Effects of parental care on skin microbial community composition in poison frogs
Data files
Nov 23, 2024 version files 6.76 MB
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data_files.zip
6.76 MB
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README.md
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Abstract
Early exposure to microbes can have lasting influences on the assembly and functionality of the host’s microbiota, leaving a life-long footprint on host health and disease resilience. Studies addressing how microbial acquisition is facilitated by parental care have mostly explored vertical transmission in humans and species with agricultural relevance. Anuran vertebrates offer the opportunity to examine dynamics in microbial community composition across life stages as a function of parental investment. In this study, we investigate vertical transmission of bacteria during parental care in a poison frog (Dendrobatidae), where dedicated fathers transport their offspring piggyback from terrestrial clutches to aquatic nurseries. We extracted DNA from tissues and skin-swabs and amplified the V4 region of the 16S rRNA gene. We performed two separate sequencing runs for laboratory collected samples and field-collected samples in a paired-end configuration (Roy J Carver Biotechnology Center, University of Illinois). Data from both sequencing runs that were used for the analysis described in the publication are provided in the form of the original phyloseq objects, together with the metadata, phylogenetic tree and scripts to reproduce the results. Using a laboratory cross-foster experiment, we demonstrated that frogs performing tadpole transport serve as a source of skin microbes for tadpoles on their back. To study how transport impacts the microbial skin communities of tadpoles in an ecologically relevant setting, we sampled cohabiting parenting and pond-spawning frogs and their tadpoles in their natural habitat. We found more diverse microbial communities associated with tadpoles of poison frogs compared to a non-poison frog, but no higher degree of similarity between adults and tadpoles of transporting species relative to a non-transporting frog. Using a field experiment, we confirmed that tadpole transport can result in the persistent colonization of tadpoles by isolated microbial taxa associated with the caregiver's skin, albeit often at low prevalence. This is the first study to describe vertical transmission of skin microbes in anuran amphibians. The provided data contains information on the skin microbiome associated with tadpoles and adults of wild populations of two poison frog and one leptodactylid species that might be integrated in other comparative studies. This is also the first study describing skin-associated bacterial communities of poison frog tadpoles, to our knowledge
README
This dataset contains all original phyloseq data files and code to process, analyse and plot the data published in the manuscript "Effects of parental care on skin microbial community composition in poison frogs".
The csv file 'Overview' contains a list of all provided files, file type and use of files.
Data files and scripts are organised in two subfolders: 'lab data' and 'field data'.
The 'laboratory_data' folder contains the 16S rRNA sequencing datasets (original phyloseq object, metadata table and phylogenetic tree) or analysis files (R scripts) for the cross-foster experiment performed in the laboratory as well as the ddPCR data table used to analyse bacterial load from anuran embryos and jellies.
The csv file 'Overview_variables_laboratory' contains the detailed variable description of the metadata tables provided for lab datafiles.
The 'field data' folder contains the 16S rRNA (original phyloseq object, metadata table and phylogenetic tree) and ITS (phyloseq object and metadata table for Bd+ individuals) or analysis files (R scripts) for the comparison of tadpoles and adults of wild populations.
The csv file 'Overview_variables_field' contains the detailed variable description of the metadata tables provided for field datafiles.
Methods
Detailed methodological information for each experiment can be found in the associated manuscript. In short, Qiagen PowerSoil Pro Kit was used to extract DNA from all swabs and tissue samples collected from frogs, tadpoles or their environment. Samples were pooled and the V4 region of the 16S rRNA gene was amplified using 515F (GTGYCAGCMGCCGCGGTAA) and 806R (GGACTACNVGGGTWTCTAAT) primers (Bletz et al., 2017) and barcoded using standard Illumina unique dual indices (UDIs). We performed two separate sequencing runs: Laboratory collected samples were sequenced in a 2x300nt paired-end configuration on an Illumina MiSeq v3 run, field collected samples in a 2x250nt paired-end configuration on a NovaSeq 6000 SP Flowcell (Roy J Carver Biotechnology Center, University of Illinois). We annotated in-line barcodes based on the first 7 bases of each sequencing read (umi-tools, Smith et al., 2017), split out reads that matched each known barcode combination (grep, GNU Project, 1998), trimmed the remaining primer sequences from the sequencing reads (cutadapt, Martin, 2011) counted the number of sequencing reads in each file and removed files (including negative controls) with low read numbers (<100 reads) from the dataset. We processed the remaining reads with the R Divisive Amplicon Denoising Algorithm package "dada2" (version 1.28.0) (Callahan et al., 2016). Taxonomy was assigned using the Silva 138 database (Ref NR99) (Quast et al., 2012). The count table and the taxonomy table were integrated into a phyloseq object using the R package "phyloseq" (version 1.44.0) (McMurdie & Holmes, 2013). The object as well as sample-associated data and phylogenetic trees used for downstream data analysis are provided with all analysis scripts.