Development of HuMiChip for Functional Profiling of Human Microbiomes | |
Tu, Qichao1; He, Zhili1; Li, Yan2; Chen, Yanfei3; Deng, Ye1; Lin, Lu4; Hemme, Christopher L.1; Yuan, Tong1; Van Nostrand, Joy D.1; Wu, Liyou1; Zhou, Xuedong2; Shi, Wenyuan5; Li, Lanjuan3; Xu, Jian4; Zhou, Jizhong1,6,7 | |
2014-03-04 | |
发表期刊 | PLOS ONE |
卷号 | 9期号:3页码:1 |
摘要 | Understanding the diversity, composition, structure, function, and dynamics of human microbiomes in individual human hosts is crucial to reveal human-microbial interactions, especially for patients with microbially mediated disorders, but challenging due to the high diversity of the human microbiome. Here we have developed a functional gene-based microarray for profiling human microbiomes (HuMiChip) with 36,802 probes targeting 50,007 protein coding sequences for 139 key functional gene families. Computational evaluation suggested all probes included are highly specific to their target sequences. HuMiChip was used to analyze human oral and gut microbiomes, showing significantly different functional gene profiles between oral and gut microbiome. Obvious shifts of microbial functional structure and composition were observed for both patients with dental caries and periodontitis from moderate to advanced stages, suggesting a progressive change of microbial communities in response to the diseases. Consistent gene family profiles were observed by both HuMiChip and next generation sequencing technologies. Additionally, HuMiChip was able to detect gene families at as low as 0.001% relative abundance. The results indicate that the developed HuMiChip is a useful and effective tool for functional profiling of human microbiomes. |
文章类型 | Article |
WOS标题词 | Science & Technology |
DOI | 10.1371/journal.pone.0090546 |
关键词[WOS] | PROBE DESIGN CRITERIA ; CORE GUT MICROBIOME ; PHYLOGENETIC MICROARRAY ; INTESTINAL MICROBIOTA ; COMMUNITY COMPOSITION ; GENE MICROARRAYS ; AMINO-ACIDS ; HOST ; PERIODONTITIS ; METABOLISM |
收录类别 | SCI |
语种 | 英语 |
WOS研究方向 | Science & Technology - Other Topics |
WOS类目 | Multidisciplinary Sciences |
WOS记录号 | WOS:000332475500065 |
引用统计 | |
文献类型 | 期刊论文 |
条目标识符 | http://ir.qibebt.ac.cn/handle/337004/6175 |
专题 | 单细胞中心组群 |
作者单位 | 1.Univ Oklahoma, Dept Microbiol & Plant Biol, Inst Environm Genom, Norman, OK 73019 USA 2.Sichuan Univ, State Key Lab Oral Dis, West China Hosp Stomatol, Chengdu 610064, Peoples R China 3.Zhejiang Univ, State Key Lab Diag & Treatment Infect Dis, Affiliated Hosp 1, Hangzhou 310003, Zhejiang, Peoples R China 4.Chinese Acad Sci, Qingdao Inst Bioenergy & Bioproc Technol, Qingdao, Shandong, Peoples R China 5.Univ Calif Los Angeles, Sch Dent, Los Angeles, CA 90024 USA 6.Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Div Earth Sci, Berkeley, CA 94720 USA 7.Tsinghua Univ, State Key Joint Lab Environm Simulat & Pollut Con, Sch Environm, Beijing 100084, Peoples R China |
推荐引用方式 GB/T 7714 | Tu, Qichao,He, Zhili,Li, Yan,et al. Development of HuMiChip for Functional Profiling of Human Microbiomes[J]. PLOS ONE,2014,9(3):1. |
APA | Tu, Qichao.,He, Zhili.,Li, Yan.,Chen, Yanfei.,Deng, Ye.,...&Zhou, Jizhong.(2014).Development of HuMiChip for Functional Profiling of Human Microbiomes.PLOS ONE,9(3),1. |
MLA | Tu, Qichao,et al."Development of HuMiChip for Functional Profiling of Human Microbiomes".PLOS ONE 9.3(2014):1. |
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