The Veterinary Microbiome Project

Beyond the Microbiome: Functional Gut Markers & What They Are Really Telling You with Betsy Redmond, Innovative Pet Lab

Most gut health conversations stop at the bacteria. Betsy Redmond wants to know what the body itself is doing.

Betsy Redmond is a microbiologist and co-founder of Innovative Pet Lab, a functional stool testing company that brings human clinical gut markers to dogs and cats. In this episode, Dr. Lily Chen sits down with Betsy to walk through five functional markers that can identify gut inflammation, immune dysfunction, intestinal permeability, pancreatic insufficiency, and dysbiosis before a pet ever reaches a diagnosis.

KEY INSIGHTS

• Fecal calprotectin is a direct measure of neutrophil-driven gut inflammation. A pet can have chronically elevated calprotectin long before developing full enteropathy, and catching it early gives clinicians a real window to intervene.

• Secretory IgA is the first line of immune defense at the gut lining. When it is too high, the body is actively fending off a threat. When it is too low, the immune system may not be defending itself at all.

• Fecal zonulin reflects intestinal permeability. NSAIDs, certain bacteria, and chronic inflammation can all drive it up. Saccharomyces boulardii has been shown to bring it down alongside low secretory IgA.

• Pancreatic elastase measures overall pancreatic enzyme output. A gray area between adequate function and insufficiency exists in pets just as it does in people, and borderline low levels in senior dogs can respond to digestive enzyme support.

• Beta-glucuronidase, when elevated, signals bacterial overgrowth interfering with the liver's phase II detoxification pathway. Bringing the number down with a supplement without fixing the microbiome is mopping the floor without turning off the faucet.

RESOURCES
Innovative Pet Lab: https://www.innovativepetlab.com
Instagram: @innovativepetlab

CONNECT WITH DR. LILY CHEN
Instagram: @dr.lilychen @the.unicorn.vet

Integrative Pet Wellness Center: https://integrativepet.com

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Real science. Real cases. And a little magic.

How medicinal mushrooms work as prebiotic fiber, immune trainers, and microbiome modulators, and what to look for on the label before you recommend one.Mushrooms, Microbiome & the Unifying Principle of Health with Dr. Rob Silver.

Most conversations about the microbiome start and end with bacteria.

Dr. Silver is an integrative veterinarian, nutraceutical formulator, and one of the most recognized experts in veterinary mycology in North America. In this episode, Dr. Lily Chen sits down with Dr. Silver to explore the growing research on mushrooms and the microbiome. They cover why beta-glucans are only part of the story, how to dose mushrooms for wellness versus therapeutic versus critical cases, which species to reach for first for gut health, and what to look for on a mushroom label when most of the industry still looks like the Wild West.

KEY INSIGHTS:

✨ Mushrooms are not just a source of beta-glucans. They also contain alpha-glucans, chitin, mannoproteins, and secondary metabolites, each of which has different effects on the immune system, gut barrier, and microbiome. Thinking of them as a single-fiber supplement undersells what they actually do.

✨ When gut bacteria ferment chitin from mushrooms, one of the byproducts is N-acetyl D-glucosamine, the same compound used clinically for leaky gut and inflammatory enteritis. The mushroom is essentially producing its own gut repair component.

✨ Of all the mushrooms studied for microbiome benefit, lion's mane has the most evidence. It has been used in Traditional Chinese Medicine for GI conditions for hundreds of years, and modern research is now showing benefits for inflammatory enteritis, gut barrier function, short-chain fatty acids, and the gut-brain axis.

✨ Reishi is the other standout for microbiome work, particularly for its hepatoprotective properties, its role in epilepsy through the gut-brain axis, and its use alongside turkey tail in oncology cases.

✨ Mushroom dosing is simpler than most clinicians assume. Using Traditional Chinese Medicine dosing tiers as a framework: one to three grams of dried powder for wellness, three to six grams for therapeutic cases, and three to nine grams for severe or critical cases in a 70 kg human. Scale down by body weight using Clark's law.

✨ A major quality problem exists in the mushroom supplement industry. Dr. Silver analyzed 11 turkey tail products for pets and found that only six had enough beta-glucans to qualify as a real mushroom product. The rest were primarily myceliated grain. Look for beta-glucan content on the label and always ask for a third-party certificate of analysis.

✨ Mushrooms improve vaccine duration of immunity. Pre-conditioning with mushrooms for two to four weeks before a booster in a dog with a low titer has been shown in multiple studies to produce a more robust and durable protective response.

✨ Routine prophylactic deworming without testing is not medically justified. Test first, then choose the right treatment. And when microbiome support is strong, the gut environment itself becomes more resistant to parasitic burden.

