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ORIGINAL RESEARCH article

Front. Microbiol.
Sec. Systems Microbiology
Volume 15 - 2024 | doi: 10.3389/fmicb.2024.1443292
This article is part of the Research Topic Expert Opinions: Save the Microbes to Save the Planet View all 9 articles

Comparative Metagenomics of Microbial Communities and Resistome in Southern Farming Systems: Implications for Antimicrobial Stewardship and Public Health

Provisionally accepted
Agnes Kilonzo-Nthenge Agnes Kilonzo-Nthenge 1*Iftekhar M. Rafiqullah Iftekhar M. Rafiqullah 2Michael J. Netherland, Jr Michael J. Netherland, Jr 2Maureen S. Nzomo Maureen S. Nzomo 1Abdullah Mafiz Abdullah Mafiz 1Samuel N. Nahashon Samuel N. Nahashon 1Nur A. Hasan Nur A. Hasan 3,4*
  • 1 Department of Food and Animal Sciences, Tennessee State University, Nashville, Tennessee, United States
  • 2 Center of Bioinformatics and Computational Biology (CBCB), EzBiome Inc., Gaithursburg, MD, United States
  • 3 EzBiome Inc., Gaithursburg, MD, United States
  • 4 Center for Bioinformatics and Computational Biology, University of Maryland, College Park, United States

The final, formatted version of the article will be published soon.

    Agricultural practices significantly influence microbial diversity and the distribution of virulence and antimicrobial resistance (AMR) genes, with implications for ecosystem health and food safety. This study used metagenomic sequencing to analyze 60 samples (30 per state) including water, soil, and manure (10 each) from Alabama (a mix of cattle and poultry sources) and Tennessee (primarily from cattle). The results highlighted a rich microbial diversity, predominantly comprising Bacteria (67%) and Viruses (33%), with a total of over 1,950 microbial species identified. The dominant bacterial phyla were Proteobacteria, Cyanobacteria, Actinobacteria, Firmicutes, and Bacteroidetes, with the viral communities primarily represented by Phixviricota and Uroviricota. Distinct state-specific microbial profiles were evident, with Alabama demonstrating a higher prevalence of viral populations and unique bacterial phyla compared to Tennessee. The influence of environmental and agricultural practices was reflected in the microbial compositions: soil samples were notably rich in Actinobacteria, water samples were dominated by Proteobacteria and Cyanobacteria, and manure samples from Alabama showed a predominance of Actinobacteria. Further analyses, including diversity assessment and enterotype clustering, revealed complex microbial structures. Tennessee showed higher microbial diversity and phylogenetic complexity across most sample types compared to Alabama, with poultry-related samples displaying distinct diversity trends. Principal Coordinate Analysis (PCoA) highlighted notable state-specific variations, particularly in manure samples. Differential abundance analysis demonstrated elevated levels of Deinococcus and Ligilactobacillus in Alabama, indicating regional effects on microbial distributions. The virulome analysis revealed a significant presence of virulence genes in samples from Alabama. The community resistome was extensive, encompassing 109 AMR genes across 18 antibiotic classes, with manure samples displaying considerable diversity. Ecological analysis of the interactions between AMR gene

    Keywords: microbial community, Antimicrobial resistance (AMR), Cattle and Poultry Farming, Alabama, Tennessee, Food Safety

    Received: 06 Jun 2024; Accepted: 14 Oct 2024.

    Copyright: © 2024 Kilonzo-Nthenge, Rafiqullah, Netherland, Jr, Nzomo, Mafiz, Nahashon and Hasan. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    * Correspondence:
    Agnes Kilonzo-Nthenge, Department of Food and Animal Sciences, Tennessee State University, Nashville, 37209, Tennessee, United States
    Nur A. Hasan, EzBiome Inc., Gaithursburg, 20742, MD, United States

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