Key points
- Red grouse provide a relatively unique opportunity to study the gut microbiome of a wild-type bird in detail.
- This study is the first to identify the gut microbiome in red grouse in detail, by extracting DNA directly from the gut contents of 15 individual birds from Scotland.
- The research identified a catalogue of highly diverse microorganisms specialised to help grouse digest their fibre-heavy diet of heather.
- This included 12 microbes, 11 of which were species that have not been previously catalogued.
- This modern DNA sequencing approach can aid our understanding of how diet, environment and health interact through the microbiome could help guide strategies that support grouse populations.
Background
Our gut health plays a huge role in overall nutrition. The gut microbiome is also crucial in understanding nutrition in birds. However, research on this rather niche topic has mostly focused on farmed species, such as chickens. More recently, an increasing number of studies have examined wild bird populations, revealing some of the factors that influence the microbes found in their guts.
Assessing the gut of wild bird species in non-invasive ways is challenging. Researchers usually rely on taking a quick swab from a bird rather than whole samples of gut contents. This limits their ability to accurately represent the microbes in the large and small intestine.
The caecal sac (caecum), located towards the end of the digestive tract, plays a crucial role in breaking down fibrous food. In herbivorous (plant-eating) bird species, the caecum is longer than in non-herbivorous species, allowing more time for fermentation of tough plant material. As a gamebird, the red grouse provides a relatively unique opportunity to study the gut microbiome in more detail. These gamebirds are shot in the autumn when there is a surplus and the digestive tracts are a waste product from the industry, so can be used for scientific research.
Red grouse are particularly interesting to study. Despite their ‘wild’ status, they are relatively closely related to chickens. They also feed on a very tough, fibre-heavy diet of heather. Microbes in their caecum allow them to break down complex plant fibres.
What they did
Scientists collected samples from the caeca of 15 wild red grouse legally shot during the 2023 Scottish grouse shooting season. The birds came from three locations in Scotland, with five samples from each site.
The researchers extracted DNA from the gut contents. Using advanced DNA sequencing (metagenomics), the study is the first to explore the gut microbes of red grouse in detail.
After filtering out the DNA from the host animal itself and the DNA genome of heather (their main food source), the remaining sequences represent microbial genomes. These DNA blueprints of bacteria are known as Metagenome-Assembled Genomes (MAGs).
From this DNA, they were able to reconstruct the full genomes of 12 different microbes. They also identified 18 high-quality viral genomes from the data including two proviruses (viruses that are integrated into bacterial genomes) and 16 other free viruses.
What they found
The researchers discovered a highly diverse community of microorganisms that help grouse digest their fibre-heavy diet of heather. The MAGs (microbial genomes) came from five main bacterial groups (phyla), with the largest group being Bacillota_A, particularly the class Clostridia.
The most common bacterium across all samples was a species of Helicobacter_B, which made up about 26% of the bacterial reads, but in some birds it accounted for over 60%. Of the 12 microbes identified, 11 genomes could not be assigned to a known species, suggesting that red grouse may host new species of bacteria not previously catalogued. The one genome that could be classified to species was within the Ruminoccacaeae family, a poorly understood group previously detected in the guts of cattle, sheep and deer. Many of the microbes had carbohydrate-active enzymes, which help break down tough plant materials. The genus Prevotella stood out as especially important for fibre digestion.
Researchers classified 18 high-quality of viral genomes. Most were likely to be bacteriophages – viruses that infect bacteria not the host animal. Rather than being harming, many bacteriophages actually help balance the gut microbiome, in some cases, keeping harmful bacteria in check.
The study also identified some microbial genes linked to antimicrobial resistance. One was a particularly strong antibiotic called vancomycin. This doesn’t mean the grouse are ill or being treated with antibiotics as these resistance genes might be naturally occurring in the environment or gut. Although their presence doesn’t necessarily signal danger yet, it is a noteworthy observation for understanding environmental or health pressures affecting grouse. The relevance of these genes for ecological or gut health is currently unknown and more research is needed to better understand this.
What this means
Birds do not produce their own fibre-fermenting enzymes, so grouse rely entirely on their gut microbes to break down the nutrients from heather. The modern sequencing method used in this study may allow further research to look at how microbial communities contribute directly to gamebird health, productivity and survival.
Overall, the grouse gut community contained bacteria capable of digesting cellulose and hemicellulose, complex fibres found in heather stems and leaves. Prevotella was the only bacterium identified with the ability to break down xylooligosaccharides, smaller fibre fragments created when hemicellulose is broken apart. Some microbes also carried enzymes for breaking down chemical defences in heather leaves, which normally make plant harder to digest.
The researchers found limited ability to digest starch and metabolise sulphur, which makes sense given that heather is low in these compared to seeds or grains. These findings suggest that the gut microbiome of red grouse is highly specialised for the nutrient profile of upland heather moorlands, rather than a broad range of plant foods.
Understanding how diet, environment and health interact through the microbiome could help guide management to promote a gut-friendly diet or reduce exposure to stressors that might disturb microbial balance.
Read the original paper
Amhad, A., Fletcher, K., Hesford, N. & Glendinning, L. (2025). Metagenomics reveals fibre fermentation and AMR pathways in red grouse (Lagopus scotica) microbiota. BMC Microbiology, 25: 1-11
Photo credit: Laurie Campbell