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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
Source PublicationPLOS ONE
Volume9Issue:3Pages:1
Abstract

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.

SubtypeArticle
WOS HeadingsScience & Technology
DOI10.1371/journal.pone.0090546
WOS KeywordPROBE DESIGN CRITERIA ; CORE GUT MICROBIOME ; PHYLOGENETIC MICROARRAY ; INTESTINAL MICROBIOTA ; COMMUNITY COMPOSITION ; GENE MICROARRAYS ; AMINO-ACIDS ; HOST ; PERIODONTITIS ; METABOLISM
Indexed BySCI
Language英语
WOS Research AreaScience & Technology - Other Topics
WOS SubjectMultidisciplinary Sciences
WOS IDWOS:000332475500065
Citation statistics
Document Type期刊论文
Identifierhttp://ir.qibebt.ac.cn/handle/337004/6175
Collection单细胞中心组群
Affiliation1.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
Recommended Citation
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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