Metagenome-Assembled Genomes (MAGs) and Ecological Metadata of the Microbiome in Irish Beef Processing Chains

Project Summary

This dataset provides 4,475 Metagenome-Assembled Genomes (MAGs) recovered from four commercial beef processing environments over summer and winter seasons. The collection represents a comprehensive genomic catalog of microbial dynamics across different facilities, seasons, and processing surface types.

📌 How to cite: If you use this database in your research, please cite the original publication:

Rahman, A. U., et al. (2026). Metagenomic profiling reveals how ecological and processing drivers shape the beef microbiome from farm to fork. Food Research International. [10.1016/j.foodres.2026.119939] [https://www.sciencedirect.com/science/article/pii/S0963996926016236?via%3Dihub]

Bioinformatics Pipeline & Column Definitions:

Assembly: MEGAHIT (contig generation).

Binning: MetaBAT2 (bin recovery).

Quality Metrics: CheckM2 was utilized for the Completeness and Contamination columns.

Clustering: SGB_ID (Species Genome Bins) were defined using fastANI.

Taxonomy: Lineages assigned via GTDB-tk (Reference Data Version R214).

MAG_ID: Matches the filenames in the ZIP archive (excluding the extension).

Linkage to Raw Data:

All MAGs are linked via the Sample_ID and Run columns to the raw shotgun metagenomic data deposited at NCBI under BioProject PRJNA1233666