Abstract
The composition of gut bacterial communities is strongly influenced by the host diet in many animal taxa. For birds, the effect of diet on the microbiomes has been documented through diet manipulation studies. However, for wild birds, most studies have drawn on literature-based information to decipher the dietary effects, thereby, overlooking individual variation in dietary intake. Here we examine how naturally consumed diets influence the composition of the crop and cloacal microbiomes of twenty-one tropical bird species, using visual and metabarcoding-based identification of consumed diets and bacterial 16S rRNA microbiome sequencing. We show that diet intakes vary markedly between individuals of the same species and that literature-based dietary guilds grossly underestimate intraspecific diet variability. Furthermore, despite an effect of literature-based dietary guild assignment of host taxa, the composition of natural diets does not align with crop and cloacal microbiome similarity. However, host-taxon specific gut bacterial lineages are positively correlated with specific diet items, indicating that certain microbes associate with different diet components in specific avian hosts. Consequently, microbiome composition is not congruent with the overall consumed diet composition of species, but specific components of a consumed diet lead to host-specific effects on gut bacterial taxa.
Highlights
A b and cloacal microbiomes were characterized through sequencing the v4 region of the bacterial 16S rRNA gene
To explore whether specific gut bacterial symbionts of different host taxa are associated with different dietary items (Fig. 1b), we tested for correlations between the 30 most abundant bacterial genera and the proportion of order-level diet items in each individual using the taxa.env.correlation function in the microbiomeSeq p ackage[31]. These analyses revealed that certain bacterial genera were positively correlated with certain dietary items (Fig. 4 and Table S8) and that the taxonomy of bacterial symbionts associated with the same diet item differed between host orders, suggesting that host-taxon specific microbes are affected by the same dietary items in different bird taxa
We investigated the influence of naturally consumed diets on the crop and the cloacal microbiomes of multiple tropical wild bird species
Summary
A b and cloacal microbiomes were characterized through sequencing the v4 region of the bacterial 16S rRNA gene. We tested two alternative hypotheses related to the effect of diets on crop and cloacal microbiomes (Fig. 1). If consumed diet similarity is a strong determinant of wild avian gut microbiomes, we expected individuals consuming compositionally similar diets to harbour similar crop and cloacal microbiomes, irrespective of host taxonomy (Fig. 1a). We compared the crop and cloacal microbiomes of the same individuals, testing the assumption that the avian stomach acts as a barrier for passage of microbes from the foregut to the h indgut[24], expecting that microbial communities in the crop and the cloaca would be compositionally different. Anatomical gut modifications associated with powered flight has led to gut microbial restrictions in birds (e.g., increased individual variation and less stability of gut microbiomes in smaller birds)[9,10], and we further predicted that smaller birds with shorter digestive t racts[10] would have more shared bacterial sequences in the two regions
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