What Rita Hogan Wants Dog Parents To Know About Antibiotics And Gut Recovery

Antibiotics can be lifesaving for dogs when they are truly needed. But according to canine herbalist Rita Hogan, pet parents should also understand what antibiotics can do to the gut—and why supporting the microbiome afterward deserves attention.

Hogan takes a very conservative approach to antibiotic use and encourages dog parents to think beyond the immediate infection. Her concern is that antibiotics don't affect only the bacteria responsible for an illness. They can also disrupt communities of microorganisms that normally live throughout the digestive tract.

Research supports the broader concern that antimicrobial medications can significantly alter the canine intestinal microbiome and can increase antimicrobial-resistant bacteria during and after use.

For Hogan, that makes two questions equally important:

Does my dog truly need an antibiotic?

And, if the answer is yes:

What am I going to do to support their gut afterward?

Antibiotics Can Affect More Than The Infection

One of Hogan's strongest statements about antibiotics is:

“Antibiotics create a mass extinction event in the gut where 70–80% of your dog's immune system resides.”

The exact percentage of the immune system located in the gut isn't a particularly useful or well-established measurement in dogs. However, the broader idea behind Hogan's statement is important: the intestinal tract contains extensive immune tissue, and interactions between the gut microbiota and the immune system play an important role in canine gastrointestinal and overall health.

Antibiotics are designed to inhibit or destroy bacteria. Unfortunately, they don't necessarily affect only the bacteria causing a problem.

Studies in dogs have documented changes in intestinal microbial populations following antimicrobial exposure. Researchers have also observed changes in antimicrobial-resistant organisms in the intestinal tract during antibiotic use.

That doesn't mean antibiotics are inherently bad.

It means they should have a reason for being used.

Don't Use Antibiotics “Just To Be Safe”

One of Hogan's simplest recommendations is also one of her most important:

“Never give antibiotics ‘just to be safe.’”

This idea closely aligns with modern veterinary antimicrobial stewardship.

The American Animal Hospital Association recommends limiting antimicrobial therapy to appropriate clinical indications and considering approaches such as diagnostic testing, supportive care, watchful waiting, or delayed prescribing in situations where a bacterial infection is uncertain or may resolve without antibiotics.

Unnecessary antibiotic exposure isn't harmless. In addition to possible medication side effects, inappropriate antibiotic use contributes to antimicrobial resistance—a growing concern in both veterinary and human medicine.

If you're unsure why your dog is being prescribed an antibiotic, reasonable questions to ask your veterinarian include:

Why do you suspect a bacterial infection?

Would testing help determine whether an antibiotic is necessary?

Could we safely monitor the condition first?

Is this the narrowest appropriate antibiotic for the suspected infection?

How long does my dog need to take it?

The purpose of these questions isn't to avoid antibiotics at all costs. It's to make sure they have a clear job to do.

Antibiotics Don't Work Against Viruses

Hogan also emphasizes:

“Never give antibiotics for a viral condition.”

Antibiotics target bacteria, not viruses.

However, there is an important distinction for pet parents to understand. A dog with a viral illness can sometimes develop a secondary bacterial infection. In those situations, a veterinarian may determine that antibiotics are appropriate for the bacterial complication even though they do not address the underlying virus.

This is another reason antibiotics should be based on an individual dog's clinical situation rather than used automatically.

When Are Antibiotics Appropriate?

Hogan recommends:

“Antibiotics should be given in life threatening situations only.”

Her philosophy reflects an intentionally conservative approach to antimicrobial exposure.

Current veterinary antimicrobial-stewardship guidelines are somewhat broader. Antibiotics should be reserved for situations in which there is an appropriate clinical indication, but the bacterial infection does not necessarily have to be life-threatening before antibiotic use is justified.

For example, some confirmed bacterial infections may warrant antimicrobial care before they become emergencies.

The common ground between these perspectives is important:

Antibiotics shouldn't be automatic.

