人类微生物组计划第二阶段-人类微生物组整合计划：人体...

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The Integrative Human Microbiome Project: Dynamic Analysis of Microbiome-Host Omics Profiles during Periods of Human Health and Disease
The Integrative HMP (iHMP) Research Network Consortium
人类微生物组整合计划：人体健康与疾病期间微生物组-宿主组学数据的动态分析
整合HMP（iHMP）研究网络联盟
DOI: http://dx.doi.org/10.1016/j.chom.2014.08.014

Abstract：
Much has been learned about the diversity and distribution of human-associated microbial communities, but we still know little about the biology of the microbiome, how it interacts with the host, and how the host responds to its resident microbiota. The Integrative Human Microbiome Project (iHMP, http://hmp2.org), the second phase of the NIH Human Microbiome Project, will study these interactions by analyzing microbiome and host activities in longitudinal studies of disease-specific cohorts and by creating integrated data sets of microbiome and host functional properties. These data sets will serve as experimental test beds to evaluate new models, methods, and analyses on the interactions of host and microbiome. Here we describe the three models of microbiome-associated human conditions, on the dynamics of preterm birth, inflammatory bowel disease, and type 2 diabetes, and their underlying hypotheses, as well as the multi-omic data types to be collected, integrated, and distributed through public repositories as a community resource.
我们对人体微生态的多样性和分布已经认识不少了，但我们对于微生物组如何与宿主交互、宿主对定居的微生物如何应答这一微生物组生物学仍然知之甚少。人类微生物组整合计划/The Integrative Human Microbiome Project (iHMP, http://hmp2.org)，NIH（美国国立卫生研究院）人类微生物组计划的第二阶段，在特定疾病人群的纵向研究中通过分析微生物组和宿主活动，以及创建微生物组和宿主功能特点的整合数据集来研究这些相互作用。这些数据集将作为用来评估宿主与微生物组间交互的新模式、方法和分析法的试验测试平台。这里我们对三种微生物组相关患者模型，动态变化中的早产、炎症性肠病和Ⅱ型糖尿病进行了阐述，包括可能的发病假说，以及作为社区资源通过公共库收集、整合与发布的多组学数据类型。

These three examples of microbiome-associated human conditions will provide innovative, freely available, multi-omic data of properties analyzed in both the microbiome and host with which to explore the behavior of the human microbiome over the course of complex conditions using preterm birth, onset of IBD, and onset of T2D as dynamic model systems. In addition, they will help lay the foundation for shared protocols and analysis methods for highly detailed studies of the microbiome’s basic biology and translational potential. ——————Data produced by the iHMP Consortium will be routinely released, and ongoing feedback is encouraged on how best to leverage these resources. For those interested in participating in the iHMPConsortium or learning more about the iHMP data sets or tools, please either contact the corresponding author or send an inquiry via the iHMP portal (http://hmp2.org).
这三种微生物组相关患者样本将为我们提供创新、易获取、多组学的微生物组和宿主双方面特性分析数据，通过早产、IBD、Ⅱ型糖尿病发病的复杂病程这些动态模型系统，探索人体微生物组的行为。另外，它们共享的实验方案和分析方法将为微生物组基础生物学及其转化潜力的详尽研究打下基础。iHMP联盟生成的数据会定期发布，我们鼓励就如何最大化利用好这些数据不断给我们反馈。有兴趣参与iHMP联盟研究，或者想进一步了解iHMP数据集或研究工具的，欢迎联系通讯作者，或者通过iHMP门户进行查询(http://hmp2.org)。


