학술논문
APOLLO: A genome-scale metabolic reconstruction resource of 247,092 diverse human microbes spanning multiple continents, age groups, and body sites.
Document Type
Author
Heinken A; School of Medicine, University of Galway, Galway, Ireland.; Ryan Institute, University of Galway, Galway, Ireland.; Inserm UMRS 1256 NGERE, University of Lorraine, Nancy, France.; Hulshof TO; School of Medicine, University of Galway, Galway, Ireland.; Ryan Institute, University of Galway, Galway, Ireland.; Nap B; School of Medicine, University of Galway, Galway, Ireland.; Ryan Institute, University of Galway, Galway, Ireland.; Martinelli F; School of Medicine, University of Galway, Galway, Ireland.; Ryan Institute, University of Galway, Galway, Ireland.; Basile A; School of Medicine, University of Galway, Galway, Ireland.; Department of Biology, University of Padova, Padova, Italy.; O'Brolchain A; University of Galway, Galway, Ireland.; O'Sullivan NF; University College Cork, Cork, Ireland.; Gallagher C; University of Galway, Galway, Ireland.; Magee E; University College Dublin, Dublin, Ireland.; McDonagh F; University College Dublin, Dublin, Ireland.; Lalor I; University of Galway, Galway, Ireland.; Bergin M; University of Galway, Galway, Ireland.; Evans P; University College Dublin, Dublin, Ireland.; Daly R; University of Galway, Galway, Ireland.; Farrell R; University of Galway, Galway, Ireland.; Delaney RM; University College Cork, Cork, Ireland.; Hill S; University College Cork, Cork, Ireland.; McAuliffe SR; University College Cork, Cork, Ireland.; Kilgannon T; University of Galway, Galway, Ireland.; Fleming RMT; School of Medicine, University of Galway, Galway, Ireland.; Thinnes CC; School of Medicine, University of Galway, Galway, Ireland.; Ryan Institute, University of Galway, Galway, Ireland.; Thiele I; School of Medicine, University of Galway, Galway, Ireland.; Ryan Institute, University of Galway, Galway, Ireland.; Division of Microbiology, University of Galway, Galway, Ireland.; APC Microbiome Ireland, Cork, Ireland.
Source
Country of Publication: United States NLM ID: 101680187 Publication Model: Electronic Cited Medium: Internet NLM ISO Abbreviation: bioRxiv Subsets: PubMed not MEDLINE
Subject
Language
English
Abstract
Computational modelling of microbiome metabolism has proved instrumental to catalyse our understanding of diet-host-microbiome-disease interactions through the interrogation of mechanistic, strain- and molecule-resolved metabolic models. We present APOLLO, a resource of 247,092 human microbial genome-scale metabolic reconstructions spanning 19 phyla and accounting for microbial genomes from 34 countries, all age groups, and five body sites. We explored the metabolic potential of the reconstructed strains and developed a machine learning classifier able to predict with high accuracy the taxonomic strain assignments. We also built 14,451 sample-specific microbial community models, which could be stratified by body site, age, and disease states. Finally, we predicted faecal metabolites enriched or depleted in gut microbiomes of people with Crohn's disease, Parkinson disease, and undernourished children. APOLLO is compatible with the human whole-body models, and thus, provide unprecedented opportunities for systems-level modelling of personalised host-microbiome co-metabolism. APOLLO will be freely available under https://www.vmh.life/.
Competing Interests: Declaration of interests The authors declare no conflict of interest.
Competing Interests: Declaration of interests The authors declare no conflict of interest.