scholarly journals The amphibian microbiome exhibits poor resilience following pathogen-induced disturbance

2021 ◽  
Author(s):  
Andrea J. Jani ◽  
Jessie Bushell ◽  
Cédric G. Arisdakessian ◽  
Mahdi Belcaid ◽  
Daniel M. Boiano ◽  
...  
Keyword(s):  
Microbial Community ◽  
Batrachochytrium Dendrobatidis ◽  
Recovery Period ◽  
Stable State ◽  
Amphibian Skin ◽  
Unifrac Distance ◽  
Microbiome Composition ◽  
Relative Abundances ◽  
Community Variability ◽  
Bacterial Groups

AbstractInfectious pathogens can disrupt the microbiome in addition to directly affecting the host. Impacts of disease may be dependent on the ability of the microbiome to recover from such disturbance, yet remarkably little is known about microbiome recovery after disease, particularly in nonhuman animals. We assessed the resilience of the amphibian skin microbial community after disturbance by the pathogen, Batrachochytrium dendrobatidis (Bd). Skin microbial communities of laboratory-reared mountain yellow-legged frogs were tracked through three experimental phases: prior to Bd infection, after Bd infection (disturbance), and after clearing Bd infection (recovery period). Bd infection disturbed microbiome composition and altered the relative abundances of several dominant bacterial taxa. After Bd infection, frogs were treated with an antifungal drug that cleared Bd infection, but this did not lead to recovery of microbiome composition (measured as Unifrac distance) or relative abundances of dominant bacterial groups. These results indicate that Bd infection can lead to an alternate stable state in the microbiome of sensitive amphibians, or that microbiome recovery is extremely slow—in either case resilience is low. Furthermore, antifungal treatment and clearance of Bd infection had the additional effect of reducing microbial community variability, which we hypothesize results from similarity across frogs in the taxa that colonize community vacancies resulting from the removal of Bd. Our results indicate that the skin microbiota of mountain yellow-legged frogs has low resilience following Bd-induced disturbance and is further altered by the process of clearing Bd infection, which may have implications for the conservation of this endangered amphibian.

scholarly journals Assembly of the amphibian microbiome is influenced by the effects of land-use change on environmental reservoirs

2020 ◽  
Author(s):  
Elle M. Barnes ◽  
Steve Kutos ◽  
Nina Naghshineh ◽  
Marissa Mesko ◽  
Qing You ◽  
...  
Keyword(s):  
New York ◽  
Land Use ◽  
Microbial Community ◽  
Community Composition ◽  
Batrachochytrium Dendrobatidis ◽  
Pathogenic Fungus ◽  
Microbial Community Composition ◽  
Canopy Cover ◽  
Amphibian Skin ◽  
Regional Species Pool

0AbstractA growing focus in microbial ecology is understanding of how beneficial microbiome function is created and maintained through both stochastic and deterministic assembly mechanisms. This study explores the role of both the environment and disease in regulating the composition of microbial species pools in the soil and local communities of an amphibian host. To address this, we compared the microbiomes of over 200 Plethodon cinereus salamanders along a 65km land-use gradient in the greater New York metropolitan area and paired these with associated soil cores. Additionally, we characterized the diversity of bacterial and fungal symbionts that putatively inhibit the pathogenic fungus Batrachochytrium dendrobatidis. We predicted that if soil functions as the main regional species pool to amphibian skin, variation in skin microbial community composition would correlate with changes seen in soil. We found that salamanders share many microbial taxa with their soil environment but that these two microbiomes exhibit key differences, especially in the relative abundances of the bacteria phyla Acidobacteria, Actinobacteria, and Proteobacteria and the fungal phyla Ascomycota and genus Basidiobolus. Microbial community composition varied with changes in land-use associated factors such as canopy cover, impervious surface, and concentrations of the soil elements Al, Ni, and Hg, creating site-specific compositions. In addition, high dissimilarity among individual amphibian microbiomes across and within sites suggest that both stochastic and deterministic mechanisms guide assembly of microbes onto amphibian skin, with likely consequences in disease preventative function.