They should be chosen intentionally, for the right patient, for the right reason, and for an appropriate amount of time.

If your dog has a potentially serious bacterial infection, avoiding a necessary antibiotic because of concerns about the microbiome could create a much greater health risk.

Gut support should complement appropriate veterinary care—not replace it.

What Happens To The Gut After Antibiotics?

Hogan believes pet parents often overlook what happens after the prescription bottle is empty.

Her position is direct:

“Damage must be repaired.”

Researchers have demonstrated that antibiotics can produce measurable changes in the canine microbiome, although the degree of disruption and recovery varies according to the antibiotic, the dog's health, diet, duration of therapy, and other factors.

In other words, there isn't one universal recovery timeline.

Some microbial populations may rebound relatively quickly. Others may take considerably longer to normalize, and the microbiome may not necessarily return to exactly the same composition it had before antibiotic exposure.

Hogan encourages dog parents to think of recovery as a process rather than something that happens automatically the day antibiotics stop.

Rita Hogan's Gut Recovery Priorities

Hogan's approach to post-antibiotic support includes several components:

“Recovery includes prebiotics/probiotics, fermented foods, beneficial yeast, gut lining repair, and watching for yeast overgrowth.”

These strategies are designed around supporting microbial diversity, nourishing beneficial organisms, and supporting the gastrointestinal environment.

Research into probiotics, prebiotics, and other microbiome-supportive interventions in dogs is growing, but the evidence is still developing. A 2024 veterinary review described evidence for prebiotics, probiotics, and related “biotics” as promising but still emerging, particularly for gastrointestinal disorders.

A small 2025 study involving 14 healthy dogs found that probiotic supplementation was associated with more favorable microbiome measures following antibiotic exposure compared with dogs that did not receive probiotics. The small study size means the results shouldn't be interpreted as proof that every probiotic works for every dog, but the findings add to growing interest in targeted microbiome support.

This is also why choosing a probiotic shouldn't simply mean grabbing any product labeled “probiotic.”

Different organisms, strains, combinations, doses, and products may behave differently.

Prebiotics Feed The Microbiome

Probiotics receive much of the attention in gut health discussions, but Hogan also emphasizes prebiotics.

Prebiotics are compounds that can serve as substrates for beneficial microorganisms already living in the intestinal tract.

In practical terms, supporting the microbiome isn't only about adding bacteria.

It's also about creating an intestinal environment where beneficial organisms have the resources they need to thrive.

Diet therefore becomes an important part of the conversation.

A veterinarian or qualified canine nutrition professional can help determine which foods and fibers are appropriate for an individual dog, particularly when gastrointestinal disease, cancer, pancreatitis, allergies, or other medical conditions are present.

What About Fermented Foods And Beneficial Yeast?

Hogan also incorporates fermented foods and beneficial yeasts into her approach.

Fermentation introduces microorganisms and microbial metabolites that can influence the gastrointestinal environment. However, not every fermented food intended for humans is appropriate for dogs.

Salt, sugar, spices, onions, garlic, sweeteners, and other ingredients can make some fermented foods unsuitable.

That's why “feed fermented foods” shouldn't automatically translate into sharing whatever happens to be in your refrigerator.

The individual food, quantity, and dog's health need to be considered.

Rita's Unusual Recommendation: Save A Stool Sample

Perhaps the most memorable recommendation on Hogan's list is:

“Freeze a turd and label if your dog has never had antibiotics.”

The idea behind this recommendation is microbiome preservation.

A stool sample collected before antibiotic exposure theoretically represents the dog's microbiota before that disruption occurred.

Research into fecal microbiota transplantation, commonly called FMT, is expanding in veterinary medicine. FMT involves transferring microorganisms from fecal material into another gastrointestinal environment with the goal of influencing the recipient's microbiome.

But this is an emerging area of veterinary medicine—not a do-it-yourself therapy.

Studies of FMT in dogs have produced promising findings in some situations, but results remain variable. A 2026 randomized trial evaluating oral FMT in dogs with tylosin-responsive enteropathy found inconsistent benefits and concluded that further research and optimized protocols are needed.

