a larger number of bacteria were reduced on tadpoles’ skin when exposed to the higher concentration of chlorothalonil. We detected four presumed Bd-inhibitory bacteria being suppressed on tadpoles exposed to the fungicide. Our results suggest that exposure to a widely used fungicide could be impacting host-associated bacterial communities, potentially disrupting an amphibian protective trait against pathogens.

scholarly journals Skin Microbiome in Patients with Hand Eczema and Healthy Controls: A Three-week Prospective Study

2021 ◽  
Author(s):  
Line Brok Nørreslet ◽  
Berit Lilje ◽  
Anna Cäcilia Ingham ◽  
Sofie Marie Edslev ◽  
Maja-Lisa Clausen ◽  
...  
Keyword(s):  
Prospective Study ◽  
Disease Severity ◽  
Amplicon Sequencing ◽  
Hand Eczema ◽  
Skin Microbiome ◽  
Healthy Controls ◽  
16S Rrna Amplicon Sequencing ◽  
Chronic Hand Eczema ◽  
Α Diversity ◽  
Underlying Mechanisms

The pathogenesis of chronic hand eczema remains unclear. Insights into the skin microbiome in hand eczema and its potential relevance to disease severity may help to elucidate the underlying mechanisms of hand eczema. The aim of this study was to characterize the microbiome in patients with hand eczema and healthy controls. A 5-visit prospective study was conducted over a period of 3 weeks. At each visit, bacterial swabs were taken from the hands of patients with hand eczema and controls. The microbiome was examined using DNA extraction and 16S rRNA amplicon sequencing (V3–V4 regions). Fifty patients with hand eczema and 50 controls were included (follow-up rate=100%). The baseline bacterial α-diversity was reduced on the hands of patients with hand eczema compared with controls (effect size=–0.31; 95% confidence interval (95% CI) –0.50; –0.11; p = 0.003). The dysbiosis on the patients’ hands was stable over the study period, was associated with disease severity, and was characterized by reduced bacterial diversity and different bacterial community compositions.

scholarly journals SKIOME Project: a curated collection of skin microbiome datasets enriched with study-related metadata

2021 ◽  
Author(s):  
Giulia Agostinetto ◽  
Davide Bozzi ◽  
Danilo Porro ◽  
Maurizio Casiraghi ◽  
Massimo Labra ◽  
...  
Keyword(s):  
Data Science ◽  
Data Retrieval ◽  
Amplicon Sequencing ◽  
Full Potential ◽  
Skin Microbiome ◽  
Data Accessibility ◽  
16S Rrna Amplicon Sequencing ◽  
Comprehensive Collection ◽  
Microbiome Research ◽  
Microbiome Data

Large amounts of data from microbiome-related studies have been (and are currently being) deposited on international public databases. These datasets represent a valuable resource for the microbiome research community and could serve future researchers interested in integrating multiple datasets into powerful meta-analyses. However, this huge amount of data lacks harmonization and is far from being completely exploited in its full potential to build a foundation that places microbiome research at the nexus of many subdisciplines within and beyond biology. Thus, urges the need for data accessibility and reusability, according to FAIR (Findable, Accessible, Interoperable, and Reusable) principles, as supported by National Microbiome Data Collaborative and FAIR Microbiome. To tackle the challenge of accelerating discovery and advances in skin microbiome research, we collected, integrated and organized existing microbiome data resources from human skin 16S rRNA amplicon sequencing experiments. We generated a comprehensive collection of datasets, enriched in metadata, and organized this information into data frames ready to be integrated into microbiome research projects and advanced post-processing analysis, such as data science applications (e.g. machine learning). Furthermore, we have created a data retrieval and curation framework built on three different stages to maximize the retrieval of datasets and metadata associated with them. Lastly, we highlighted some caveats regarding metadata retrieval and suggested ways to improve future metadata submissions. Overall, our work resulted in a curated skin microbiome datasets collection accompanied by a state-of-the-art analysis of the last 10 years of the skin microbiome field.

scholarly journals Most of the Dominant Members of Amphibian Skin Bacterial Communities Can Be Readily Cultured

2015 ◽  
Vol 81 (19) ◽  
pp. 6589-6600 ◽  
Author(s):  
Jenifer B. Walke ◽  
Matthew H. Becker ◽  
Myra C. Hughey ◽  
Meredith C. Swartwout ◽  
Roderick V. Jensen ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Batrachochytrium Dendrobatidis ◽  
Amplicon Sequencing ◽  
Reference Database ◽  
Rrna Gene ◽  
Amphibian Skin ◽  
Amphibian Species ◽  
Content Type ◽  
Average Percentage ◽  
Culture Independent

