In Cottontail Rabbits
Cottontail rabbits have a particular way of digesting food. They are called “hindgut fermenters”. They share this trait with horses, guinea pigs, koalas, elephant, , porcupines and beavers. In these types of animals, a large sac at the end of their small intestine, called the cecum acts as a fermentation chamber (brewery) to provide them with the nutrients they need to survive. But cottontail rabbits are not born with the ability to obtain their nutrients from the plants that adult rabbits eat. In domestic rabbits, that ability developes between 2 and 4 weeks of age. (ref)
Animals can only absorb nutrients through their small intestine. Cows and other ruminants also have dysbiosis problems. But in their case, the fermentation chamber is their rumen that sits ahead of their small intestine (photo of cow rumen). The nutrients fermented there are absorbed as they pass through the small intestine. In rabbits, that won't work, because the cecum is to far along in the system. To get around that, rabbits re-eat their feces, getting the nutrients as it passes through their small intestine for a second time.
Do you remember Horton Hears A Who? Within all adult bunnies live an enormous zoo of microorganisms that process the foods the rabbit eats, making the nutrients in it available to the bunny. Some of these organisms are bacteria, but others are microscopic protozoa, fungi and yeast. They are all of a particular sort called anaerobes, which means they can only survive where there is no air or oxygen. The mix of organisms is called a flora. It changes from hour to hour depending on the foods consumed; synthesizing nutrients from the high cellulose plants that wild rabbits normally eat. Most of these synthesized products are called fatty acids, or volatile free fatty acids. One particular organism will liberate one product, only to have it consumed by another and the original organism itself consumed. As the acidity of the cecum changes, one organism will prosper, modifying the contents to support another organism that then flourishes. This goes on again and again, meal after meal, day after day in fore-gut fermenters, and in rabbits too.
The same dysbiosis problem occurs in domestic baby rabbits, but it is more fulminating and fatal in cottontails because of their smaller size and nervous temperament. At the NIH, I studied these organisms in domestic rabbits and guinea pigs.
We think the primary microbes involved in this fermentation process in rabbits include the non-sporulated, gram-negative anaerobic bacilli, Bacteroides, Proprionobacteria, and Butyrivibrio. But other species of gram negative and metachromatic bacteria, fusiform rods, ovals, large, ciliated protozoa, Isotrichia; and a rabbit-specific yeast, Cyniclomyces guttulatulus also take part.
When I tried to grow these organisms in the past ,it was very frustrating. Many are very fragile. They must be grown in complicated systems that exclude all oxygen and the more sensitive ones, in broth or on petri dishes , are quickly crowded out by the tougher species. That is why ordinary veterinary diagnostic laboratories do not report their presence. When laboratories report back that rabbits die of E. coli, or another gram negative aerobic bacteria or clostridia, you can usually just infer that survival problems in the protective anaerobic bacteria flora were the underlying root problem.
A similar ("faunation") process occurs in all grass-eating and leaf-grazing animals. The most research on the dynamics of cellulose fermentation is work done in cattle but much the fermentation process and type of organisms involved appears to be quite similar in rabbits. When the proper cecal organisms are not provided, the process goes terribly wrong, causing changes in the bunny’s acid/base balance and the liberation of toxins that are quickly fatal. A similar ,but slower,problem in fore-gut fermenters is called SARA .