Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.
Koonkie Inc., Menlo Park, California 94025, USA.
Sci Data. 2017 Apr 11;4:170035. doi: 10.1038/sdata.2017.35.
Advances in high-throughput sequencing are reshaping how we perceive microbial communities inhabiting the human body, with implications for therapeutic interventions. Several large-scale datasets derived from hundreds of human microbiome samples sourced from multiple studies are now publicly available. However, idiosyncratic data processing methods between studies introduce systematic differences that confound comparative analyses. To overcome these challenges, we developed GutCyc, a compendium of environmental pathway genome databases (ePGDBs) constructed from 418 assembled human microbiome datasets using MetaPathways, enabling reproducible functional metagenomic annotation. We also generated metabolic network reconstructions for each metagenome using the Pathway Tools software, empowering researchers and clinicians interested in visualizing and interpreting metabolic pathways encoded by the human gut microbiome. For the first time, GutCyc provides consistent annotations and metabolic pathway predictions, making possible comparative community analyses between health and disease states in inflammatory bowel disease, Crohn's disease, and type 2 diabetes. GutCyc data products are searchable online, or may be downloaded and explored locally using MetaPathways and Pathway Tools.
高通量测序技术的进步正在改变我们对人体微生物群落的认识，这对治疗干预措施具有重要意义。现在有几个来自数百个人类微生物组样本的大型数据集可从多个研究中获得。然而，研究之间特有的数据处理方法会引入系统差异，从而混淆比较分析。为了克服这些挑战，我们开发了 GutCyc，这是一个由 418 个人类微生物组数据集组装而成的环境途径基因组数据库 (ePGDB) 的汇编，使用 MetaPathways 进行构建，从而实现可重复的功能宏基因组注释。我们还使用 Pathway Tools 软件为每个宏基因组生成代谢网络重建，使对可视化和解释人类肠道微生物组编码的代谢途径感兴趣的研究人员和临床医生能够获得这些信息。GutCyc 首次提供了一致的注释和代谢途径预测，使得在炎症性肠病、克罗恩病和 2 型糖尿病的健康和疾病状态之间进行比较社区分析成为可能。GutCyc 的数据产品可以在线搜索，也可以使用 MetaPathways 和 Pathway Tools 下载并在本地探索。
