Flexibility and resilience of great tit (Parus major) gut microbiomes to changing diets

Abstract

Background: Gut microbial communities play important roles in nutrient management and can change in response to host diets. The extent of this flexibility and the concomitant resilience is largely unknown in wild animals. To untangle the dynamics of avian-gut microbiome symbiosis associated with diet changes, we exposed Parus major (Great tits) fed with a standard diet (seeds and mealworms) to either a mixed (seeds, mealworms and fruits), a seed, or a mealworm diet for 4 weeks, and examined the flexibility of gut microbiomes to these compositionally different diets. To assess microbiome resilience (recovery potential), all individuals were subsequently reversed to a standard diet for another 4 weeks. Cloacal microbiomes were collected weekly and characterised through sequencing the v4 region of the 16S rRNA gene using Illumina MiSeq.

Results: Initial microbiomes changed significantly with the diet manipulation, but the communities did not differ significantly between the three diet groups (mixed, seed and mealworm), despite multiple diet-specific changes in certain bacterial genera. Reverting birds to the standard diet led only to a partial recovery in gut community compositions. The majority of the bacterial taxa that increased significantly during diet manipulation decreased in relative abundance after reversion to the standard diet; however, bacterial taxa that decreased during the manipulation rarely increased after diet reversal CONCLUSIONS: The gut microbial response and partial resilience to dietary changes support that gut bacterial communities of P. major play a role in accommodating dietary changes experienced by wild avian hosts. This may be a contributing factor to the relaxed association between microbiome composition and the bird phylogeny. Our findings further imply that interpretations of wild bird gut microbiome analyses from single-time point sampling, especially for omnivorous species or species with seasonally changing diets, should be done with caution. The partial community recovery implies that ecologically relevant diet changes (e.g., seasonality and migration) open up gut niches that may be filled by previously abundant microbes or replaced by different symbiont lineages, which has important implications for the integrity and specificity of long-term avian-symbiont associations.

Keywords: 16S rRNA gene; Bacterial communities; Community flexibility; Community resilience; Gut symbionts; Illumina MiSeq.

Fig. 1

a. Contents of standard, mixed, seed and mealworm diets, with a schematic timeline of the experiment. b. Predicted flexible (toward three diet groups) and resilient (recovery after the diet reversal) microbiome responses to dietary changes in Parus major. Filled grey circles represent recovery of gut microbiomes if the communities are resilient, while open grey circles represent potential outcomes if microbiomes are not resilient

Fig. 2

Mean ASV richness (a) and Shannon’s diversity index (b) of gut microbial communities in initial, after the diet manipulation and after the diet reversal. Letters above each boxplot represent the pairwise differences between different groups (Dunn’s post-hoc test) and different letters indicate significant differences

Fig. 3

a. Non-Metric Multidimensional Scaling (NMDS) plot of bacterial communities for initial, mixed, mealworm, seed, and reversed diets (ellipses indicate 95% CI; stress = 0.166). Shapes represent the sex of each individual. b. Relative abundances of bacterial phyla in gut microbiomes under different diets. c. Relative abundance of macronutrients in 100 g of each diet

Fig. 4

Relative abundances of the 25 most common bacterial genera in the cloacal swabs of P. major on the initial diet, after diet manipulation and after diet reversal are shown in the bar graphs. Unclassified genera are indicated with a “U”, following the closest taxonomic level classification (i.e., family or order). Individual birds are represented with their name codes on the x-axis. Top ten significantly differentially abundant genera (divided between comparison groups) are given between panels. Positive log₂-fold values represent increase of certain genera in bottom panel compared to the top panel. Empty columns indicate samples that did not sequence or failed the quality filtering step