High-throughput microbiome profiling and co-occurrence with antibiotic resistance genes in <i>Lucilia sericata</i>

Abstract Blow flies such as Lucilia sericata (Diptera: Calliphoridae) serve important ecological functions as decomposers. However, due to their close association with decaying organic matter, they also play potential roles as reservoirs of pathogenic bacteria and antimicrobial resistance genes (ARGs). In this study, we characterized the bacterial communities and targeted key antibacterial resistance markers of L. sericata specimens using 16S rRNA gene metabarcoding and targeted PCR screening. The microbiome was dominated by Dysgonomonas, Vagococcus, Pseudomonas, Ignatzschineria, and Providencia with geographic variation in community structure. Flies from Chungnam exhibited the lowest microbial diversity, while samples from Jeonnam and Gyeonggi showed greater richness and evenness. Beta diversity analyses confirmed geographic structuring of bacterial communities, with semi-urban and rural locations harboring more diverse taxa. Notably, opportunistic pathogens such as Proteus mirabilis and Providencia were detected alongside a range of ARGs (blaTEM, ermB, sul1, aac(6′)-Ib-cr, cat and mecA) and integron elements (intI and intII), suggesting that L. sericata may act as a reservoir of clinically important microbes and resistance genes.