Integrative Multi-Omic Analysis of the Vaginal and Related Microbiomes in Pregnancy: Sample Collection, Assays, and Data Generation Workflow
Samples from pregnant women and neonates will be collected at clinics associated with Virginia Commonwealth University and the Global Alliance to Prevent Prematurity and Stillbirth (GAPPS). Health questionnaires will be administered and samples collected from multiple body sites over multiple visits throughout pregnancy, at delivery, at discharge, and at follow-up visits. Neonates will be sampled at delivery, discharge, and follow-up visits. A multi-omic approach will probe properties of the host and microbial communities to generate an integrative, longitudinal, and comprehensive data set of 16S rRNA gene surveys, mass spectrometry-based lipidomic profiles, and cytokine assays. A subset of samples will be subjected to wholemetagenome and metatranscriptome sequencin for cultivation and isolation of bacterial strains for genome sequencing, and for generation of interactomemaps
妊娠中产道与相关微生物组的整合多组学分析：样本采集、测定和数据生成工作流程图
孕妇和新生儿标本在弗吉尼亚联邦大学和预防早产死胎全球联盟(GAPPS)附属的诊所采集。整个孕期、分娩、出院和随访期间，通过多次出诊从身体多个部位采集标本，并进行健康调查问卷。新生儿在分娩、出院和随访时采样。应用多组学方法测定宿主和微生态的特点，生成16S rRNA基因检查的整合、纵向与全面的数据集，质谱法脂类组学数据，和细胞因子测定。一部分属于完整宏基因组和宏转录组测序的样本将培养分离细菌菌株，进行基因组测序，并生成相互作用组地图。


Characterizing the Gut Microbial Ecosystem for Diagnosis and Therapy in Inflammatory Bowel Disease: Sample Collection, Assay, and Data Generation Workflow
Samples from Crohn’s disease patients, ulcerative colitis patients, and non-IBD controls are collected at Massachusetts General Hospital (adult new onset), Emory University (pediatric new onset), Cincinnati Children’s Hospital (pediatric new onset), and Cedars-Sinai Medical Center (adult established). From each patient, three different types of samples are collected: longitudinal stool samples, periodic biopsies, and regularly scheduled blood samples. Biopsies are collected as clinically indicated, blood during clinical visits, and stool samples are self-collected by participants at home and shipped directly to a centralized handling and aliquotting pipeline. Multi-omic data generation (primarily, but not entirely, nucleotide sequence- and mass spectroscopy-based) provides microbial, host, and mixed profiles including 16S rRNA gene surveys, whole metagenome and metatranscriptome shotgun sequences, metabolite and protein profiles, single-cell assays, whole virome shotgun sequences, and serological profiles. Each sample is further accompanied by clinical (bloods/biopsies) or self-reported environmental and dietary (stools) metadata.
表征肠道微生态与炎症性肠病的治疗：样本采集、测定和数据生成流程图
克罗恩病、溃疡性结肠炎患者和非IBD对照组的样本分别在麻省综合医院（成人初发病人）、艾莫利大学（儿科初发病人）、辛辛那提儿童医院（儿科新发病人）和西达赛奈医疗中心（成人建册病人）采集。每个患者采集三种不同标本：纵向粪便样本、定期组织活检和定期血样。活检在临床指导下采集，血样在就诊时采集，粪便样本由受试者在家中自行采集并直送分装流水线中心处理。多组学数据生成（主要但不完全是核苷酸序列和质谱法）提供微生物、宿主和混合数据，包括16S rRNA 基因检查、完整宏基因组和宏转录组鸟枪法测序、代谢产物和蛋白数据，单细胞测定，完整病毒组鸟枪法测序，以及血清学数据。每个样本进一步收集临床（血样/活检）或环境和饮食（粪便）自行上报元数据。


Microbiome and Host Changes during Respiratory and Other Stress Conditions in Individuals at Risk for Type 2 Diabetes: Sample Collection, Assay, and Data Generation Workflow
All samples are collected at the Stanford Clinical & Translational Research Unit. From each patient in every visit, blood sample and microbiome sample (including nasal swabs and stool and urine samples) are collected. ……帖子字数限制略
Ⅱ型糖尿病风险个体在呼吸和其它应激状态下微生物组和宿主的变化：标本采集、测定和数据生成流程图
所有标本在斯坦福临床和转化研究部采集。在每个患者每次就诊时采集血样和微生物组样本（包括鼻咽拭子和粪便、尿液样本）。多组学数据生成（主要但不完全是核苷酸序列和质谱法）提供微生物谱系构成图、宏基因组、宏转录组和宏蛋白组；宿主的蛋白数据、细胞因子和自身抗体数据；完整的代谢组学数据。每个样本进一步收集临床（血样）或应激水平、环境和饮食（粪便和尿）自行上报元数据。


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