Comparative studies of the microbiota in whole-body mosquitoes from natural populations and laboratory-reared specimens are scarce, particularly in tropical countries like Colombia, where understanding microbial patterns is critical for effective disease control and vector management. This study examines the bacterial microbiota of Aedes aegypti by comparing field-collected mosquitoes from 3 Colombian regions (Southern Amazon, Central Andean region, and Northern Caribbean coast) with laboratory strains (Rockefeller, Otanche, andTolima).These regions are highly endemic for dengue and are associated with lineage 1 of Ae. aegypti, known for its elevated vector competence. Using next-generation sequencing of the 16S rRNA gene with Illumina technology, we found that field-collected mosquitoes exhibited significantly higher alpha and beta diversity compared to laboratory-reared specimens. Field mosquitoes were enriched with bacterial families such as Acetobacteraceae, Lactobacillaceae, and Bacillaceae, while laboratory mosquitoes showed a greater abundance of Enterobacteriaceae. Differential abundance analysis revealed that Acetobacter and Bacillus predominated in field mosquitoes, whereas Asaia, Cedacea, and Chryseobacterium were more common in laboratory specimens. Notably, Pseudomonas and Acinetobacter were consistently abundant across all samples. Our findings suggest that environmental factors, such as habitat and diet, significantly influence the bacterial composition and diversity of Ae. aegypti in Colombia. Future research should further explore how these factors, alongside genetic components, shape mosquito–micro-biota interactions and their implications for disease transmission and vector competence.

Graphical Abstract