A genome-scale metabolic reconstruction resource of 247,092 diverse human microbes spanning multiple continents, age groups, and body sites.

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Tác giả: Arianna Basile, Maeve Bergin, Rachel Daly, Rose Mary Delaney, Phoebe Evans, Ronan Farrell, Ronan M T Fleming, Celine Gallagher, Almut Heinken, Saoirse Hill, Timothy Otto Hulshof, Trevor Kilgannon, Ian Lalor, Eimer Magee, Filippo Martinelli, Saoirse Roisin McAuliffe, Francesca McDonagh, Bram Nap, Amy O'Brolchain, Neil Francis O'Sullivan, Ines Thiele, Cyrille C Thinnes

Ngôn ngữ: eng

Ký hiệu phân loại:

Thông tin xuất bản: United States : Cell systems , 2025

Mô tả vật lý:

Bộ sưu tập: NCBI

ID: 179752

 Genome-scale modeling of microbiome metabolism enables the simulation of diet-host-microbiome-disease interactions. However, current genome-scale reconstruction resources are limited in scope by computational challenges. We developed an optimized and highly parallelized reconstruction and analysis pipeline to build a resource of 247,092 microbial genome-scale metabolic reconstructions, deemed APOLLO. APOLLO spans 19 phyla, contains >
 60% of uncharacterized strains, and accounts for strains from 34 countries, all age groups, and multiple body sites. Using machine learning, we predicted with high accuracy the taxonomic assignment of strains based on the computed metabolic features. We then built 14,451 metagenomic sample-specific microbiome community models to systematically interrogate their community-level metabolic capabilities. We show that sample-specific metabolic pathways accurately stratify microbiomes by body site, age, and disease state. APOLLO is freely available, enables the systematic interrogation of the metabolic capabilities of largely still uncultured and unclassified species, and provides unprecedented opportunities for systems-level modeling of personalized host-microbiome co-metabolism.
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