Abstract
Despite the microbiome’s key role in health and fitness, little is known about the environmental factors shaping the gut microbiome of wild birds. With habitat fragmentation being recognised as a major threat to biological diversity, we here determined how forest structure influences the bacterial species richness and diversity of wild great tit nestlings (Parus major). Using an Illumina metabarcoding approach which amplifies the 16S bacterial ribosomal RNA gene, we measured gut microbiota diversity and composition from 49 great tit nestlings, originating from 23 different nests that were located in 22 different study plots across a gradient of forest fragmentation and tree species diversity. Per nest, an average microbiome was determined on which the influence of tree species (composition and richness) and forest fragmentation (fragment area and edge density) was examined and whether this was linked to host characteristics (body condition and fledging success). We found an interaction effect of edge density with tree species richness or composition on both the microbial richness (alpha diversity: Chao1 and Shannon) and community structure (beta diversity: weighted and unweighted UniFrac). No significant short-term impact was observed of the overall faecal microbiome on host characteristics, but rather an adverse effect of specific bacterial genera on fledging success. These results highlight the influence of environmental factors on the microbial richness as well as the phylogenetic diversity during a life stage where the birds’ microbiota is shaped, which could lead to long-term consequences for host fitness.
Highlights
During the past two decades, the gut microbiome has attracted considerable research attention because of its role in a host’s physiology and health status
With the transition from nestling to fledgling being a key moment in the development of altricial birds and with gut microbiota characteristics and nestling body condition in great tits being linked to each other (Teyssier et al, 2018a), we explored the hypothesis that forest-driven changes in the microbiome can affect important host parameters including body condition and bird survival after fledgling
When selecting the 5 most abundant genera in all nests, the genera Staphylococcus, Bacillus, Lactobacillus, and Carnobacterium belonging to the Class Bacilli, together with genus Burkholderia-Paraburkholderia belonging to the Class Betaproteobacteria were most prevalent in the great tit microbiome (Supplementary Data 3)
Summary
During the past two decades, the gut microbiome has attracted considerable research attention because of its role in a host’s physiology and health status. The microbiota of the gastrointestinal tract plays a fundamental role in food digestion, pathogen defence, stimulation of the immune system, gut and central nervous system functioning, life-history traits and behaviour. Despite its pivotal role in host health, research on the gut microbiota of avian species has lagged behind mammalian research and is dominated by studies of agriculturally important birds as well as birds of conservation interest (Grond et al, 2018). Studies examining the gastrointestinal flora are rather scarce and mostly focusing on juvenile birds of which the gut microbiota is still undergoing substantial changes (Zhu et al, 2017; Teyssier et al, 2018a). Foodassociated microbial communities may, vary by location and the food quality can pose a differential selection pressure on the gut microbiota (Grond et al, 2018; Davidson et al, 2020). Teyssier et al (2018b) showed that adult house sparrows from urban areas hosted microbial communities with lower diversity and fewer metabolic functions compared to rural populations
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