R. Roehe

Protozoal populations drive system-wide variation in the rumen microbiome

The paper identifies two rumen community types linked to protozoal populations and shows their impact on microbial interactions and metabolite profiles.

KOunt - A reproducible KEGG orthologue abundance workflow

KOunt quantifies KEGG orthologue abundance in metagenomes using a reproducible SnakeMake pipeline.

MAGpy: a reproducible pipeline for the downstream analysis of metagenome-assembled genomes (MAGs)

MAGpy is a Snakemake pipeline that annotates and characterizes metagenome-assembled genomes by comparing them to public databases and performing quality checks and phylogenetic analysis.

Assembly of hundreds of microbial genomes from the cow rumen reveals novel microbial species encoding enzymes with roles in carbohydrate metabolism

The paper assembles 220 high-quality microbial genomes from cow rumen metagenomic data, revealing novel species with carbohydrate metabolism enzymes and improving metagenomic classification.