The PathoChip, a functional gene array for assessing pathogenic properties of diverse microbial communities
The PathoChip, a functional gene array for assessing pathogenic properties of diverse microbial communities
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DOI：
10.1038/ismej.2013.88
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发表时间：
2013-10-01
期刊：
影响因子：
11
通讯作者：
Zhou, Jizhong
中科院分区：
文献类型：
--
作者：
Lee, Yong-Jin;van Nostrand, Joy D.;Zhou, Jizhong
环境中存在的病原体对人类、植物和动物的健康构成严重威胁，最近的疫情证明了这一点。由于许多病原体可以在环境中生存和繁殖，因此了解它们在环境中的种群动态和致病潜力是很重要的。为了评估不同生境下的致病潜力，我们开发了一个功能基因阵列PathoChip，它由与主要毒力因子相关的关键毒力基因组成，如黏附、定植、移动、入侵、毒素、免疫逃避和铁摄取。从13个毒力因子中筛选出3715个最佳探针，覆盖1397个微生物种(2336株)的7417个编码序列。通过计算验证了该基因芯片的特异性，大约98%的探针提供了物种水平或物种水平以下的特异性，证明了它具有良好的检测目标序列的能力和高分辨能力。我们将这个阵列应用于来自土壤、海水和人类唾液的社区样本，以评估自然环境中毒力基因的出现。在胁迫条件下，与相应的对照相比，毒力基因的丰度和多样性都增加了，这表明在气候变暖或石油泄漏等环境扰动下，病原菌的丰度可能会增加。统计分析表明，携带毒力基因的微生物群落对环境扰动有反应，环境扰动驱动了毒力基因丰度和分布的变化。病理芯片为鉴定微生物种群中的毒力基因、检测毒力基因对环境扰动的响应以及确定微生物群落的致病潜力提供了有用的工具。
Pathogens 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.