Genomic Characterization of Bacterial Isolates from Aerobic Fermentation of Oolong Tea Dregs: Antimicrobial Resistance, Virulence, and Lignocellulose-Degrading Potential
TL;DR
Comparative 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.
Abstract
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.