Redefining the human oral mycobiome with improved practices in amplicon-based taxonomy: discovery of Malassezia as a prominent commensal.
Redefining the human oral mycobiome with improved practices in amplicon-based taxonomy: discovery of Malassezia as a prominent commensal.
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通过改进基于扩增子的分类学实践重新定义人类口腔真菌组：发现马拉色菌作为一种重要的共生菌。
DOI：
10.1371/journal.pone.0090899
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发表时间：
2014
期刊：
影响因子：
3.7
通讯作者：
Strausbaugh LD
中科院分区：
文献类型：
--
作者：
Dupuy AK;David MS;Li L;Heider TN;Peterson JD;Montano EA;Dongari-Bagtzoglou A;Diaz PI;Strausbaugh LD
真菌是一个庞大而复杂的群体，越来越多地被认为是新出现的威胁。它们作为健康修饰剂的作用要求准确描绘人类中的真菌群落。作为进入气道和胃肠道的入口点，口腔中的真菌与几个生物区室有关。我们已经修订了基于序列的分类分配的现行做法，并采用改进来解决健康人口腔中存在的真菌属的问题。采用稳健的提取方法，对唾液中的内转录间隔区1（ITS 1）扩增子进行大规模平行、高通量测序，调查人类口腔真菌生物群系。通过与策展的参考数据集进行比较来分配分类，然后使用经验确定的BLAST E值匹配统计进行过滤（10 - 42）。命名修正通过将单个真菌属的冗余名称结合起来进一步完善了结果。经过这些管理步骤，大约三分之二的最初确定的属被淘汰。与一项类似的宏基因组研究和几项早期的基于培养的研究相比，我们的研究结果改变了目前对口腔真菌组的概念，特别是发现了马拉色菌属的高患病率和丰度。马拉色菌以前被鉴定为皮肤的重要病原体，最近被报道为头和耳的背部和背部的主要真菌属，这是马拉色菌在人类口腔中的首次报道。这项研究的结果与其他人关于核心真菌生物群的许多共识成员的存在以及个体受试者的独特模式的一致性很好。这项研究对无条件接受由自动分配产生的冗长的社区成员名单提出了警告，为增强基于序列的真菌调查的可能生物相关性提供了路线图，并为了解真菌在口腔健康和疾病中的作用奠定了基础。
Fungi are a large, complex group, increasingly recognized as emerging threats. Their roles as modifiers of health mandate accurate portrayals of fungal communities in humans. As an entry point into the airways and gastrointestinal tract, fungi in the mouth are relevant to several biocompartments. We have revised current practices in sequence-based taxonomy assignments and employed the improvements to address the question of the fungal genera present in the healthy human mouth. The human oral mycobiome was surveyed using massively parallel, high throughput sequencing of internal transcribed spacer 1 (ITS1) amplicons from saliva following robust extraction methods. Taxonomy was assigned by comparison to a curated reference dataset, followed by filtering with an empirically determined BLAST E-value match statistic (10−42). Nomenclature corrections further refined results by conjoining redundant names for a single fungal genus. Following these curation steps, about two-thirds of the initially identified genera were eliminated. In comparison with the one similar metagenomic study and several earlier culture-based ones, our findings change the current conception of the oral mycobiome, especially with the discovery of the high prevalence and abundance of the genus Malassezia. Previously identified as an important pathogen of the skin, and recently reported as the predominant fungal genus at the nostril and backs of the head and ear, this is the first account of Malassezia in the human mouth. Findings from this study were in good agreement with others on the existence of many consensus members of the core mycobiome, and on unique patterns for individual subjects. This research offered a cautionary note about unconditional acceptance of lengthy lists of community members produced by automated assignments, provided a roadmap for enhancing the likely biological relevance of sequence-based fungal surveys, and built the foundation for understanding the role of fungi in health and disease of the oral cavity.
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影响因子：
5.4
作者：
Hawksworth DL;Crous PW;Redhead SA;Reynolds DR;Samson RA;Seifert KA;Taylor JW;Wingfield MJ;Abaci O;Aime C;Asan A;Bai FY;de Beer ZW;Begerow D;Berikten D;Boekhout T;Buchanan PK;Burgess T;Buzina W;Cai L;Cannon PF;Crane JL;Damm U;Daniel HM;van Diepeningen AD;Druzhinina I;Dyer PS;Eberhardt U;Fell JW;Frisvad JC;Geiser DM;Geml J;Glienke C;Gräfenhan T;Groenewald JZ;Groenewald M;de Gruyter J;Guého-Kellermann E;Guo LD;Hibbett DS;Hong SB;de Hoog GS;Houbraken J;Huhndorf SM;Hyde KD;Ismail A;Johnston PR;Kadaifciler DG;Kirk PM;Kõljalg U;Kurtzman CP;Lagneau PE;Lévesque CA;Liu X;Lombard L;Meyer W;Miller A;Minter DW;Najafzadeh MJ;Norvell L;Ozerskaya SM;Oziç R;Pennycook SR;Peterson SW;Pettersson OV;Quaedvlieg W;Robert VA;Ruibal C;Schnürer J;Schroers HJ;Shivas R;Slippers B;Spierenburg H;Takashima M;Taşkın E;Thines M;Thrane U;Uztan AH;van Raak M;Varga J;Vasco A;Verkley G;Videira SI;de Vries RP;Weir BS;Yilmaz N;Yurkov A;Zhang N
通讯作者：
Zhang N
影响因子：
3.7
作者：
Diaz PI;Dupuy AK;Abusleme L;Reese B;Obergfell C;Choquette L;Dongari-Bagtzoglou A;Peterson DE;Terzi E;Strausbaugh LD
通讯作者：
Strausbaugh LD
影响因子：
9.4
作者：
Buzina, W;Lass-Flörl, C;Marth, E
通讯作者：
Marth, E
影响因子：
5.4
作者：
Hawksworth DL
通讯作者：
Hawksworth DL
影响因子：
3
作者：
Blackwell, Meredith
通讯作者：
Blackwell, Meredith