The gut mycobiome of the Human Microbiome Project healthy cohort.
The gut mycobiome of the Human Microbiome Project healthy cohort.
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DOI：
10.1186/s40168-017-0373-4
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发表时间：
2017-11-25
期刊：
影响因子：
15.5
通讯作者：
Petrosino JF
中科院分区：
文献类型：
--
作者：
Nash AK;Auchtung TA;Wong MC;Smith DP;Gesell JR;Ross MC;Stewart CJ;Metcalf GA;Muzny DM;Gibbs RA;Ajami NJ;Petrosino JF
大多数描述健康和患病状态下的人类肠道微生物组的研究都强调细菌成分，但真菌微生物组（即真菌组）作为我们微生物组的基本组成部分开始获得认可。迄今为止，人类肠道真菌组研究主要以疾病为中心或以一小群健康个体为中心。为了贡献人类真菌组的现有知识，我们通过对内部转录间隔区 2 (ITS2) 区域以及 18S rRNA 基因进行测序，研究了人类微生物组计划 (HMP) 队列的肠道真菌组。通过 ITS2 测序对 317 HMP 粪便样本进行了分析。与细菌多样性相比，粪便真菌多样性显着较低。酵母在样本中占主导地位，包括前 15 个最丰富属中的 8 个属。具体而言，真菌群落的特点是酵母菌属、马拉色菌属和念珠菌属的高流行，其中酿酒酵母、限制性酵母菌和白色念珠菌操作分类单位 (OTU) 分别存在于 96.8%、88.3% 和 80.8% 的样本中。真菌群落的志愿者之间和志愿者内部存在高度的变异性。然而，在大约 1 年期间捐赠的所有样本中，分别在 92.2%、78.3% 和 63.6% 的志愿者中发现了酿酒酵母、限制性酿酒酵母和白色念珠菌 OTU。宏基因组和18S rRNA基因测序数据与ITS2结果一致；然而，ITS2 测序为相对低丰度的真菌组成分提供了更高的分辨率。与细菌群落相比，人类肠道菌群多样性较低，以酵母菌为主，包括酵母菌、马拉色菌和念珠菌。 HMP 队列中志愿者之间和志愿者内部的变异性都很高，这表明与细菌群落不同，随着时间的推移，一个人的真菌组与自己的相似度并不比与另一个人的相似度高。尽管如此，大多数样本中仍然存在几种真菌，这证明核心肠道真菌群可能存在。与宏基因组和 18S rRNA 基因测序数据相比，ITS2 测序数据提供了更高分辨率的真菌组成员资格，这表明它是研究粪便样本真菌组的更灵敏的方法。本文的在线版本 (10.1186/s40168-017-0373-4) 包含补充材料，可供授权用户使用。
Most studies describing the human gut microbiome in healthy and diseased states have emphasized the bacterial component, but the fungal microbiome (i.e., the mycobiome) is beginning to gain recognition as a fundamental part of our microbiome. To date, human gut mycobiome studies have primarily been disease centric or in small cohorts of healthy individuals. To contribute to existing knowledge of the human mycobiome, we investigated the gut mycobiome of the Human Microbiome Project (HMP) cohort by sequencing the Internal Transcribed Spacer 2 (ITS2) region as well as the 18S rRNA gene. Three hundred seventeen HMP stool samples were analyzed by ITS2 sequencing. Fecal fungal diversity was significantly lower in comparison to bacterial diversity. Yeast dominated the samples, comprising eight of the top 15 most abundant genera. Specifically, fungal communities were characterized by a high prevalence of Saccharomyces, Malassezia, and Candida, with S. cerevisiae, M. restricta, and C. albicans operational taxonomic units (OTUs) present in 96.8, 88.3, and 80.8% of samples, respectively. There was a high degree of inter- and intra-volunteer variability in fungal communities. However, S. cerevisiae, M. restricta, and C. albicans OTUs were found in 92.2, 78.3, and 63.6% of volunteers, respectively, in all samples donated over an approximately 1-year period. Metagenomic and 18S rRNA gene sequencing data agreed with ITS2 results; however, ITS2 sequencing provided greater resolution of the relatively low abundance mycobiome constituents. Compared to bacterial communities, the human gut mycobiome is low in diversity and dominated by yeast including Saccharomyces, Malassezia, and Candida. Both inter- and intra-volunteer variability in the HMP cohort were high, revealing that unlike bacterial communities, an individual’s mycobiome is no more similar to itself over time than to another person’s. Nonetheless, several fungal species persisted across a majority of samples, evidence that a core gut mycobiome may exist. ITS2 sequencing data provided greater resolution of the mycobiome membership compared to metagenomic and 18S rRNA gene sequencing data, suggesting that it is a more sensitive method for studying the mycobiome of stool samples. The online version of this article (10.1186/s40168-017-0373-4) contains supplementary material, which is available to authorized users.
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影响因子：
3.7
作者：
Frykman PK;Nordenskjöld A;Kawaguchi A;Hui TT;Granström AL;Cheng Z;Tang J;Underhill DM;Iliev I;Funari VA;Wester T;HAEC Collaborative Research Group (HCRG)
通讯作者：
HAEC Collaborative Research Group (HCRG)
DOI：
10.1038/ismej.2012.8
发表时间：
2012-08
期刊：
The ISME journal
影响因子：
--
作者：
通讯作者：
--
DOI：
10.1016/j.diagmicrobio.2010.04.005
发表时间：
2011-08-01
影响因子：
2.9
作者：
Chen, Yu;Chen, Zhenjing;Li, Lanjuan
通讯作者：
Li, Lanjuan
影响因子：
2.7
作者：
Alfellani, Mohammed A.;Stensvold, C. Rune;Clark, C. Graham
通讯作者：
Clark, C. Graham
影响因子：
3
作者：
Blackwell, Meredith
通讯作者：
Blackwell, Meredith