Bees face several ecological and physiological challenges due to poor nutrition and abiotic stress. This dissertation explores various aspects related to these challenges, including the microbial ecology of honey bees and the alfalfa leafcutting bee, as well as the cold physiology of the alfalfa leafcutting bee. The first study delves into the dynamics of gut microbiota in overwintering adult worker honey bees, Apis mellifera. Through 16S rRNA gene amplicon sequencing, variations in the microbial composition among the bee strains, due to types of storage conditions, and the month of storage were examined. Overall, in this study a stable gut microbiota was observed in the bees both in the indoor and outdoor storage conditions during the winter months with slight differences in the abundance of bacterial species between bee strains. This study highlights the resilience of honey bee gut microbiota under cold stress conditions. The second study was focused on assessing the gut microbial ecology in the solitary bee, Megachile rotundata. The study investigated the significance of gut microbiota in these bees and in particular the effect of the Apilactobacillus clade on the larval and prepupal development, their weight, and survival. Results indicate that reliance on non-host specific environmental bacteria may not significantly impact the fitness of M. rotundata. The study highlights the role of environmentally collected bacteria in shaping bee nutrition and health. The third study explored the regulation of diapause initiation in the M. rotundata. By analyzing the gene expression using RNA-seq during diapause initiation, the research identified differentially expressed genes associated with oxidative stress, cell signaling, and other diapause-related pathways. The study provides insights into the molecular differences between diapausing and non diapausing individuals, contributing to a broader understanding of the cold physiology of M. rotundata. Together, these multi ‘omics’ studies contribute invaluable knowledge to the fields of bee biology, ecology and physiology, offering insights into the intricate relationships between bees, their microbiota, and the environmental factors influencing their life cycle.