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The PathoChip, a functional gene array for assessing pathogenic properties of diverse microbial communities
Lee, Yong-Jin1,2; van Nostrand, Joy D.1,2; Tu, Qichao1,2; Lu, Zhenmei1,2,3; Cheng, Lei1,2; Yuan, Tong1,2; Deng, Ye1,2; Carter, Michelle Q.4; He, Zhili1,2; Wu, Liyou1,2; Yang, Fang5; Xu, Jian6; Zhou, Jizhong1,2,7,8
2013-10-01
Source PublicationISME JOURNAL
Volume7Issue:10Pages:1974-1984
AbstractPathogens present in the environment pose a serious threat to human, plant and animal health as evidenced by recent outbreaks. As many pathogens can survive and proliferate in the environment, it is important to understand their population dynamics and pathogenic potential in the environment. To assess pathogenic potential in diverse habitats, we developed a functional gene array, the PathoChip, constructed with key virulence genes related to major virulence factors, such as adherence, colonization, motility, invasion, toxin, immune evasion and iron uptake. A total of 3715 best probes were selected from 13 virulence factors, covering 7417 coding sequences from 1397 microbial species (2336 strains). The specificity of the PathoChip was computationally verified, and approximately 98% of the probes provided specificity at or below the species level, proving its excellent capability for the detection of target sequences with high discrimination power. We applied this array to community samples from soil, seawater and human saliva to assess the occurrence of virulence genes in natural environments. Both the abundance and diversity of virulence genes increased in stressed conditions compared with their corresponding controls, indicating a possible increase in abundance of pathogenic bacteria under environmental perturbations such as warming or oil spills. Statistical analyses showed that microbial communities harboring virulence genes were responsive to environmental perturbations, which drove changes in abundance and distribution of virulence genes. The PathoChip provides a useful tool to identify virulence genes in microbial populations, examine the dynamics of virulence genes in response to environmental perturbations and determine the pathogenic potential of microbial communities.
SubtypeArticle
KeywordVirulence Genes Functional Gene Array Climate Warming Oil-contamination Caries
WOS HeadingsScience & Technology ; Life Sciences & Biomedicine
DOI10.1038/ismej.2013.88
WOS KeywordGEOCHIP-BASED ANALYSIS ; PROBE DESIGN CRITERIA ; SEA OIL PLUME ; ESCHERICHIA-COLI ; OLIGONUCLEOTIDE MICROARRAY ; BACTERIAL VIRULENCE ; ELEVATED CO2 ; WATER ; SOIL ; IDENTIFICATION
Indexed BySCI
Language英语
WOS Research AreaEnvironmental Sciences & Ecology ; Microbiology
WOS SubjectEcology ; Microbiology
WOS IDWOS:000324869400009
Citation statistics
Document Type期刊论文
Identifierhttp://ir.qibebt.ac.cn/handle/337004/6000
Collection单细胞中心组群
Affiliation1.Univ Oklahoma, Inst Environm Genom, Norman, OK 73019 USA
2.Univ Oklahoma, Dept Microbiol & Plant Biol, Norman, OK 73019 USA
3.Zhejiang Univ, Coll Life Sci, Hangzhou 310003, Zhejiang, Peoples R China
4.USDA, Produce Safety & Microbiol Unit, Western Reg Res Ctr, ARS, Albany, CA USA
5.Qingdao Municipal Hosp, Oral Res Ctr, Qingdao, Shandong, Peoples R China
6.Chinese Acad Sci, Qingdao Inst Bioenergy & Bioproc Technol, Qingdao, Shandong, Peoples R China
7.Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Div Earth Sci, Berkeley, CA 94720 USA
8.Tsinghua Univ, Sch Environm, State Key Joint Lab Environm Simulat & Pollut Con, Beijing 100084, Peoples R China
Recommended Citation
GB/T 7714
Lee, Yong-Jin,van Nostrand, Joy D.,Tu, Qichao,et al. The PathoChip, a functional gene array for assessing pathogenic properties of diverse microbial communities[J]. ISME JOURNAL,2013,7(10):1974-1984.
APA Lee, Yong-Jin.,van Nostrand, Joy D..,Tu, Qichao.,Lu, Zhenmei.,Cheng, Lei.,...&Zhou, Jizhong.(2013).The PathoChip, a functional gene array for assessing pathogenic properties of diverse microbial communities.ISME JOURNAL,7(10),1974-1984.
MLA Lee, Yong-Jin,et al."The PathoChip, a functional gene array for assessing pathogenic properties of diverse microbial communities".ISME JOURNAL 7.10(2013):1974-1984.
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