Hannah Zulueta The Approach · Digestive
Why I Stopped Reaching For Probiotics
Adding more bacteria to a compromised gut is not my first move, and the research is less settled than the label suggests.
This is one of the first questions I get from owners of dogs with chronic gut problems. They have already bought three brands. They want to know which one I like. My honest answer is that I do not start there anymore, and the reasoning took me several years and a lot of reading to arrive at.
The one thing
A weak gut is not an empty gut.
The mental picture behind probiotics is a garden bed that has been stripped bare, waiting for seed. That picture fits a few dogs. For most of the chronic cases I see, the bed is not bare. It is waterlogged. The soil will not drain, nothing planted in it takes root, and adding more seed to standing water does not produce a garden.
In TCM terms, that is Spleen Qi Deficiency. The job is to restore the transforming function first. Once the ground drains, the flora that belong there come back on their own, and that is what I have watched happen case after case.
The assumption
What we assume a probiotic does
The assumption is straightforward. Your dog’s gut is short of good bacteria. You supply good bacteria. The good bacteria move in, settle down, and rebuild the population.
Every part of that sentence has been tested in the last decade, and the results are more complicated than the marketing.
Swallowing an organism and establishing it are two different events, and the research separates them cleanly.
The research
What the studies actually found
Select a study to see what it tested and what it found.
Some people are permissive. Some people are resistant. The same pill does different things in different guts.
This is the study behind everything I say about the latest and greatest strain. There is no strain that works for everyone, because the deciding factor is the gut receiving it rather than the organism arriving.
The exact scenario where probiotics are prescribed most confidently is where they performed worst.
Read that finding again. Doing nothing at all restored the microbiome faster than supplementing it. This is one study in a small human cohort, and it needs replication. But it is the study that made me stop treating post-antibiotic probiotics as automatic.
Included because it is interesting, flagged because it is disputed.
I am including this with its criticism attached because I would rather you see the whole picture. The line I take from it is the author’s own: probiotics deserve to be treated like a drug rather than like a food supplement.
The canine evidence, gathered in one place, and it is thinner than most people assume.
Diet is the lever. That is not my opinion talking. It is the conclusion of the largest review of the canine literature, and it is the reason my work starts in the bowl.
Sixty dogs, three arms, and no clear winner.
Worth sitting with the placebo number. Most acute diarrhea in an otherwise healthy dog resolves in under five days on its own. Whatever you gave the dog on day one will look like it worked.
My own gut
I have tried them on myself
I have slight Spleen Qi deficiency. It is mild and I manage it, and it means my own digestion is a reasonably sensitive instrument for this question.
I have taken a lot of probiotics over the years, including whichever strain was being described as the latest and greatest at the time. The trendy ones make me double over. Not mildly. Doubled over, waiting for it to pass, wondering why the thing that was supposed to fix my digestion had just wrecked it.
My body sorted me into the resistant group before I ever read the study that named the categories.
That experience is what makes me cautious when an owner tells me a friend’s dog did beautifully on a particular brand. I believe them. I also know their dog is not this dog.
Honest practice
The gastroenterologist with 30 pills
I have heard of a gastroenterologist who handles this problem in the only way that fully respects it. He gives a patient 30 pills, 15 different products in pairs. The patient takes one product per day, keeps notes, and reports back on what happened.
Then he recommends based on the response, rather than on the theory.
There is something admirable in that. He is running a small trial in one patient because he understands that the published averages cannot tell him what will happen in this particular gut. He is not pretending to know in advance.
Notice what that approach concedes. If the right product could be selected from the label, the strain list or the colony count, you would not need to run the experiment. The experiment exists because the prediction is not reliable.
What I do instead
I switched to herbs and never looked back
When I moved from Western probiotics to Chinese herbal formulas, I expected to miss something. I did not. There was no gap where the probiotics used to be.
The reason, as I understand it now, is that the two approaches are aimed at different targets. A probiotic supplies organisms. A formula like Shen Ling Bai Zhu San changes the environment those organisms live in. It strengthens transformation, drains the dampness that is drowning the bed, and firms up a gut wall that has been leaking.
What I find compelling is that the laboratory research on this formula points the same way, and one experiment in particular settles the mechanism.
That last line is the whole argument in one sentence. The formula does not work instead of the microbiome. It works through it. Strip the flora out and the herbs stop doing anything, which tells you the herbs were never the active agent. They were restoring the conditions that let the resident population do its job.
The picture repeats across the other work on this formula. In a Crohn’s-like colitis model it raised the tight junction proteins ZO-1, occludin and claudin-5 while lowering the inflammatory cytokines TNF-alpha, IL-6 and IL-1-beta, and restored microbial balance. In a lactose-induced diarrhea model in rats it reduced fecal water content and shifted colonic fermentation and short-chain fatty acid production. In a chronic diarrhea model it restored barrier function through tight junction upregulation alongside microbiome change.
These are animal models rather than trials in dogs, and I want to be plain about that. What they give me is a mechanism that matches what I see clinically, which is a different and more useful thing than a product claim.
Fix the soil and the seed you already have will grow. That is the whole difference.
The sequence
Order of operations
This is not a rejection of probiotics. It is a disagreement about where they belong in the sequence. Anyone who has read my yeast protocol will recognize this: probiotics live in the third stage, never the first.
