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ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Meat Safety and Quality » Research » Publications at this Location » Publication #401034

Research Project: Holistic Tactics to Advance the Microbiological Safety and Quality of the Red Meat Continuum

Location: Meat Safety and Quality

Title: Characterizing the collective dynamics of microbial interactions in environmental multi-species biofilm using shotgun metagenomics

item PALANISAMY, VIGNESH - Texas A&M University
item CHITLAPILLY DASS, SAPNA - Texas A&M University
item Wang, Rong
item Bosilevac, Joseph - Mick

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 3/15/2023
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: Objective: To compare the metagenomic profile of mixed species biofilms collected from three beef-processing plants across two timepoints. Experimental Design & Analysis: A total of 79 floor drain biofilm samples were collected from three beef-processing plants, A, B, and C, from five different locations, namely, Hot Scale, Hotbox, Cooler, Processing, and Grinding over two time periods, 2017-18 and 2021. The sequencing yielded a total of 29,600,359 potential microbial reads. The reads were processed by Kraken2 for assigning taxonomy1, assembly was performed by the program MEGAHIT2, MG-RAST, a web-server was used for functional annotation3, the program NCBI-AMR Finder4 was used to identify the antibiotic resistance genes (ARGs), horizontal gene transfer (HGT) among the bacteria were identified by the program WAAFLE and mobile genetic elements (MGEs) were identified using MOB-suite5. Statistical analysis was performed in R. Key Results: Diversity analysis showed higher alpha diversity among all of the samples (Figure 1). Core microbiome analysis identified Pseudomonas, Psychrobacter and Acinetobacter to be the three most prevalent genera across all of the samples. Functional analysis showed highly metabolically active microbiome with abundance of genes in metabolism, transport and especially in biofilm formation such as flagellar assembly, chemotaxis, and quorum sensing. Moreover, horizontal gene transfer (HGT) analysis identified the transfer of various functional genes such as transposases, polymerases, permeases and flagellar proteins between the micro-organisms. The presence of various antibiotic resistance genes (ARGs), including QAC efflux genes, was identified. How can this information be applied in the industry? 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 disrupt these highly communicative microbial networks.