Effects of parental care on skin microbial community composition in poison frogs

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, Un..., 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 rema..., , 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 metad...