{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,10]],"date-time":"2026-09-10T10:13:11Z","timestamp":1789035191488,"version":"build-2803163510"},"reference-count":43,"publisher":"MDPI AG","issue":"18","license":[{"start":{"date-parts":[[2026,9,10]],"date-time":"2026-09-10T00:00:00Z","timestamp":1788998400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Foods"],"abstract":"<jats:p>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 &gt; 95%), Pantoea (ANI &gt; 95%), and both Pseudomonas isolates (ANI &gt; 95%), while the Bacillus and Stenotrophomonas isolates showed ANI &lt; 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.<\/jats:p>","DOI":"10.3390\/foods15183201","type":"journal-article","created":{"date-parts":[[2026,9,10]],"date-time":"2026-09-10T09:13:03Z","timestamp":1789031583000},"page":"3201","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Genomic Characterization of Bacterial Isolates from Aerobic Fermentation of Oolong Tea Dregs: Antimicrobial Resistance, Virulence, and Lignocellulose-Degrading Potential"],"prefix":"10.3390","volume":"15","author":[{"given":"Ziheng","family":"Zeng","sequence":"first","affiliation":[{"name":"School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-4171-1356","authenticated-orcid":false,"given":"Ren","family":"Ke","sequence":"additional","affiliation":[{"name":"School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marsena Jasiel","family":"Ismaiah","sequence":"additional","affiliation":[{"name":"School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guanming","family":"Ye","sequence":"additional","affiliation":[{"name":"School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaoqing","family":"Yu","sequence":"additional","affiliation":[{"name":"School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shuning","family":"Lan","sequence":"additional","affiliation":[{"name":"School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiarui","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Han","family":"Yu","sequence":"additional","affiliation":[{"name":"Biotechnology and Food Engineering Program, Guangdong Technion-Israel Institute of Technology, Shantou 515063, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-0908-9935","authenticated-orcid":false,"given":"Huiyu","family":"Liu","sequence":"additional","affiliation":[{"name":"Biotechnology and Food Engineering Program, Guangdong Technion-Israel Institute of Technology, Shantou 515063, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kin Sum","family":"Leung","sequence":"additional","affiliation":[{"name":"School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lu","family":"Zhang","sequence":"additional","affiliation":[{"name":"School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8175-7069","authenticated-orcid":false,"given":"Jetty Chung-Yung","family":"Lee","sequence":"additional","affiliation":[{"name":"School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6357-4285","authenticated-orcid":false,"given":"Olivier","family":"Habimana","sequence":"additional","affiliation":[{"name":"Biotechnology and Food Engineering Program, Guangdong Technion-Israel Institute of Technology, Shantou 515063, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,9,10]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"12150","DOI":"10.1080\/10408398.2022.2099343","article-title":"Extraction methods, physiological activities and high value applications of tea residue and its active components: A review","volume":"63","author":"Miao","year":"2022","journal-title":"Crit. 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