Nasopharyngeal and oropharyngeal microbiome of goat farmers and rural residents in the Netherlands

This dataset consists of a ready-to-use phyloseq S4 object (ps_filtered_zenodo.Rds) containing three components: An amplicon sequence variant (ASV) table A taxonomy table Sample metadata (a separate metadata description file is included (Metadata_codebook_microbiome.xlsx) Additional metadata can be made available upon request. The dataset was generated by processing paired-end 16S rRNA gene sequencing reads using the DADA2 pipeline (Callahan et al., 2016; v1.16.0), with the following parameters: maxEE = 2 and truncLen = c(200, 150). ASVs were inferred directly from quality-filtered reads. The data has undergone pre-processing steps to remove contamination and low quality samples (see details below in the notes). The analysis scripts associated with this dataset are available via Zenodo at 10.5281/zenodo.15773127, which is a release archived from the GitHub repository: https://github.com/BeatriceCornuHewitt/URT_microbiome_livestock_exposure Note: The phyloseq object provided here has undergone downstream filtering and decontamination. For detailed information on data cleaning and preprocessing steps used in subsequent analyses, please refer to the script 3_clean_phyloseq.Rmd in 10.5281/zenodo.15773127. This phyloseq is the resulting data from this processing script. In brief, pre-processing involved: Removal of contaminants and low-quality samples by applying the decontam package and manual checks, and filtering samples with low DNA concentration or read counts. This resulted in 904 NP (824 from residents, 80 from goat farmers) and 1,046 OP samples (951 from residents, 95 from goat farmers) for analysis.本数据集包含一个可直接使用的phyloseq S4对象（ps_filtered_zenodo.Rds），内含三类组件：扩增子序列变异体（amplicon sequence variant, ASV）表、分类学表以及样本元数据（附带独立的元数据说明文件Metadata_codebook_microbiome.xlsx）。 额外元数据可应申请提供。 本数据集通过DADA2流程（Callahan等，2016；v1.16.0）处理双端16S rRNA基因测序读段生成，所用参数为：maxEE = 2及truncLen = c(200, 150)。研究人员直接从质量过滤后的读段中推断得到ASV。该数据已完成去污染与低质量样本剔除等预处理步骤（详见下文备注）。 本数据集配套的分析脚本可通过Zenodo平台的10.5281/zenodo.15773127获取，该存档源自GitHub仓库：https://github.com/BeatriceCornuHewitt/URT_microbiome_livestock_exposure 备注： 本次提供的phyloseq对象已完成下游过滤及去污染处理。如需了解后续分析所用的数据清洗与预处理步骤的详细信息，请查阅10.5281/zenodo.15773127中的3_clean_phyloseq.Rmd脚本，本phyloseq对象即由该处理脚本生成。简言之，预处理流程包括：通过decontam包结合人工校验剔除污染样本与低质量样本，并过滤DNA浓度或读段计数过低的样本。最终得到904份NP样本（其中824份来自居民、80份来自山羊养殖户）与1046份OP样本（其中951份来自居民、95份来自山羊养殖户）用于后续分析。