ABSTRACTCurrently, it is estimated that only 0.001% to 15% of bacteria in any given system can be cultured by use of commonly used techniques and media, yet culturing is critically important for investigations of bacterial function. Despite this situation, few studies have attempted to link culture-dependent and culture-independent data for a single system to better understand which members of the microbial community are readily cultured. In amphibians, some cutaneous bacterial symbionts can inhibit establishment and growth of the fungal pathogenBatrachochytrium dendrobatidis, and thus there is great interest in using these symbionts as probiotics for the conservation of amphibians threatened byB. dendrobatidis. The present study examined the portion of the culture-independent bacterial community (based on Illumina amplicon sequencing of the 16S rRNA gene) that was cultured with R2A low-nutrient agar and whether the cultured bacteria represented rare or dominant members of the community in the following four amphibian species: bullfrogs (Lithobates catesbeianus), eastern newts (Notophthalmus viridescens), spring peepers (Pseudacris crucifer), and American toads (Anaxyrus americanus). To determine which percentage of the community was cultured, we clustered Illumina sequences at 97% similarity, using the culture sequences as a reference database. For each amphibian species, we cultured, on average, 0.59% to 1.12% of each individual's bacterial community. However, the average percentage of bacteria that were culturable for each amphibian species was higher, with averages ranging from 2.81% to 7.47%. Furthermore, most of the dominant operational taxonomic units (OTUs), families, and phyla were represented in our cultures. These results open up new research avenues for understanding the functional roles of these dominant bacteria in host health.

scholarly journals Seasonal and ontogenetic variation of skin microbial communities and relationships to natural disease dynamics in declining amphibians

2015 ◽  
Vol 2 (7) ◽  
pp. 140377 ◽  
Author(s):  
Ana V. Longo ◽  
Anna E. Savage ◽  
Ian Hewson ◽  
Kelly R. Zamudio
Keyword(s):  
Bacterial Diversity ◽  
Batrachochytrium Dendrobatidis ◽  
Developmental Stages ◽  
Pathogenic Fungus ◽  
Natural Populations ◽  
Amplicon Sequencing ◽  
Protective Role ◽  
Skin Microbiome ◽  
Skin Bacteria

Recently, microbiologists have focused on characterizing the probiotic role of skin bacteria for amphibians threatened by the fungal disease chytridiomycosis. However, the specific characteristics of microbial diversity required to maintain health or trigger disease are still not well understood in natural populations. We hypothesized that seasonal and developmental transitions affecting susceptibility to chytridiomycosis could also alter the stability of microbial assemblages. To test our hypothesis, we examined patterns of skin bacterial diversity in two species of declining amphibians ( Lithobates yavapaiensis and Eleutherodactylus coqui ) affected by the pathogenic fungus Batrachochytrium dendrobatidis ( Bd ). We focused on two important transitions that affect Bd susceptibility: ontogenetic (from juvenile to adult) shifts in E. coqui and seasonal (from summer to winter) shifts in  L. yavapaiensis . We used a combination of community-fingerprinting analyses and 16S rRNA amplicon sequencing to quantify changes in bacterial diversity and assemblage composition between seasons and developmental stages, and to investigate the relationship between bacterial diversity and pathogen load. We found that winter-sampled frogs and juveniles, two states associated with increased Bd susceptibility, exhibited higher diversity compared with summer-sampled frogs and adult individuals. Our findings also revealed that hosts harbouring higher bacterial diversity carried lower Bd infections, providing support for the protective role of bacterial communities. Ongoing work to understand skin microbiome resilience after pathogen disturbance has the potential to identify key taxa involved in disease resistance.

scholarly journals Habitat disturbance Linked with Host Microbiome Dispersion and Bd Dynamics in Temperate Amphibians

2021 ◽  
Author(s):  
Wesley James Neely ◽  
Sasha E Greenspan ◽  
Leigha M Stahl ◽  
Sam D Heraghty ◽  
Vanessa M Marshall ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Population Health ◽  
Batrachochytrium Dendrobatidis ◽  
Habitat Disturbance ◽  
Skin Microbiome ◽  
Amphibian Skin ◽  
Community Interactions ◽  
Microbiome Composition ◽  
Habitat Disturbances ◽  
Anthropogenic Habitat

