Gut microbiota structure differs between honey bees in winter and summer

Lucie Kešnerová; Olivier Emery; Michaël Troilo; Joanito Liberti; Berra Erkosar; Philipp Engel

Performing universal 16S rRNA qPCR, we found that total bacterial loads differed between 348 the three bee types across the sampled hives. Both winter bees and nurses had higher 349 bacterial loads than foragers ( Fig. 2A , Permutation ANOVA P=1e-4, followed by Tukey HSD 350 test, P=5.1e-9 and 1.66e-6 respectively) confirming our previous results from the single 351 hive. Winter bees also showed a trend towards higher bacterial loads than nurses, but this 352 difference was not statistically significant ( Fig. 2A The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/703512 doi: bioRxiv preprint Page 18 of 44 4A). Therefore, while the gut communities of the three bee types differed from each other, 379 they seemed to be similarly variable among each other. 380 We next assessed differences in the absolute abundance of individual community members 381 to reveal the directionality of community changes. We first looked at the seven phylotypes 382 that were monitored by qPCR over two years (Fig. 2E) . Consistent with our previous results 383 (Fig. 1C) , Bifidobacterium, Lactobacillus Firm4, Lactobacillus Firm5, and Bartonella had 384 increased levels (Permutation ANOVA on three groups P=1e-4, followed by Tukey, P<2e-4), 385 while Frischella had decreased levels in winter bees compared to foragers (Fig. 2E , 386 Permutation ANOVA p=2e-04 followed by Tukey HSD test P=2.79e-3). The only two 387 phylotypes showing abundance patterns inconsistent with the results from the two year 388 sampling were Snodgrassella and Gilliamella. Snodgrassella did not experience any 389 differences in absolute abundance (Fig. 2E , Permutation ANOVA P=1.87e-1), illustrating 390 that a proportional change in the community, as found when looking at the relative 391 community composition (Fig. 2D) , does not necessarily imply a change in abundance. When 392 comparing nurses and winter bees, only Bartonella and Frischella showed differences in 393 their absolute abundance. While Bartonella had markedly increased levels, Frischella 394 abundance went down in winter bees as compared to nurses ( Figure 2E) . We confirmed 395 these changes by carrying out qPCR on the same samples with the phylotype-specific 396 primers used for the monthly sampling as presented above (Supplementary Fig. S5 ). Except 397 for Lactobacillus Firm5, which showed a significant difference between nurses and winter 398 bees in the qPCR but not in the amplicon sequencing data, the results of the two 399 approaches were surprisingly congruent corroborating our conclusion that the microbiota 400 of nurses, foragers, and winter bees markedly differs in the composition of these seven 401 major community members. The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/703512 doi: bioRxiv preprint