Diet-associated gut microbiome analysis

Author: Jiyan Xu
Date: 2026-07-24

Overview

This project analyzes gut microbiome profiles from a healthy cohort in Freiburg across dietary patterns (omnivore, vegetarian, vegan), using 16S rRNA gene sequencing. The study investigates how dietary patterns influence microbial composition, microbial conditional association networks, and host physiological parameters.

Project structure

Project/
├── README.md
├── scripts/     # analysis scripts
├── data/input/  # input data for analyses
├── data/tmp/    # intermediate data
└── res/         # figures and tables

Data

Raw sequencing data are available at the NCBI Sequence Read Archive (SRA) under accession PRJNA1499606.

Reproducibility

Analysis overview

• Clinical demographic and biomarker data overview
• Nutrient dimension reduction
• Alpha and beta diversity analyses of gut microbiome
• Mediation analysis between dietary pattern, gut microbiome and blood biomarkers
• Microbial conditional association networks

Requirements

• R (version 4.4.3)

The analysis was performed in R and requires the following packages:

• Data manipulation: tidyverse
• Data visualization: ggplot2, scales，ggrepel, ggbeeswarm, ggpubr, ggalluvial, svglite
• Microbiome analysis: phyloseq, vegan
• Dimension reduction and clustering: factoextra, dendextend, ggdendro
• Statistical analysis: broom, car, mediation
• Network analysis: igraph, tidygraph, ggraph, huge, glasso, pulsar, SPRING

Contact

Jiyan Xu
PhD Student
Max Delbrück Center for Molecular Medicine (MDC)
Charité – Universitätsmedizin Berlin

Email: jiyan.xu [at] mdc-berlin.de

Citation

If you use this code, please cite:

Xu et al., A nutrient-derived dietary gradient links gut microbiome composition, network structure, and host physiology, 2026 (in preparation)