Santos-Matos, G. | Search bioRxiv

bioRxiv2026

Competition between co-localized gut symbionts underlies inter-individual variation in the honeybee gut microbiota

Microbes in the animal gut compete to colonize spatially restricted host niches. However, whether competition for space drives inter-individual variation among hosts, and which factors determine the outcome of such competition, remain poorly understood. Here, we investigated competitive interactions of the western honeybee gut symbiont Frischella perrara with other members of the bee gut microbiota. Shotgun metagenomics analysis of individual bees revealed that F. perrara is negatively correlated with a specific species of the genus Gilliamella. Co-colonization of microbiota-depleted bees with these two bacteria resulted in their competitive exclusion. The outcome of this competition depended on the relative number of bacteria each bee received and benefited Gilliamella when one of the two type VI secretion systems of F. perrara was mutated. Using fluorescently tagged strains, high-resolution microscopy, and gut region-specific quantification, we show that both bacteria localize to the same host niche in the ileum of mono-colonized bees, indicating competition in a spatially restricted host niche. Moreover, both microbes protected against infection, promoting bee health. This competition provides an explanatory mechanism underlying variation in the occurrence of F. perrara across honeybee colonies and highlights the importance of gut spatial structure and microbial competition in shaping microbiome composition and inter-individual variability.

microbiology↗

bioRxiv2025

Priority effects determine community composition at the strain level in the honeybee gut microbiota

Gut microbial communities often differ at the strain level among individual hosts, but the mechanisms driving this variation remain poorly understood. One potential factor is priority effects, a process in which differences in the timing and order of microbial colonization influence subsequent community assembly ("first come, first served" dynamics). We hypothesize that such priority effects operate at the strain level within species, where closely related bacteria exhibit niche overlap, and that these dynamics can lead to community divergence even under similar environmental conditions. We tested these predictions, using the gut microbiota of honeybees, which harbor conserved microbial communities that differ in strain composition among individual bees. We sequentially colonized microbiota-depleted honeybees with two distinct microbial communities composed of the same twelve core microbiota species but different strains, ensuring that individuals shared species-level composition but differed at the strain level. We found that firstcomer strains consistently dominated the resulting communities, suggesting strong priority effects. Dropout experiments in which the firstcomer strain of a species was removed led to only partial increases in the colonization success of the conspecific latecomer, suggesting that both intra- and inter-species interactions contribute to priority effects. Our findings highlight the significant role of priority effects in strain-level community assembly and reveal their influence in shaping the specialized gut microbiota of honeybees, with important implications for the development of probiotic strategies in beekeeping. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=134 SRC="FIGDIR/small/689826v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@b0930eorg.highwire.dtl.DTLVardef@8687c5org.highwire.dtl.DTLVardef@3ba838org.highwire.dtl.DTLVardef@a10c3e_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