Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota
Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota
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DOI：
10.1038/nbt.3703
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发表时间：
2017-01-01
影响因子：
46.9
通讯作者：
Thiele, Ines
中科院分区：
文献类型：
--
作者：
Magnusdottir, Stefania;Heinken, Almut;Thiele, Ines
来自人类肠道宏基因组数据的基因组尺度代谢模型可以用作阐明微生物群落如何调节人类代谢和健康的框架。我们介绍了AGORA（通过重建和分析组装肠道生物），这是一种为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。使用该资源，我们确定了用于Bacteroides caccae ATCC 34185的限定生长培养基。我们还表明，模拟物种之间的相互作用取决于每个物种的代谢潜力和营养物质。AGORA重建可以整合宏基因组或16 S 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的手动管理的代谢重建提供起点。AGORA与Recon 2完全兼容，Recon 2是人体代谢的全面代谢重建，将促进宿主-微生物组相互作用的研究。
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.