Ulloa M. A. auteur aut IRD Serrano A. V. auteur aut IRD Camelo L. C. auteur aut IRD Guyot Romain auteur aut IRD Vela D. auteur aut IRD Muñoz A. R. auteur aut IRD text journalArticle eng text/pdf reformatted digital access Drosophila species serve as key models for microbiota research due to their relatively simple microbial communities. However, microbial diversity and dynamics in Neotropical Andean Drosophila remain underexplored. Here we applied shotgun metagenomics to characterize the microbiota of 24 Neotropical Drosophila species from Ecuador, reconstructing 64 high-quality bacterial genomes predominantly from Acetobacteraceae and Enterobacterales. Microbial communities were consistently dominated by yeasts, lactic acid bacteria, acetic acid bacteria, and Wolbachia. Comparative analyses revealed no strong correlation between host phylogeny and microbial community composition, suggesting environmental factors and microbial interactions shape these communities. Notably, shifts in relative abundances indicate dynamic ecological succession and metabolic cooperation among microbes. These findings expand genomic resources for Drosophila-associated bacteria and highlight the complex ecological processes influencing host-microbiota relationships in natural populations. specialized Neotropical Drosophila spp Metagenome-assembled genomes (MAGs) Microbiota Gut bacteria Phylogenetic analysis EQUATEUR 084 020 084 16 1 6601 [15 p.] 2026 2045-2322 https://www.documentation.ird.fr/hor/fdi:010096412 10.1038/s41598-026-36282-y 2045-2322 [F B010096412] https://www.documentation.ird.fr/hor/fdi:010096412 https://horizon.documentation.ird.fr/exl-doc/pleins_textes/2026-03/010096412.pdf IRD - Base Horizon / Pleins textes 2026-03-11 2026-03-11 fdi:010096412 fre