Diarrhoea

Unlike most other mammals, lagomorphs aka rabbits produce two types of droppings, faecal pellets (the round, dry ones you usually see in the litterbox) and cecotrophes. The latter are produced in a region of the rabbit's digestive tract called the cecum, a blind-end pouch located at the junction of the small and large intestines. The cecum contains a natural community of bacteria and fungi that provide essential nutrients and may even protect the rabbit from potentially harmful pathogens.

How does the rabbit get those essential nutrients? She eats the cecotrophes as they exit the anus. The rabbits blissful expression when she's engaging in cecotrophy (the ingestion of cecotrophes) will tell you that she finds this anything but disgusting. In fact, rabbits deprived of their cecotrophes will eventually succumb to malnutrition. Cecotrophes are not faeces. They are nutrient-packed dietary items essential to your companion rabbit's good health.

A rabbit may produce cecotrophes at various times during the day, and this periodicity may vary from rabbit to rabbit. Some produce cecotrophes in the late morning, some in the late afternoon, and some at night. In any case, they usually do this when you're not watching (quite polite of them). This might be why some people refer to cecotrophes as "night droppings," though cecotrophes are not always produced at night.

Normal Poops & Cecotrophes
Anyone who lives with a bunny has seen a faecal pellet. These are the small, brown "cocoa puffs" that (we hope) end up in the litterbox. They should be relatively spherical, somewhat dry and friable, and composed mostly of undigested fibre. Rabbits do not ordinarily re-ingest faecal pellets, though a few bunnies seem to enjoy an occasional faecal pellet hors d'ouevre with no harm.

A normal cecotrophe resembles a dark brown mulberry, or tightly bunched grapes. It is composed of small, soft, shiny pellets, each coated with a layer of rubbery mucus, and pressed into an elongate mass. The cecotrophe has a rather pungent odour, as it contains a large mass of beneficial cecal bacteria. When the bunny ingests the cecotrophe, the mucus coat helps protect the bacteria as they pass through the stomach, then re-establish in the cecum.

Diarrhoea - What Does it Mean? 
True diarrhoea (unformed, watery faeces) is relatively rare in adult rabbits. It can be caused by intestinal parasites, such as coccidia (Eimeria spp.), roundworms, tapeworms, or anything that inflames the intestinal lining. Your rabbit savvy vet will be able to examine a faecal sample (you should probably provide the vet with a fresh sample both faecal and cecal pellets, if possible) to examine them for signs of parasitic infection. More often, true diarrhoea is seen in infant and juvenile rabbits.

Perhaps the most common complaint regarding rabbit health is the problem of mushy or runny stool sticking to the bunny's anal area and creating a nasty, stinky mess. In most cases (in adult rabbits, at least), this mass is made of poorly formed cecotrophes that have the consistency of toothpaste, rather than the normal form of bunched, squishy pellets.

The cecum is a delicately balanced ecosystem. If the intestine is moving too slowly, or if the rabbit is getting a diet too rich in digestible carbohydrates and too low in crude fibre, the complex population of bacteria in the cecum can become "unbalanced." This condition is known as cecal disbiosis. To read further about Cecal Disbiosis see the Poopy Butt section.

Common Causes of Runny Stool in Adult Rabbits
Mechanical Problems

• Obesity
  An overweight rabbit may produce normally formed cecotrophes, but because she cannot properly reach down to grab them as they emerge from the chute, these soft pellets can become squashed under the bunny as she flexes and bends around to get them. Weight reduction is the answer here, and this is as difficult for rabbits as it is for humans. Switching from low quality commercial pellets to a high-fibre, low-calorie grass-based pellet can make a great difference. Replace any starchy treats with fresh herb treats. And, painful as it may be, exercise is one of the best ways to burn more calories than bunny takes in. As we all should know, that's the bottom line when it comes to slimming down.

