Bacterial enrichment methods for metagenomic analysis of mosquito midgut microbiota

Mosquito midguts contain diverse microbial communities that influence host biology and pathogen transmission. However, metagenomic studies are challenged by the large proportion of host DNA. Here, we compared three DNA extraction methods for Aedes aegypti midguts: standard extraction without filtration, extraction after a filtration step, and the QIAamp Microbiome kit designed for host DNA depletion. We quantified host and bacterial DNA, profiled bacterial diversity from SSU rRNA reads, and reconstructed metagenome-assembled genomes (MAGs).