HELIUS project on oral and gut microbiomes

Interdisciplinary project within the UvA Research Priority Area - Personal Microbiome Health, using HELIUS oral and gut microbiome data

Data

Two microbiome data types from the HELIUS cohort, processed in parallel:

• 16S rRNA amplicon sequencing — throat and nose swabs
• Shotgun metagenomics — tongue and throat swabs

Raw sequencing output and clinical/metadata are cleaned into phyloseq/table objects in data/processed/ (see scripts/1a_datacleaning_helius.R and scripts/1b_datacleaning_biome.R).

Analysis pipeline

Scripts in scripts/ are numbered in run order:

Script	Analysis
1a_datacleaning_helius.R	Clean HELIUS clinical/metadata
1b_datacleaning_biome.R	Clean and filter 16S and shotgun microbiome data into phyloseq objects
2_tableone.R	Table 1: cohort characteristics
3_relative_abundance_plots.R	Compositional (stacked bar) plots of taxon relative abundance
4_alpha_diversity_16s_throat.R	Alpha diversity, 16S throat (descriptive)
5_alpha_diversity_16s_ethnicity.R	Alpha diversity, 16S throat and nose, stratified by ethnicity
6_beta_diversity_16s.R	Beta diversity, 16S throat and nose, stratified by ethnicity (PERMANOVA, betadisper)
7_beta_diversity_16s_migration.R	Beta diversity, 16S, non-Dutch groups pooled by migration generation/acculturation
8_differential_abundance_16s.R	Differential abundance, 16S throat and nose, pairwise ethnicity comparisons (MaAsLin2)
9_upset_diffabund_16s.R	Overlap of significant differentially abundant taxa across ethnicity pairs
10_alpha_diversity_shotgun.R	Alpha diversity, shotgun tongue and throat, stratified by ethnicity

Shotgun beta diversity and differential abundance analyses, analogous to the 16S ones above, are planned but not yet implemented.

Outputs (plots, tables) are written to results/, grouped by analysis type.

Setup

Prerequisites

Install pixi:

curl -fsSL https://pixi.sh/install.sh | bash

Install the environment

Clone the repository and run the setup script:

git clone <repo-url>
cd rpa-microbiomes
chmod +x setup_pixi.sh
./setup_pixi.sh

This installs all dependencies (phyloseq, tidyverse, vegan, decontam, etc.) and additional Bioconductor packages.

Run R in the pixi environment

pixi run R

Or activate the environment shell:

pixi shell
R

Contributors

Roel van der Ploeg, Kevin Singh, Barbara Verhaar

Funding

This project was supported by an RPA-PMH seed grant