Amphibian chytridiomycosis outbreak dynamics are linked with host skin bacterial community structure - PubMed (original) (raw)

Amphibian chytridiomycosis outbreak dynamics are linked with host skin bacterial community structure

Kieran A Bates et al. Nat Commun. 2018.

Abstract

Host-associated microbes are vital for combatting infections and maintaining health. In amphibians, certain skin-associated bacteria inhibit the fungal pathogen Batrachochytrium dendrobatidis (Bd), yet our understanding of host microbial ecology and its role in disease outbreaks is limited. We sampled skin-associated bacteria and Bd from Pyrenean midwife toad populations exhibiting enzootic or epizootic disease dynamics. We demonstrate that bacterial communities differ between life stages with few shared taxa, indicative of restructuring at metamorphosis. We detected a significant effect of infection history on metamorph skin microbiota, with reduced bacterial diversity in epizootic populations and differences in community structure and predicted function. Genome sequencing of Bd isolates supports a single introduction to the Pyrenees and reveals no association between pathogen genetics and epidemiological trends. Our findings provide an ecologically relevant insight into the microbial ecology of amphibian skin and highlight the relative importance of host microbiota and pathogen genetics in predicting disease outcome.

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Conflict of interest statement

The authors declare no competing financial interests.

Figures

Fig. 1

Fig. 1

Bacterial communities of Alytes obstetricans skin across life stages and in environmental samples. a OTUs common among life stages and environmental samples. b Shannon diversity by sample type (boxes represent 25 and 75 percentile, the horizontal line is the median, whiskers are maximum and minimum values). c NMDS plot of bacterial communities based on life stage, environmental samples and population. d Stacked bar chart of the ten most abundant phyla for lake water, sediment, larvae and metamorphs. Sample sizes were: n = 63 (larvae); n = 51 (metamorphs); n = 20 (environment)

Fig. 2

Fig. 2

Bd infection profiles of Alytes obstetricans metamorph populations. a Boxplot of Bd infection intensity in metamorphs sampled in 2015 showing reduced infection intensity in enzootic populations (Chi-sq = 59.855, P < 0.0001). Boxes represent 25 and 75 percentile, the horizontal line is the median and whiskers are maximum and minimum values of infection intensity. b Bar chart of Bd infection prevalence in metamorphs. Enzootic populations are coloured in blue, epizootic populations are coloured in red. Sample sizes were: Enzootic = 32 (Acherito = 14, Lhurs = 11, Puits d’Arious = 7); Epizootic = 19 (Arlet = 16, Ansabere = 3)

Fig. 3

Fig. 3

Bacterial community profiles of Alytes obstetricans metamorph skin from enzootic and epizootic populations. a Shannon diversity of metamorph populations. Epizootic populations are in red and enzootic populations are blue. Boxes represent 25 and 75 percentile; the horizontal line is the median and whiskers are maximum and minimum values. b NMDS plot based on Bray−Curtis distances displaying beta diversity of enzootic and epizootic populations. c Stacked bar chart of abundant bacterial phyla for each metamorph population. d Map showing location of enzootic and epizootic populations. Map generated using ArcGIS version 10.0 (

http://www.esri.com/software/arcgis

) with the World Imagery Basemap. Source: Esri, DigitalGlobe, GeoEye, Earthstar, Geographics, CNES/Airbus DS, USDA, USGS, AeroGRID, IGN, the GIS User Community. Sample sizes were: Enzootic = 32 (Acherito = 14, Lhurs = 11, Puits d’Arious = 7); Epizootic = 19 (Arlet = 16, Ansabere = 3)

Fig. 4

Fig. 4

Heatmap displaying the normalised relative abundance of the top 20 bacterial OTUs from enzootic and epizootic populations identified from indicator analysis. Sample sizes were: Enzootic = 32 (Acherito = 14, Lhurs = 11, Puits d’Arious = 7); Epizootic = 19 (Arlet = 16, Ansabere = 3)

Fig. 5

Fig. 5

Bd genetics across space and time in the Pyrenees. a Phylogeny of Bd isolates collected from the Pyrenees and other European localities. Red stars indicate bootstrap values of 100. b PCA plot of identified SNPs from Bd isolates from all localities. c PCA plot of identified Bd SNPs from Pyrenean lakes only. Sample sizes were: n = 6 (Ansabere); n = 7 (Arlet); n = 26 (Acherito); n = 14 (Lhurs); n = 6 (Puits d’Arious), n = 22 (other European isolates)

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