Quantitative microbiome profiling of honey bee (Apis mellifera) guts is predictive of winter colony loss in northern Virginia (USA)

For the past 15 years, the proportion of honey bee hives that fail to survive winter has averaged ~ 30% in the United States. Winter hive loss has significant negative impacts on agriculture, the economy, and ecosystems. Compared to other factors, the role of honey bee gut microbial communities in driving winter hive loss has received little attention. We investigate the relationship between winter survival and honey bee gut microbiome composition of 168 honey bees from 23 hives, nine of which failed to survive through winter 2022. We found that there was a substantial difference in the abundance and community composition of honey bee gut microbiomes based on hive condition, i.e ., winter survival or failure. The overall microbial abundance, as assessed using Quantitative Microbiome Profiling (QMP), was significantly greater in hives that survived winter 2022 than in those that failed, and the average overall abundance of each of ten bacterial genera was also greater in surviving hives. There were no significant differences in alpha diversity based on hive condition, but there was a highly significant difference in beta diversity. The bacterial genera Commensalibacter and Snodgrassella were positively associated with winter hive survival. Logistic regression and random forest machine learning models on pooled ASV counts for the genus data were highly predictive of winter outcome, although model performance decreased when samples from the location with no hive failures were excluded from analysis. As a whole, our results show that the abundance and community composition of honey bee gut microbiota is associated with winter hive loss, and can potentially be used as a diagnostic tool in evaluating hive health prior to the onset of winter. Future work on the functional characterization of the honey bee gut microbiome’s role in winter survival is warranted.