Engineered symbiont biosensor maps micron-scale sugar gradients in the honeybee gut

Abstract

The honeybee gut microbiota plays a key role in shaping host health and susceptibility to disease. Yet, the nutrient environment it experiences within the gut remains poorly characterized. In particular, little is known about the spatial distribution of nutrients across this community, as resolving such fine gradients in vivo has been technically challenging. Here, we engineer the native honeybee symbiont Snodgrassella alvi as a living biosensor to quantify the bioavailability of the dietary sugar arabinose within the gut. By expanding the genetic toolkit for S. alvi through chromosomal integration of high-burden genes and a suite of low-strength promoters, we achieve stable multi-gene expression without compromising host colonization. The resulting biosensor generates a specific, dose-dependent response to arabinose in situ, enabling visualization of sugar gradients across gut-associated bacterial biofilms at micron-scale resolution. Using this system, we show that diet-derived arabinose distribution is highly heterogeneous and can be influenced by the metabolic activity of co-colonizing Gilliamella species. These findings highlight how diet composition and microbial specialization generate fine-scale microenvironments within the gut. More broadly, this work further establishes S. alvi as a genetically tractable platform for in situ probing of microbial metabolism and nutrient distribution.