Application of next-generation sequencing (NGS) for disease diagnosis in the beehive

Honey bee ( Apis mellifera ) populations face increasing threats from pathogens, parasites, and synergistic interactions among pathogens and stressors that contribute to colony losses. Traditional hive health monitoring relies on visual inspections, mite counts, and targeted diagnostics, which are labor-intensive, expertise-dependent, and often detect infections only at advanced stages. Next-generation sequencing (NGS), specifically 16S rRNA gene and ITS amplicon sequencing, offers a powerful culture-independent approach for simultaneous detection of bacterial and fungal microbes in beehive samples (larvae, honey, bee tissue). This technology is particularly relevant for exotic pet medicine, where veterinarians may be consulted by beekeepers to investigate brood diseases in managed honey bee colonies. This paper reviews the application of 16S rRNA gene amplicon sequencing in apiculture and presents clinical case studies demonstrating its diagnostic utility. Longitudinal monitoring of brood nest samples revealed dynamic changes in Melissococcus plutonius abundance. In other cases, 16S rRNA gene amplicon sequencing excluded suspected European foulbrood (EFB) and documented co-infections involving agents such as Enterococcus faecalis and Paenibacillus dendritiformis (the latter representing the first reported detection in honey bee colonies in the U.S.). These findings highlight the ability of 16S rRNA gene amplicon sequencing to detect bacterial pathogens, reveal microbial community shifts, and differentiate primary from secondary microbes when combined with clinical context. 16S rRNA gene amplicon sequencing can support early intervention and avoidance of unnecessary antibiotics amid rising resistance concerns. By equipping exotic pet veterinarians with these tools, this approach enhances diagnostic accuracy for bee-related consultations, supports antimicrobial stewardship, and contributes to the welfare of pollinators as part of broader exotic animal practice. Despite challenges including cost, bioinformatics requirements, sample processing, and interpretation of complex datasets, 16S rRNA gene amplicon sequencing integration into routine apicultural practice shows promise for improved colony resilience and reduced losses.