• Arthritis or other Skeletal Disorders
  Similarly, a rabbit who is suffering from degenerative joint problems in the spine, hips, or other areas, may not be able to reach cecotrophes easily. He ends up sitting on some of them, and squashing them into his fur. Arthritis can be treated by your veterinarian. Common remedies include various NSAIDs (Non-Steroidal Anti-inflammatory Drugs), and dietary supplements.

Dietary Problems

• Incorrect Diet
  Rabbits, like horses and cattle, are strict herbivores. The rabbit intestine--and its normal bacterial flora--has evolved to feed almost exclusively on grass and herbs. Does your rabbit get starchy treats such as oatmeal, crackers, bread or sweets? Some rabbits with very sensitive intestines can suffer from runny cecotrophes even from commercial pellets. Fruit, as healthy as it is for humans, can be too much of a good thing for rabbits. The high level of sugar and starch in table fruit makes them too rich for a bunny except as a very small, occasional treat. A diet too rich in digestible starch is one of the most common causes of runny cecotrophes in companion rabbits.

• Insufficient Indigestible Fiber
  A rabbit should be fed unlimited grass hay, such as timothy or Meadow. Alfalfa hay is too rich in calories and protein for daily feeding. A rabbit who cannot nibble constantly on high-fibre grass or hay may suffer from a lack of tonus in the gut muscles. Normal peristalsis (muscular movements that push food through the gut) may become sluggish. This causes the passage of food through the cecum to slow down, and the normal rate of bacterial "flushing" from the cecum is disrupted, promoting cecal disbiosis. The high fibre content of grass hay also helps to "dilute" the starch of other dietary items, and helps to provide a healthy intestinal environment. A balanced and healthy diet is truly key to preventing intestinal problems such as cecal disbiosis (and its associated mushy stool).

• Hidden Health Problems
  When a rabbit is ill, in pain, or is suffering from emotional stress, a typical physiological response is slowing of the normal peristaltic movements of the intestine. This results in cecal disbiosis, with all the accompanying problems of runny stool, and possible inflammation of the intestinal lining (enteritis). Some of the most common causes of intestinal slowdown (and hence, cecal disbiosis) in rabbits include pain/stress due to - Dental problems, Urinary Tract Infections, Upper Respiratory Infections & EC.

Further causes of diarrhoea can include

• The administration of drugs or antibiotics. 

• Viruses and pathogen bacterial overgrowth of e.g. Corynebacteria sp., Clostridia sp., Pasteurella sp. and Escherichia coli cause enteritis. The occurence of Salmonella sp. is, however, rare in rabbits. 

• The presence of intestinal parasites such as trematodes (flukes), cestodes (tapeworms), nematodes and protozoa such as Giardia and Coccidia, can also lead to digestive disorders in rabbits, with onset of stasis and diarrhoea.

Any of these conditions must be diagnosed and treated by a rabbit-savvy veterinarian familiar with such problems and their appropriate treatment. Until a cryptic health disorder is diagnosed and treated, chronic runny stool will likely persist. Therefore, it's wise to have your messy-bottomed bunny undergo a thorough wellness check, especially if his diet and weight are normal and healthy. Once an underlying source of pain/stress is treated, the runny stool often resolves on its own. But if the condition is not treated, it can progress and eventually result in a potentially life-threatening condition, ileus - or GI stasis, in which peristalsis stops completely.

Keeping Bunny Comfortable in the Meantime
While you and your veterinarian are treating the problems that caused the runny stool, it's still important to keep the bunny clean and comfortable. Dried cecotrophes stuck to the rear end are not only smelly and uncomfortable, they also attract flies, and can result in life-threatening fly strike. To prevent this, be sure to learn how to give your bunny a butt bath--SAFELY. ( see links below)

Resolving runny stool in a rabbit is not always a simple matter. It may require dietary changes, good husbandry, and sometimes extensive diagnostic work and treatment by your veterinarian. But it will all be worth it for a long life filled with happy, nose-wiggling love and a nice, clean bum.

Original material sourced - with relevant edits, from:
The Mystery of Rabbit Poop - by Dana Krempels, Ph.D.

