Unraveling the coevolutionary dynamics of phage and bacterial protein warfare occurring in the drains of beef-processing plants

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

Submitted to: Microorganisms
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/14/2026
Publication Date: 2/18/2026
Citation: Palanisamy, V., Bosilevac, J.M., Barkhouse, D.A., Velez, S.E., Chitlapilly Dass, S. 2026. Unraveling the coevolutionary dynamics of phage and bacterial protein warfare occurring in the drains of beef-processing plants. Microorganisms. 14(2). Article 493. https://doi.org/10.3390/microorganisms14020493.
DOI: https://doi.org/10.3390/microorganisms14020493

Interpretive Summary: Bacteriophages, viruses that infect and kill bacteria, and bacterial survival mechanisms were studied in beef processing plants by identifying all the kinds of bacteria present. Analysis revealed phage genes involved in infecting common environmental bacteria and bacterial genes that defend against these viruses. Some phage genes enable counterattacks against bacterial defenses, illustrating a virus-bacteria competition. These findings improve our understanding of bacteria-phage interactions in beef processing environments and may inform strategies to control harmful microorganisms in these settings thereby improving the safety of meat.

Technical Abstract: Phages, the most abundant entities on Earth, exhibit a complex interplay with bacteria,especially within environmental biofilms, resulting in an ecological arms race. This study investigates the interaction between phages and bacteria in the drains of beef-processing plants using high-throughput sequencing and metagenomic analysis. Metagenomic data collected from 75 drain samples from beef-processing plants were analyzed to investigate phage–bacterial interactions. First, assembled contigs were screened to identify viral sequences, which were then taxonomically annotated to determine the viral composition, including phages. Functional annotation of these viral sequences provided information about the viral genes and their roles in bacterial interactions specifically associated with attack and counterattack of bacteria. In parallel, bacterial contigs were examined to identify genes associated with antiphage defense systems, providing insights into the strategies adapted by bacteria to resist phage infection. Taxonomic annotation of viral sequences from the bulk metagenomic data revealed the presence of phages targeting Pseudomonas, Klebsiella, and Enterococcus. The higher abundance of Pseudomonas phages aligns with our previous study, where Pseudomonas was identified as the dominant bacterial genus, suggesting potential copersistence of phages and their hosts. Functional annotation of phage contigs revealed infective and lysis-related genes,highlighting their potential role in bacterial attack. Conversely, bacterial contigs encoded antiphage defense systems, including CRISPR-Cas, restriction–modification, and other defense-related genes. The study also uncovered the presence of anti-CRISPR proteins in phages, suggesting a counterattack on the bacterial defense. These findings provide evidence for phage attack, bacterial defense, and phage counterattack and may showcase the ongoing coevolutionary arms race between phages and bacteria. While this evidence looks promising, these results remain preliminary and further studies are needed to validate these findings. Still, this study provides a foundational understanding of bacteria–phage coexistence in beef-processing plant drains and paves the way for further explorations of these intricate interactions and their possible applications in controlling pathogenic microorganisms within biofilms.