Genomic Characterization of Bacterial Isolates from Aerobic Fermentation of Oolong Tea Dregs: Antimicrobial Resistance, Virulence, and Lignocellulose-Degrading Potential

The global tea industry generates millions of tons of waste annually, yet the bacteria capable of degrading this recalcitrant biomass remain poorly characterized. This study performed whole-genome sequencing and comparative genomic analysis of six bacterial strains isolated from oolong tea residue fermentation: Bacillus sp., Paenibacillus sp., Pantoea sp., two Pseudomonas isolates, and Stenotrophomonas sp. Genome sizes ranged from 3.61 to 6.33 Mbp, with GC content from 43.2% to 66.5%. Average nucleotide identity (ANI) analysis confirmed species-level identification for Paenibacillus (ANI > 95%), Pantoea (ANI > 95%), and both Pseudomonas isolates (ANI > 95%), while the Bacillus and Stenotrophomonas isolates showed ANI < 95% to all reference genomes, suggesting potential taxonomic novelty requiring further characterization. Antimicrobial resistance genes were detected only in Bacillus (cat86, dfrG) and Pantoea (oqxB). Genome-wide MGE profiling identified 349 MGE-associated genes across all six strains, including 101 IS elements, 61 integron-associated genes, and 183 plasmid-associated genes; tetracycline resistance-associated gene homologs were additionally detected in four strains below CARD thresholds. Virulence-associated gene profiling revealed that the 32 factors identified in Pseudomonas isolates primarily encode motility, biofilm formation, and secretion system components, traits associated with environmental adaptation rather than pathogenicity. Carbohydrate-active enzyme (CAZyme) annotation identified conserved plant biomass-degrading capabilities across all isolates. Descriptive comparisons suggested potential differences in enzyme profiles relative to isolation time: early-stage isolates appeared to harbor more hemicellulose-degrading enzymes, while late-stage isolates showed more lignin- and polyphenol-related enzyme annotations; however, these patterns require experimental validation. This genomic resource provides a foundation for understanding bacterial adaptation to tea waste environments and informs candidate strain selection for future inoculant development studies.