Antibiotic resistance is one of the most serious global health threats we face today. It occurs when bacteria adapt and learn how to survive exposure to antibiotics that once killed them. Over time, these surviving bacteria multiply, and infections become harder, slower, or sometimes impossible to treat. This problem does not exist in isolation. It affects people, animals, and the environment simultaneously, which is why antibiotic resistance is considered a One Health issue.
One way resistance develops is through genetic exchange. Bacteria can share DNA with one another, including genes that make them resistant to antibiotics. These genes are often carried on mobile pieces of DNA called plasmids or transposons, which act like genetic “USB drives,” moving resistance traits from one bacterium to another, even across species. Every time antibiotics are used, they increase the selective pressure that favors these resistant organisms.
Because of this growing crisis, researchers are actively looking for ways to reduce antibiotic use whenever possible. Probiotics are often suggested as a supportive tool because they can help maintain gut balance, reduce digestive upset, and potentially lower the need for antibiotics.
A new peer-reviewed study published in Frontiers in Veterinary Science examined this issue in depth. Researchers tested 10 popular probiotic products marketed for dogs and cats1. They assessed whether the bacteria in these products were resistant to commonly used antibiotics and whether they carried genes known to confer antibiotic resistance. Across these products, researchers identified 19 different antibiotic resistance genes.
This matters because bacteria living in a pet’s gut do not exist in isolation. Resistance genes can be shared with other bacteria, including potentially harmful ones. Once those genes are established, future infections in pets may become more difficult to treat. Because humans and animals share environments and, in many cases, bacteria, these resistance genes can also contribute to risks beyond pets alone.
One of the most striking findings involved Enterococcus faecium2. This species is widely used in pet probiotics and has a long history of use for managing diarrhea because of Purina’s popular product, Fortiflora. In this study, it was the most frequently included probiotic species and also the one that carried the highest number of antibiotic resistance genes. Enterococcus faecium as a species is well known for its ability to acquire and exchange resistance genes. This makes it inherently higher risk, especially with long-term or repeated exposure.
Some of the probiotic products tested showed resistance to antibiotics used in both veterinary and human medicine3. That overlap is particularly concerning, as it increases the potential for shared resistance challenges across species.
The takeaway is not that all probiotics are dangerous, but that they require the same level of scientific scrutiny as any other biologically active product. Rotating probiotic strains rather than using the same one continuously may help reduce selective pressure. Avoiding long-term use of higher-risk species, such as Enterococcus faecium, is another prudent step. This is why I no longer recommend E. faecium–based products, even though I have formulated probiotics with this strain in the past. Our understanding has evolved, and we now know more about the risks than we did years ago.
An important part of this conversation is where probiotic strains come from. Species-specific strains derived from healthy, wild ancestors, such as wolves, offer a compelling alternative. Wolves have not been exposed to antibiotics, industrial agriculture, or modern pharmaceutical pressures. Their gut bacteria evolved in an environment without synthetic antibiotics, which dramatically reduces the likelihood that these microbes carry or have ever selected for antibiotic resistance genes.
Using carefully screened, species-appropriate strains rooted in a dog’s evolutionary history aligns with the goal of supporting gut health without contributing to the broader resistance problem. These strains are more likely to be compatible with a dog’s immune system and less likely to serve as reservoirs for transferable resistance genes.
Stronger Safety Studies for Pet Probiotics
The researchers behind the Frontiers in Veterinary Science study recommend stronger safety standards for pet probiotics, similar to those already in place for livestock. This includes mandatory screening of probiotic strains before they reach the market and avoiding strains that carry resistance genes, especially those that can spread easily between bacteria.
One of the earliest and most well-known pet probiotics was Purina FortiFlora, which helped popularize the idea of probiotics for pets. As the science advances, however, it is becoming clear that tradition and familiarity are not enough. Probiotic selection needs to be based on current genomic safety data, resistance risk, and long-term ecological impact.
Antibiotic resistance did not develop overnight, and it will not be solved with a single intervention. Thoughtful probiotic choices, reduced unnecessary antibiotic use, and higher safety standards are all part of protecting the health of pets, people, and the ecosystems we share.