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 52 Alterations of fecal microbiome characteristics by dietary soy isoflavone ingestion in growing pigs infected with porcine reproductive and respiratory syndrome virus

2020 ◽  
Vol 98 (Supplement_3) ◽  
pp. 30-31
Author(s):  
Brooke N Smith ◽  
Stephen A Fleming ◽  
Mei Wang ◽  
Ryan N Dilger
Keyword(s):  
Control Diet ◽  
Growing Pigs ◽  
Respiratory Syndrome Virus ◽  
Post Inoculation ◽  
Long Term Effects ◽  
Unifrac Distance ◽  
Fecal Microbiome ◽  
Microbiome Composition ◽  
Time Points ◽  
Experimental Treatments

Abstract Porcine reproductive and respiratory syndrome virus (PRRSV) is an economically-important disease and ingestion of soy isoflavones (ISF) may benefit PRRSV-infected pigs due to demonstrated anti-inflammatory and anti-viral properties. The objective of this study was to quantify long-term effects of ISF consumption on fecal microbiome characteristics under disease challenge. In total, 96 weaned barrows were group-housed in a BSL-2 containment facility and allotted to 1 of 3 experimental treatments that were maintained throughout the wean-to-finish study: non-infected pigs receiving an ISF-devoid control diet (NC, n=24), and infected pigs receiving either the control diet (PC, n=36) or that supplemented with total ISF in excess of 1,600 mg/kg (ISF, n=36) (Table 1). Following a 7-day adaptation, pigs were inoculated intranasally with either a sham-control (PBS) or live PRRSV (1×105 TCID50/mL, strain NADC20). Fecal samples were collected from 48 individual pigs at pre-infection (-2 days post-inoculation, DPI), peak-infection (10 DPI), and post-infection (144 DPI) time-points and extracted DNA was used for 16S bacterial rRNA sequencing. Differences in bacterial communities among diet groups were evaluated using UniFrac distance matrices (weighted and unweighted) in QIIME. All other data were analyzed by one-way ANOVA performed on transformed data using R. Across all time-points, only minimal differences were observed due to ISF alone. At 10 DPI, PRRSV infection reduced Prevotella 9 genera abundance from approximately 20% to less than 10%, but the specific function of this variety in pigs is unclear. The most notable finding was decreased relative abundance of Actinobacteria at 144 DPI between non-infected and infected treatments (P < 0.05), which is consistent with various dysbioses observed in other disease models. Our findings indicate that differences present were mainly due to PRRSV infection and not strongly influenced by ISF ingestion, which implies previously observed performance benefits conferred by dietary ISF are not likely due to changes in microbiome composition.

scholarly journals The phyllosphere microbiome of host trees contributes more than leaf phytochemicals to variation in the Agrilus planipennis Fairmaire gut microbiome structure

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Judith Mogouong ◽  
Philippe Constant ◽  
Pierre Legendre ◽  
Claude Guertin
Keyword(s):  
Microbial Community ◽  
Gut Microbiome ◽  
Strong Predictor ◽  
Emerald Ash Borer ◽  
Agrilus Planipennis ◽  
Food Sources ◽  
Microbiome Composition ◽  
Living Organisms ◽  
Insect Gut ◽  
Gut Microbial Community

AbstractThe microbiome composition of living organisms is closely linked to essential functions determining the fitness of the host for thriving and adapting to a particular ecosystem. Although multiple factors, including the developmental stage, the diet, and host-microbe coevolution have been reported to drive compositional changes in the microbiome structures, very few attempts have been made to disentangle their various contributions in a global approach. Here, we focus on the emerald ash borer (EAB), an herbivorous pest and a real threat to North American ash tree species, to explore the responses of the adult EAB gut microbiome to ash leaf properties, and to identify potential predictors of EAB microbial variations. The relative contributions of specific host plant properties, namely bacterial and fungal communities on leaves, phytochemical composition, and the geographical coordinates of the sampling sites, to the EAB gut microbial community was examined by canonical analyses. The composition of the phyllosphere microbiome appeared to be a strong predictor of the microbial community structure in EAB guts, explaining 53 and 48% of the variation in fungi and bacteria, respectively. This study suggests a potential covariation of the microorganisms associated with food sources and the insect gut microbiome.

