Comparative Metagenomics of Soda Lakes and the Rumen Reveals Novel Microbial Lineages and CAZyme Diversity
Oliyad Jeilu et al., 2025
This project presents a comparative metagenomic analysis of microbial communities and carbohydrate-active enzyme (CAZyme) repertoires in two contrasting environments: Ethiopian soda lakes and the ruminant gut (rumen).
Using shotgun metagenomic sequencing, we reconstructed metagenome-assembled genomes (MAGs), profiled taxonomic and functional diversity, annotated metabolic pathways and CAZymes, and analyzed codon usage bias.
This repository contains all analysis scripts, from quality control and assembly to downstream visualization and interpretation.
Analyses were performed primarily on Swedish national high-performance computing clusters:
- Dardel, PDC Center for High Performance Computing (KTH Royal Institute of Technology)
- UPPMAX, Uppsala Multidisciplinary Center for Advanced Computational Science
Workflows were implemented using Bash shell scripts and Conda-based environments for reproducible dependency management. Downstream statistical analyses and visualizations were conducted in R (v4.3+).
Scripts are modular, organized by analysis stage, and executable on any Linux-based HPC or workstation with appropriate dependencies installed.