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Characterization of the microbial community is essential for understanding the symbiotic relationships between microbes and host insects.  Chrysomya megacephala  is a vital resource, a forensic insect, a pollinator, and a vector for enteric bacteria, protozoa, helminths, and viruses. However, research on its microbial community is incomprehensive, particularly at the pupal stage, which comprises approximately half of the entire larval development stage and is important entomological evidence in forensic medicine. For the first time, this study investigated the bacterial communities of  C. megacephala  pupae at different ages using third-generation sequencing technology. The results showed that  C. megacephala  has a diverse and dynamic bacterial community. Cluster analysis at ≥ 97% similarity produced 154 operational taxonomic units (OTUs) that belonged to 10 different phyla and were distributed into 15 classes, 28 orders, 50 families, 88 genera, and 130 species. Overall, the number of bacterial OTUs increased with the development of pupae, and the relative abundance of  Wolbachia  in the Day5 group was significantly lower than that in the other groups. Within the pupal stage, Proteobacteria, Firmicutes, and Bacteroidetes were the dominant phyla of bacteria. At the genus level,  Wolbachia  and  Ignatzschineria  coexisted, a rarely known feature. In addition, we found  Erysipelothrix rhusiopathiae , the etiological agent of swine erysipelas, which is rarely identified in insects. This study enriches the understanding of the microbial community of  C. megacephala  and provides a reference for better utilization and control of  C. megacephala.

Diversity and dynamics of bacteria at the Chrysomya megacephala pupal stage revealed by third-generation sequencing