人类微生物组计划：修订间差异

人类微生物组计划（HMP）
所有人	美國國立衛生研究院
啓動日期	2008年
关闭日期	2012年
網站	commonfund.nih.gov/hmp

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2022年5月13日 (五) 02:46的版本

人类微生物组计划（英語：Human Microbiome Project，缩写：HMP）是美國國立衛生研究院(NIH)于2008年发起的一项旨在鉴定与阐明和人类健康与疾病相关的微生物（人類微生物组）功能的计划^[1]，计划耗时五年，总投资达1.150亿美元。这和类似的美国国立卫生研究院赞助微生物（Microbiome）项目的最终目的都是测试人类微生物变化如何与人类健康或疾病有关。这个主题目前还不十分清楚。

貢獻機構

人类微生物组计划(HMP)涉及許多研究機構的參與，包括斯坦福大學、布羅德研究所(Broad Institute)、弗吉尼亞聯邦大學、華盛頓大學、東北大學、麻省理工學院、貝勒醫學院等。貢獻包括數據評估、參考序列數據集的構建、倫理和法律研究、技術開發等。

第一階段（2007-2014年）

第一階段(HMP1)包括來自許多機構的研究工作^[2]。 HMP1 設定了以下目標^[3]：

開發一組參考微生物基因組序列並對人類微生物組進行初步表徵
探索疾病與人類微生物組變化之間的關係
開髮用於計算分析的新技術和工具
建立資源庫
研究人類微生物組研究的倫理、法律和社會影響

第二階段（2014-2016年）

2014年，美國國立衛生研究院(NIH)啟動了該項目的第二階段，即綜合人類微生物組項目 (Integrative Human Microbiome Project, 缩写：iHMP)。 iHMP 的目標是提供資源以創建人類微生物組的完整特徵，重點是了解微生物群在健康和疾病狀態中的存在^[4]。正如美國國立衛生研究院(NIH)所述，項目任務如下：

綜合人類微生物組項目(iHMP)將使用多種“組學”技術從三個不同的微生物組相關條件隊列研究中創建來自微生物組和宿主的生物學特性的綜合縱向數據集^[4]。

該項目包括在多個機構開展的三個子項目。研究方法包括 16S rRNA 基因分析、全基因組鳥槍法測序、全基因組測序、元轉錄組學、代謝組學/脂質組學和免疫蛋白質組學。 iHMP 的主要發現於2019年被發布^[5]。

里程碑

參考數據庫被建立

2012年6月13日，美國國立衛生研究院院長法蘭西斯·柯林斯（Francis S. Collins）宣布了人类微生物组计划項目的一個重要里程碑。該公告還附有一系列協調文章於同一天在《[[自然 (期刊)|自然》^[6]^[7]和包括公共科學圖書館 (PLoS) 在內的多個期刊上發表^[8]^[9]^[10]^[11]^[12]^[13]。通過使用基因組測序技術繪製健康人類的正常微生物組成，HMP 的研究人員創建了一個參考數據庫和人類正常微生物變化的邊界^[14]。

参阅

参考文献

^ Human Microbiome Project: Diversity of Human Microbes Greater Than Previously Predicted. ScienceDaily. [8 March 2012].
^ Human Microbiome Project / Funded Research. The NIH Common Fund. [8 March 2012].
^ Human Microbiome Project / Program Initiatives. The NIH Common Fund. [8 March 2012].
^ ^4.0 ^4.1 NIH Human Microbiome Project - About the Human Microbiome. hmpdacc.org. [2018-03-30] （英语）.
^ NIH Human Microbiome Portfolio Analysis Team. A review of 10 years of human microbiome research activities at the US National Institutes of Health, Fiscal Years 2007-2016. Microbiome. 2019, 7 (1): 31. ISSN 2049-2618. PMC 6391833 . PMID 30808411. doi:10.1186/s40168-019-0620-y （英语）.
^ Human Microbiome Project Consortium. A framework for human microbiome research. Nature. June 2012, 486 (7402): 215–21. Bibcode:2012Natur.486..215T. PMC 3377744 . PMID 22699610. doi:10.1038/nature11209.
^ Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature. June 2012, 486 (7402): 207–14. Bibcode:2012Natur.486..207T. PMC 3564958 . PMID 22699609. doi:10.1038/nature11234.
^ Faust K, Sathirapongsasuti JF, Izard J, Segata N, Gevers D, Raes J, Huttenhower C. Microbial co-occurrence relationships in the human microbiome. PLOS Computational Biology. 2012, 8 (7): e1002606. Bibcode:2012PLSCB...8E2606F. PMC 3395616 . PMID 22807668. doi:10.1371/journal.pcbi.1002606.
^ Abubucker S, Segata N, Goll J, Schubert AM, Izard J, Cantarel BL, Rodriguez-Mueller B, Zucker J, Thiagarajan M, Henrissat B, White O, Kelley ST, Methé B, Schloss PD, Gevers D, Mitreva M, Huttenhower C. Metabolic reconstruction for metagenomic data and its application to the human microbiome. PLOS Computational Biology. 2012, 8 (6): e1002358. Bibcode:2012PLSCB...8E2358A. PMC 3374609 . PMID 22719234. doi:10.1371/journal.pcbi.1002358.
^ Segata N, Haake SK, Mannon P, Lemon KP, Waldron L, Gevers D, Huttenhower C, Izard J. Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples. Genome Biology. June 2012, 13 (6): R42. PMC 3446314 . PMID 22698087. doi:10.1186/gb-2012-13-6-r42.
^ Cantarel BL, Lombard V, Henrissat B. Complex carbohydrate utilization by the healthy human microbiome. PLOS ONE. 2012, 7 (6): e28742. Bibcode:2012PLoSO...728742C. PMC 3374616 . PMID 22719820. doi:10.1371/journal.pone.0028742 .
^ Wu YW, Rho M, Doak TG, Ye Y. Oral spirochetes implicated in dental diseases are widespread in normal human subjects and carry extremely diverse integron gene cassettes. Applied and Environmental Microbiology. August 2012, 78 (15): 5288–96. PMC 3416431 . PMID 22635997. doi:10.1128/AEM.00564-12.
^ PLOS Collections: Article collections published by the Public Library of Science. collections.plos.org. [2018-04-15] （英语）.
^ Manuscript Summaries