An important part of this conversation is where probiotic strains come from. Species-specific strains derived from healthy, wild ancestors, such as wolves, offer a compelling alternative. Wolves have not been exposed to antibiotics, industrial agriculture, or modern pharmaceutical pressures. Their gut bacteria evolved in an environment without synthetic antibiotics, which dramatically reduces the likelihood that these microbes carry or have ever selected for antibiotic resistance genes.
Using carefully screened, species-appropriate strains rooted in a dog’s evolutionary history aligns with the goal of supporting gut health without contributing to the broader resistance problem. These strains are more likely to be compatible with a dog’s immune system and less likely to serve as reservoirs for transferable resistance genes.
The researchers behind the Frontiers in Veterinary Science study recommend stronger safety standards for pet probiotics, similar to those already in place for livestock. This includes mandatory screening of probiotic strains before they reach the market and avoiding strains that carry resistance genes, especially those that can spread easily between bacteria.
One of the earliest and most well-known pet probiotics was Purina FortiFlora, which helped popularize the idea of probiotics for pets. As the science advances, however, it is becoming clear that tradition and familiarity are not enough. Probiotic selection needs to be based on current genomic safety data, resistance risk, and long-term ecological impact.
Antibiotic resistance did not develop overnight, and it will not be solved with a single intervention. Thoughtful probiotic choices, reduced unnecessary antibiotic use, and higher safety standards are all part of protecting the health of pets, people, and the ecosystems we share.
We know probiotics are very beneficial for gut health, and we now know that choosing the right stains are important. The right choices help animals cope with life in today’s challenging times.
Today’s domestic dogs face modern challenges their wild counterparts never faced: highly processed diets, increased environmental pollutants and frequent medications, chronic low-grade inflammation and an impaired gut microbiome. Additionally, the GI tract of dogs is much different than humans. Don’t assume human probiotics will get the job done. Here's what to look for when selecting an effective, high-quality probiotic for your canine companion.
My Top 10 Favorite Probiotic Strains
The gut is the control center of your dog’s overall wellbeing. The gastrointestinal tract doesn’t just digest food; it educates the immune system, helps regulate inflammation, communicates directly with the brain, and plays a central role in behavior, mood, and resilience to stress. Each probiotic strain has a unique “job description,” producing different compounds, interacting with immune cells in distinct ways, and influencing different physiological systems. When we match the right probiotic strains to a dog’s specific needs, we can create profound, whole-body benefits that go far beyond firmer stools.
Because the digestive tracts of canines evolved to handle a significant bacterial load from the food they consume, your dog’s GI tract must maintain a healthy level of good bacteria to keep populations of bad bacteria in check and prevent digestive issues and other health problems. Without colonies of friendly bacteria in the gut, they have an increased risk of developing disease, and day-to-day emotional or physical stressors exacerbate that risk.
When choosing a probiotic, here are 10 important strains to look for, and why.
Lactobacillus fermentum K9-2: Strengthening the Gut Barrier and Calming Inflammation
Lactobacillus fermentum K9-2 is a canine-specific strain that excels at supporting the integrity of the intestinal lining. A healthy gut barrier acts like a finely tuned filter, allowing nutrients to pass through while keeping inflammatory molecules, toxins, and pathogens out of the bloodstream.
When this barrier becomes compromised, a cascade of chronic inflammation can follow, often showing up as itchy skin, food sensitivities, joint discomfort, or immune imbalance. L. fermentum K9-2 helps reinforce tight junctions between intestinal cells, reducing permeability and quieting inflammatory signaling. Clinically, this often translates into better stool quality, improved nutrient absorption, and a more balanced immune response throughout the body4.
Lactobacillus casei K9-1: Restoring Microbial Balance and Reducing Harmful Bacteria
Lactobacillus casei K9-1 plays an important role in maintaining microbial harmony within the gut. One of its key functions is suppressing overgrowth of opportunistic organisms such as Clostridium species, which are frequently associated with diarrhea, gas, and toxin production.
By producing organic acids and other antimicrobial compounds, L. casei K9-1 creates an intestinal environment that favors beneficial microbes while discouraging pathogens. This strain works synergistically with L. fermentum K9-2, supporting digestive stability and contributing to more consistent, well-formed stools, especially in dogs with a history of gastrointestinal upset5.
