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Volume 7, Issue 4

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

Abstract

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 () and the Eurasian blue tit ().

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 . From metagenome assemblies, we obtained complete mitochondrial genomes from the host species and from spp., while metagenome-assembled genomes documented new prokaryotic species.

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.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): antimicrobial resistance , Cyanistes caeruleus , FONA beta-lactamase , gut microbiome , Isospora , metagenomics , Parus major , Serratia fonticola and siadenovirus
Funding
This study was supported by the:
  • Leverhulme Trust (Award ECF-2018-700)
    • Principal Award Recipient: GabrielleL Davidson
  • Isaac Newton Trust
    • Principal Award Recipient: GabrielleL Davidson
© 2025 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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2025-04-28
2026-03-16

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Faecal metagenomes of great tits and blue tits provide insights into host, diet, pathogens and microbial biodiversity
Access Microbiology 7, 000910.v3 (2025); https://doi.org/10.1099/acmi.0.000910.v3
/content/journal/acmi/10.1099/acmi.0.000910.v3
/content/journal/acmi/10.1099/acmi.0.000910.v3
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