Honey bee gut bacterial communities’ characterisation across different ecosystem qualities in the department of Boyacá, Colombia

Honey bees (Apis mellifera) are essential pollinators that play a crucial role in ecosystem functioning. Recent studies have examined their gut microbiota to better understand ecological interactions and the impacts of anthropogenic disturbances. However, few have explored how ecosystem quality, shaped by the availability of natural resources and influenced by both anthropogenic disturbance and climatic seasonality, affects honey bees, especially in Colombia, where beekeeping is mainly artisanal. In this study, we describe the gut bacterial communities of 80 honey bee workers collected from local apiaries across three municipalities in the Boyacá department, Colombia, using amplicon-based 16S-rRNA sequencing. We conducted a cross-sectional comparison of three apiaries with varying environmental qualities and a longitudinal study of a hive relocated from a disturbed area to a more natural environment. Our analyses indicate that ecosystem quality, as mediated by human disturbance and seasonal environmental variation, can influence the relative abundances and diversity metrics of bacterial communities in environments where apiaries are located. Furthermore, favourable environmental conditions within the ecosystem promote the relative abundance of beneficial bacteria such as Bombilactobacillus spp., Lactobacillus spp., and Bifidobacterium asteroides, which play key roles in nectar and pollen metabolism and regulate pathogen activity. In contrast, disturbed ecosystems reduce the abundance of beneficial bacteria and increase opportunistic bacteria, potentially compromising physiological processes essential to bee health. This study provides the first insights into the impact of ecosystem quality on honey bee gut microbiota in the country, highlighting the importance of maintaining healthy ecosystems to support these pollinators.