外部链接

Human Microbiome Project
Data Analysis and Coordination Center （页面存档备份，存于互联网档案馆）
The CIHR Canadian Microbiome Initiative （页面存档备份，存于互联网档案馆）
The International Human Microbiome Consortium （页面存档备份，存于互联网档案馆）
2006, Lay summary of colon microbiome study（页面存档备份，存于互联网档案馆） (the actual study: Gill et al., 2006 （页面存档备份，存于互联网档案馆）)
Olivia Judson Microbes ‘R’ Us （页面存档备份，存于互联网档案馆） New York Times 22 July 2009
Gina Kolata Good Health? （页面存档备份，存于互联网档案馆） Thank Your 100 Trillion Bacteria （页面存档备份，存于互联网档案馆） New York Times 13 June 2012

[1] Human Microbiome Project: Diversity of Human Microbes Greater Than Previously Predicted. ScienceDaily. [8 March 2012].

[2] Human Microbiome Project / Funded Research. The NIH Common Fund. [8 March 2012].

[3] Human Microbiome Project / Program Initiatives. The NIH Common Fund. [8 March 2012].

[:0-4] 4.0 ^4.1 NIH Human Microbiome Project - About the Human Microbiome. hmpdacc.org. [2018-03-30] （英语）.

[5] NIH Human Microbiome Portfolio Analysis Team. A review of 10 years of human microbiome research activities at the US National Institutes of Health, Fiscal Years 2007-2016. Microbiome. 2019, 7 (1): 31. ISSN 2049-2618. PMC 6391833 . PMID 30808411. doi:10.1186/s40168-019-0620-y （英语）.

[6] Human Microbiome Project Consortium. A framework for human microbiome research. Nature. June 2012, 486 (7402): 215–21. Bibcode:2012Natur.486..215T. PMC 3377744 . PMID 22699610. doi:10.1038/nature11209.

[7] Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature. June 2012, 486 (7402): 207–14. Bibcode:2012Natur.486..207T. PMC 3564958 . PMID 22699609. doi:10.1038/nature11234.

[8] Faust K, Sathirapongsasuti JF, Izard J, Segata N, Gevers D, Raes J, Huttenhower C. Microbial co-occurrence relationships in the human microbiome. PLOS Computational Biology. 2012, 8 (7): e1002606. Bibcode:2012PLSCB...8E2606F. PMC 3395616 . PMID 22807668. doi:10.1371/journal.pcbi.1002606.

[9] Abubucker S, Segata N, Goll J, Schubert AM, Izard J, Cantarel BL, Rodriguez-Mueller B, Zucker J, Thiagarajan M, Henrissat B, White O, Kelley ST, Methé B, Schloss PD, Gevers D, Mitreva M, Huttenhower C. Metabolic reconstruction for metagenomic data and its application to the human microbiome. PLOS Computational Biology. 2012, 8 (6): e1002358. Bibcode:2012PLSCB...8E2358A. PMC 3374609 . PMID 22719234. doi:10.1371/journal.pcbi.1002358.

[10] Segata N, Haake SK, Mannon P, Lemon KP, Waldron L, Gevers D, Huttenhower C, Izard J. Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples. Genome Biology. June 2012, 13 (6): R42. PMC 3446314 . PMID 22698087. doi:10.1186/gb-2012-13-6-r42.

[11] Cantarel BL, Lombard V, Henrissat B. Complex carbohydrate utilization by the healthy human microbiome. PLOS ONE. 2012, 7 (6): e28742. Bibcode:2012PLoSO...728742C. PMC 3374616 . PMID 22719820. doi:10.1371/journal.pone.0028742 .

[12] Wu YW, Rho M, Doak TG, Ye Y. Oral spirochetes implicated in dental diseases are widespread in normal human subjects and carry extremely diverse integron gene cassettes. Applied and Environmental Microbiology. August 2012, 78 (15): 5288–96. PMC 3416431 . PMID 22635997. doi:10.1128/AEM.00564-12.