Lactobacillus reuteri PCR7: Natural Antimicrobial Support and Immune Modulation
Lactobacillus reuteri PCR7 is particularly valuable for its ability to produce reuterin, a naturally occurring antimicrobial substance that selectively inhibits harmful bacteria without wiping out beneficial flora. This targeted approach helps preserve microbial diversity, which is essential for long-term gut health.
In addition to its antimicrobial effects, L. reuteri PCR7 supports immune modulation, helping the immune system respond appropriately rather than excessively. This is especially helpful for dogs dealing with allergies, chronic infections, or inflammatory conditions. An added benefit of this strain is its support of oral health, which matters more than most people realize, as oral microbes directly influence gut and systemic health6.
Pediococcus acidilactici PCLL01: Digestive Resilience and Gas Reduction
Pediococcus acidilactici PCLL01 is a hardy strain that survives passage through stomach acid and bile, allowing it to reach the intestines intact. It is particularly effective at reducing gas, bloating, and diarrhea, making it a great choice for dogs with sensitive stomachs or stress-related digestive issues. This strain supports overall microbial diversity and helps stabilize the gut during dietary transitions, travel, or boarding. By improving digestive efficiency and reducing fermentation-related gas, P. acidilactici PCLL01 contributes to greater comfort and predictability for dogs prone to digestive volatility.
7.
Bifidobacterium Species: Fueling the Gut Lining and Supporting Immune Balance
Bifidobacterium species are foundational organisms in a healthy canine colon. Their primary role is fermenting dietary fibers into short-chain fatty acids such as butyrate, which serve as a primary energy source for intestinal cells. These compounds help maintain a healthy gut lining, reduce inflammation, and support immune tolerance.
In dogs, adequate levels of Bifidobacterium are associated with improved stool quality, reduced gut inflammation, and stronger immune defenses. These strains are especially important for dogs with inflammatory bowel disease, food sensitivities, or chronic immune-mediated conditions
8.
Optibiome® BS50 Bacillus subtilis: Digestive Efficiency and Antioxidant Support
Optibiome® BS50 is a spore-forming Bacillus subtilis strain designed to withstand harsh digestive conditions. Rather than permanently colonizing the gut, it exerts its benefits as it passes through, modulating the microbial environment and enhancing digestive enzyme activity. This strain improves stool consistency by supporting the breakdown and absorption of proteins, fats, and carbohydrates.
It also contributes to improved antioxidant status, helping counteract oxidative stress associated with aging, chronic inflammation, and environmental toxins. BS50 is particularly beneficial for senior dogs, active dogs, and those recovering from illness or metabolic stress
9.
MuniSpore® Bacillus clausii CS108: Microbiome Protection During Antibiotic Use
MuniSpore® Bacillus clausii CS108 stands out for its resistance to both stomach acid and many commonly used antibiotics. This makes it an excellent choice during and after antibiotic therapy, when the gut microbiome is most vulnerable. CS108 helps reduce antibiotic-associated diarrhea and supports immune resilience during times of physiological stress.
Its benefits extend beyond the gut, supporting respiratory and systemic immune function, which is especially valuable for dogs with recurrent infections or weakened immune systems10.
Lactobacillus rhamnosus GG: Allergy Relief and Gut-Brain Axis Support
Lactobacillus rhamnosus GG is one of the most researched probiotic strains in both human and veterinary medicine. In dogs, it is particularly well known for reducing allergic reactivity by promoting immune tolerance and balancing inflammatory pathways. This strain also plays a meaningful role in the gut-brain axis, producing metabolites that influence neurotransmitter signaling.
By supporting communication between the gut and nervous system, L. rhamnosus GG can help improve stress resilience, emotional stability, and behavioral balance in sensitive or reactive dogs11.
Saccharomyces boulardii: Rapid Diarrhea Control and Gut Lining Protection
Saccharomyces boulardii is a probiotic yeast with unique therapeutic benefits. It works quickly to halt diarrhea by binding toxins, inhibiting pathogenic microbes, and supporting fluid balance in the intestines. Because it is resistant to antibiotics, it can be used safely alongside conventional treatments.
