Gut Microbiota Interactions in Rabbit Health Systems

Rabbits possess a highly specialised hindgut fermentation system in which the caecum and colon host dense microbial communities that ferment dietary fibre into short-chain fatty acids (SCFAs) and other metabolites essential for energy homeostasis, mucosal integrity and immune modulation. Caecotrophy—the reingestion of soft faeces—is a behavioural adaptation that recycles microbial proteins, vitamins and live bacteria, reinforcing host–microbiota co-development. Dietary components, age and health status jointly shape the bacteriome along the gastrointestinal tract, with Firmicutes, Bacteroidetes and Proteobacteria dominating distinct niches from stomach to colon. Dysbiosis in this ecosystem underlies common disorders such as epizootic rabbit enteropathy, while targeted nutritional interventions—altering fibre composition, supplementing probiotics or insect-derived fats—can restore microbial balance, enhance barrier function and boost disease resistance. Current advances integrate high-throughput sequencing, metabolomics and transcriptomics to map host–microbiota crosstalk, guiding strategies to improve rabbit welfare, productivity and translational insights into herbivore gut health.

Research from Nature Portfolio

Seminal work has dissected the microbial shifts underlying post-weaning enteropathy induced by low-fibre regimens, demonstrating that reduced Firmicutes and butyrate-producing taxa coincide with overgrowth of Proteobacteria and mucin-degrading bacteria, leading to epithelial inflammation and impaired SCFA production. Another foundational study characterised differential bacterial assemblages in hard versus soft faeces of rex rabbits, linking high-weight individuals to enriched populations of YS2/Cyanobacteria and Ruminococcaceae in hard pellets and to Akkermansia and Ruminococcus in soft faeces. Metabolic pathway predictions suggest that variations in xenobiotic biodegradation and phenolic compound synthesis may underpin growth and caecotrophy, offering new hypotheses for microbiota-driven optimisation of rabbit performance.

Gut Microbiota Interactions in Rabbit Health Systems publication trend

The graph below shows the total number of articles in gut microbiota interactions in rabbit health systems across all publications each year (not limited to Nature Index journals).

Technical terms

Caecotrophy: Behaviour of reingesting soft faeces to recover nutrients and live microbes.

Caecum: Blind-ended hindgut chamber where microbial fermentation of fibre occurs.

Short-chain fatty acids (SCFAs): Metabolites such as acetate, propionate and butyrate produced by bacterial fermentation.

Firmicutes, Bacteroidetes, Proteobacteria: Major bacterial phyla that dominate gut communities and influence host metabolism.

Dysbiosis: Disruption of microbial balance associated with disease states.

Holobiont: The host organism together with its associated microbiota.

Metabolome: The complete set of small-molecule metabolites in a biological sample.

Bacteriome: The collective genome of all bacterial inhabitants of an ecosystem.

References

1. A multi-omics dataset of the response to early plant polysaccharide ingestion in rabbits. Scientific Data (2024).
2. The ratios of dietary non-fibrous carbohydrate (NFC) to neutral detergent fiber (NDF) influence intestinal immunity of rabbits by regulating gut microbiota composition and metabolites. Frontiers in Microbiology (2023).
3. Impact of coprophagy prevention on the growth performance, serum biochemistry, and intestinal microbiome of rabbits. BMC Microbiology (2023).
4. The bacterial communities associated with fecal types and body weight of rex rabbits. Scientific Reports (2015).
5. Antimicrobial Effects of Black Soldier Fly and Yellow Mealworm Fats and Their Impact on Gut Microbiota of Growing Rabbits. Animals (2020).
6. The underlying microbial mechanism of epizootic rabbit enteropathy triggered by a low fiber diet. Scientific Reports (2018).
7. Characterization of Bacterial Microbiota Composition along the Gastrointestinal Tract in Rabbits. Animals (2020).