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...早期接触微生物可对宿主微生物群（microbiota）的组装与功能产生持久影响，进而在宿主健康与疾病抗性上留下终身印记。针对双亲抚育如何促进微生物获得的研究，多聚焦于人类与具有农业重要性的物种的垂直传播。无尾两栖类（anuran vertebrates）为我们提供了研究“以双亲投入为变量的生命各阶段微生物群落组成动态”的绝佳模型。本研究以箭毒蛙（Dendrobatidae）为研究对象，探究其双亲抚育过程中的细菌垂直传播机制——这类蛙类的雄性亲代会背负幼体从陆地卵团转移至水生育苗场。我们从组织与皮肤拭子中提取DNA，并扩增16S核糖体RNA（16S rRNA）基因的V4区域。本研究分别对实验室采集样本与野外采集样本开展双端测序（由Roy J Carver生物技术中心完成，原文此处略有截断）。各项实验的详细方法学信息可参见相关论文。简言之，本研究使用Qiagen PowerSoil Pro试剂盒，从蛙类、蝌蚪及其生境采集的拭子与组织样本中提取DNA。样本混匀后，采用515F（引物序列：GTGYCAGCMGCCGCGGTAA）与806R（引物序列：GGACTACNVGGGTWTCTAAT）引物（Bletz等，2017）扩增16S rRNA基因V4区域，并通过Illumina标准独特双索引（UDIs）进行条码标记。本研究分两轮独立测序：实验室采集样本采用Illumina MiSeq v3平台进行2×300nt双端测序，野外采集样本则采用NovaSeq 6000 SP流动槽开展2×250nt双端测序（由伊利诺伊大学Roy J Carver生物技术中心完成）。我们基于每条测序读段的前7个碱基注释内嵌条码（umi-tools，Smith等，2017），分离出匹配各已知条码组合的读段（grep，GNU项目，1998），并对剩余读段进行修剪（原文此处略有截断）。本数据集包含本研究发表于论文"Effects of parental care on skin microbial community composition in poison frogs"中的全部原始phyloseq（phyloseq）数据文件，以及用于数据处理、分析与可视化的代码。名为"Overview"的CSV文件列出了本数据集提供的全部文件、文件类型及文件用途。数据文件与脚本分为两个子文件夹："lab data"与"field data"。"laboratory_data"文件夹包含实验室交叉抚育实验的16S rRNA测序数据集（原始phyloseq对象、元数据表与系统发育树）及分析文件（R脚本），同时包含用于分析无尾类胚胎与胶状卵团细菌载量的数字PCR（ddPCR）数据表。名为"Overview_variables_laboratory"的CSV文件详细说明了实验室数据集元数据表的变量含义。"field data"文件夹包含16S rRNA测序数据（原始phyloseq对象、元数据表与系统发育树）及ITS测序数据（phyloseq对象与元数据……，原文此处略有截断）。