Evaluating gut microbial community dynamics in Bombus terrestris queens during diapause: a comparison of relative and absolute quantification methods

Abstract

While relative abundance data have revealed compositional shifts in the gut microbiome of bumblebees before and after diapause, such data alone cannot reliably assess microbial load dynamics. Notably, the gut microbiome’s temporal variation during diapause remains unexplored, particularly in terms of absolute quantification. Here, we conducted a longitudinal experiment to investigate the temporal variation in gut microbiome of bumblebees during diapause (0, 30, and 60 days) using both relative quantitative and absolute quantitative data. Our study based on absolute quantification data showed a simplification of microbial network structure, a reduced observed richness of alpha diversity, and a decline in the core bacterial genus Gilliamella during diapause—contrary to trends inferred from our study based on relative abundance data and previous research. We propose that temporal variation of gut microbiome may be associated with the host’s fasting state and isolation from environmental microbes during diapause, which could contribute to a reduction in microbial load. Therefore, we advocate for cautious interpretation of relative abundance data and emphasize the importance of absolute quantification in ecological and host-associated microbiome research.