Shotgun-metagenomics reveals a highly diverse and communal microbial network present in the drains of three beef-processing plants

Vignesh Palanisamy; Joseph M Bosilevac; Darryll A Barkhouse; Sarah E Velez; Sapna Chitlapilly Dass

doi:10.3389/fcimb.2023.1240138

Shotgun-metagenomics reveals a highly diverse and communal microbial network present in the drains of three beef-processing plants

Front Cell Infect Microbiol. 2023 Sep 8:13:1240138. doi: 10.3389/fcimb.2023.1240138. eCollection 2023.

Authors

Vignesh Palanisamy¹, Joseph M Bosilevac², Darryll A Barkhouse³, Sarah E Velez³, Sapna Chitlapilly Dass¹

Affiliations

¹ Department of Animal Science, Texas A&M University, College Station, TX, United States.
² U. S. Department of Agriculture, Roman L. Hruska U.S. Meat Animal Research Center, Clay Center, Lincoln, NE, United States.
³ Molecular Center of Excellence, Invisible Sentinel, bioMerieux Inc., Philadelphia, PA, United States.

Abstract

Background: Multi-species biofilms pose a problem in various environments, especially food-processing environments. The diversity of microorganisms in these biofilms plays a critical role in their integrity and protection against external biotic and abiotic factors. Compared to single-species biofilms, mixed-species biofilms are more resistant to various stresses, including antimicrobials like sanitizers. Therefore, understanding the microbiome composition and diversity in biofilms and their metabolic potential is a priority when developing intervention techniques to combat foodborne pathogens in food processing environments.

Methods: This study aimed to describe and compare the microbiome profile of 75 drain biofilm samples obtained from five different locations (Hotscale, Hotbox, Cooler, Processing, & Grind room) of three beef-processing plants (Plant A, B & C) taken over two timepoints 2017-18 (T1) and 2021 (T2) by shotgun sequencing.

Results: Core microbiome analysis found Pseudomonas, Psychrobacter, and Acinetobacter to be the top three prevalent genera among the plants and locations. Alpha diversity analysis demonstrated a high diversity of microbiome present in all the plants and locations across the time points. Functional analysis showed the high metabolic potential of the microbial community with abundance of genes in metabolism, cell-adhesion, motility, and quorum sensing. Moreover, Quaternary Ammonium Compound (QAC) resistance genes were also observed, this is significant as QAC sanitizers are commonly used in many food processing facilities. Multi-functional genes such as transposases, polymerases, permeases, flagellar proteins, and Mobile Genetic Elements (MGEs) were found suggesting these are dynamic microbial communities that work together to protect themselves against environmental stresses through multiple defense mechanisms.

Conclusion: This study provides a framework for understanding the collective microbial network spanning a beef processing system. The results can be used to develop intervention strategies to best control these highly communicative microbial networks.

Keywords: antimicrobial resistance; beef-processing plants; biofilms; core microbiome; horizontal gene transfer; shotgun metagenomics.

Grants and funding

Portions of this work were supported by USDA-NIFA-AFRI award 2020-67017-30776 and Beef Checkoff and the Foundation for Meat and Poultry Research and Education (USDA-REE Agreement Number/FAIN: 58-3040-1-006).