Mycobiome: Approaches to analysis of intestinal fungi.
Mycobiome: Approaches to analysis of intestinal fungi.
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DOI：
10.1016/j.jim.2015.04.004
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发表时间：
2015-06
影响因子：
2.2
通讯作者：
Funari, Vincent A.
中科院分区：
文献类型：
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作者：
Tang, Jie;Iliev, Iliyan D.;Brown, Jordan;Underhill, David M.;Funari, Vincent A.
细菌16S rDNA的大规模平行测序（MPSS）已被广泛用于表征人和小鼠胃肠道的微生物组成。然而，真菌菌群（mycobiota）分析技术仍然相对欠发达。与16S分析相比，真菌菌群分析最常见的目标真菌内部转录间隔1 （ITS1）的大小和序列背景是高度可变的。使用代表性胃肠道真菌建立已知的“模拟”文库，我们研究了这种序列变异性如何影响来自Illumina Miseq和Ion Torrent PGM测序管道的数据质量。此外，虽然高质量的细菌16S序列数据库的存在有助于分析细菌16S谱，但这样一个公认的数据库尚未出现，以促进真菌ITS序列表征，我们观察到，在公开的真菌参考数据库中，ITS1序列表示的冗余和不一致影响了肠道中物种的定量和注释。为了解决这个问题，我们构建了一个人工整理的参考数据库，优化了胃肠道真菌的注释。这个靶向宿主相关真菌（THF）数据库包含1817个ITS1序列，代表了以前在人类和小鼠肠道中发现的属的序列多样性。我们观察到，在分析小鼠胃肠道测序数据时，该数据库在全面性、分类分配准确性和计算效率方面始终优于三种常见的ITS数据库替代品。
Massively parallel sequencing (MPSS) of bacterial 16S rDNA has been widely used to characterize the microbial makeup of the human and mouse gastrointestinal tract. However, techniques for fungal microbiota (mycobiota) profiling remain relatively under-developed. Compared to 16S profiling, the size and sequence context of the fungal Internal Transcribed Spacer 1 (ITS1), the most common target for mycobiota profiling, are highly variable. Using representative gastrointestinal tract fungi to build a known “mock” library, we examine how this sequence variability affects data quality derived from Illumina Miseq and Ion Torrent PGM sequencing pipelines. Also, while analysis of bacterial 16S profiles is facilitated by the presence of high-quality well-accepted databases of bacterial 16S sequences, such an accepted database has not yet emerged to facilitate fungal ITS sequence characterization, and we observe that redundant and inconsistent ITS1 sequence representation in publically available fungal reference databases affect quantitation and annotation of species in the gut. To address this problem, we have constructed a manually curated reference database optimized for annotation of gastrointestinal fungi. This Targeted Host-associated Fungi (THF) database contains 1,817 ITS1 sequences representing sequence diversity in genera previously identified in human and mouse gut. We observe that this database consistently outperforms three common ITS database alternatives on comprehensiveness, taxonomy assignment accuracy and computational efficiency in analyzing sequencing data from the mouse gastrointestinal tract.
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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：
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影响因子：
46.9
作者：
Loman, Nicholas J.;Misra, Raju V.;Pallen, Mark J.
通讯作者：
Pallen, Mark J.
DOI：
10.1126/science.1221789
发表时间：
2012-06-08
期刊：
Science (New York, N.Y.)
影响因子：
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作者：
Iliev ID;Funari VA;Taylor KD;Nguyen Q;Reyes CN;Strom SP;Brown J;Becker CA;Fleshner PR;Dubinsky M;Rotter JI;Wang HL;McGovern DP;Brown GD;Underhill DM
通讯作者：
Underhill DM
影响因子：
4.9
作者：
GARDES, M;BRUNS, TD
通讯作者：
BRUNS, TD
影响因子：
64.8
作者：
通讯作者：
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