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Analysis of Bacterial Communities by 16S rRNA Gene Sequencing in a Melon-Producing Agro-environment

Abstract

Cantaloupe melons, which have been responsible of an increasing number of foodborne disease outbreaks, may become contaminated with microbial pathogens during production. However, little information is available on the microbial populations in the cantaloupe farm environment. The purpose of this work was to characterize the bacterial communities present on cantaloupe farms. Fruit, soil, and harvester hand rinsates were collected from two Mexican cantaloupe farms, each visited three times. Microbiome analysis was performed by sequencing 16sRNA and analyzed using qiime2 software. Correlations were determined between sample type and microbial populations. The α and β diversity analysis identified 2777 sequences across all samples. The soil samples had the highest number and diversity of unique species (from 130 to 1329 OTUs); cantaloupe (from 112 to 205 OTUs), and hands (from 67 to 151 OTUs) had similar diversity. Collectively, Proteobacteria was the most abundant phyla (from 42 to 95%), followed by Firmicutes (1–47%), Actinobacteria (< 1 to 23%), and Bacteroidetes (< 1 to 4.8%). The most abundant genera were Acinetobacter (20–58%), Pseudomonas (14.5%), Erwinia (13%), and Exiguobacterium (6.3%). Genera with potential to be pathogenic included Bacillus (4%), Salmonella (0.85%), Escherichia-Shigella (0.38%), Staphylococcus (0.32%), Listeria (0.29%), Clostridium (0.28%), and Cronobacter (0.27%), which were found at lower frequencies. This study provides information on the cantaloupe production microbiome, which can inform future research into critical food safety issues such as antimicrobial resistance, virulence, and genomic epidemiology.

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Acknowledgements

We are thankful to CONACYT for the scholarship granted to Victor Mercado-Guajardo. We also thank the farm manages and workers which with their interest in food safety, provided their permission to conduct this study in their farms.

Funding

This research was supported by the Consejo Nacional de Ciencia y Tecnología de Mexico (CONACYT) grant # A1-S-25033; USDA-NIFA [2018-07410, 2019-67017-29642], and the U.S. Food and Drug Administration, under award number HHSF223201710406P. CONACYT granted a scholarship to Victor Mercado-Guajardo.

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All authors contributed substantially to (1) conception and design or data acquisition and analysis, (2) drafting or critical revision of the manuscript, and (3) approval of the final submitted version.

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Correspondence to Santos García.

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Permission was obtained for sampling from farm managers and oral consent from farm workers as per the Universidad Autónoma de Nuevo León-Emory University Institutional Review Board (IRB00035460)–approved protocol-

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Franco-Frías, E., Mercado-Guajardo, V., Merino-Mascorro, A. et al. Analysis of Bacterial Communities by 16S rRNA Gene Sequencing in a Melon-Producing Agro-environment. Microb Ecol 82, 613–622 (2021). https://doi.org/10.1007/s00248-021-01709-8

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Keywords

  • Cantaloupe farms
  • 16 s RNA
  • Sequencing
  • Bacterial population