'Omics from Source to Sink: Microbiome of a Stream Irrigation System and its Potential Impact

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PROJECT SUMMARY- ‘Omics from Source to Sink: Microbiome of a Stream Irrigation System and Its Potential Impact 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 human and environmental health and aligns with the COBRE mission of “how environmental microbes impact human health” as it aims to use ‘omics approaches to define relationships between environmental microbiome and its potential impacts on human health. Soft rot pectinolytic bacterial plant pathogens (SRP) macerate plant tissues of vegetable crops, producing a niche for foodborne human pathogens (FBP) and enabling the latter to colonize fresh produce. Our specific aims are: (I) Determine the composition and structure of the microbiomes of stream irrigation systems by amplicon and shotgun sequence analyses, and (II) determine the role that microbes in irrigation water play in establishing niches for FBP by internalization and in vivo interspecies interactions. Application of new technologies will permit more precise identification of microbial communities and results of this study will elucidate the interactions between SRP and FBP 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 FBP 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 FBP and their interactions with SRP. Our projected results are expected to have important positive impacts on improving our understanding of evaluating risk factors and help to resolve poorly understood mechanisms. This impact aligns with NIH’s mission to seek fundamental knowledge to enhance health and reduce illness.