"In rabbits, health of the digestive system is considered as the basis of the general health of the animal. There is no specific and unique cause that leads to a disruption of digestive transit, but a combination of factors: stress, the shift from a milk diet to an herbivore diet in weaning rabbits, hygiene, parasites, molting and trichobezoar (mass of fur hair in the stomach) and dental problems. In response, rabbits respond with intestinal disturbances characterized by the onset of diarrhea. Newborns are not much concerned because they are protected by milk produced by the doe, which has antibacterial properties that prevent the growth of pathogenic bacteria. Newly weaned 4- to 7-week-olds suffer mainly from enterotoxemia with the almost complete destruction of the intestinal flora. After this age, young rabbits and adults suffer from mucoid enteritis, with partial destruction of the bacterial flora."
Bacterial Enteritis and Diarrhea in Weaned and Adult Rabbits - MediRabbit

Diarrhoea in Kits
One of the most common signs associated with sudden death in baby rabbits is diarrhoea, which can appear very quickly and kill in a matter of hours. Thus, it is of vital importance that any baby rabbit showing signs of lethargy, inappetence (not wanting to eat), or runny stool be taken immediately to an experienced rabbit veterinarian for emergency, life-saving treatment. Delaying even for an hour or two can mean the difference between life and death.

Young rabbits respond badly to stress, transport (especially during the post-weaning period), to unidentified noises, to a new environment and to new persons or animals. Modifications of the diet or a diet low in fibres can, furthermore, lead to digestive disorders. Usually, food alone is not the main trigger of diarrhoea, but rather its composition, such as a low percentage of crude fibre, too rich in carbohydrates or proteins, too finely ground food or improper watering, or the introduction of a new sort of vegetable or fruit.

True diarrhoea is more prevalent in baby rabbits than in adults, especially if the babies have been taken from their mother before they are ready for weaning. Sadly, many baby rabbits are weaned too young to be away from their mothers. Instead of being allowed to nurse for a full, normal eight weeks, they are taken away while they are still "cute" and marketable--often as young as four weeks. This can spell death for many of them.

Without mother's antibodies, complex organic compounds and proper pH environment her milk provides to help protect the baby's intestines, these babies are highly susceptible to over-proliferation of foreign bacteria. One of the most common culprits of runny stool in baby rabbits is accidental infection by the common human intestinal bacterium, Escherichia coli. This is transmitted from humans to baby rabbits during handling, since these bacteria are all over us, not just in our intestines. Handling an unweaned infant rabbit without properly washing and disinfecting one's hands is a good way to transmit these opportunistic pathogens. Even a loving kiss on a too-young baby rabbit's lips can kill. Until a young rabbit is at least eight weeks old, she should not be taken from her mother, as mother's milk affords protection against E. coli and other bacteria until the baby's own immune system can handle them.

Another pathogen that can cause diarrhoea in baby rabbits is Eimeria spp., the causative agent of coccidiosis. The reproductive sporocysts of these protist parasites can usually be seen in the faeces of the host, so your vet may wish to examine the faecal sample of the affected rabbit for signs of coccidial sporocysts.

IF YOUR KIT HAS DIARRHOEA - KEEP IT WARM AND QUIET.
A dehydrated baby rabbit can easily become hypothermic, which is not only life-threatening, but can interfere with the efficacy of the treatments below.
Towel-wrapped warm water bottles or bags are a safe source of heat. Then get the kit to a vet IMMEDIATELY.

"An infant lagomorph presenting with runny stool will often be close to death within hours of onset if the
condition is not treated immediately and aggressively. Such animals succumb primarily to dehydration,
but inflammation and shock are often contributing factors."
Emergency protocol for diarrhoea in infant and juvenile rabbits - by Dana Krempels, Ph.D

Mucoid & Bacterial Enteritis, Enterotoxemia
A more chronic form of Entertoxemia, is mucoid enteropathy. This painful, life-threatening condition is often caused by imbalance of the cecal flora and can result in an  impacted cecum. Faecal pellets are generally absent; instead, the rabbit produces and eliminates excessive amounts of mucus. Mucoid diarrhoea is also sometimes observed in growing rabbits and nursing does. The watery faeces are mixed with mucus, a translucent and gelatinous substance. This particular type of enteritis has various causes, including bacterial overgrowth as stated above, or nutritional deficiencies (lack of water and food low in fibre).

