HMP中健康人样本的肠道真菌菌群调查

Title：
The gut mycobiome of the Human Microbiome Project healthy cohort

DOI：
10.1186/s40168-017-0373-4

Abstract：
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.

All Authors：
Andrea K Nash , Thomas A Auchtung , Matthew C Wong , Daniel P Smith , Jonathan R Gesell , Matthew C Ross , Christopher J Stewart , Ginger A Metcalf , Donna M Muzny , Richard A Gibbs , Nadim J Ajami, Joseph F Petrosino

First Authors：
Andrea K Nash

Correspondence：
Joseph F Petrosino

内容要点：

本研究选取人类微生物组计划中的317份粪便样本，对转录间隔区2（ITS2）区域进行测序，分析健康人群的肠道真菌群。真菌多样性显著低于细菌多样性，酵母在所有样本中占主要部分，在丰度最高的15个真菌属中占据了8个。真菌属水平的酵母属、马拉色氏霉菌属、假丝酵母属，以及OTU水平的酿酒酵母、白色念珠菌、限制性马拉色菌存在于大多数样本中。个体内及个体间的肠道真菌群落差异较大。