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

Pallen, Mark J., Ponsero, Alise Jany, Telatin, Andrea, Moss, Cara Jane, Baker, David, Heavens, Darren and Davidson, Gabrielle L. (2025) Faecal metagenomes of great tits and blue tits provide insights into host, diet, pathogens and microbial biodiversity. Access Microbiology, 7 (4). pp. 1-13. ISSN 2516-8290

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Abstract

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 Kraken2 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 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.

Item Type:	Article
Uncontrolled Keywords:	antimicrobial resistance,cyanistes caeruleus,fona beta-lactamase,gut microbiome,isospora,metagenomics,parus major,serratia fonticola,siadenovirus,microbiology,microbiology (medical) ,/dk/atira/pure/subjectarea/asjc/2400/2404
Faculty \ School:	Faculty of Medicine and Health Sciences > Norwich Medical School
UEA Research Groups:	Faculty of Medicine and Health Sciences > Research Centres > Metabolic Health
Related URLs:	https://www.scopus.com/pages/publication...
Depositing User:	LivePure Connector
Date Deposited:	15 May 2026 14:52
Last Modified:	15 May 2026 14:52
URI:	https://ueaeprints.uea.ac.uk/id/eprint/103046
DOI:	10.1099/acmi.0.000910.v3

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