PIENTER URT microbiome baseline analysis code
Creators: name: Odendaal, Mari-Lee
Publisher: name: Zenodo
Year: 2024
Subjects: upper respiratory tract
microbiome
microbiota
human lifespan
host
environment
health outcomes
population-wide
16S-rRNA sequencing

description: This code accompanies the manuscript 'Host and environmental factors shape upper airway microbiota and respiratory health across the human lifespan'. How to cite this material: 10.5281/zenodo.10854139

Description

This repository contains the Rmd-scripts (scripts/) and functions (src/) used to generate results (results/). The code below was ran in R (v4.3.1).

Scripts for data analysis

Data preprocessing



1.1_create_phyloseq.Rmd : Merge phyloseq objects generated by the in-house DADA2 pipeline.

1.2_find_contaminants.Rmd: Identify contaminants with the decontam R-package and our manually filtering step

1.3_clean_phyloseq.Rmd: Cleaning of the microbiome dataset based on cut-offs determined in 1.5_explore_phyloseq.Rmd and 1.2_find_contaminants.Rmd.

1.4_clean_variables.Rmd: Cleaning and merging the questionnaire data with the cleaned phyloseq object (Script not shown).

1.5_explore_phyloseq.Rmd: Exploration of the raw and cleaned phyloseq objects (Script not shown).

1.6_identify_clusters.Rmd: Identifying nasopharyngeal and oral microbial clusters.


Alpha-/beta-diversity & cluster analyses



2.1_alpha_diversity.Rmd : Microbial diversity and density across age per niche.

2.2_beta_diversity.Rmd : Beta-diversity analyses (PERMANOVA) and visualisation (PCoA plots) for age category and niches.

2.3_distances.Rmd : Exploration of the dissimilarity indices across age and per niche.

2.4_cluster_analysis.Rmd : Further exploration of the microbial cluster generated in 1.6_identify_clusters.Rmd.


High-level association analyses



3.1_correlation_variables.Rmd : Correlation analysis with the metadata variables.

3.2_host_characteristics.Rmd : High-level association analysis between the URT microbiota and host, environmental and health characteristics.


Diversity, density and ASV/genus-level analyses



4.1_diff_abundance_age.Rmd : Differential abundance of ASVs across age

4.2_density_diversity_sex.Rmd : Microbial diversity and density between sex across age per niche.

4.3_diff_abundance_sex_nasopharynx.Rmd : Differential abundance of ASVs between sex across age in the nasopharyngeal microbiota

4.4_diff_abundance_sex_oral.Rmd : Differential abundance of genera between sex across age in the oral microbiota

4.5_social_contact_related_patterns.Rmd : Social contact-related patterns (density, diversity and composition) in adults

4.6_smoking_drinking_antibiotics_related_patterns : Smoking, drinking and antibiotics use-related patterns (density, diversity and composition)in adults

4.7_season_symptoms_pneumonia_related_patterns.Rmd : Season, Symptoms and pneumonia-related patterns (density, diversity and composition)

4.8_streptococcus_14.Rmd : Correlation between ASV Streptococcus (14) and Streptococcus pneumoniae


Other analyses



geographical_map.Rmd : Geographical map of the distribution of PIENTER-3 participants across the Netherlands.

SRA_upload.Rmd : Script used to prepare data for SRA-upload.


The .html-output of all the scripts can be found the results-folder.