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

Authors: PALANISAMY, VIGNESH - Texas A&M University; Bosilevac, Joseph - Mick; BARKHOUSE, DARRYLL - Biomerieux, Inc; VELEZ, SARAH - Biomerieux, Inc; CHITLAPILLY DASS, SAPNA - Texas A&M University

Submitted to: Frontiers in Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/8/2023
Publication Date: N/A
Citation: N/A

Interpretive Summary: In beef processing plants complex communities of bacteria called biofilms can be found. Biofilms can resist stress and sanitizers to protect pathogens and spoilage bacteria if they are present. Therefore, understanding the composition and metabolic activity of biofilms is crucial to controlling their growth, but much is unknown about how biofilms compare from place to place and year to year. This study compared the biofilms from five different locations in three different beef-processing plants over two years. Analysis identified the most common bacteria present in the biofilms and how diverse the communities were at each location, processing plant, and time. The biofilms had highly active communities that expressed many genes associated with growth at cold temperatures and that provided resistance to commonly used sanitizers. By understanding the biofilm networks spanning a beef processing plant, better ways to improve the safety and quality of beef products can be developed.

Technical Abstract: Multi-species biofilms are a significant 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 crucial to developing intervention techniques to combat foodborne pathogens in food processing environments. 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. Core microbiome analysis found Pseudomonas, Psychrobacter, and Acinetobacter were 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 a highly metabolically active 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 most food processing facilities employ QAC as sanitizers. Evidence supporting Horizontal Gene Transfer (HGT), was found with multi-functional genes such as transposases, polymerases, permeases, flagellar proteins, Mobile Genetic Elements (MGEs). These observations demonstrate dynamic microbial communities that work together to protect themselves against environmental stresses through multiple defense mechanisms. 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.