Development of HuMiChip for functional profiling of human microbiomes.
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...
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2014-01-01
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| Series: | PLoS ONE |
| Online Access: | https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0090546&type=printable |
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| author | Qichao Tu Zhili He Yan Li Yanfei Chen Ye Deng Lu Lin Christopher L Hemme Tong Yuan Joy D Van Nostrand Liyou Wu Xuedong Zhou Wenyuan Shi Lanjuan Li Jian Xu Jizhong Zhou |
| author_facet | Qichao Tu Zhili He Yan Li Yanfei Chen Ye Deng Lu Lin Christopher L Hemme Tong Yuan Joy D Van Nostrand Liyou Wu Xuedong Zhou Wenyuan Shi Lanjuan Li Jian Xu Jizhong Zhou |
| author_sort | Qichao Tu |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-c6943372dc4341cf8be0d2ecbb686880 |
| institution | DOAJ |
| issn | 1932-6203 |
| language | English |
| publishDate | 2014-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj-art-c6943372dc4341cf8be0d2ecbb6868802025-08-20T03:01:14ZengPublic Library of Science (PLoS)PLoS ONE1932-62032014-01-0193e9054610.1371/journal.pone.0090546Development of HuMiChip for functional profiling of human microbiomes.Qichao TuZhili HeYan LiYanfei ChenYe DengLu LinChristopher L HemmeTong YuanJoy D Van NostrandLiyou WuXuedong ZhouWenyuan ShiLanjuan LiJian XuJizhong ZhouUnderstanding 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.https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0090546&type=printable |
| spellingShingle | Qichao Tu Zhili He Yan Li Yanfei Chen Ye Deng Lu Lin Christopher L Hemme Tong Yuan Joy D Van Nostrand Liyou Wu Xuedong Zhou Wenyuan Shi Lanjuan Li Jian Xu Jizhong Zhou Development of HuMiChip for functional profiling of human microbiomes. PLoS ONE |
| title | Development of HuMiChip for functional profiling of human microbiomes. |
| title_full | Development of HuMiChip for functional profiling of human microbiomes. |
| title_fullStr | Development of HuMiChip for functional profiling of human microbiomes. |
| title_full_unstemmed | Development of HuMiChip for functional profiling of human microbiomes. |
| title_short | Development of HuMiChip for functional profiling of human microbiomes. |
| title_sort | development of humichip for functional profiling of human microbiomes |
| url | https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0090546&type=printable |
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