DOI: 10.5061/dryad.2ngf1vhzc
title: Poison frog microbiome metagenomics data

description: Shifts in microbiome community composition can impact function, and in
 host-associated microbial communities, these functional changes can have
 ramifications for the host in addition to the microbes. It is of interest
 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
 alkaloids that the frogs sequester from their diet and use for defense.
 There are demonstrated antimicrobial effects of these poison frog
 alkaloids, however how they affect the structure of the skin microbial
 community is unknown. To test this, we first characterized microbial
 communities from field-collected Dendrobatid frogs across a range of
 alkaloid levels. Then we conducted a laboratory experiment to monitor the
 effect of the common, commercially available alkaloid decahydroquinoline
 (DHQ) on the microbiome of two frog species with contrasting alkaloid
 loads in nature. In both the field and lab experiments, we found that
 alkaloid-exposed microbiomes are more phylogenetically diverse, with an
 increase in diversity especially among rare taxa. To better understand the
 isolate-specific behavior in response to alkaloids, we cultured microbial
 isolates from chemically defended poison frog skin and found that many
 isolates exhibited either enhanced growth or were not impacted by the
 addition of DHQ. To further explore microbial response to alkaloids, we
 sequenced the metagenomes from chemically defended and undefended frogs
 and observed a greater diversity of genes associated with nitrogen and
 carbon metabolism. From this data, we hypothesized that some strains may
 be able to metabolize the alkaloids as a source of carbon and/or nitrogen.
 To test this, we used stable isotope tracing coupled to nanoSIMS, which
 supported the idea that some of these isolates 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, such as
 alkaloid metabolism, 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: # Metagenomics data
 [https://doi.org/10.5061/dryad.2ngf1vhzc](https://doi.org/10.5061/dryad.2ngf1vhzc) The metagenomic data come from two species of frogs collected in the wild, *Oophaga sylvatica* and *Allobates femoralis,* as well as samples from these frogs reared in the laboratory, before (Day 12) and after (Day 19) being fed with the alkaloid decahydroquinoline.   ## Description of the data and file structure See `Metagenomics_metadata.xlsx` for details on specimen.  * **Sample Number**: Sample identifier, corresponds with FASTQ file names.  * **Experiment Type**: Either field (samples taken from frogs from the wild) or lab (samples taken from frogs in related alkaloid feeding experiment) * **Frog Number**: Either a number associated with samples from the wild, or the frog identifier from the feeding experiment. Blanks mean frogs were not assigned a number.  * **Frog Species**: Either Oophaga sylvatica (Sylvatica) or Allobates femoralis (Femoralis) * **Treatment**: For those frogs in the lab subset, denotes whether they were fed DHQ (toxic) or not (non-toxic) * **Day**: For those frogs in the lab subset, denotes which day the sample is from, either 19 (post DHQ feeding) or 12 (pre DHQ feeding).  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