Unraveling the genetic traits and functional diversity of the pan-genome in Pantoea dispersa

Abstract

Background

Medical devices are crucial in modern healthcare, but commonly used clinical tools such as cotton swabs can be easily contaminated by microorganisms (such as Pantoea), becoming vectors for pathogens and leading to patient infections or more severe outcomes. Despite the dual nature of the Pantoea that has garnered significant attention, research investigating Pantoea dispersa (P. dispersa) remains limited. This study conducted a pan-genome analysis of three isolates and 57 P. dispersa strains from NCBI to investigate their evolutionary relationships, population structure, and functional characteristics.

Results

Whole-genome analysis revealed high genomic diversity among 60 strains of P. dispersa, identifying 6,791 orthologous gene clusters (OGs), with core genes accounting for 45.1% and accessory genes accounting for 54.9%. Additionally, 2,185 gene clusters were not annotated in the reference genome. Further analysis demonstrated that 782 gene clusters were annotated as 406 VFs that were unevenly distributed among different strains and primarily associated with nutritional or metabolic factors, motility, and immune modulation. This study also identified four VFs genes related to the type III secretion system (T3SS) and observed some VFs present only in specific genetic clusters. In the analysis of antibiotic resistance genes (ARGs), 12 ARGs were identified, with nine being highly conserved across all isolates, and resistance mechanisms primarily involved antibiotic efflux and antibiotic target alteration. Secondary metabolite analysis identified 289 gene clusters, with 23 matching known gene clusters, while the rest were new discoveries, including arylpolyene, NRPS, and terpene types. These results reveal the complex virulence factors (VFs) and secondary metabolite genes in P. dispersa, providing significant insights into its genetic diversity and biological significance.

Conclusion

This study provides the first pan-genome framework for P. dispersa, along with a map of its VFs, ARGs, and secondary metabolite gene clusters. This study provides a deep insight into the genetic diversity and potential biological significance of P. dispersa, offering valuable references for leveraging its unique strain characteristics and metabolic capabilities in industrial production and clinical therapy.