期刊
NATURE BIOTECHNOLOGY
卷 35, 期 1, 页码 81-89出版社
NATURE PUBLISHING GROUP
DOI: 10.1038/nbt.3703
关键词
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资金
- Luxembourg National Research Fund (FNR) ATTRACT program grant [FNR/A12/01, FNR/A10/03]
- CORE program grant [CORE/11/BM/1186762]
- Proof-of-Concept grant [PoC15/11014639]
- Aides a la Formation-Recherche [FNR/6951193, FNR/6783162, FNR/9964547]
- FNR [6847110]
- US Department of Energy, Offices of Advanced Scientific Computing Research and the Biological and Environmental Research as part of the Scientific Discovery Through Advanced Computing program [DE-SC0010429]
Genome-scale metabolic models derived from human gut metagenomic data can be used as a framework to elucidate how microbial communities modulate human metabolism and health. We present AGORA (assembly of gut organisms through reconstruction and analysis), a resource of genome-scale metabolic reconstructions semi-automatically generated for 773 human gut bacteria. Using this resource, we identified a defined growth medium for Bacteroides caccae ATCC 34185. We also showed that interactions among modeled species depend on both the metabolic potential of each species and the nutrients available. AGORA reconstructions can integrate either metagenomic or 16S rRNA sequencing data sets to infer the metabolic diversity of microbial communities. AGORA reconstructions could provide a starting point for the generation of high-quality, manually curated metabolic reconstructions. AGORA is fully compatible with Recon 2, a comprehensive metabolic reconstruction of human metabolism, which will facilitate studies of host-microbiome interactions.
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