Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine

Heinken, Almut; Hertel, Johannes; Acharya, Geeta; Ravcheev, Dmitry A.; Nyga, Malgorzata; Okpala, Onyedika Emmanuel; Hogan, Marcus; Magnúsdóttir, Stefanía; Boneschi, Filippo Martinelli; Nap, Bram; Preciat, German; Edirisinghe, Janaka N.; Henry, Christopher S.; Fleming, Ronan M. T.; Thiele, Ines

doi:10.1038/s41587-022-01628-0

articleNature BiotechnologyJan 19, 2023HYBRID OA

Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine

AHAlmut Heinken JHJohannes Hertel GAGeeta Acharya DADmitry A. Ravcheev MNMalgorzata Nyga

Inserm · Ollscoil na Gaillimhe – University of Galway · +13 more institutions

PubMed

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Abstract

The human microbiome influences the efficacy and safety of a wide variety of commonly prescribed drugs. Designing precision medicine approaches that incorporate microbial metabolism would require strain- and molecule-resolved, scalable computational modeling. Here, we extend our previous resource of genome-scale metabolic reconstructions of human gut microorganisms with a greatly expanded version. AGORA2 (assembly of gut organisms through reconstruction and analysis, version 2) accounts for 7,302 strains, includes strain-resolved drug degradation and biotransformation capabilities for 98 drugs, and was extensively curated based on comparative genomics and literature searches. The microbial reconstructions…

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Topics & keywords

Topics

Keywords

Microbiome
Computational biology
Personalized medicine
Human microbiome
Precision medicine
Genome
Genomics
Metabolomics

UN Sustainable Development Goals

Good health and well-being

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