The gut microbiota of three avian species living in sympatry

Abstract

Background: Evolutionary divergence and genetic variation are often linked to differences in microbial community structure and diversity. While environmental factors and diet heavily influence gut microbial communities, host species contributions are harder to quantify. Closely related species living in sympatry provide a unique opportunity to investigate species differences without the confounding effects of habitat and dietary variation. We therefore compared and contrasted the gut microbiota of three sympatric plover species: the widespread Kittlitz's and white-fronted plovers (Anarhynchus pecuarius and A. marginatus) and the endemic and vulnerable Madagascar plover (A. thoracicus).

Results: We found no significant differences in the beta diversity (composition) of the gut microbiota of the three species. However, A. thoracicus exhibited higher intraspecific compositional similarity (i.e. lower pairwise distances) than the other two species; this pattern was especially pronounced among juveniles. By contrast, microbial alpha diversity varied significantly among the species, being highest in A. pecuarius, intermediate in A. marginatus and lowest in A. thoracicus. This pattern was again stronger among juveniles. Geographical distance did not significantly affect the composition of the gut microbiota, but genetic relatedness did.

Conclusion: While patterns of microbial diversity varied across species, the lack of compositional differences suggests that habitat and diet likely exert a strong influence on the gut microbiota of plovers. This may be enhanced by their precocial, ground-dwelling nature, which could facilitate the horizontal transmission of microbes from the environment. We hypothesise that gut microbiota diversity in plovers primarily reflects the ecological pool of microbiota, which is subsequently modified by host-specific factors including genetics. The reduced microbial and genetic diversity of the endemic A. thoracicus may hinder its ability to adapt to environmental changes, highlighting the need for increased conservation efforts for this vulnerable species.

Keywords: Endemic; Genetics; Gut microbiota; Holobiont; Madagascar; Plovers.

Fig. 1

Evolutionary divergence and a summary of the key differences between the three plover species [33, 36, 41]

Fig. 2

Relative abundances (as percentages) of of core gut microbiota decomposed by: A phyla and C families. Each species is represented by two age classes (adults and juveniles). Core taxa are defined as microbial taxa present in at least 95% of the samples. Venn diagrams representing B shared and unique ASVs among the three plover species, and D shared ASVs weighted by relative abundance

Fig. 3

Composition differences (beta diversity) among adult individuals of the three plover species. The results of Principal Component Analyses (PCoA) are shown for A Bray-Curtis dissimilarities and C Weighted UniFrac distances. Results from PERMANOVAs including p and $R^2$ values are also given. B and D show the results of Bayesian pairwise models; asterisks indicate variables that are significantly associated with microbiota dissimilarity/distance (i.e. the 95% credible intervals do not overlap zero). AM-AM, AP-AP and AT-AT denote pairwise comparisons among pairs of individuals of the same species and are indicated in bold. AM-AT, AP-AM and AP-AT indicate pairwise comparisons among pairs of individuals of different species

Fig. 4

Composition differences (beta diversity) among adult individuals of the three plover species. The results of Principal Component Analyses (PCoA) are shown for A Bray-Curtis dissimilarities and C Weighted UniFrac distances. Results from PERMANOVAs including p and $R^2$ values are also given. B and D show the results of Bayesian pairwise models; asterisks indicate variables that are significantly associated with microbiota dissimilarity/distance (i.e. the 95% credible intervals do not overlap zero) AM-AM, AP-AP and AT-AT denote pairwise comparisons among pairs of individuals of the same species and are indicated in bold. AM-AT, AP-AM and AP-AT indicate pairwise comparisons among pairs of individuals of different species. E Bar plot showing differentially abundant microbial genera between A. thoracicus and A. pecuarius based on the output of MaAsLin2. Coefficients are presented for genera with corrected p-values < 0.05 and correspond to log2(fold change). Taxa that are less abundant in A. thoracicus compared to A. pecuarius are highlighted in red, while Taxa that are more abundant in A. thoracicus compared to A. pecuarius are highlighted in blue

Fig. 5

Microbiota diversity A) Shannon diversity index and B) Faith PD for adults and juveniles of the three plover species. The boxplots display the raw data, representing the interquartile range, with the horizontal line inside each box indicating the median and the vertical lines illustrating the spread and variability of the data. Upper and lower 95% confidence intervals are indicated for each species comparison, with intervals not crossing zero (i.e. significant differences) depicted in black