Strains, functions and dynamics in the expanded Human Microbiome Project

Lloyd-Price Jason; Mahurkar Anup; Ahnavard Gholamali R.; Rabtree Jonathan C.; Rvis Joshua O.; Hall A. B. Rantley; Rady Arthur B.; Reasy Heather H. C.; McCracken Carrie; Giglio Michelle G.; McDonald Daniel; Franzosa Eric A.; Knight Rob; White Owen; Huttenhower Curtis

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Strains, functions and dynamics in the expanded Human Microbiome Project

机译：扩大的人类微生物组计划中的菌株，功能和动力学

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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.

机译：人类微生物组中基线微生物和功能多样性的表征已使微生物组相关疾病，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人类微生物组计划提供了迄今为止最广泛的此类特征之一。在这里，我们介绍了该研究的第二波数据，包括针对265个个体中多个时间点的不同身体部位的1,631个新的元基因组（总计2,355个）。我们应用了更新的配置文件和组装方法，以提供微生物组个性化的新特征。菌株鉴定揭示了特定于身体部位的亚种进化枝；它还量化了在分离基因组中代表性不足的系统发育多样性物种。全身功能分析将途径分为通用的，人体富集的和人体部位富集的子集。最后，时间分析将微生物变化分解为快速变化，中等变化和稳定的子集。这项研究进一步增进了我们对人类基本微生物多样性的了解，并有助于了解个性化微生物组的功能和动力学。

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《Nature》 |2017年第7674期|61-66|共6页
作者
Lloyd-Price Jason; Mahurkar Anup; Ahnavard Gholamali R.; Rabtree Jonathan C.; Rvis Joshua O.; Hall A. B. Rantley; Rady Arthur B.; Reasy Heather H. C.; McCracken Carrie; Giglio Michelle G.; McDonald Daniel; Franzosa Eric A.; Knight Rob; White Owen; Huttenhower Curtis;
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作者单位

Harvard TH Chan Sch Publ Hlth, Biostat Dept, Boston, MA 02115 USA|Broad Inst, Cambridge, MA 02142 USA;

Univ Maryland, Sch Med, Inst Gnome Sci, Baltimore, MD 21201 USA;

Harvard TH Chan Sch Publ Hlth, Biostat Dept, Boston, MA 02115 USA|Broad Inst, Cambridge, MA 02142 USA;

Univ Maryland, Sch Med, Inst Gnome Sci, Baltimore, MD 21201 USA;

Univ Maryland, Sch Med, Inst Gnome Sci, Baltimore, MD 21201 USA;

Broad Inst, Cambridge, MA 02142 USA;

Univ Maryland, Sch Med, Inst Gnome Sci, Baltimore, MD 21201 USA;

Univ Maryland, Sch Med, Inst Gnome Sci, Baltimore, MD 21201 USA;

Univ Maryland, Sch Med, Inst Gnome Sci, Baltimore, MD 21201 USA;

Univ Maryland, Sch Med, Inst Gnome Sci, Baltimore, MD 21201 USA;

Univ Calif San Diego, Dept Pediat, La Jolla, CA 92093 USA;

Harvard TH Chan Sch Publ Hlth, Biostat Dept, Boston, MA 02115 USA|Broad Inst, Cambridge, MA 02142 USA;

Univ Calif San Diego, Dept Pediat, La Jolla, CA 92093 USA|Univ Calif San Diego, Dept Comp Sci & Engn, La Jolla, CA 92093 USA;

Univ Maryland, Sch Med, Inst Gnome Sci, Baltimore, MD 21201 USA;

Harvard TH Chan Sch Publ Hlth, Biostat Dept, Boston, MA 02115 USA|Broad Inst, Cambridge, MA 02142 USA;

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收录信息美国《科学引文索引》(SCI);美国《工程索引》(EI);美国《生物学医学文摘》(MEDLINE);美国《化学文摘》(CA);
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1. Strains, functions and dynamics in the expanded Human Microbiome Project (vol 550, pg 61, 2017) [J] . Lloyd-Price Jason, Mahurkar Anup, Rahnavard Gholamali, Nature . 2017,第7679期

机译：扩大的人类微生物组计划中的菌株，功能和动力学（2017年第550卷，第61页）
2. The Integrative Human Microbiome Project: Dynamic Analysis of Microbiome-Host Omics Profiles during Periods of Human Health and Disease [J] . Proctor Lita M. Cell Host & Microbe . 2014,第3期

机译：一体化人类微生物组计划：人类健康和疾病时期微生物组-宿主组学特征的动态分析
3. New Insights into Human Nostril Microbiome from the Expanded Human Oral Microbiome Database (eHOMD): a Resource for the Microbiome of the Human Aerodigestive Tract [J] . Isabel F. Escapa, Tsute Chen, Yanmei Huang, mSystems . 2018,第6期

机译：来自扩大人口腔微生物数据库（EHOMD）的人鼻孔微生物组的新见解（EHOMD）：用于人气衰弱道的微生物组的资源
4. The human microbiome: Opportunities for dynamics, systems, and control (based on the IFAC blog post translate or die) [C] . Travis E. Gibson American Control Conference . 2016

机译：人类微生物组：动力学，系统和控制的机会（基于IFAC博客文章的翻译或死亡）
5. Guidelines for the use of expanded polystyrene (EPS)-block geofoam for the function of lightweight fill in road embankment projects. [D] . Arellano, David. 2005

机译：关于在路堤工程中使用轻质填料功能的发泡聚苯乙烯（EPS）块状泡沫塑料使用指南。
6. Strains functions and dynamics in the expanded Human Microbiome Project [O] . Jason Lloyd-Price, Anup Mahurkar, Gholamali Rahnavard, -1

机译：扩大的人类微生物组计划中的菌株功能和动力学
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Strains, functions and dynamics in the expanded Human Microbiome Project

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