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Dysbiosis is the condition that results when the natural flora of the gut are thrown out of balance. When used for rabbits, it usually means that harmful bacteria out-compete the "good" bacteria in the digestive tract or certain types of "good" bacteria are too proliferate.[1]:76

E. coli routinely proliferates in any rabbit with dysbiosis.[2]:199

Signs and Symptoms

  • pain
  • watery or mucoid diarrhea
  • lethargy
  • hypothermia
  • shock
  • anorexia or eating only when prompted
  • gas
  • GI stasis
  • repetitive actions such as reaching down repeatedly to eat cecum and coming up without anything to chew
  • repetitive motions such as twisting and stretching the hips/pelvis/lower back-- distinct from the up and down of rubbing a gaseous or static belly on the floor, which my also be present


Common causes of dysbiosis in the rabbit include the following:[2]:193,198-199[1]:76

  • A carbohydrate-rich diet or too many high-carbohydrate, high-fat treats fed at once.
  • Inappropriate antibiotic therapy. (e.g. clindamycin, lincomycin, ampicillin, amoxicillin, amoxicillin-clavulanic acid, cephalosporins, many penicillins, and erythromycin)
  • Bacterial (e.g. Salmonella, Pseudomonas, Campylobacter)
  • GI Dysbiosis is common in immuno-compromised, elderly rabbits, and rabbits who have dental issues such as malocclusion, extraction, root atrophy, or gum disease.

Cecal Dysbiosis

Dysbiosis in the cecum can be acute but is sometimes chronic and comorbid with other conditions that make it hard for a rabbit to get enough fiber and maintain other aspects of their digestive health including maintaining a balanced stomach pH. Cecal dysbiosis results in conditions such as poopy butt/intermittent soft stool (ISS). Commonly this means that the rabbit is incapable of consuming cecum in a meaningful way and this interruption of their digestive cycle can be life-threatening.


Dysbiosis may present as non-obstructive bloat or an atypical GI stasis with or without presence of soft stool/malformed cecum. Palliative treatments include incubation with warm towels, heating discs, and/or pain medications to encourage physical movement/prevent shock. Gas or low GI motility may gentle require massage. Poor eating may necessitate assisted syringe feeding/hydration with critical care and/or subcutaneous fluids to sustain kidney function and GI motility. Molar trims, withholding carbohydrate rich or sugary treats, and being really attentive to your rabbit's appetite and fecal/cecal eliminations are key, necessary ongoing care for rabbits predisposed to recurring dysbiosis.

Medications that have been prescribed for this condition are as follows:

  • Simethicone - If gas is present, otc infant simethicone 20mg oral suspension can help relieve bloating.
  • Meloxicam - This palliative can be used for pain management when obstructive bloat/stasis have been ruled out.
  • Buprenorphine - This narcotic has been prescribed only in emergencies to keep a rabbit from going into shock pre-differential diagnosis between bloat/stasis from obstruction vs dysbiosis.
  • Metoclopromide - Increases gut motility by stimulating smooth muscle contractions in the GI tract.
  • Cholestyramine - (oral suspension, USP) actually a cholesterol medication with an off-label use that lowers bile acids in a rabbit's body and acts as a binding agent for the cecal discharge to solidify it and make it easier for a rabbit to consume. Must be administered solo and away from other medications.
  • Metronidazole - Antibiotic that specifically targets e. coli and clostridium to help bring those levels down to normal.

See also