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Microbiome function predicts amphibian chytridiomycosis disease dynamics.

Kieran A Bates1,2,3, Ulf Sommer4, Kevin P Hopkins5

  • 1Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK. kieran.bates@zoo.ox.ac.uk.

Microbiome
|March 11, 2022
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Summary

Amphibian skin microbes significantly impact Batrachochytrium dendrobatidis (Bd) infection outcomes. Multi-omics analysis reveals that microbial community structure and function predict Bd disease dynamics, identifying key bacterial taxa and metabolites associated with resistance.

Keywords:
AmphibianBatrachochytrium dendrobatidisChytridiomycosisMetabolomeMicrobiomeMulti-omics

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Area of Science:

  • Amphibian disease ecology
  • Microbiome research
  • Pathogen-host interactions

Background:

  • The fungal pathogen Batrachochytrium dendrobatidis (Bd) poses a global threat to amphibian populations.
  • Amphibian skin microbiome composition is linked to Bd infection outcomes, but its functional role remains unclear.

Purpose of the Study:

  • To investigate the functional importance of amphibian skin microbial communities in the context of Bd infections.
  • To assess how Bd infection alters microbiome structure and function in midwife toads (Alytes obstetricans).

Main Methods:

  • Utilized high-throughput sequencing (16S rRNA, ITS2), shotgun metagenomics, and metabolomics on wild and experimentally infected midwife toads.
  • Compared microbiome and metabolome profiles between Bd-exposed and control toads, and across wild populations with different disease dynamics.

Main Results:

  • Bd infection induced dynamic changes in skin microbiome taxonomic and functional profiles in both wild and experimental settings.
  • Specific bacterial taxa (e.g., Sphingobacterium) were associated with Bd resistance and influenced disease outcome, contradicting functional redundancy.
  • Microbe-metabolite integration highlighted influential taxa and pathways, such as bacterial environmental sensing and resource competition, driving infection outcomes.

Conclusions:

  • Bd infection significantly alters amphibian skin microbiome composition and function.
  • Multi-omics analyses robustly predict Bd disease dynamics and identify potential biomarkers for infection.