vmh

name	vmh
description	Virtual Metabolic Human (VMH) database — human and gut microbiome metabolism integrated with nutrition and disease knowledge for GEM interpretation. Use when: (1) Contextualizing gapseq / AGORA-style models, (2) Linking metabolites, microbes, and nutrition, (3) Browsing human–microbiome metabolic resources. Portal: https://www.vmh.life. Pair with gapseq for reconstruction; do not treat VMH entries as measured fluxes in your sample.
license	MIT
category	utilities
tags	["VMH","GEMs","metabolism","database","gut"]
upstream	https://www.vmh.life

Virtual Metabolic Human (VMH)

Portal: https://www.vmh.life

Citation

Noronha, A. et al. The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. Nucleic Acids Res. 47, D614–D624 (2019). https://doi.org/10.1093/nar/gky992

See also docs/references.md.

Analytical thinking

VMH is a knowledge/integration database (human + gut microbial metabolism, nutrition, disease links), not a shotgun profiler. Use it to interpret genome-scale models and metabolites after gapseq (or related GEM tools).

Resource	Role
gapseq	Build/fill models from your genomes/MAGs
vmh	Browse/integrate human–microbiome metabolic knowledge
kegg / dram	Pathway annotation alternatives

Decision tree

Metabolic modeling need?
├─ Reconstruct model from MAG → gapseq
├─ Interpret vs human/gut/nutrition knowledge → vmh
├─ Distill annotations without full GEM → dram
└─ KO maps → kegg (license)

Related skills

gapseq · dram · kegg · public-databases · microbial-mining