Metabolic diversity of Paenibacillus: Pan-genome insights on carbohydrate-active enzymes and biosynthetic gene clusters

Paenibacillus is a genus of Gram-positive bacteria and a prominent secondary metabolite producer, yet its intrinsic metabolic potential remains largely underexplored. The study aimed to identify promising genes in Paenibacillus genomes, using popular bioinformatics platforms and tools, including BV-BRC, antiSMASH, BiG-SCAPE, BAGEL4, and dbCAN3. In this study, 63 Paenibacillus reference genomes from NCBI were selected, and other associated data were recorded. Pan-genome analysis revealed that the genus Paenibacillus harbours an open pan-genome, characterized by a large number of cloud genes (279,455), alongside 856 shell genes and 41 soft-core genes, indicating significant genomic diversity. A total of 176 prophage regions were detected, approximately 48.3% of which were intact, suggesting that prophage acquisition substantially contributes to the open pan-genome of Paenibacillus . BV-BRC identified 213 protein families associated with essential cellular functions and diverse metabolic activities. In total, 736 BGCs were detected by antiSMASH, representing 36 distinct classes. The most prevalent clusters included terpene and terpene-precursor (191, 22.06%), NRPS and NRPS-like (172, 19.86%), and cyclic lactone autoinducer (87, 10.05%). Integration of antiSMASH and BiG-SCAPE analyses revealed 131 biosynthetic gene clusters (BGCs) that showed no similarity to characterized MIBiG entries and did not cluster into gene cluster families. In addition, novelBGC detected 596 BGCs, 111 of which exhibited a novelty score ≥0.6. BAGEL4 predicted 180 bacteriocin and RiPP gene clusters, with sactipeptide (50), lasso peptide (40), and PoyA (34)- type clusters being the most prevalent. CAZyme profiling revealed that GH (44.97%) and GT (26.82%) were the most abundant CAZyme families in Paenibacillus genomes. Our study highlights that Paenibacillus genomes harbour a vast array of BGCs and CAZyme families, emphasizing their potential as prolific producers of biotechnologically significant enzymes and metabolites.