The Gut Microbial Composition Is Species-Specific and Individual-Specific in Two Species of Estrildid Finches, the Bengalese Finch and the Zebra Finch

Abstract

Microbial communities residing in the gastrointestinal tracts of animals have profound impacts on the physiological processes of their hosts. In humans, host-specific and environmental factors likely interact together to shape gut microbial communities, resulting in remarkable inter-individual differences. However, we still lack a full understanding of to what extent microbes are individual-specific and controlled by host-specific factors across different animal taxa. Here, we document the gut microbial characteristics in two estrildid finch species, the Bengalese finch (Lonchura striata domestica) and the zebra finch (Taeniopygia guttata) to investigate between-species and within-species differences. We collected fecal samples from breeding pairs that were housed under strictly controlled environmental and dietary conditions. All individuals were sampled at five different time points over a range of 120 days covering different stages of the reproductive cycle. We found significant species-specific differences in gut microbial assemblages. Over a period of 3 months, individuals exhibited unique, individual-specific microbial profiles. Although we found a strong individual signature in both sexes, within-individual variation in microbial communities was larger in males of both species. Furthermore, breeding pairs had more similar microbial profiles, compared to randomly chosen males and females. Our study conclusively shows that host-specific factors contribute structuring of gut microbiota.

Keywords: Bengalese finch; birds; gut microbiota; host-specific factors; inter-individual differences; symbionts; temporal stability; zebra finch.

FIGURE 1

The relative abundance of microbial families in gut samples from (A) the Bengalese Finches and (B) the zebra finches through the different phases of the reproductive cycle: at incubation, 5 days (D5), 10 days (D10), 35 days (D35), and 100 days (D100) after hatching the youngest chick, respectively. Rare phyla with relative abundances below 1% are not shown.

FIGURE 2

Comparisons of Shannon’s diversity index. (A) Among the host species (Bengalese Finches and zebra finches). (B) In males of both species across five different sampling times: at incubation, 5 days (D5), 10 days (D10), 35 days (D35), and 100 days (D100) after hatching of the youngest chick, respectively. The significance was determined based on the linear mixed model, at p-values ≤ 0.05 (*), p ≤ 0.01 (**), and p ≤ 0.001 (***). In the box plots, the line within indicates the median and the lower and upper boundary of the boxes indicates the 25th and 75th percentile, respectively. Whiskers above and below the boxes correspond to the range of 1.5 times the inter-quartile range (IQR) above and below the 25th and 75th percentile, respectively.

FIGURE 3

Principal coordinate analysis plots of the dissimilarities of zebra Finch and the Bengalese finch gut microbiota. Distances were computed using the (A) Jaccard and (B) Bray–Curtis dissimilarity index, and the (C) unweighted (D) weighted UniFrac distance metric.

FIGURE 4

The differentially abundant phyla between the zebra finches and the Bengalese finches. Bars represent OTUs that are significantly differentially abundant between the two host species. OTUs with a log₂–fold–change larger than zero are more abundant in the zebra finches (blue bars), while the OTUs with a log₂–fold–change smaller than zero are more abundant in the Bengalese finches (purple bars).