Evolutionary dynamics of type VI secretion systems in fruit fly-associated Enterobacter

Species in the genus <i>Enterobacter</i> are widely distributed and occupy diverse ecological niches. Although many species within this genus have been extensively isolated and characterized, their symbiotic associations with Tephritidae fruit flies remain understudied, particularly through comparative genomic analyses. To address this gap, we conducted a whole-genome comparative analysis of thirteen <i>Enterobacter</i> strains isolated from the most economically significant fruit fly species: <i>Anastrepha fraterculus</i>, <i>Bactrocera dorsalis</i>, <i>Bactrocera zonata</i>, <i>Ceratitis capitata</i>, and <i>Zeugodacus cucurbitae</i>. The results revealed that different fruit flies harbor distinct <i>Enterobacter</i> species, with <i>Enterobacter hormaechei</i> being the most prevalent across hosts. Notably, distinct <i>E. hormaechei</i> subspecies were associated with specific hosts, suggesting a potential host-driven adaptation and coevolution. Pangenome analysis highlighted a dynamic genetic structure among these strains, with significant differences in the core, shell, and species-specific gene composition. The high proportion of metabolism-related genes in the core genome suggests a conserved role in essential biological functions, whereas the enrichment of mobile genetic elements (prophages and transposons) and cell motility genes within the shell and species-specific genomes highlights the genomic plasticity and potential host-specific adaptations. Three distinct subtypes of T6SS (type VI secretion systems) gene clusters, T6SS_C1, T6SS_C2, and T6SS_C3, were detected across <i>Enterobacter</i> strains. T6SS_C1 and T6SS_C2 were identified in most <i>Enterobacter</i> strains, whereas T6SS_C3 cluster was restricted to a single isolate. Although these clusters contained thirteen core T6SS genes, they were characterized by different gene synteny and effector/immunity gene content, suggesting that different <i>Enterobacter</i> strains may utilize distinct mechanisms for interbacterial interactions, host manipulation, and environmental adaptation. Overall, our findings reveal the genetic basis of the symbiosis between <i>Enterobacter</i> species and fruit flies, shedding light on their evolutionary dynamics, diversity of T6SS, and functional traits. These results open new avenues for developing microbiome-based strategies for pest management, including the targeted manipulation of microbial communities to enhance sterile insect technique (SIT) outcomes.