Genome-Guided Insights into Xenobiotic Biodegradation and Secondary Metabolite Bioprocess Potential in Enterobacter pseudoroggenkampii G2.8

Fipronil is a phenylpyrazole agrochemical widely used in agriculture and livestock production, posing persistent challenges of environmental contamination due to its toxicity and the formation of stable transformation products. Genome-based analyses provide a powerful framework for exploring the biotechnological potential of environmental microorganisms. The G2.8 isolate, obtained from fipronil-contaminated soil, was initially classified as Enterobacter chengduensis; however, taxonomic reassessment based on whole-genome sequencing combined with average nucleotide identity and digital DNA-DNA hybridization (ANI/dDDH ≈97%) reclassified this strain as Enterobacter pseudoroggenkampii. The occurrence of this species in a contaminated environmental niche highlights its relevance beyond previously reported clinical or plant-associated contexts and supports its potential role in bioremediation. The draft genome of E. pseudoroggenkampii G2.8 was assembled and subjected to rigorous quality assessment and functional annotation using genome-scale approaches. Functional analyses revealed 14 biosynthetic gene clusters, including non-ribosomal peptide synthetases, hybrid NRPS/polyketide synthases, and siderophore-related clusters, indicating potential for secondary metabolite production. In addition, genes encoding oxidoreductases, hydrolases, and esterases associated with xenobiotic transformation were identified, supporting the experimentally observed capacity of this strain to degrade fipronil and its toxic metabolites. Within a One Health framework, the genome exhibited only intrinsic antimicrobial resistance determinants, mainly related to efflux systems and chromosomal β-lactamases, with no evidence of mobile resistance elements, supporting an environmental safety profile. Overall, genome-guided functional and comparative analyses provide a robust foundation for identifying metabolic pathways involved in both biosynthesis and biodegradation, positioning E. pseudoroggenkampii G2.8 as a promising genome-guided candidate for metabolite-driven environmental biotechnology and reinforcing the value of microbial genomics in the development of sustainable bioprocesses.