One variable at a time is the discipline that makes all of this legible. Change three things at once and you have learned nothing, whichever way the dog goes.
The exceptions
When I would still use one
Two situations move a probiotic up my list. Both are specific, and neither is the default case walking through my door.
On the first one. A double-blinded, placebo-controlled study in dogs with chronic enteropathy found that S. boulardii added to standard treatment achieved better control of clinical signs than standard treatment alone, with improvements in stool frequency, stool consistency and body condition. Twenty dogs, not randomized, which makes it a signal rather than a settled answer. It is still the best canine evidence I have seen for any product in this category.
Notice what both exceptions have in common. There is a specific reason, tied to something observed in this dog, and the probiotic is doing a defined job rather than being added because the gut is unwell and something should probably be given.
What this looks like in practice
The cases that taught me this
The dogs who reach me have usually been through the aisle already. A four-year-old with chronic intermittent loose stool, mucus and urgency, whose panel showed her primary butyrate producer had gone absent entirely. A six-year-old who could not hold weight, with biopsy-confirmed duodenitis and blunted villi. Another whose fecal came back positive for Clostridium, whose owner was handed a probiotic on the way out of urgent care and was not thrilled about it.
In each of those cases the probiotic question came up early, and in each of them it was not the lever that moved. What moved them was taking the load off the food, then rebuilding the transforming function, then watching one change at a time.
In one of those cases I did keep a yeast-based product in the plan, for exactly the reason described above. In another I took the probiotic out of the written plan entirely, because it was not doing identifiable work and it was making the picture harder to read.
Work with me
If you have a shelf of these and nothing has changed
That is the most common version of this conversation. Three or four products, some improvement that did not hold, and a dog whose stool is still telling you something is wrong. The useful next step is usually to work out which pattern you are in and what the gut is failing to do, then build the food and the formula around that answer. Book a consultation and we will start there.
Related reading: leaky gut, your dog’s digestion, East and West, and where probiotics sit in the yeast protocol.
Sources
Where this comes from
- Zmora N, Zilberman-Schapira G, Suez J, and others. Personalized gut mucosal colonization resistance to empiric probiotics is associated with unique host and microbiome features. Cell. 2018;174(6):1388-1405.e21. PubMed.
- Suez J, Zmora N, Zilberman-Schapira G, and others. Post-antibiotic gut mucosal microbiome reconstitution is impaired by probiotics and improved by autologous FMT. Cell. 2018;174(6):1406-1423.e16.
- Rao SSC, Rehman A, Yu S, Martinez de Andino N. Brain fogginess, gas and bloating: a link between SIBO, probiotics and metabolic acidosis. Clin Transl Gastroenterol. 2018;9:162. Full text. See also the published letters of concern regarding this study’s design, including Sachdeva and colleagues.
- Jensen AP, Bjørnvad CR. Clinical effect of probiotics in prevention or treatment of gastrointestinal disease in dogs: a systematic review. J Vet Intern Med. 2019;33(5):1849-1864. Full text.
- Shmalberg J, and others. A randomized, double blinded, placebo-controlled clinical trial of a probiotic or metronidazole for acute canine diarrhea. Full text.
- D’Angelo S, Fracassi F, Bresciani F, and others. Effect of Saccharomyces boulardii in dogs with chronic enteropathies: double-blinded, placebo-controlled study. Veterinary Record. 2018;182:258. PubMed.
On Shen Ling Bai Zhu San
- Gao Q, Tian W, Yang H, and others. Shen-Ling-Bai-Zhu-San alleviates the imbalance of intestinal homeostasis in dextran sodium sulfate-induced colitis mice by regulating gut microbiota and inhibiting NLRP3 inflammasome activation. J Ethnopharmacol. 2024;319(Pt 1):117136. PubMed. This is the study containing the microbiota-depleted arm.
- Shen-Ling-Bai-Zhu-San alleviates Crohn’s disease-like colitis by modulating fatty acid degradation via the PPAR pathway. J Ethnopharmacol. 2025. PubMed.
- Shen-Ling-Bai-Zhu-San and its derived polysaccharide ameliorate the severity of diarrhea induced by high lactose via modification of colonic fermentation. Full text.
- Chen R, Lin YL, Gao XL, and others. Shen Ling Bai Zhu San promotes gut IgA+ plasma cells to alleviate chronic diarrhea in mice via increasing systemic glutamine. J Ethnopharmacol. 2026;355:120544.
The information on Daily Dog Food Recipes is intended for nutritional, informational and educational purposes only. Nothing here is intended to diagnose, cure, treat or prevent any disease or illness. Please consult your veterinarian about your dog’s medical care, and do not stop or start a supplement your veterinary team has prescribed without speaking to them first.
Hannah Zulueta obtained her Certificate in Canine Nutrition from CASI Institute. She is also studying for her Doctorate in Acupuncture, Traditional Chinese Medicine, and Herbalism from the esteemed Pacific College of Health and Medicine. If you’re as keenly interested in health for yourself, visit her website for human health: Satori Acupuncture and Herbs.
She resides in San Diego with her three dogs, Maggie, Orbit, and Mr. Higgins.
She is available for one on one consultations. She develops evidence-based recipes that meet both NRC and AAFCO nutritional standards while integrating the therapeutic food principles of Traditional Chinese Veterinary Medicine into her formulations.
Additionally, you can find her sharing free content on Instagram.
