Development and application of the human intestinal tract chip, a phylogenetic microarray: analysis of universally conserved phylotypes in the abundant microbiota of young and elderly adults.
Development and application of the human intestinal tract chip, a phylogenetic microarray: analysis of universally conserved phylotypes in the abundant microbiota of young and elderly adults.
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DOI：
10.1111/j.1462-2920.2009.01900.x
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发表时间：
2009-07
影响因子：
5.1
通讯作者：
de Vos WM
中科院分区：
文献类型：
--
作者：
Rajilić-Stojanović M;Heilig HG;Molenaar D;Kajander K;Surakka A;Smidt H;de Vos WM
在本文中，我们提出的小亚基核糖体RNA（SSU rRNA）基因的可变区的多样性的计算机评估的基础上，生态系统特定的策展数据库，描述了一个探针设计程序的基础上，两个高变区具有最小的冗余和测试的潜力，这样的探针设计策略的设计一个灵活的微阵列平台。这导致了用于研究人类胃肠道微生物群的系统发育微阵列的开发和应用-被称为人类肠道芯片（HITChip）。根据1140种独特微生物的SSU rRNA基因的两个高变区（同一性< 98%），在分析超过16000个人肠道SSU rRNA序列后，设计了超过4800个专用的平铺寡核苷酸探针。将这些HITChip探针与一组不同的人肠道样品和SSU rRNA克隆杂交，以验证其指纹图谱和定量潜力。极好的再现性（中位数皮尔逊相关系数为0.99），获得以下杂交与T7聚合酶转录在体外产生的SSU rRNA基因扩增子。用相对丰度低至总微生物群的0.1%的40种不同代表性扩增子的人工混合物观察到线性剂量反应。对10个个体（5个年轻人和5个老年人）连续采集的3个粪便样本的分析揭示了时间动态，并证实了成人肠道微生物群是一个个体特异性和相对稳定的生态系统。对稳定部分的进一步分析允许在近似属水平（90%序列相似性）鉴定通用微生物群核心。该核心由放线菌门、拟杆菌门和厚壁菌门的成员组成。HITChip作为一种系统发育指纹分析工具，具有相对定量的可能性，有可能弥合我们在定量和定性描述人类胃肠道微生物群组成方面的知识差距。
In this paper we present the in silico assessment of the diversity of variable regions of the small subunit ribosomal RNA (SSU rRNA) gene based on an ecosystem-specific curated database, describe a probe design procedure based on two hypervariable regions with minimal redundancy and test the potential of such probe design strategy for the design of a flexible microarray platform. This resulted in the development and application of a phylogenetic microarray for studying the human gastrointestinal microbiota – referred as the human intestinal tract chip (HITChip). Over 4800 dedicated tiling oligonucleotide probes were designed based on two hypervariable regions of the SSU rRNA gene of 1140 unique microbial phylotypes (< 98% identity) following analysis of over 16 000 human intestinal SSU rRNA sequences. These HITChip probes were hybridized to a diverse set of human intestinal samples and SSU rRNA clones to validate its fingerprinting and quantification potential. Excellent reproducibility (median Pearson's correlation of 0.99) was obtained following hybridization with T7 polymerase transcripts generated in vitro from SSU rRNA gene amplicons. A linear dose–response was observed with artificial mixtures of 40 different representative amplicons with relative abundances as low as 0.1% of total microbiota. Analysis of three consecutively collected faecal samples from ten individuals (five young and five elderly adults) revealed temporal dynamics and confirmed that the adult intestinal microbiota is an individual-specific and relatively stable ecosystem. Further analysis of the stable part allowed for the identification of a universal microbiota core at the approximate genus level (90% sequence similarity). This core consists of members of Actinobacteria, Bacteroidetes and Firmicutes. Used as a phylogenetic fingerprinting tool with the possibility for relative quantification, the HITChip has the potential to bridge the gaps in our knowledge in the quantitative and qualitative description of the human gastrointestinal microbiota composition.
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影响因子：
4.4
作者：
Fogarty, LR;Voytek, MA
通讯作者：
Voytek, MA
影响因子：
5.1
作者：
Bodrossy, L;Stralis-Pavese, N;Sessitsch, A
通讯作者：
Sessitsch, A
影响因子：
56.9
作者：
Gill, Steven R.;Pop, Mihai;Nelson, Karen E.
通讯作者：
Nelson, Karen E.
DOI：
10.1099/00207713-44-4-812
发表时间：
1994-10-01
期刊：
INTERNATIONAL JOURNAL OF SYSTEMATIC BACTERIOLOGY
影响因子：
--
作者：
COLLINS, MD;LAWSON, PA;FARROW, JAE
通讯作者：
FARROW, JAE
影响因子：
4.4
作者：
Guschin, DY;Mobarry, BK;Mirzabekov, AD
通讯作者：
Mirzabekov, AD