The Department of Biochemistry & Molecular Medicine, School of Medicine and Health Sciences, George Washington University Medical Center, Washington, DC, United States of America.
McCormick Genomic and Proteomic Center, George Washington University, Washington, DC, United States of America.
PLoS One. 2019 Sep 11;14(9):e0206484. doi: 10.1371/journal.pone.0206484. eCollection 2019.
A comprehensive knowledge of the types and ratios of microbes that inhabit the healthy human gut is necessary before any kind of pre-clinical or clinical study can be performed that attempts to alter the microbiome to treat a condition or improve therapy outcome. To address this need we present an innovative scalable comprehensive analysis workflow, a healthy human reference microbiome list and abundance profile (GutFeelingKB), and a novel Fecal Biome Population Report (FecalBiome) with clinical applicability. GutFeelingKB provides a list of 157 organisms (8 phyla, 18 classes, 23 orders, 38 families, 59 genera and 109 species) that forms the baseline biome and therefore can be used as healthy controls for studies related to dysbiosis. This list can be expanded to 863 organisms if closely related proteomes are considered. The incorporation of microbiome science into routine clinical practice necessitates a standard report for comparison of an individual's microbiome to the growing knowledgebase of "normal" microbiome data. The FecalBiome and the underlying technology of GutFeelingKB address this need. The knowledgebase can be useful to regulatory agencies for the assessment of fecal transplant and other microbiome products, as it contains a list of organisms from healthy individuals. In addition to the list of organisms and their abundances, this study also generated a collection of assembled contiguous sequences (contigs) of metagenomics dark matter. In this study, metagenomic dark matter represents sequences that cannot be mapped to any known sequence but can be assembled into contigs of 10,000 nucleotides or higher. These sequences can be used to create primers to study potential novel organisms. All data is freely available from https://hive.biochemistry.gwu.edu/gfkb and NCBI's Short Read Archive.
在进行任何试图改变微生物组以治疗疾病或改善治疗效果的临床前或临床研究之前，必须全面了解健康人体肠道中栖息的微生物的类型和比例。为了满足这一需求，我们提出了一种创新的可扩展的综合分析工作流程、一个健康人体参考微生物组列表和丰度图谱（GutFeelingKB），以及一个具有临床适用性的新型粪便生物群落报告（FecalBiome）。GutFeelingKB 提供了一个由 157 个生物体组成的列表（8 个门、18 个纲、23 个目、38 个科、59 个属和 109 个种），这些生物体构成了基线生物群落，因此可用于与菌群失调相关的研究作为健康对照。如果考虑密切相关的蛋白质组，则可以将该列表扩展到 863 个生物体。将微生物组科学纳入常规临床实践需要一个标准报告，用于将个体的微生物组与不断增长的“正常”微生物组数据知识库进行比较。FecalBiome 和 GutFeelingKB 的基础技术满足了这一需求。该知识库可用于监管机构评估粪便移植和其他微生物组产品，因为它包含了来自健康个体的生物体列表。除了生物体及其丰度列表外，本研究还生成了一组宏基因组暗物质的组装连续序列（contigs）。在本研究中，宏基因组暗物质代表无法映射到任何已知序列但可以组装成 10000 个核苷酸或更长的 contigs 的序列。这些序列可用于创建研究潜在新型生物体的引物。所有数据均可从 https://hive.biochemistry.gwu.edu/gfkb 和 NCBI 的 Short Read Archive 免费获得。