scholarly journals Food Starch Structure Impacts Gut Microbiome Composition

mSphere ◽  
2018 ◽  
Vol 3 (3) ◽  
Author(s):  
Frederick J. Warren ◽  
Naoki M. Fukuma ◽  
Deirdre Mikkelsen ◽  
Bernadine M. Flanagan ◽  
Barbara A. Williams ◽  
...  
Keyword(s):  
Small Intestine ◽  
Microbial Community ◽  
Gut Microbiome ◽  
Nutritive Value ◽  
Human Diet ◽  
Fermentation Products ◽  
Microbiome Composition ◽  
Starch Fermentation ◽  
Starch Structure

ABSTRACT Starch is a major source of energy in the human diet and is consumed in diverse forms. Resistant starch (RS) escapes small intestinal digestion and is fermented in the colon by the resident microbiota, with beneficial impacts on colonic function and host health, but the impacts of the micro- and nanoscale structure of different physical forms of food starch on the broader microbial community have not been described previously. Here, we use a porcine in vitro fermentation model to establish that starch structure dramatically impacts microbiome composition, including the key amylolytic species, and markedly alters both digestion kinetics and fermentation outcomes. We show that three characteristic food forms of starch that survive digestion in the small intestine each give rise to substantial and distinct changes in the microbiome and in fermentation products. Our results highlight the complexity of starch fermentation processes and indicate that not all forms of RS in foods are degraded or fermented in the same way. This work points the way for the design of RS with tailored degradation by defined microbial communities, informed by an understanding of how substrate structure influences the gut microbiome, to improve nutritive value and/or health benefits. IMPORTANCE Dietary starch is a major component in the human diet. A proportion of the starch in our diet escapes digestion in the small intestine and is fermented in the colon. In this study, we use a model of the colon, seeded with porcine feces, in which we investigate the fermentation of a variety of starches with structures typical of those found in foods. We show that the microbial community changes over time in our model colon are highly dependent on the structure of the substrate and how accessible the starch is to colonic microbes. These findings have important implications for how we classify starches reaching the colon and for the design of foods with improved nutritional properties.

scholarly journals Alterations of fecal microbiome characteristics by dietary soy isoflavone ingestion in growing pigs infected with porcine reproductive and respiratory syndrome virus

2020 ◽  
Vol 98 (6) ◽  
Author(s):  
Brooke N Smith ◽  
Stephen A Fleming ◽  
Mei Wang ◽  
Ryan N Dilger
Keyword(s):  
Control Diet ◽  
Fecal Microbiota ◽  
Growing Pigs ◽  
Respiratory Syndrome Virus ◽  
Post Inoculation ◽  
Unifrac Distance ◽  
Infectious Dose ◽  
Fecal Microbiome ◽  
Microbiome Composition ◽  
Experimental Treatments

Abstract Porcine reproductive and respiratory syndrome virus (PRRSV) is an economically important disease, and the ingestion of soy isoflavones (ISF) may benefit PRRSV-infected pigs due to demonstrated anti-inflammatory and antiviral properties. The objective of this study was to quantify the effects of ISF consumption on fecal microbiome characteristics at different timepoints across a disease challenge and determine whether any changes, if present, elude to potential biological mechanisms for previously observed performance benefits. In total, 96 weaned barrows were group-housed in a Biosafety Level-2 containment facility and allotted to one of three experimental treatments that were maintained throughout the study: noninfected pigs receiving an ISF-devoid control diet (NEG, n = 24) and infected pigs receiving either the control diet (POS, n = 36) or that supplemented with total ISF in excess of 1,600 mg/kg (ISF, n = 36). Following a 7-d adaptation, pigs were inoculated intranasally with either a sham-control (phosphate-buffered saline) or live PRRSV (1 × 105 median tissue culture infectious dose[TCID]50/mL, strain NADC20). Fecal samples were collected from 48 individual pigs at pre-infection (−2 d post-inoculation [DPI]), peak-infection (10 DPI), and post-infection (144 DPI) timepoints. Extracted DNA was used to quantify fecal microbiota profiles via 16S bacterial rRNA sequencing. Differences in bacterial communities among diet groups were evaluated with principal coordinate analysis and permutational multivariate analysis of variance using UniFrac distance matrices based on both unweighted and weighted UniFrac distances using QIIME 2. All other data were analyzed by one-way ANOVA performed on square root transformations using R. Across all timepoints, only a few differences were observed due to ISF alone mainly in lowly abundant genera. The most notable differences observed were decreased relative abundance of Actinobacteria at 144 DPI between noninfected and infected treatments (P < 0.05), which is consistent with various dysbioses observed in other disease models. Our findings indicate that the differences present were mainly due to PRRSV-infection alone and not strongly influenced by diet, which implies that previously observed performance benefits conferred by dietary ISF are not likely due to the changes in microbiome composition.

