Fecal Microbiome and Metabolome Signatures of Severe and Attenuated Familial Adenomatous Polyposis

This repository contains the analysis code for the paper "Fecal Microbiome and Metabolome Signatures ofSevere and Attenuated Familial Adenomatous Polyposis".

Overview

Familial Adenomatous Polyposis (FAP) is an early-onset colorectal cancer syndrome. This study integrates gut microbiome profiles (16S rRNA), fecal metabolomics (LC-MS), and clinical blood biochemistry to identify robust multi-omic signatures that track with disease severity (Classical vs. Attenuated phenotypes).

The pipeline performs quality control, batch correction, taxonomic/metabolomic profiling, and integrated multi-omic analysis combining taxonomy, metabolomics and blood biochemistry test results to predict and characterize FAP.

Repository Structure

The analysis is organized into a sequential series of R Markdown notebooks and helper scripts:

Directory/File	Description
python/metabolomics_data_preprocessing.ipynb	Pre-processing: Preprocessing and ID mapping of raw metabolomics data.
R/00_process_metadata.Rmd	Cohort Definition: Cleaning clinical metadata and defining study groups (FAP vs. Control).
R/01_QC.Rmd	Microbiome QC: Rarefaction curves, prevalence filtering, and sequencing depth evaluation.
R/02_compare_batches.Rmd	Batch Correction: Evaluation and correction of batch effects (Batch 22 vs. 24).
R/03_taxonomic_analysis.Rmd	Microbiome: Figure 1: Alpha/Beta diversity analysis and differential abundance testing.
R/04_metabolomic_analysis.Rmd	Metabolome: Figure 2: PCA, univariate enrichment analysis, and KEGG pathway over-representation analysis (ORA).
R/05_multiomic_analysis.Rmd	Integration: Figure 3: Logistic regression classification (AUC analysis) and multi-omic module discovery using MintTea.
R/statistics.R	Helper functions for statistical tests (Wilcoxon, Permutation ANCOVA).
R/visualization.R	Custom ggplot2 themes and plotting wrappers.
R/utils.R	Small helper functions.