Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
Nat Biotechnol. 2017 Jan;35(1):81-89. doi: 10.1038/nbt.3703. Epub 2016 Nov 28.
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.
从人类肠道宏基因组数据中衍生出的基因组规模代谢模型可作为阐明微生物群落如何调节人类代谢和健康的框架。我们提出了 AGORA（通过重建和分析构建肠道生物体），这是一个为 773 种人类肠道细菌半自动生成的基因组规模代谢重建资源。使用此资源，我们为 Bacteroides caccae ATCC 34185 确定了一种定义明确的生长培养基。我们还表明，模型物种之间的相互作用取决于每个物种的代谢潜力和可用的营养素。AGORA 重建可以整合宏基因组或 16S rRNA 测序数据集，以推断微生物群落的代谢多样性。AGORA 重建可以为生成高质量、手动编辑的代谢重建提供起点。AGORA 与 Recon 2 完全兼容，这是人类代谢的综合代谢重建，将有助于宿主-微生物组相互作用的研究。
