Caecal microflora
There is a range of micro-organisms in the caecum that can break down molecules of fibre to release nutrients that can be absorbed across the caecal wall. The caecal microflora is composed of gram-positive and gram-negative rods, cocci, filaments, coccobacilli and spirochaetes . Cellulolytic bacteria, such as Eubacterium cellulosolvens and pectinolytic and xylanolytic bacteria, such Prevotella ruminicola, have been cultured (Combes et al., 2013, 4) Species such as Bifidobacterium, Endophorus, Clostridium, Streptococcus and Acuformis have also been identified (Cheeke, 1987, 3). Later studies used DNA sequencing identified a complex microbiota in the caecum and revealed that it is genetically unique to rabbits. Most of the microbiota represent new species not previously identified (Abecia et al., 2007, 1).
Firmicutes spp. dominate (> 90%) in the caecal microflora with fewer Bacteroidetes (4%). Lactobacillus, Streptococcus and Escherichia coli are either absent or present in low quantities (Combes et al., 2013, 4).
The rabbit caecum also harbours a unique population of methanogenic archaea that utilise hydrogen released in fibre degradation to produce acetate and to reduce carbon dioxide to methane (Rodríguez-Romero et al., 2013, 6). There is a difference in the microbial population of farmed and wild rabbits, which reflects the difference in their diet (Abecia et al., 2012, 2)
In other parts of the intestinal tract, the yeast, Cyniclomyces guttulatus is present is the stomach and large intestine. Entamoeba cuniculi is a large sluggish amoeba that is found in large numbers in the lumen of the large intestine. The flagellate, Giardia duodenalis can be found in the duodenum but not does not cause clinical disease. Eutrichomastix, Lactobacillus is absent from all part of the digestive tract. In addition to digestion of food, the intestinal microbiota plays an important role in digestive health and immune processes.
The composition of the caecal microflora does not remain constant and is affected by several factors including age, diet, management, the presence of pathogens and individual differences (Eshar & Weese, 2014, 5). It is also influenced by the time of day. Caecal pH shows a diurnal rhythm linked with feeding behaviour. It is most alkaline in the morning and most acid in mid-afternoon. Ammonia and volatile fatty acids produced by caecal degradation and fermentation cause fluctuations in caecal pH affect the population of caecal microorganisms.
1 Abecia, L., Fondevila, M., Balcells, J., Edwards, J. E., Newbold, C. J., & McEwan, N. R. (2007). Effect of antibiotics on the bacterial population of the rabbit caecum. FEMS Microbiology Letters, 272(2), 144–153. https://doi.org/10.1111/j.1574-6968.2007.00746.x
2 Abecia, L., Rodríguez-Romero, N., Yañez-Ruiz, D. R., & Fondevila, M. (2012). Biodiversity and fermentative activity of caecal microbial communities in wild and farm rabbits from Spain. Anaerobe, 18(3), 344–349. https://doi.org/10.1016/j.anaerobe.2012.04.004
3 Cheeke, P. R. (1987). Rabbit Feeding and Nutrition. Academic Press. https://new.harcourt-brown.co.uk/media/documents/cheeke-5.pdf/view
4 Combes, S., Fortun-Lamothe, L., Cauquil, L., & Gidenne, T. (2013). Engineering the rabbit digestive ecosystem to improve digestive health and efficacy. Animal, 7(9), 1429–1439. https://doi.org/https://doi.org/10.1017/S1751731113001079
5 Eshar, D., & Weese, J. S. (2014). Molecular analysis of the microbiota in hard feces from healthy rabbits (Oryctolagus cuniculus) medicated with long term oral meloxicam. BMC Veterinary Research, 10(1), 62. https://doi.org/10.1186/1746-6148-10-62
6 Rodríguez-Romero, N., Abecia, L., & Fondevila, M. (2013). Microbial ecosystem and fermentation traits in the caecum of growing rabbits given diets varying in neutral detergent soluble and insoluble fibre levels. Anaerobe, 20, 50–57. https://doi.org/https://doi.org/10.1016/j.anaerobe.2013.02.001