Bacterial enteritis develops very rapidly, within 3 to 4 days and may cause death before the appearance of diarrhoea. The bacteria causing intestinal enteritis are known as Clostridia perfrigens and Escherichia coli. In healthy rabbits the number of E. coli bacteria present in the droppings is low (102-103/g drops), but in diarrhoea they are systematically present in high number. The bacterium produces toxins, but it has been shown that these alone do not lead to the onset of diarrhoea. Escherichia coli is occasionally found together with coccidia. For diarrhoea to occur there must be another stress on the rabbit, such as unbalanced feeding or a thermal shock.

Clostridia perfrigens exists in 5 forms and is classified according to the production of toxins. These toxins induce local lesions in the intestine, but their action may also affect distant organs such as the liver and the kidney. See Enterotoxemia, below.

Escherichia coli possess five general mechanisms to invade the intestine and cause the disease. Sometimes there is production of toxins. The bacterium invades the intestine by adhering on the villi of enterocytes and begins to proliferate. The presence of toxins stimulates the secretion of water and electrolytes by the intestinal mucosa. Proliferation of bacteria and production of toxin together can lead to diarrhoea. See Enterotoxemia, below.

Treatment of Bacterial Enteritis
As the disease develops very rapidly, treatment of bacterial enteritis often comes too late. Antibiotics and sulfonamide drugs will help prevent the growth of pathogen bacteria. Anti-diarrhoea product can help stop the diarrhoea as can the administration of drugs to bind toxins released by pathogen bacteria. Probiotic powders or paste, although controversial, will help the growth of the endemic healthy bacterial flora.

If the rabbit is dehydrated, subcutaneous fluids should be given. If the rabbit refuses to eat, it must be forced food, using a syringe.

In the case of yeast overgrowth, this can be treated by reduced the carbohydrates sources in the diet, or with nystatin.

Enterotoxemia
Enterotoxemia, a life-threatening disease, results from toxins produced by specific bacteria that overgrow in a rabbit’s GI tract. These toxins are absorbed into the bloodstream and affect many organs in the rabbit’s body, often resulting in death in a very short time. Young rabbits, especially those newly weaned, are especially susceptible to the disease when they are fed a high-starch diet because their digestive system does not yet have the normal amounts of microbial flora, as does that of a healthy adult rabbit. Any rabbit, especially those fed a high-starch or high-sugar diet or those on inappropriate antibiotics, can develop enterotoxemia.

Essentially, the disease is a poisoning of a rabbit’s system, and it is caused by the overgrowth of pathogenic bacteria, notably Clostridium spiroforme and E. coli. All rabbits house low levels of pathogenic bacteria in their body. In a healthy rabbit, the organisms live in the intestinal tract without causing problems. However, under certain conditions the microorganisms proliferate, producing rapid onset of severe illness.

Diet plays a major role in setting up conditions favourable to the pathogenic bacteria. High-starch or refined carbohydrate foods (e.g., crackers, cereals, bananas) are highly fermentable. Pelleted foods that are cereal-based or that contain grain fall into this category. Rapid fermentation in the cecum upsets the pH, creating an environment more hospitable to dangerous bacteria. Compounding the problem is the lack of fibre; the rabbit is not eating enough grass hay, which means that the cecum does not empty as it should.

Thus, poor diet plays a major role in the disease. Stress and inappropriate antibiotics may also be factors.

It must be noted that although the disease can cause rapid decline, when enterotoxemia is caused by inappropriate antibiotics, whether administered as a single dose or more long-term, a rabbit may not succumb until many days after the administration of the medication. Therefore, the cause of death may not be obvious.

