Dog Got the Runs? Don’t Run to Antibiotics Just Yet

Diarrhea is one of the most common reasons pet owners call or visit their veterinarian. Few things feel more urgent than a dog or cat with “the runs.” Even though humans rarely run to the doctor’s office for an occasional bout of diarrhea, pet owners tend to want a solution more immediately.  

For decades, medications such as metronidazole or tylosin were the standard first-line treatment for pets with loose stool. These antibiotics became synonymous with quickly “fixing” diarrhea, reassuring owners and clinicians alike. Today, however, research shows that this approach may be outdated, unnecessary, and can sometimes even delay recovery.  

Acute diarrhea is almost always caused by non-bacterial factors, such as stress, sudden dietary changes, parasites, viral triggers, or simple dietary indiscretion after a pet gets into something they shouldn’t. In these common scenarios, antibiotics do not target the underlying cause and have no meaningful impact on how quickly a pet recovers. In fact, new research shows that most cases of uncomplicated diarrhea (sudden, self-limiting diarrhea in an otherwise healthy dog or cat with no signs of systemic illness) do not require antibiotics, and antibiotics may actually prolong recovery by disrupting the gut ecosystem we’re trying to heal. 

Why Antibiotics Aren’t the First Answer Anymore 

Modern studies show that many forms of acute, non-complicated diarrhea resolve with supportive care alone, including dietary modification, probiotic or postbiotic supplementation, and hydration management. In fact, one of the most impactful findings comes from microbiome research showing metronidazole can induce significant dysbiosis, reducing key beneficial bacteria, decreasing short-chain fatty acid production, and delaying normalization of gut function. 

In controlled trials, dogs receiving metronidazole showed measurable negative changes in microbiome composition for weeks after treatment, even after their stools normalized. While metronidazole has long been considered a “safe” gastrointestinal (GI) antibiotic, these studies challenge that assumption and highlight potential long-term consequences. 

Additionally, global veterinary and human medical organizations continue to issue strict guidance on antimicrobial stewardship. Overuse of antibiotics, especially when used for self-limiting GI disease (sudden gastrointestinal upset that resolves on its own), contributes to the accelerating problem of antimicrobial resistance. Simply put, we need to reserve antibiotics for cases in which they are truly warranted. 

The evidence is clear: for most cases of acute diarrhea, first steps should focus on diet and microbiome support, not reflexive antibiotic use. Dietary modification remains one of the most powerful tools clinicians have, with highly digestible therapeutic GI diets consistently resolving uncomplicated diarrhea. These formulas typically rely on easily digestible proteins and carbohydrates, modified-fat levels, mixed sources of soluble fiber, and, when appropriate, novel or hydrolyzed proteins for suspected food-responsive disease.  

Microbiome-directed therapies have also changed how we approach acute diarrhea, shifting the focus from suppressing signs with antibiotics to actively supporting mucosal health and microbial resilience. Well-studied probiotic organisms have been shown in clinical trials to shorten the duration of diarrhea. For example, a randomized, placebo-controlled trial of an anti-diarrheal probiotic product in dogs with acute, uncomplicated diarrhea demonstrated a significantly shorter duration of diarrhea and faster resolution rate in the probiotic group compared with placebo.  

Beyond live microbes, postbiotics are emerging as a promising treatment option. Consensus definitions now describe postbiotics as inanimate microbial preparations that still confer health benefits to the host, and a growing body of work highlights their ability to modulate immune responses, enhance gut barrier integrity, and influence microbial metabolites without the formulation and stability challenges that accompany live cultures like probiotics. Early canine studies suggest that specific blends of prebiotics and postbiotics can beneficially shift the gut microbiome and support gastrointestinal health, underscoring the potential of these “non-living” microbial interventions as part of a modern, microbiome-conscious approach to diarrhea management. 

Additionally, fecal microbiota transplantation (FMT), once limited to specialty settings, is now available in various formats for veterinary practice, including fresh donor fecal suspensions, rectal enemas, and increasingly, commercially produced freeze-dried oral capsules that provide consistent dosing and improved safety. FMT involves transferring a processed fecal microbiome from a carefully screened healthy donor into a recipient torestore a balanced, functional microbial community. Research shows that FMT can quickly restore microbial balance, decrease dysbiosis scores, and improve outcomes. These benefits align perfectly with the broader goal of modern GI medicine: to correct the underlying disruption rather than merely suppress clinical signs. 

While most cases of acute, uncomplicated diarrhea do not require antibiotics, there are still situations in which antimicrobial therapy is not only appropriate but essential. Pets showing systemic illness, such as fever, lethargy, dehydration, marked abdominal pain, or blood in the stool, warrant a broader diagnostic workup and may benefit from targeted antibiotic therapy when a true bacterial infection is confirmed or strongly suspected.In these cases, antibiotics are used strategically to address documented or highly likely bacterial involvement, support stabilization, and prevent life-threatening complications. The key is not to eliminate antibiotics altogether, but to ensure they are used judiciously, evidence-based, and reserved for cases where the benefits clearly outweigh the risks. 

What This Means for Veterinary Teams, Pet Owners, and Pet Industry 

The move away from reflexive antibiotic intervention represents a meaningful evolution in veterinary medicine; however, it may seem difficult initially, especially when clients expect a quick prescription. Yet the facts are clear: diet- and microbiome-focused therapies are now the first line of care. With highly digestible GI diets, targeted probiotics and postbiotics, functional fibers, hydration support, and clear decision points for further diagnostics, clinicians can address the underlying causes of most acute diarrhea cases directly. This process not only prevents the risks of unnecessary antibiotics but also results in a more rapid resolution, fewer relapses, and enhanced long-term GI resilience. For pet owners, it is empowering; instead of taking drugs that can upset the normal flow of things in the gut, they can actually use targeted nutrition for recovery, with the support oftheir veterinarian, who provides evidence-based counseling. 

These emerging best practices also have relevant implications for the pet food sector. As veterinarians pay even more attention to microbiome-friendly, highly digestible, and functionally formulated diets as first-line therapy, there is increased demand for clinically substantiated, formulation transparency, and GI-focused claims that are based on science. Companies need to focus more on digestibility testing, functional fiber systems, and postbiotic technologies that are relevant to modern GI care as well, and this is where BSM Partners step in.  

As the industry’s leading partner in research and product development, BSM works with brands to innovate with evidence-based formulas grounded in peer-reviewed science and performance testing. BSM provides veterinary teams with easily accessible, research-informed educational material and allows brands to provide precise, empathetic consumer messaging that brings pet owners into line with veterinary guidelines. Through the integration of scientific rigor, clinical expertise, and strategic communication, BSM trains brands to develop new lines of GI-supportive products for modern veterinary practice.  

Nutrition is likely to assume a more meaningful role in both its management and prevention as the clinical relevance of antimicrobial stewardship grows. The future of digestive health in pets is set to be more effective and scientific than it has ever been, thanks to veterinary professionals, pet owners, and industry partners like BSM working together. 

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About the Author

Dr. Katy Miller works as the Director of Veterinary Services at BSM Partners. She earned her veterinary degree at Ross University and completed her clinical year at Louisiana State University. She previously served for 11 years as the Director of Dog and Cat Health and Nutrition for Mud Bay where she earned multiple certifications and specialized in pet food nutrition, prior to which she practiced general and emergency medicine for seven years. She is also a competitive three-day eventer, licensed falconer, and claims only two (Golden and Mini Doxie) of their nine dogs.