Wild dendrobatid microbiomes - fungi
Data files
Dec 12, 2024 version files 2.92 GB
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README.md
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Abstract
Shifts in microbiome community composition can have large effects on host health. It is therefore important to understand how perturbations, like those caused by the introduction of exogenous chemicals, modulate microbiome community composition. In poison frogs within the family Dendrobatidae, the skin microbiome is exposed to the alkaloids that the frogs sequester from their diet and use for defense. Given the demonstrated antimicrobial effects of these poison frog alkaloids, these compounds may be structuring the skin microbial community. To test this, we first characterized microbial communities from chemically defended and closely related non-defended frogs from Ecuador. Then we conducted a laboratory experiment to monitor the effect of the alkaloid decahydroquinoline (DHQ) on the microbiome of a single frog species. In both the field and lab experiments, we found that alkaloid-exposed microbiomes are more species rich and phylogenetically diverse, with an increase in rare taxa. To better understand the strain-specific behavior in response to alkaloids, we cultured microbial strains from poison frog skin and found the majority of strains exhibited either enhanced growth or were not impacted by the addition of DHQ. Additionally, stable isotope tracing coupled to nanoSIMS suggests that some of these strains are able to metabolize DHQ. Taken together, these data suggest that poison frog chemical defenses open new niches for skin-associated microbes with specific adaptations, including the likely metabolism of alkaloids, that enable their survival in this toxic environment. This work helps expand our understanding of how exposure to exogenous compounds like alkaloids can impact host microbiomes.
Other data related to this manuscript can be found in the following locations:
https://doi.org/10.5061/dryad.5qfttdzd5, Wild dendrobatid frog microbiomes - bacteria
https://doi.org/10.5061/dryad.gxd2547t1, Oophaga sylvatica decahydroquinoline quantification
https://doi.org/10.5061/dryad.9ghx3ffqn, Ecuadorian Dendrobatid frog alkaloid profiles
https://doi.org/10.5061/dryad.tdz08kq62, Feeding experiment microbiome - bacteria
https://doi.org/10.5061/dryad.4mw6m90hn, Feeding experiment microbiome - fungi
https://doi.org/10.5061/dryad.2ngf1vhzc, Poison frog microbiome metagenomics data
https://doi.org/10.5061/dryad.9cnp5hqrm, Wild dendrobatid microbiomes – fungi
README: Wild dendrobatid microbiomes - fungi
https://doi.org/10.5061/dryad.9cnp5hqrm
ITS amplicon sequencing data from poison frogs collected from Ecuador in 2019
Other data related to this manuscript can be found in the following locations:
https://doi.org/10.5061/dryad.5qfttdzd5, Wild dendrobatid frog microbiomes - bacteria\
https://doi.org/10.5061/dryad.gxd2547t1, Oophaga sylvatica decahydroquinoline quantification\
https://doi.org/10.5061/dryad.9ghx3ffqn, Ecuadorian Dendrobatid frog alkaloid profiles\
https://doi.org/10.5061/dryad.tdz08kq62, Feeding experiment microbiome - bacteria\
https://doi.org/10.5061/dryad.4mw6m90hn, Feeding experiment microbiome - fungi\
https://doi.org/10.5061/dryad.2ngf1vhzc, Poison frog microbiome metagenomics data\
https://doi.org/10.5061/dryad.9cnp5hqrm, Wild dendrobatid microbiomes – fungi
Data and file structure
Metadata details can be found in wild_fungi_metadata.xlsx
- sample.names: Names of samples that correspond to FASTQ files.
- Plate: 96 well plate number for library preps
- sample.number: Sample identifier, used in library preps
- FrogID: Frog identifier, used to link with alkaloid data. Blanks denote frog was not given this type of identifier number.
- Species: Frog species
- Population: Geographic location of frog collection.
- Toxic: Categorized into toxic (contains both high and medium alkaloid quantities) and non-toxic (referred to as low alkaloids in the associated paper)
- Province: Province of frog collection location. Blanks denote information not recorded.
- Sex: Frog sex. Entries with question marks denote uncertainty, generally meaning ovaries or testes were not found but appearance suggests the indicated sex. Blanks denote information not recorded.
- Weight: Frog weight in grams. Blanks correspond to measurements not taken.
- Length: Snout-vent length in millimeters. Blanks correspond to measurements not taken.
Samples with mostly blank rows correspond to samples that, when processed, had illegible identifiers that could not be associated with a frog species or location.