Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.
ISME J. 2013 Oct;7(10):1974-84. doi: 10.1038/ismej.2013.88. Epub 2013 Jun 13.
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.
环境中的病原体对人类、植物和动物的健康构成严重威胁，最近的疫情就证明了这一点。由于许多病原体可以在环境中存活和繁殖，因此了解它们在环境中的种群动态和致病潜力非常重要。为了评估不同生境中的致病潜力，我们开发了一种功能基因芯片，即 PathoChip，该芯片由与主要毒力因子（如粘附、定植、运动、侵袭、毒素、免疫逃避和铁摄取）相关的关键毒力基因构建而成。从 13 种毒力因子中筛选出 3715 个最佳探针，涵盖了来自 1397 种微生物物种（2336 株）的 7417 个编码序列。PathoChip 的特异性通过计算进行了验证，大约 98%的探针在种水平或以下提供了特异性，证明了其具有很高的区分能力，能够检测目标序列的出色能力。我们将该芯片应用于土壤、海水和人唾液的群落样本中，以评估自然环境中毒力基因的存在情况。与相应的对照相比，应激条件下毒力基因的丰度和多样性都增加了，这表明在环境扰动（如变暖或溢油）下，致病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，这导致了毒力基因丰度和分布的变化。PathoChip 为识别微生物种群中的毒力基因、研究毒力基因对环境扰动的动态响应以及确定微生物群落的致病潜力提供了一种有用的工具。
