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ARS Home » Pacific West Area » Albany, California » Western Regional Research Center » Produce Safety and Microbiology Research » Research » Publications at this Location » Publication #401706

Research Project: Elucidating the Factors that Determine the Ecology of Human Pathogens in Foods

Location: Produce Safety and Microbiology Research

Title: Microbiome profiles of an organic agricultural environment microcosm: A window to bacteriophage-bacterial population dynamics and the evolution of antibiotic resistance in the agricultural environment microbiome

item Zhang, Yujie
item KITAZUMI, AI - Texas Tech University
item Liao, Yen-Te
item DE LOS REYES, BENILDO - Texas Tech University
item Wu, Vivian

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 3/3/2023
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: Agricultural microbiomes are major reservoirs of antibiotic resistance genes (ARGs), posing continuous risks to human health. Viruses, mostly bacteriophages, are important members of the natural agricultural microbiome and can co-exist and co-evolve with bacteria. The objective of this study was to investigate the role of bacteriophages on the transmission of antibiotic resistance genes (ARGs) in natural agricultural environments. A total of 5 different sample types, including animal feces, soil, and surface water, were collected from an organic farm. Further, the profile and diversity of bacterial and viral microbiota from each sample were determined using metagenomic sequencing. The profiles of bacteriome indicated the highest abundance of Bacteroidetes and Firmicutes phyla in animal feces with varying Bacteroidetes/Firmicutes ratios between herbivorous and omnivorous farm animals. The most predominant composition in abiotic samples was the phylum Proteobacteria. Compared to the bacteriome profiles, the trends in virome indicated much broader diversity with more specific signatures between the biotic and abiotic samples. Overall, viruses belonging to the Orders Picornavirales, Caudovirales, and Tubulavirales were the most predominant across the agricultural samples. Additionally, the similarities within and between biotic and abiotic components of agricultural environment based on ARG-associated bacteria alone were much lower than that of total bacteriome composition. However, there were high similarities in the profiles of ARG-associated viruses across the biotic and abiotic components. Moreover, the predictive models of phage-bacterial interactions on bipartite ARG transfer networks indicated that phages belonging to the order Caudovirales, particularly in the Siphoviridae family, contained diverse ARG types in different samples. Their interaction with various bacterial hosts further implied the critical roles of bacteriophages on ARG transmission across bacterial populations. Our findings provided a novel insight into the potential mechanism of phage-mediated ARG transmission and their correlation with resistome evolution in natural agricultural environments.