Poison frog microbiome metagenomics data
Data files
Dec 12, 2024 version files 74 GB
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114_R1_001.fastq.gz
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Metagenomics_metadata.xlsx
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README.md
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Abstract
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 - 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: Metagenomics data
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, 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