Rabbits have a very high mortality rate with this disease, and it can happen very suddenly.

Pain (e.g., hunched appearance, inability to stretch out; unmoving; teeth grinding)

Signs of Enterotoxemia
A rabbit with enterotoxemia may exhibit signs of:

• Pain (eg hunched appearance, inability to stretch out, unmoving, teeth grinding)

• Soiled hindquarters

• Depression; lethargy

• Anorexia

• Weight loss

• Abdominal distension

• Diarrhoea (brown or greenish brown; watery); may contain blood and/or mucus.  Mucoid enteropathy results in excessive mucus.

• Dehydration

• Hypothermia and shock

Signs such as diarrhoea, hypothermia, and shock are very serious. Some rabbits may look healthy, but succumb rapidly. Death from enterotoxemia can result within hours.

Treatment and Prognosis for Recovery from Enterotoxemia
A rabbit exhibiting signs listed above needs emergency treatment; it is likely he will require hospitalization. Emergency treatment generally includes stabilisation of the rabbit’s temperature, subcutaneous or intravenous fluids, pain medication, prokinetics (motility drugs), and syringe-feeding of a high-fibre food (e.g., Critical Care™). There are anecdotal reports about the positive effects of probiotics, and a veterinarian may incorporate them into the treatment plan.

If the rabbit is young, the chances for recovery are not as good, especially if the bunny is newly weaned and exhibiting the most serious signs of the disease. Adult rabbits are somewhat less likely to succumb to the disease, especially if treated early, put on the appropriate diet, and any inappropriate antibiotic is stopped. A low-stress environment is also beneficial.

Home Care of a Rabbit with Enterotoxemia
A diet high in fibre and low in starch and sugars will be critical in returning the rabbit to health. The caregiver can best protect the bunny by feeding that same diet for the rabbit’s lifetime. As noted early in this article, grass hay plays a pivotal role in moving food through a rabbit’s digestive system, and so an unlimited amount of fresh grass-hay is recommended on a daily basis.

Caregivers can also help reduce a rabbit’s stress by discerning what causes anxiety or fear. Helping a bunny to feel safe and protected includes building trust, proper handling, good location of the rabbit’s house, safe play and exercise time, and proper introductions to other people and animals (including other rabbits). If the situation involves kits, removing baby rabbits from the mother is stressful for them all.

Cow Pile Syndrome
Cow pile syndrome, named for its most visible characteristic, may result from a combination of factors, including genetic, environmental, and dietary. Though not a medically recognised condition, brief mention is included because of some of the similarities with cecal motility disorders.

Determining whether a rabbit is suffering from a condition that affects the cecum or colon requires the skill of an experienced rabbit veterinarian. The caregiver can assist in the process by providing astute and accurate observations about the problem. Additional factors aid in the diagnostic process, including the history of medications, description of the diet (including dates and details of change), any possible foreign materials ingested and date of occurrence(s), and stress factors. Regardless of the condition, appropriate diet plays a crucial role in the recovery and health of the rabbit.
Original material sourced - with relevant edits, from: The Mystery of Rabbit Poop - by Dana Krempels, Ph.D.
Bacterial Enteritis and Diarrhea in Weaned and Adult Rabbits - MediRabbit

"The healthy functioning of the cecum is critical to the overall health of a rabbit. Gaining an understanding of how this large organ works – and what causes disruption – will help caregivers monitor their rabbits’ health, detect early signs of cecal disorder, and take steps to prevent a bunny’s condition from worsening."
Disorders of the Cecum - House Rabbit Society

"If your rabbit has a messy bottom due to either runny stool or urine leakage, the most important thing to do is to determine the source of the problem, starting with a full exam by your rabbit-experienced veterinarian, including a full dental examination (including molars) as well as blood chemistry and blood cell counts. This can reveal undetected health problems that are manifesting as gastrointestinal or urinary tract signs. Treating these will be the ultimate way to solve the messy bottom problem."
Bathing a Rabbit's Messy Bottom - Dana Krempels