American Gut: an Open Platform for Citizen Science Microbiome Research.
American Gut: an Open Platform for Citizen Science Microbiome Research.
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DOI：
10.1128/msystems.00031-18
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发表时间：
2018-05
期刊：
影响因子：
6.4
通讯作者：
Knight R
中科院分区：
文献类型：
--
作者：
McDonald D;Hyde E;Debelius JW;Morton JT;Gonzalez A;Ackermann G;Aksenov AA;Behsaz B;Brennan C;Chen Y;DeRight Goldasich L;Dorrestein PC;Dunn RR;Fahimipour AK;Gaffney J;Gilbert JA;Gogul G;Green JL;Hugenholtz P;Humphrey G;Huttenhower C;Jackson MA;Janssen S;Jeste DV;Jiang L;Kelley ST;Knights D;Kosciolek T;Ladau J;Leach J;Marotz C;Meleshko D;Melnik AV;Metcalf JL;Mohimani H;Montassier E;Navas-Molina J;Nguyen TT;Peddada S;Pevzner P;Pollard KS;Rahnavard G;Robbins-Pianka A;Sangwan N;Shorenstein J;Smarr L;Song SJ;Spector T;Swafford AD;Thackray VG;Thompson LR;Tripathi A;Vázquez-Baeza Y;Vrbanac A;Wischmeyer P;Wolfe E;Zhu Q;American Gut Consortium;Knight R
我们表明，公民科学，在室温下通过邮件运送样本的自选队列从临床收集的队列中重新捕获了许多已知的微生物组结果，并揭示了新的结果。特别令人感兴趣的是将n = 1的研究数据与人口数据相结合，表明手术等事件后微生物组的变化程度可以超过不同环境生物群落之间的差异，以及饮食中不同植物的影响，我们通过数百个样本的非靶向代谢组学证实了这一点。尽管许多工作已经将人类微生物组与特定的表型和生活方式变量联系起来，但来自不同项目的数据一直难以整合，人类粪便中微生物和分子多样性的程度仍然未知。使用地球微生物组项目的标准化协议和来自10，000多名公民科学家的样本贡献，以及一个开放的研究网络，我们将主要来自美国，英国和澳大利亚的人类微生物组标本相互比较，并与环境样本进行比较。我们的研究结果显示，与环境样品相比，人类粪便微生物组中的β多样性范围出乎意料;证明了在室温运输期间消除过度生长影响的程序的实用性，以揭示表型相关性;揭示了人类粪便代谢组中的新分子和分子群落种类;并检查微生物组，代谢组和消费植物多样性之间的新兴联系（而不是依赖于简化的分类变量，如素食主义，这几乎没有或根本没有解释力）。我们还展示了活体数据资源和跨队列比较的实用性，以确认微生物组与精神疾病之间的现有关联，并揭示手术期间一个人体内微生物组变化的程度，为开放微生物组研究和教育提供了一个范例。重要性我们表明，公民科学，在室温下通过邮件运送样本的自选队列从临床收集的队列中重新获得许多已知的微生物组结果，并揭示了新的结果。特别令人感兴趣的是将n = 1的研究数据与人口数据相结合，表明手术等事件后微生物组的变化程度可以超过不同环境生物群落之间的差异，以及饮食中不同植物的影响，我们通过数百个样本的非靶向代谢组学证实了这一点。
We show that a citizen science, self-selected cohort shipping samples through the mail at room temperature recaptures many known microbiome results from clinically collected cohorts and reveals new ones. Of particular interest is integrating n = 1 study data with the population data, showing that the extent of microbiome change after events such as surgery can exceed differences between distinct environmental biomes, and the effect of diverse plants in the diet, which we confirm with untargeted metabolomics on hundreds of samples. Although much work has linked the human microbiome to specific phenotypes and lifestyle variables, data from different projects have been challenging to integrate and the extent of microbial and molecular diversity in human stool remains unknown. Using standardized protocols from the Earth Microbiome Project and sample contributions from over 10,000 citizen-scientists, together with an open research network, we compare human microbiome specimens primarily from the United States, United Kingdom, and Australia to one another and to environmental samples. Our results show an unexpected range of beta-diversity in human stool microbiomes compared to environmental samples; demonstrate the utility of procedures for removing the effects of overgrowth during room-temperature shipping for revealing phenotype correlations; uncover new molecules and kinds of molecular communities in the human stool metabolome; and examine emergent associations among the microbiome, metabolome, and the diversity of plants that are consumed (rather than relying on reductive categorical variables such as veganism, which have little or no explanatory power). We also demonstrate the utility of the living data resource and cross-cohort comparison to confirm existing associations between the microbiome and psychiatric illness and to reveal the extent of microbiome change within one individual during surgery, providing a paradigm for open microbiome research and education. IMPORTANCE We show that a citizen science, self-selected cohort shipping samples through the mail at room temperature recaptures many known microbiome results from clinically collected cohorts and reveals new ones. Of particular interest is integrating n = 1 study data with the population data, showing that the extent of microbiome change after events such as surgery can exceed differences between distinct environmental biomes, and the effect of diverse plants in the diet, which we confirm with untargeted metabolomics on hundreds of samples.