Lloyd-Price Jason, Mahurkar Anup, Rahnavard Gholamali, Crabtree Jonathan, Orvis Joshua, Hall A Brantley, Brady Arthur, Creasy Heather H, McCracken Carrie, Giglio Michelle G, McDonald Daniel, Franzosa Eric A, Knight Rob, White Owen, Huttenhower Curtis
Biostatistics Department, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA.
The Broad Institute, Cambridge, Massachusetts 02142, USA.
Nature. 2017 Oct 5;550(7674):61-66. doi: 10.1038/nature23889. Epub 2017 Sep 20.
The characterization of baseline microbial and functional diversity in the human microbiome has enabled studies of microbiome-related disease, diversity, biogeography, and molecular function. The National Institutes of Health Human Microbiome Project has provided one of the broadest such characterizations so far. Here we introduce a second wave of data from the study, comprising 1,631 new metagenomes (2,355 total) targeting diverse body sites with multiple time points in 265 individuals. We applied updated profiling and assembly methods to provide new characterizations of microbiome personalization. Strain identification revealed subspecies clades specific to body sites; it also quantified species with phylogenetic diversity under-represented in isolate genomes. Body-wide functional profiling classified pathways into universal, human-enriched, and body site-enriched subsets. Finally, temporal analysis decomposed microbial variation into rapidly variable, moderately variable, and stable subsets. This study furthers our knowledge of baseline human microbial diversity and enables an understanding of personalized microbiome function and dynamics.
对人类微生物组中基线微生物和功能多样性的表征，使得对微生物组相关疾病、多样性、生物地理学和分子功能的研究成为可能。美国国立卫生研究院的人类微生物组计划提供了迄今为止最广泛的此类表征之一。在此，我们介绍该研究的第二批数据，包括1631个新的宏基因组（总共2355个），这些宏基因组针对265名个体的多个身体部位，并在多个时间点进行了采样。我们应用了更新的分析和组装方法，以提供微生物组个性化的新表征。菌株鉴定揭示了特定于身体部位的亚种分支；它还对分离基因组中系统发育多样性代表性不足的物种进行了量化。全身体功能分析将通路分类为通用、人类富集和身体部位富集的子集。最后，时间分析将微生物变异分解为快速可变、中度可变和稳定的子集。这项研究进一步加深了我们对人类基线微生物多样性的了解，并有助于理解个性化微生物组的功能和动态。
