Insects often rely on symbiotic bacteria and fungi for various physiological processes, developmental stages, and defenses against parasites and diseases. Despite their significance, the associations between bacterial and fungal symbionts in Apis mellifera are not well studied, particularly in the Philippines. In this study, we collected A. mellifera from two different sites in the Municipality of Bacnotan, La Union, Philippines. A gut microbiome analysis was conducted using next-generation sequencing with the Illumina MiSeq platform. Bacterial and fungal community compositions were assessed using 16S rRNA and ITS gene sequences, respectively. Our findings confirm that adult worker bees of A. mellifera from the two locations possess distinct but comparably proportioned bacterial and fungal microbiomes. Key bacterial symbionts, including Lactobacillus, Bombilactobacillus, Bifidobacterium, Gilliamella, Snodgrassella, and Frischella, were identified. The fungal community was dominated by the yeasts Zygosaccharomyces and Priceomyces. Using the ENZYME nomenclature database and PICRUSt2 software version 2.5.2, a predicted functional enzyme analysis revealed the presence of β-glucosidase, catalase, glucose-6-phosphate dehydrogenase, glutathione transferase, and superoxide dismutase, which are involved in host defense, carbohydrate metabolism, and energy support. Additionally, we identified notable bacterial enzymes, including acetyl-CoA carboxylase and AMPs nucleosidase. Interestingly, the key bee symbionts were observed to have a negative correlation with other microbiota. These results provide a detailed characterization of the gut microbiota associated with A. mellifera in the Philippines and lay a foundation for further metagenomic studies of microbiomes in native or indigenous bee species in the region.

Honey bees provide essential pollination services in natural and agricultural ecosystems, yet little is known about honey bee-associated pathogens in Cambodia and Laos. Here, we screened 53 colonies from 10 sites, including Apis cerana (n = 28), A. mellifera (n = 18), A. dorsata (n = 4), and A. florea (n = 3), for common honey bee viruses and the microsporidian Nosema ceranae using PCR and RT-PCR assays. Six viruses—acute bee paralysis virus, black queen cell virus, deformed wing virus type A, Israeli acute paralysis virus, Kashmir bee virus, and Lake Sinai virus—and N. ceranae were detected in A. cerana and A. mellifera, with overall low detection frequencies across sites. No targets were detected in A. dorsata or A. florea; however, the limited sample sizes for these species restrict interpretation of absence. Partial gene fragment sequences showed similarity to previously reported Asian isolates, indicating consistency with known regional viral diversity. These findings provide baseline detection data for honey bee-associated pathogens in Cambodia and Laos and support the need for expanded sampling across host species and seasons to better characterize pathogen occurrence in the region.