DOI: 10.5061/dryad.s4mw6m9g9
title: Effects of parental care on skin microbial community composition in poison frogs

description: 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
description: 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
 (&lt;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.
description: 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.