Anthropogenic stressors drive microbiome assembly: A global meta-analysis of bumble bees

Bumble bees (Bombus spp. ) play a vital role in the provision of ecosystem services that benefit humans through crop pollination and supporting natural plant biodiversity. While their ecological function is well studied, the microbial communities within their gut are only beginning to be recognized for their contributions to bee health and resilience. To better understand these communities, we conducted a meta-analysis of 814 gut samples from 15 studies across 9 countries. This analysis confirmed Snodgrassella, Lactobacillus, Bifidobacterium, Bombilactobacillus, and Gilliamella as core gut taxa, and proposed the addition of Neisseriaceaeᵤnclassified and Orbaceaeᵤnclassified. Human-altered environments were identified as the most influential factor shaping microbiota composition, with indoor versus outdoor rearing showing the strongest effect. Outdoor bees collectively hosted 253% more genera and exhibited higher microbial richness, connectivity, and stability. In contrast, indoor bees showed reduced diversity and the loss of multiple environmentally-associated taxa. Based on these patterns, we propose a “captivity-sensitive core” of twelve taxa, including Frischella, Apilactobacillus, Staphylococcus, and Acinetobacter. These findings establish a robust reference for the bumble bee gut microbiome and highlight how anthropogenic environments alter microbial community structure, with implications for insect pollinator health, management, and conservation. • Human-altered environments significantly alter bumble bee microbiota composition. • Wild bees supported a substantially richer microbiota, hosting 253% more genera than their captive counterparts. • Several “core” genera persist at >50% mean prevalence across environments, including two unclassified genera. • Our findings support the application of the “missing microbe hypothesis” to understanding microbial loss in bees.