Delineation of Two Distinct Subspecies of Pantoea agglomerans-Two Faces of a Versatile Bacterium

The cosmopolitan bacterium Pantoea agglomerans is renowned for its dual nature, with some strains promoting plant growth and aiding in the suppression of pests and phytopathogens, whereas others have been linked to plant disease and opportunistic human infections. This duality hampers the biotechnological application of this bacterium and underpins the necessity for taxonomic refinement. The genomes of 295 P. agglomerans strains were subjected to phylogenomic analyses (core genome phylogeny, average nucleotide identity, and digital DNA-DNA hybridization [dDDH]), with strains consistently resolving as two coherent clades supported by proteome content analysis. Average interclade dDDH values (79.1%) fall near the proposed subspecies threshold. Comparative genomic analysis identified clade-specific orthologs, and phenotypic assays demonstrate that citrate utilization distinguishes the two clades. Based on these genotypic and phenotypic markers, we propose delineation of two subspecies of P. agglomerans, subsp. agglomerans (which includes the P. agglomerans type strain) and subsp. jekyllhydei, to reflect the dual nature of this versatile bacterial species.