Simply freezing stool at home should therefore not be interpreted as creating a medically ready fecal transplant.

Proper microbiome therapy involves considerations such as sample handling, screening for pathogens and parasites, antimicrobial-resistant organisms, storage conditions, and veterinary oversight.

If preserving your dog's microbiome interests you, discuss stool banking or microbiome testing with a veterinarian or qualified veterinary microbiome service rather than attempting an unsupervised fecal transplant.

Consider Microbiome Testing When Appropriate

Hogan also recommends:

“Test gut if possible.”

Canine microbiome testing is becoming increasingly available, and researchers are learning much more about what constitutes normal microbial variation among dogs.

A large 2026 Dog Aging Project analysis involving more than 900 dogs demonstrated just how complex the canine microbiome is, with factors such as age, diet, environment, and behavior all associated with microbial composition.

That complexity is worth remembering.

A microbiome test isn't necessarily a simple pass-or-fail test of whether your dog's gut is “good” or “bad.”

Results should be interpreted within the larger context of diet, symptoms, medications, health history, and veterinary findings.

Antibiotic Recovery Isn't About Fear

Perhaps the most useful way to interpret Hogan's recommendations is not as an argument that antibiotics should never be used.

Antibiotics have saved countless animal lives.

The better lesson is that they are powerful medications—and powerful medications deserve thoughtful use.

Don't request antibiotics simply because your dog is sick.

Don't use leftover antibiotics from another illness.

Don't assume every cough, episode of diarrhea, skin problem, or respiratory illness requires an antibiotic.

But don't avoid an antibiotic that your veterinarian believes is necessary for a bacterial infection simply because you're worried about the microbiome.

Instead, think about both sides of care:

Use antibiotics appropriately when they are truly indicated.

Then:

Pay attention to the gastrointestinal ecosystem afterward.

As Hogan emphasizes, antibiotic recovery may involve supporting beneficial organisms, feeding the microbiome, paying attention to digestion, and allowing the intestinal environment time to recover.

The goal isn't to fear antibiotics.

It's to respect them.

And to remember that caring for your dog's gut doesn't necessarily end when the infection is gone.

This article presents recommendations from canine herbalist Rita Hogan alongside current veterinary research and antimicrobial-stewardship guidance. It is intended for educational purposes and should not replace individualized veterinary care. Never discontinue, delay, or alter a prescribed antibiotic without speaking with your veterinarian.

References

Connelly S, Fanelli B, Hasan NA, Colwell RR, Kaleko M. Oral Beta-Lactamase Protects the Canine Gut Microbiome from Oral Amoxicillin-Mediated Damage. Microorganisms. 2019 May 27;7(5):150. doi: 10.3390/microorganisms7050150. PMID: 31137766; PMCID: PMC6560916.

Evangelia M. Stavroulaki, Jan S. Suchodolski, Panagiotis G. Xenoulis, Effects of antimicrobials on the gastrointestinal microbiota of dogs and cats, The Veterinary Journal, Volume 291, 2023, 105929, ISSN 1090-0233, https://doi.org/10.1016/j.tvjl.2022.105929.

Kim SJ, Chung HC, Park SY, Lee JM, Han JH. Beneficial effects of probiotics on dysbiosis of gut microbiota induced by antibiotic treatment in healthy dogs. Res Vet Sci. 2025 Aug;191:105674. doi: 10.1016/j.rvsc.2025.105674. Epub 2025 May 9. PMID: 40347600.

Rita Hogan. Subtle Signs of Illness. Webinar.

Whittemore JC, Price JM, Moyers T and Suchodolski JS (2021) Effects of Synbiotics on the Fecal Microbiome and Metabolomic Profiles of Healthy Research Dogs Administered Antibiotics: A Randomized, Controlled Trial. Front. Vet. Sci. 8:665713. doi: 10.3389/fvets.2021.665713