[13] PLOS Collections: Article collections published by the Public Library of Science. collections.plos.org. [2018-04-15] （英语）.

[14] Manuscript Summaries

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 該項目包括在多個機構開展的三個子項目。 研究方法包括 16S rRNA 基因分析、全基因組鳥槍法測序、全基因組測序、元轉錄組學、代謝組學/脂質組學和免疫蛋白質組學。 iHMP 的主要發現於2019年被發布<ref>{{Cite journal|last=NIH Human Microbiome Portfolio Analysis Team|date=2019|title=A review of 10 years of human microbiome research activities at the US National Institutes of Health, Fiscal Years 2007-2016|journal=Microbiome|language=en|volume=7|issue=1|pages=31|doi=10.1186/s40168-019-0620-y|pmid=30808411|issn=2049-2618|pmc=6391833}}</ref>。
+== 里程碑 ==
+=== 參考數據庫被建立 ===
+年6月13日，[[國立衛生研究院 (美國)|美國國立衛生研究院]]院長[[法蘭西斯·柯林斯]]（Francis S. Collins）宣布了人类微生物组计划項目的一個重要里程碑。 該公告還附有一系列協調文章於同一天在《[[自然 (期刊)|自然》<ref>{{cite journal | title = A framework for human microbiome research | journal = Nature | volume = 486 | issue = 7402 | pages = 215–21 | date = June 2012 | pmid = 22699610 | pmc = 3377744 | doi = 10.1038/nature11209 | author1 = Human Microbiome Project Consortium | bibcode = 2012Natur.486..215T }}</ref><ref>{{cite journal | title = Structure, function and diversity of the healthy human microbiome | journal = Nature | volume = 486 | issue = 7402 | pages = 207–14 | date = June 2012 | pmid = 22699609 | pmc = 3564958 | doi = 10.1038/nature11234 | author1 = Human Microbiome Project Consortium | bibcode = 2012Natur.486..207T }}</ref>和包括[[公共科學圖書館]] (PLoS) 在內的多個期刊上發表<ref>{{cite journal | vauthors = Faust K, Sathirapongsasuti JF, Izard J, Segata N, Gevers D, Raes J, Huttenhower C | title = Microbial co-occurrence relationships in the human microbiome | journal = PLOS Computational Biology | volume = 8 | issue = 7 | pages = e1002606 | date = 2012 | pmid = 22807668 | pmc = 3395616 | doi = 10.1371/journal.pcbi.1002606 | bibcode = 2012PLSCB...8E2606F }}</ref><ref>{{cite journal | vauthors = Abubucker S, Segata N, Goll J, Schubert AM, Izard J, Cantarel BL, Rodriguez-Mueller B, Zucker J, Thiagarajan M, Henrissat B, White O, Kelley ST, Methé B, Schloss PD, Gevers D, Mitreva M, Huttenhower C | title = Metabolic reconstruction for metagenomic data and its application to the human microbiome | journal = PLOS Computational Biology | volume = 8 | issue = 6 | pages = e1002358 | date = 2012 | pmid = 22719234 | pmc = 3374609 | doi = 10.1371/journal.pcbi.1002358 | bibcode = 2012PLSCB...8E2358A }}</ref><ref>{{cite journal | vauthors = Segata N, Haake SK, Mannon P, Lemon KP, Waldron L, Gevers D, Huttenhower C, Izard J | title = Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples | journal = Genome Biology | volume = 13 | issue = 6 | pages = R42 | date = June 2012 | pmid = 22698087 | pmc = 3446314 | doi = 10.1186/gb-2012-13-6-r42 }}</ref><ref>{{cite journal | vauthors = Cantarel BL, Lombard V, Henrissat B | title = Complex carbohydrate utilization by the healthy human microbiome | journal = PLOS ONE | volume = 7 | issue = 6 | pages = e28742 | date = 2012 | pmid = 22719820 | pmc = 3374616 | doi = 10.1371/journal.pone.0028742 | bibcode = 2012PLoSO...728742C | doi-access = free }}</ref><ref>{{cite journal | vauthors = Wu YW, Rho M, Doak TG, Ye Y | title = Oral spirochetes implicated in dental diseases are widespread in normal human subjects and carry extremely diverse integron gene cassettes | journal = Applied and Environmental Microbiology | volume = 78 | issue = 15 | pages = 5288–96 | date = August 2012 | pmid = 22635997 | pmc = 3416431 | doi = 10.1128/AEM.00564-12 }}</ref><ref>{{Cite web|url=http://collections.plos.org/hmp|title=PLOS Collections: Article collections published by the Public Library of Science|website=collections.plos.org|language=en|access-date=2018-04-15}}</ref>。 通過使用基因組測序技術繪製健康人類的正常微生物組成，HMP 的研究人員創建了一個參考數據庫和人類正常微生物變化的邊界<ref>[http://www.plos.org/media/press/2012/PLoS_%20HMP_Collection_Manuscript_Summaries.pdf Manuscript Summaries]</ref>。
 == 参阅 ==