Composition and development of gut microbiota in birds

Abstract

The microbes living inside vertebrates’ guts have highly important consequences for host health and fitness. In turn, microbial communities can rapidly respond to changes in host diet, for example, or environmental conditions. Hence, this relationship appears to be an essential ecological feature. However, our knowledge on how wild birds interact with microbial communities is poor, and little research has been done on non-model organisms. In this PhD thesis, I investigate factors that shape microbiota and utilize high-throughput sequencing techniques to paint a broader picture of the relationship between birds and their microbes by using three populations from two British passerines. My PhD comprised two related projects: (1) a methodological framework to best store faecal samples to analyse gut microbiomes of avian hosts, and (2) an analysis of factors influencing gut microbial communities. First, we evaluated the influence of five widespread storing methods on microbial composition of house sparrow (Passer domesticus) faecal samples (Chapter II). We were then able to analyse the influences of some intrinsic and extrinsic factors that shape the gut microbiota on blue tits (Cyanestes caeruleus), focusing on their development during nestling life. We evaluated how age impacts diversity and composition of bacterial communities and assessed the age-related changes on diet and compared them with simultaneous changes in the microbiota (Chapter III). Finally, we used experimental cross-fostering design to examine the relative contributions of environmental and genetic factors (i.e., nest of rearing and kinship) to the variation of gut bacterial assemblages (Chapter IV).

We found that there is no panacea for storing bird faeces, and until then we show that regardless of the protocol chosen, consistency throughout is a prime practice to achieve replicable and reliable results for microbial ecology. We demonstrate that the gut microbial community of blue tits colonises the gut of nestlings very quickly, with multiple colonisation events that lead to high interindividual variation, which is then reduced in adulthood. We further demonstrated that genetics have a minor role in determining microbial composition; in contrast, there are significant similarities in the compositions of the microbiota of genetically unrelated individuals who share a nest, highlighting the importance of local environment shaping gut communities. In summary, this work offers new insights into host-microbiome interactions by enabling a greater understanding of the multifaceted relationship between birds and their microbes.