Faecal metagenomes of great tits and blue tits provide insights into host, diet, pathogens and microbial biodiversity

Background The vertebrate gut microbiome plays crucial roles in host health and disease. However, there is limited information on the microbiomes of wild birds, most of which is restricted to barcode sequences. We therefore explored the use of shotgun metagenomics on the faecal microbiomes of two wild bird species widely used as model organisms in ecological studies: the great tit (Parus major) and the Eurasian blue tit (Cyanistes caeruleus). Results Short-read sequencing of five faecal samples generated a metagenomic dataset, revealing substantial variation in composition between samples. Reference-based profiling with Kraken 2 identified key differences in the ratios of reads assigned to host, diet, and microbes. Some samples showed high abundance of potential pathogens, including siadenoviruses, coccidian parasites and the antimicrobial-resistant bacterial species Serratia fonticola. From metagenome assemblies, we obtained complete mitochondrial genomes from the host species and from Isospora spp., while metagenome-assembled genomes (MAGs) documented new prokaryotic species. Conclusions Here, we have shown the utility of shotgun metagenomics in uncovering microbial diversity beyond what is possible with 16S rRNA gene sequencing. These findings provide a foundation for future hypothesis testing and microbiome manipulation to improve fitness in wild bird populations. The study also highlights the potential role of wild birds in the dissemination of antimicrobial resistance. Impact statement The community of microorganisms that lives in an animal’s gut is crucial for the host’s health. However, in wild birds, such as the great tit and Eurasian blue tit, the role of this community is poorly understood. Here, we have applied advanced DNA sequencing and computational techniques to faecal samples from these birds, revealing a rich diversity of microbes, including previously unknown species and potential pathogens. We discovered antibiotic resistance genes, raising concerns about the potential spread of resistance from wild birds to humans. This research highlights the importance of understanding gut microbes in wild birds and lays the groundwork for future efforts to manipulate their gut microbial communities to enhance their health and resilience in changing environments. Data summary The authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files.