Abstract Anthropogenic habitat disturbances can dramatically alter ecological community interactions, including host-pathogen dynamics. Recent work has highlighted the potential for habitat disturbances to alter host-associated microbial communities, but the associations between anthropogenic disturbance, host microbiomes, and pathogens are unresolved. Amphibian skin microbial communities are particularly responsive to factors like temperature, physiochemistry, pathogen infection, and environmental microbial reservoirs. Through a field survey on wild populations of Acris crepitans (Hylidae) and Lithobates catesbeianus (Ranidae), we assessed effects of habitat disturbance on environmental bacterial resevoirs, Batrachochytrium dendrobatidis (Bd) infection, and skin microbiome composition. We found higher measures of microbiome dispersion (a measure of community stability) in A. crepitans from more disturbed ponds, supporting the hypothesis that disturbance increases stochasticity in biological communties. We also found that habitat disturbance limited microbiome similarity between locations for both species, suggesting less bacterial exchange in more disturbed areas. Higher disturbance was associated with lower Bd prevalence for A. crepitans, which could signify suboptimal microclimates for Bd in disturbed habitats. In this system we use microbiome dispersion as a metric of population health. Combined, our findings show that reduced microbiome stability stemming from habitat disturbance could compromise population health, even in the absence of pathogenic infection.

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

2016 ◽  
Vol 283 (1839) ◽  
pp. 20161553 ◽  
Author(s):  
Jordan G. Kueneman ◽  
Douglas C. Woodhams ◽  
Reid Harris ◽  
Holly M. Archer ◽  
Rob Knight ◽  
...  
Keyword(s):  
Batrachochytrium Dendrobatidis ◽  
Life Stage ◽  
Skin Microbiome ◽  
Janthinobacterium Lividum ◽  
Probiotic Treatment ◽  
In Captivity ◽  
Boreal Toads ◽  
Inhibitory Bacteria

Host-associated microbiomes perform many beneficial functions including resisting pathogens and training the immune system. Here, we show that amphibians developing in captivity lose substantial skin bacterial diversity, primarily due to reduced ongoing input from environmental sources. We combined studies of wild and captive amphibians with a database of over 1 000 strains that allows us to examine antifungal function of the skin microbiome. We tracked skin bacterial communities of 62 endangered boreal toads, Anaxyrus boreas , across 18 time points, four probiotic treatments, and two exposures to the lethal fungal pathogen Batrachochytrium dendrobatidis ( Bd ) in captivity, and compared these to 33 samples collected from wild populations at the same life stage. As the amphibians in captivity lost the Bd -inhibitory bacteria through time, the proportion of individuals exposed to Bd that became infected rose from 33% to 100% in subsequent exposures. Inoculations of the Bd -inhibitory probiotic Janthinobacterium lividum resulted in a 40% increase in survival during the second Bd challenge, indicating that the effect of microbiome depletion was reversible by restoring Bd -inhibitory bacteria. Taken together, this study highlights the functional role of ongoing environmental inputs of skin-associated bacteria in mitigating a devastating amphibian pathogen, and that long-term captivity decreases this defensive function.

scholarly journals Bacterial Community in the Skin Microbiome of Frogs in a Coldspot of Chytridiomycosis Infection

2021 ◽  
Author(s):  
Milind C. Mutnale ◽  
Gundlapally S. Reddy ◽  
Karthikeyan Vasudevan
Keyword(s):  
Bacterial Community ◽  
Relative Abundance ◽  
Frog Skin ◽  
Batrachochytrium Dendrobatidis ◽  
Bacterial Community Composition ◽  
Skin Microbiome ◽  
Bacterial Phyla ◽  
Frog Species ◽  
Generation Sequencing

AbstractChytridiomycosis is a fungal disease caused by the pathogens, Batrachochytrium dendrobatidis (Bd) and B. salamandrivorans (Bsal), which has caused declines in amphibian populations worldwide. Asia is considered as a coldspot of infection, since adult frogs are less susceptible to Bd-induced mortality or morbidity. Using the next-generation sequencing approach, we assessed the cutaneous bacterial community composition and presence of anti-Bd bacteria in six frog species from India using DNA isolated from skin swabs. All the six frog species sampled were tested using nested PCR and found Bd negative. We found a total of 551 OTUs on frog skin, of which the bacterial phyla such as Proteobacteria (56.15% average relative abundance) was dominated followed by Actinobacteria (21.98% average relative abundance) and Firmicutes (13.7% average relative abundance). The contribution of Proteobacteria in the anti-Bd community was highest and represented by 175 OTUs. Overall, the anti-Bd bacterial community dominated (51.7% anti-Bd OTUs) the skin microbiome of the frogs. The study highlights the putative role of frog skin microbiome in affording resistance to Bd infections in coldspots of infection.

