Genomic Characterization of Aerobically Culturable Gut-Associated Bacteria and Yeasts Isolated from Pooled Larval Midguts of the Lesser Mealworm Alphitobius diaperinus (Coleoptera: Tenebrionidae)

Microbial communities associated with insect larvae play key roles in host nutrition, protection against pathogens, immune modulation, and represent a source of biotechnologically relevant traits. In Alphitobius diaperinus, a major poultry pest, the gut microbiota has been mainly studied at the community level, providing limited insight into the potential roles of individual microorganisms. Here, we characterized the aerobically culturable fraction of the larval gut microbiota derived from a single pooled homogenate of fifteen larvae under stable laboratory rearing conditions—an approach that uniquely enables strain-level genomic resolution, functional experimentation, and biotechnological exploitation. Ten bacterial strains and two yeasts were initially isolated; eight bacterial isolates were identical, revealing the most frequently recovered cultivable bacterial morphotype. We provide high-quality draft genomes for five members of the A. diaperinus cultivable gut microbiota—Enterobacter hormaechei subsp. xiangfangensis strain INTA AN1-1, Staphylococcus hominis subsp. novobiosepticus strain INTA AC1-4, Staphylococcus succinus subsp. succinus strain INTA AC1-8, Hyphopichia burtonii strain INTA AB1-1, and Debaryomyces fabryi strain INTA AB1-4—establishing a genome-resolved reference framework validated through a polyphasic approach. Genome-scale annotation enabled us to predict the metabolic potential and hypothesize the functional capabilities among cultivable members, providing a foundation for future studies on this economically relevant pest.