MicrobiomeEngine

16S rRNA & Metagenomics Analysis Pipeline

A pure-Python computational engine for microbiome analysis from 16S amplicon and metagenomic data.

Features

• OTU clustering simulation (97% identity threshold)
• Alpha diversity: Shannon, Simpson, Chao1, Faith's PD
• Beta diversity: Bray-Curtis dissimilarity, PCoA, PERMANOVA
• Differential abundance testing (DESeq2-style NB model, BH FDR)
• PICRUSt-style functional pathway inference
• Dysbiosis index (F/B ratio + alpha diversity composite)

Results

• 60 samples (30 healthy, 30 disease), 300 OTUs, 50 pathways
• PERMANOVA: F=1.544, p<0.0001
• Differential OTUs: 16 up, 19 down in disease
• F/B ratio: healthy=2.00, disease=7.26 (dysbiosis p=1.8e-4)

Usage

pip install numpy scipy matplotlib
python microbiome_engine.py

Tags

microbiome metagenomics 16s-rrna dysbiosis alpha-diversity permanova