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Reconstruction of genome-scale metabolic models

SS Svenja Starke
DH Danielle M. M. Harris
JZ Johannes Zimmermann
SS Sven Schuchardt
MO Mhmd Oumari
DF Derk Frank
CB Corinna Bang
PR Philip Rosenstiel
SS Stefan Schreiber
NF Norbert Frey
AF Andre Franke
KA Konrad Aden
SW Silvio Waschina
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Genome-scale metabolic models were reconstructed for bacterial genomes from the Human Reference Gut Microbiome (HRGM) genome collection [27, 61]. The HRGM collection combines isolate and metagenome-assembled genomes (MAGs) from several data sources to summarize genome sequences obtained from human fecal samples. Metabolic models were reconstructed using gapseq version 1.2 [62]. gapseq is a command-line tool for automated reconstructions of genome-scale metabolic networks, that utilizes pathway, reaction, and metabolite entries from the databases MetaCyc [63] and ModelSEED [64]. A detailed description of the genome-scale metabolic model reconstruction workflow can be found in the Supplementary Information and Supplementary Table S6.

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