Mitochondrial COI-based genetic diversity and 16S rRNA-based microbiota profiling of Aedes albopictus (Diptera: Culicidae) from urban and peri-urban non-human primate breeding facilities in Indonesia

Abstract

Aedes albopictus is a globally invasive mosquito and a competent arbovirus vector. To characterize its ecological, genetic, and microbial profiles in Indonesia, we examined populations from urban (Lodaya) and peri-urban (Dramaga) non-human primate (NHP) facilities. Ovitrap sampling conducted in January–February 2022 revealed consistently higher ovitrap indices and egg densities at urban sites, indicating that anthropogenic habitats are major drivers of proliferation. Morphological and molecular identification confirmed the presence of Ae. albopictus, and sequencing of a 643 bp cytochrome oxidase I (COI) fragment verified species identity (>99% similarity). Seven haplotypes, seven single-nucleotide polymorphisms, and one non-synonymous substitution were detected. Genetic diversity analysis showed high haplotype diversity (Hd = 1.0 urban; 0.8 peri-urban) but low nucleotide diversity (π = 0.0029), suggesting recent demographic expansion and strong gene flow across sites. Microbiota profiling of pooled larval and adult midgut samples generated 784,336 high-quality reads, dominated by Proteobacteria (64.8%), Bacteroidetes (24.6%), and Firmicutes (3.8%). The major taxa included Rahnella aquatilis, Serratia marcescens, and Asaia bogorensis, with compositions differing by geography, sex, and developmental stage. These integrative data demonstrate that Ae. albopictus exhibits ecological plasticity, limited genetic divergence, and heterogeneous microbial associations. These findings provide a baseline for vector surveillance and highlight the relevance of combining molecular barcoding and microbiota profiling within a One Health framework for arbovirus risk assessment.