Omics from source to sink: microbiome of a stream irrigation system and its potential impact

在美国，与食用受污染的新鲜农产品有关的食源性疾病被广泛报道。尽管灌溉水的重要性已得到承认，但在灌溉系统中存在的微生物群落及其在病原体传播和感染中的潜在作用的知识方面仍存在大量未被探索的空白。这项建议解决了确定环境和人类健康的潜在微生物风险因素的迫切需要。在该项目中开发的技术进步将有助于NIH-Cobre任务使用 用“组学”的方法来定义人类健康与灌溉用水中微生物群之间的关系。软腐果胶分解细菌植物病原菌(SRP)浸泡蔬菜作物的植物组织，从而为人类肠道病原菌创造生态位，使后者能够在新鲜农产品上定居。我们的目标是：(I)确定溪流灌溉系统微生物群落的组成和结构；(Ii)确定灌溉水中微生物在建立食源性病原体生态位方面的作用。新技术的应用将使微生物群落得到更准确的识别，本研究的结果将阐明SRP与肠道病原体在共同感染植物寄主时的相互作用。这项拟议的研究在基因组方法上具有创造性和原创性，并为研究肠道病原体与许多其他地区种植的食用作物之间的关系提供了一个可靠的模型。这项研究产生的知识不仅有助于了解微生物群落的一般生态学，而且更具体地说，有助于了解食源性人类病原体的动态及其与植物病原体的相互作用。我们的预测结果预计将对环境政策产生重要的积极影响，因为我们提供了强有力的证据，定义了新鲜农产品中植物和人类病原体之间的微生物相互作用以及生存和/或 使用受污染的水后，生鲜农产品上病原体的生长。

Food-borne illnesses associated with consumption of contaminated fresh produce are widely reported in the United States. Despite the recognized importance of irrigation water, a substantial unexplored gap exists in the knowledge of microbial communities present in irrigation systems and their potential roles in pathogen transmission and infection. This proposal addresses the critical need to determine potential microbial risk factors for environmental and human health. Technical advances developed in this project will contribute to the NIH-COBRE mission to use ‘omics’ approaches to define relationships between human health and microbiomes in irrigation water. Soft rot pectinolytic bacterial plant pathogens (SRP) macerate plant tissues of vegetable crops thereby producing a niche for human enteric pathogens and enabling the latter to colonize fresh produce. Our aims are: (I) To determine the composition and structure of the microbiomes of stream irrigation systems and (II) To determine the role of microbes in irrigation water in establishing niches for food-borne pathogens. Application of new technologies will permit more precise identification of microbial communities and results of this study will elucidate the interactions between SRP and enteric pathogens when co-infecting a plant host. The proposed research is creative and original in its genomic approach and provides a sound model for studying associations of enteric pathogens with edible crops grown in many other locations. Knowledge generated by this research will contribute not only to understanding the general ecology of microbial communities, but more specifically to dynamics of food-borne human pathogens and their interactions with plant pathogens. Our projected results are expected to have important positive impacts on environmental policy by providing robust evidence defining the microbial interactions between plant and human pathogens in fresh produce as well as survival and/or growth of pathogens on fresh produce following application of contaminated water.