scholarly journals Filtering artefacts in bacterial community composition can affect the outcome of dissolved organic matter biolability assays

2018 ◽  
Author(s):  
Joshua F. Dean ◽  
Jurgen R. van Hal ◽  
Han Dolman ◽  
Rien Aerts ◽  
James T. Weedon
Keyword(s):  
Organic Matter ◽  
Bacterial Community ◽  
Dissolved Organic Matter ◽  
Community Composition ◽  
Bacterial Community Composition ◽  
Amplicon Sequencing ◽  
Microbial Decomposition ◽  
16S Rrna Amplicon Sequencing ◽  
Filter Size ◽  
Carbon Dioxide Co2

Abstract. Inland waters are large contributors to global carbon dioxide (CO2) emissions, in part due to the vulnerability of dissolved organic matter (DOM) to microbial decomposition and respiration to CO2 during transport through aquatic systems. To assess the degree of this vulnerability, aquatic DOM is often incubated in standardized "biolability" assays. These assays isolate the dissolved fraction of aquatic OM by size filtration prior to incubation. We test whether this size selection has an impact on the bacterial community composition and the consequent dynamics of DOM degradation using three different filtering strategies: 0.2 μm (filtered-and-inoculated), 0.7 μm (generally the most common DOM filter size) and 106 μm ("unfiltered"). We found that bacterial community composition, based on 16S rRNA amplicon sequencing, was significantly affected by the different filter sizes. At the same time, filtering strategy also affected the DOM degradation dynamics. However, the dynamics of these two responses were decoupled, suggesting that filtration primarily influences biolability assays through bacterial abundance and the presence of their associated predators. By the end of the 41-day incubations all treatments tended to converge on a common total DOM biolability level, with the 0.7 μm filtered incubations reaching this point the quickest. These results suggest that assays to assess the total biolability of aquatic DOM should last long enough to remove filtration artefacts in the microbial population. Filtering strategy should also be taken into account when comparing results across biolability assays.

scholarly journals Early life skin microbial trajectory as a function of vertical and environmental transmission in Bornean foam-nesting frogs

2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Sarah McGrath-Blaser ◽  
Morgan Steffen ◽  
T. Ulmar Grafe ◽  
María Torres-Sánchez ◽  
David S. McLeod ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Bacterial Community Composition ◽  
Pond Water ◽  
Breeding Strategy ◽  
Skin Microbiome ◽  
Amphibian Skin ◽  
Environmental Interaction ◽  
Tadpole Skin ◽  
Foam Nest

Abstract Background The amphibian skin microbiome is an important mediator of host health and serves as a potential source of undiscovered scientifically significant compounds. However, the underlying modalities of how amphibian hosts obtain their initial skin-associated microbiome remains unclear. Here, we explore microbial transmission patterns in foam-nest breeding tree frogs from Southeast Asia (Genus: Polypedates) whose specialized breeding strategy allows for better delineation between vertically and environmentally derived microbes. To facilitate this, we analyzed samples associated with adult frog pairs taken after mating—including adults of each sex, their foam nests, environments, and tadpoles before and after environmental interaction—for the bacterial communities using DNA metabarcoding data (16S rRNA). Samples were collected from frogs in-situ in Brunei, Borneo, a previously unsampled region for amphibian-related microbial diversity. Results Adult frogs differed in skin bacterial communities among species, but tadpoles did not differ among species. Foam nests had varying bacterial community composition, most notably in the nests’ moist interior. Nest interior bacterial communities were discrete for each nest and overall displayed a narrower diversity compared to the nest exteriors. Tadpoles sampled directly from the foam nest displayed a bacterial composition less like the nest interior and more similar to that of the adults and nest exterior. After one week of pond water interaction the tadpole skin microbiome shifted towards the tadpole skin and pond water microbial communities being more tightly coupled than between tadpoles and the internal nest environment, but not to the extent that the skin microbiome mirrored the pond bacterial community. Conclusions Both vertical influence and environmental interaction play a role in shaping the tadpole cutaneous microbiome. Interestingly, the interior of the foam nest had a distinct bacterial community from the tadpoles suggesting a limited environmental effect on tadpole cutaneous bacterial selection at initial stages of life. The shift in the tadpole microbiome after environmental interaction indicates an interplay between underlying host and ecological mechanisms that drive community formation. This survey serves as a baseline for further research into the ecology of microbial transmission in aquatic animals.

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