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.