DOI: 10.5061/dryad.4mw6m90hn
title: Feeding experiment microbiome - fungi

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: # Oophaga sylvatica experimental microbiome - fungi
 [https://doi.org/10.5061/dryad.4mw6m90hn](https://doi.org/10.5061/dryad.4mw6m90hn) This data was generated in a controlled feeding experiment to test for the role of the alkaloid decahydroquinoline (DHQ) in shaping the skin microbiome of the poison frog Oophaga sylvatica. Samples were collected in a time series from animals that were in the experimental group (DHQ-fed) and control group (vehicle control fed). Metadata can also be found as an uploaded csv data file. The variables of which are: * **SampleName**: Sample Name that corresponds to FASTA files * **PlateNumber**: 96 well plate used for library prep * **WellNumber**: Well number within the 96 well plate for library prep * **SampleID**: Tracking number for library prep processing * **FrogSpecies**: Either AF (Allobates femoralis) or OS (Oophaga sylvatica) * **FrogNumber**: Frog identifier used throughout feeding experiment. Box designate samples of the frog housing that were taken to monitor environmental change over time. * **Day**: Day of the experiment, where day 1 corresponds to the first day of the acclimation period, day 8 refers to the first day of the "pre" period * **Swab**: Number of swab. Different from day because frogs were not swabbed during the acclimation period, so the second swab occurs on day 8 * **Date**: Date of swab collection * **Treatment**: Toxic were fed decahydroquinoline, non-toxic were fed vehicle control * **PrePostMid:** Pre period is before alkaloid feeding (Days 8 - 12), post samples are days 17 and on, and mid are days 13-16.  * **Combined:** Combining the Species, Treatment, and PrePostMid columns.  Some samples did not contain any fungal reads, and therefore have empty data files.  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