Characterizing the Human Mycobiota: A Comparison of Small Subunit rRNA, ITS1, ITS2, and Large Subunit rRNA Genomic Targets.
Characterizing the Human Mycobiota: A Comparison of Small Subunit rRNA, ITS1, ITS2, and Large Subunit rRNA Genomic Targets.
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DOI：
10.3389/fmicb.2018.02208
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发表时间：
2018
影响因子：
5.2
通讯作者：
Taylor MW
中科院分区：
文献类型：
--
作者：
Hoggard M;Vesty A;Wong G;Montgomery JM;Fourie C;Douglas RG;Biswas K;Taylor MW
在过去的十年里，人们对人类微生物组的兴趣急剧增加。然而，这项研究的大部分都集中在细菌上，而对它们的真菌的组成和作用还知之甚少。此外，已经应用了各种方法，研究之间的可比性尚不清楚。这项研究比较了四对针对小亚基(SSU)rRNA(18S)、ITS1、ITS2和大亚基(LSU)rRNA(26S)基因组区域的引物对准确描述人类真菌生物群典型真菌群落的能力。21个真菌模拟群落类群的所有四个目标区都能够被充分扩增和测序。混合模拟群落分析显示，每个引物对准确描述复杂群落的能力存在显著差异。其目标地区的表现优于路易斯安那州立大学和SSU。在ITS区中，ITS1在混合群落中不能产生解脂雅罗维菌和所有三种马拉色菌的序列。这些发现在对人类鼻腔和小鼠排泄物样本的研究中得到了进一步的支持。基于这些分析，以前使用ITS1、SSU或LSU标记的研究可能会忽略由ITS2标记识别的关键分类群。到目前为止，在人类真菌区系研究中常用的方法中，我们建议选择ITS2标记。进一步研究最近开发的真菌引物选项对于最终确定未来人类真菌生物区系研究应标准化的最佳方法学方法至关重要。
Interest in the human microbiome has increased dramatically in the last decade. However, much of this research has focused on bacteria, while the composition and roles of their fungal counterparts remain less understood. Furthermore, a variety of methodological approaches have been applied, and the comparability between studies is unclear. This study compared four primer pairs targeting the small subunit (SSU) rRNA (18S), ITS1, ITS2, and large subunit (LSU) rRNA (26S) genomic regions for their ability to accurately characterize fungal communities typical of the human mycobiota. All four target regions of 21 individual fungal mock community taxa were capable of being amplified adequately and sequenced. Mixed mock community analyses revealed marked variability in the ability of each primer pair to accurately characterize a complex community. ITS target regions outperformed LSU and SSU. Of the ITS regions, ITS1 failed to generate sequences for Yarrowia lipolytica and all three Malassezia species when in a mixed community. These findings were further supported in studies of human sinonasal and mouse fecal samples. Based on these analyses, previous studies using ITS1, SSU, or LSU markers may omit key taxa that are identified by the ITS2 marker. Of methods commonly used in human mycobiota studies to date, we recommend selection of the ITS2 marker. Further investigation of more recently developed fungal primer options will be essential to ultimately determine the optimal methodological approach by which future human mycobiota studies ought to be standardized.
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影响因子：
16.6
作者：
Duvallet C;Gibbons SM;Gurry T;Irizarry RA;Alm EJ
通讯作者：
Alm EJ
影响因子：
15.5
作者：
Cope EK;Goldberg AN;Pletcher SD;Lynch SV
通讯作者：
Lynch SV
影响因子：
6.4
作者：
Cleland, Edward John;Bassioni, Ahmed;Wormald, Peter-John
通讯作者：
Wormald, Peter-John
DOI：
10.1111/j.1365-2222.2012.03987.x
发表时间：
2012-05
期刊：
Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology
影响因子：
--
作者：
Agbetile J;Fairs A;Desai D;Hargadon B;Bourne M;Mutalithas K;Edwards R;Morley JP;Monteiro WR;Kulkarni NS;Green RH;Pavord ID;Bradding P;Brightling CE;Wardlaw AJ;Pashley CH
通讯作者：
Pashley CH
影响因子：
2.9
作者：
Comacle, Pauline;Belaz, Sorya;Robert-Gangneux, Florence
通讯作者：
Robert-Gangneux, Florence