Genomic fingerprint of polyethylene-degrading bacteria

Polyethylene (PE) is ubiquitous in modern environments yet remains highly recalcitrant, accumulating due to inefficient and poorly understood microbial degradation. Here, we used a comparative genomics framework to identify genetic features associated with the PE-degrading phenotype by analyzing 97 bacterial genomes with experimental evidence of PE degradation alongside 87 phylogenetically balanced control genomes lacking documented activity. Genome-wide functional annotation and orthology inference revealed a coherent set of gene families, significantly enriched in PE-degraders, including extracellular proteins, oxidoreductases, membrane transport systems, regulatory and stress-response functions consistent with growth at hydrophobic, high-molecular-weight carbon source. To assess whether a minimal genomic signature could discriminate degraders from controls, we applied an integer linear programming (ILP) approach to presence/absence and copy-number-thresholded orthogroup matrices. This analysis identified a single copy-number enriched major facilitator superfamily (MFS) transporter orthogroup (OG0000361) as the most parsimonious discriminator, indicating a modular and recurrently recruited functional trait rather than a conserved degradation locus. Genomic neighborhood analysis further showed that OG0000361 is repeatedly embedded near redox and regulatory genes despite lacking conserved synteny, supporting context-dependent coupling between transport capacity and oxidative processing of PE-derived intermediates. Together, these results define a genomic fingerprint of PE-associated metabolism and provide a mechanistically grounded framework for identifying and engineering bacterial systems for plastic biotransformation.