S. boulardii also enhances secretory IgA production, which helps protect the gut lining and reduce inflammation. I often recommend this strain for acute diarrhea, antibiotic-associated digestive upset, and inflammatory bowel flares12.
Lactiplantibacillus plantarum LP815: A GABA-Producing Probiotic for Emotional Balance
Lactiplantibacillus plantarum LP815 represents an exciting advancement in probiotic science. This strain naturally produces GABA, or gamma-aminobutyric acid, an inhibitory neurotransmitter that calms the nervous system by regulating how quickly neurons fire. Unlike conventional calming supplements that act temporarily and systemically, LP815 works within the gut to influence the gut-brain axis, creating more sustained emotional balance.
By supporting vagal nerve signaling and neurotransmitter regulation, LP815 can help dogs feel calmer, sleep more soundly, and respond more appropriately to stress.
LP815 Clinical Observations: Supporting Calmer, More Emotionally Balanced Dogs
In clinical observations, nearly half of dogs receiving LP815 showed signs of anxiety at baseline, with over a quarter exhibiting aggression. After four weeks of supplementation, dogs experienced reduced fear- and noise-based aggression, more consistent and restful sleep, improved mood stability, better energy balance, and faster emotional recovery after owner departure.
Importantly, no adverse effects were reported across more than 1,120 doses, and dogs of all breeds and diets tolerated the strain exceptionally well13. These findings underscore the powerful connection between gut health and emotional well-being.
Wolf Ancestors
Most modern companion dogs seem far removed from their ancient roots. Yet a fascinating new study shows that traces of wolf ancestry are present in nearly every dog today. These are not the dramatic wolf genetics we see in intentionally hybridized breeds. Instead, they are small but meaningful genetic signatures that remained in dog lineages long after domestication began. These traces appear to have shaped size, smell, behavior, and even a dog's ability to thrive in different environments created by humans.
The study, published in the Proceedings of the National Academy of Sciences, was led by researchers from the American Museum of Natural History and the Smithsonian’s National Museum of Natural History. The findings shed new light on how dogs evolved alongside humans and how they continued to exchange genetic material with wolves long after our partnership began. This discovery deepens our understanding of canine biology, and, for those of us who love dogs, it also highlights the profound connection between our pets and their ancient ancestors.
Your dog’s microbiome evolved in the wild, through thousands of years of adaptation to fresh meat-based diets, environmental exposures, and natural selection. Probiotics sourced from healthy, wild canids, like wolves, offers a significant evolutionary advantage.
Choosing Probiotics With Purpose
When selected thoughtfully, probiotics become powerful tools for supporting not just digestive health, but overall immune balance, inflammation control, and emotional resilience. Each strain discussed here offers a distinct and complementary benefit, reinforcing the importance of targeted, strain-specific probiotic support. By nourishing your dog’s microbiome with intention, you’re supporting health from the inside out, where true wellness begins.
Sources and References:
- 1 Front. Vet. Sci., 21 October 2024
- 2 Front. Cell. Infect. Microbiol., 27 July 2023
- 3 PRN Brill April 2018
- 4 Journal of Functional Foods 2019 May
- 5 Frontiers in Microbiology 2020
- 6 J Prev Med Hyg 2022 Oct 17
- 7 J Appl Microbiol 2014 Mar
- 8 Front. Vet. Sci., 13 January 2022
- 9 Gut Microbes 2022
- 10 Nutraingredients
- 11 Food Funct . 2020 Dec
- 12 Aliment Pharmacol Ther. 2015 Oct
- 13 Animals (Basel). 2025 Aug 4
- 14 Proceedings National Academy Sciences, Nov 24, 2025
About Karen Shaw Becker, DVM, CVH, CVA, CCRT
Veterinarian Dr. Karen Shaw Becker believes biologically appropriate food and an animal's immediate environment are essential in determining health, vitality, and lifespan. She has spent her career as a wildlife and exotic animal veterinarian and small animal clinician, empowering animal guardians to make intentional lifestyle decisions to enhance the well-being of their animals.