scholarly journals Tadpole body size and behaviour alter the social acquisition of a defensive bacterial symbiont

2019 ◽  
Vol 6 (9) ◽  
pp. 191080 ◽  
Author(s):  
Carl N. Keiser ◽  
Trina Wantman ◽  
Eria A. Rebollar ◽  
Reid N. Harris
Keyword(s):  
Body Size ◽  
Batrachochytrium Dendrobatidis ◽  
Amphibian Skin ◽  
Disease Epidemiology ◽  
Janthinobacterium Lividum ◽  
Exposed Individual ◽  
The Social ◽  
Microbial Symbionts ◽  
Protection Against Infection ◽  
Skin Bacterium

Individual differences in host phenotypes can generate heterogeneity in the acquisition and transmission of microbes. Although this has become a prominent factor of disease epidemiology, host phenotypic variation might similarly underlie the transmission of microbial symbionts that defend against pathogen infection. Here, we test whether host body size and behaviour influence the social acquisition of a skin bacterium, Janthinobacterium lividum , which in some hosts can confer protection against infection by Batrachochytrium dendrobatidis , the causative agent of the amphibian skin disease chytridiomycosis. We measured body size and boldness (time spent in an open field) of green frog tadpoles and haphazardly constructed groups of six individuals. In some groups, we exposed one individual in each group to J. lividum and, in other groups, we inoculated a patch of aquarium pebbles to J. lividum . After 24 h, we swabbed each individual to estimate the presence of J. lividum on their skin. On average, tadpoles acquired nearly four times more bacteria when housed with an exposed individual compared to those housed with a patch of inoculated substrate. When tadpoles were housed with an exposed group-mate, larger and ‘bolder’ individuals acquired more bacteria. These data suggest that phenotypically biased acquisition of defensive symbionts might generate biased patterns of mortality from the pathogens against which they protect.

scholarly journals Phylogenetic investigation of skin sloughing rates in frogs: relationships with skin characteristics and disease-driven declines

2019 ◽  
Vol 286 (1896) ◽  
pp. 20182378 ◽  
Author(s):  
Michel E. B. Ohmer ◽  
Rebecca L. Cramp ◽  
Craig R. White ◽  
Peter S. Harlow ◽  
Michael S. McFadden ◽  
...  
Keyword(s):  
Batrachochytrium Dendrobatidis ◽  
Phylogenetic Signal ◽  
Interspecific Variation ◽  
Phylogenetic Position ◽  
Turnover Rates ◽  
Amphibian Skin ◽  
Amphibian Species ◽  
Wide Range ◽  
Skin Morphology ◽  
And Function

Amphibian skin is highly variable in structure and function across anurans, and plays an important role in physiological homeostasis and immune defence. For example, skin sloughing has been shown to reduce pathogen loads on the skin, such as the lethal fungus Batrachochytrium dendrobatidis ( Bd ), but interspecific variation in sloughing frequency is largely unknown. Using phylogenetic linear mixed models, we assessed the relationship between skin turnover rate, skin morphology, ecological traits and overall evidence of Bd -driven declines. We examined skin sloughing rates in 21 frog species from three continents, as well as structural skin characteristics measured from preserved specimens. We found that sloughing rate varies significantly with phylogenetic group, but was not associated with evidence of Bd -driven declines, or other skin characteristics examined. This is the first comparison of sloughing rate across a wide range of amphibian species, and creates the first database of amphibian sloughing behaviour. Given the strong phylogenetic signal observed in sloughing rate, approximate sloughing rates of related species may be predicted based on phylogenetic position. While not related to available evidence of declines, understanding variation in sloughing rate may help explain differences in the severity of infection in genera with relatively slow skin turnover rates (e.g. Atelopus ).

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