Characterization of the Drosophila crop microbiome reveals infection-induced dysbiosis and tissue-specific inducible immune response

Drosophila melanogaster serves as an established model for exploring microbiome-host-pathogen interactions owing to its genetic tractability and conserved innate immune system. Although the gut microbiome has been well characterized, the crop - an important foregut organ responsible for food storage - remains unexplored, with limited understanding of its resident microbiome, infection-induced microbiome changes, and immune response to infection. This study provides the first comprehensive taxonomic characterization of the Drosophila crop microbiome, identifying a structured microbial community dominated by five core bacterial families, including Acetobacteraceae, Anaplasmataceae, Lactobacillaceae, Pseudomonadaceae, and Thermoactinomycetaceae. Analysis of alpha and beta diversity metrics revealed that oral infection induced microbiome dysbiosis in the crop, with significant shift in microbiome composition and diversity. Comparative analyses revealed distinct, tissue-specific microbial responses between the crop and gut following infection. Moreover, infection elicited a robust antimicrobial peptide (AMP) response in the crop, with significant upregulation of Diptericin and Cecropin A1 . Collectively, these findings establish the Drosophila crop as a dynamic niche for microbial colonization that undergoes infection-induced dysbiosis and mounts a local AMP-mediated immune response. These results offer new insights into the spatial organization of host-microbe interactions in the Drosophila and lay a groundwork for future studies of tissue-specific microbiome-immune dynamics.