DOI: 10.5061/dryad.5qfttdzd5
title: Wild dendrobatid frog microbiomes - bacteria

description: 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 -
 bacteriahttps://doi.org/10.5061/dryad.gxd2547t1, Oophaga sylvatica
 decahydroquinoline quantificationhttps://doi.org/10.5061/dryad.9ghx3ffqn,
 Ecuadorian Dendrobatid frog alkaloid
 profileshttps://doi.org/10.5061/dryad.tdz08kq62, Feeding experiment
 microbiome - bacteriahttps://doi.org/10.5061/dryad.4mw6m90hn, Feeding
 experiment microbiome - fungihttps://doi.org/10.5061/dryad.2ngf1vhzc,
 Poison frog microbiome metagenomics
 datahttps://doi.org/10.5061/dryad.9cnp5hqrm, Wild dendrobatid microbiomes
 – fungi
description: # Wild dendrobatid frog microbiomes
 [https://doi.org/10.5061/dryad.5qfttdzd5](https://doi.org/10.5061/dryad.5qfttdzd5) 16S amplicon sequencing data from poison frogs collected in Ecuador in 2019. Other data related to this manuscript can be found in the following locations: [https://doi.org/10.5061/dryad.5qfttdzd5](https://doi.org/10.5061/dryad.5qfttdzd5), Wild dendrobatid frog microbiomes - bacteria [https://doi.org/10.5061/dryad.gxd2547t1](https://doi.org/10.5061/dryad.gxd2547t1), Oophaga sylvatica decahydroquinoline quantification [https://doi.org/10.5061/dryad.9ghx3ffqn](https://doi.org/10.5061/dryad.9ghx3ffqn), Ecuadorian Dendrobatid frog alkaloid profiles [https://doi.org/10.5061/dryad.tdz08kq62](https://doi.org/10.5061/dryad.tdz08kq62), Feeding experiment microbiome - bacteria [https://doi.org/10.5061/dryad.4mw6m90hn](https://doi.org/10.5061/dryad.4mw6m90hn), Feeding experiment microbiome - fungi [https://doi.org/10.5061/dryad.2ngf1vhzc](https://doi.org/10.5061/dryad.2ngf1vhzc), Poison frog microbiome metagenomics data [https://doi.org/10.5061/dryad.9cnp5hqrm](https://doi.org/10.5061/dryad.9cnp5hqrm), Wild dendrobatid microbiomes – fungi ## 16S sample metadata Metadata details can be found in `wild_bacteria_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.