A human gut metagenome-assembled genome catalogue spanning 41 countries supports genome-scale metabolic models.

Summary

HRGM2 delivers 155,211 near-complete gut genomes from 4,824 species across 41 countries, substantially expanding diversity and quality over prior catalogues. The resource improves species/strain profiling and underpins automated, high-confidence genome-scale metabolic models, facilitating analysis of disease-associated microbial metabolic networks.

Key Findings

• Compiled 155,211 non-redundant, near-complete genomes (≥90% completeness, ≤5% contamination) from 4,824 species across 41 countries.
• Expanded genome count by 66% and species diversity by 50% versus UHGG, improving species/strain resolution and resistome surveys.
• Exclusive use of near-complete genomes enabled high-confidence, automated genome-scale metabolic models and revealed disease-associated microbial metabolic interactions.

Clinical Implications

Enhances translational microbiome research for metabolic syndrome, diabetes, and obesity by enabling reliable prediction of microbial metabolic capacities and interactions that influence host endocrine-metabolic homeostasis.

Limitations

• Potential sampling biases remain despite broad geographic coverage.
• MAG-based reconstructions, while near-complete, may still miss plasmids or low-abundance genomic regions affecting metabolic inference.

Future Directions

Expand underrepresented populations and longitudinal sampling; link models to host phenotypes and metabolomics; validate predicted microbial metabolic interactions experimentally and clinically.