RESOURCES:

Real Mushrooms: https://www.realmushrooms.com

WellPet Dispensary: https://wellpetdispensary.com

Dr. Robert Silver DVM

Instagram: @docrobsilver

CONNECT WITH DR. LILY CHEN

Instagram: @dr.lilychen @the.unicorn.vet

Threads: @the.unicorn.vet

Linkedin: Lily Chen DVM & The Unicorn Vet

INTEGRATIVE PET WELLNESS CENTER https://integrativepet.com

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Real science. Real cases. And a little magic.

How Traditional Chinese Veterinary Medicine and acupuncture complement microbiome medicine to address the root patterns behind chronic GI disease.

What if the missing piece in your most stubborn chronic GI case was not another drug, another diet, or another diagnostic, but a needle placed in exactly the right point?

Dr. Nell Ostermeier has been practicing integrative veterinary medicine for over 22 years. She is a certified veterinary acupuncturist, educator, and founder of the Everyday Acupuncture Veterinary Community, a growing global network of veterinarians using Traditional Chinese Veterinary Medicine in practice.

In this episode, Dr. Lily Chen sits down with Dr. Ostermeier to explore how acupuncture and TCVM work alongside microbiome medicine to address the root patterns beneath chronic GI disease. They cover the spleen-stomach partnership in TCM, why stress triggers GI symptoms through the liver organ system, how PC6 and Stomach 36 influence the gut through measurable neurological pathways, and which herbal formulas veterinarians can reach for even without full TCM training.

KEY INSIGHTS:

✨ In Traditional Chinese Veterinary Medicine, the spleen and stomach are considered partners. Diarrhea generally points to the spleen. Vomiting generally points to the stomach. But neither can truly be in balance without the other.

✨ The spleen in TCM encompasses the functions of the pancreas and the intestinal microvilli, including transforming food, absorbing nutrients, and transporting them through the body. The ancient Chinese were more right than they knew.

✨ Stress-triggered GI symptoms involve the liver organ in TCM. When the liver is out of balance, it puts pressure on the spleen-stomach apparatus, which is why stress so often shows up as diarrhea, IBS, or IBD flares.

✨ PC6, one of the most highly researched acupuncture points, reduces nausea and supports the gut through its long-loop reflex into the brainstem, influencing the vagus nerve, parasympathetic outflow, and neurotransmitters like serotonin, GABA, and dopamine.

✨ For stress-triggered GI cases, Dr. Ostermeier reaches for Xiao Yao San, also known as Happy Wanderer. For chronic or senior patients with depleted digestive energy, she reaches for Liu Jun Zi Tang, known as Six Gentle Pets in the Kan herbal line.

✨ Removing the spleen does not change the TCM treatment approach. Spleen acupuncture points are still used because the functions the organ represented, digestive transformation, blood building, and immune modulation, still need to be supported.

✨ Acupuncture was originally designed to maintain balance and prevent imbalance, not to correct it. Senior patients especially benefit from a regular monthly maintenance interval to prevent the slow return of patterns that have structural or degenerative roots.

✨ TCM allows clinicians to treat patterns even when a definitive Western diagnosis has not yet been reached. If an animal is showing signs of liver congestion or spleen weakness, those patterns can be addressed right now while the workup continues.

RESOURCES:

Everyday Acupuncture Veterinary Community:

The Every Day Acupuncture Vet Community

Private Veterinarian-Only Facebook Group:

Every Day Acupuncture For Veterinarians

Dr. Nell Ostermeier's Website: https://www.peopleandpet.com/

CONNECT WITH DR. NELL OSTERMEIER

Instagram: @people.and.pet

Linktree: @Dr.Nell

CONNECT WITH DR. LILY CHEN

Instagram: @dr.lilychen

Instagram: the.unicorn.vet

Threads: @the.unicorn.vet

Linkedin: Lily Chen DVM & The Unicorn Vet

INTEGRATIVE PET WELLNESS CENTER https://integrativepet.com

UNICORN ACADEMY https://theunicorn.academy

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Real science. Real cases. And a little magic.

Dr. Margo Roman has been practicing integrative veterinary medicine since 1978. She started her own hospital in 1983, was the first woman to complete the IVAS acupuncture course, and has spent the last 30 years raising seven generations of antibiotic-free donor dogs on seven organic acres in Massachusetts. She did not call it FMT. She called it Microbiome Restorative Therapy, and the distinction matters.

In this episode, Dr. Lily Chen sits down with Dr. Roman to talk about why terrain preparation changes everything, how medical ozone works alongside microbiome restoration to break down biofilm and oxygenate the gut before a transplant, and what happens when you stop just throwing poop at a problem and actually rebuild the environment it needs to survive in. They also talk about a parvo case that turned around in an hour and a half, a human story that will stop you in your tracks, and what 48 years of refusing to give up on a patient actually looks like in practice.

KEY INSIGHTS

• Dr. Roman coined the term Microbiome Restorative Therapy because FMT alone misses the point. If the gut terrain is not prepared to receive and sustain the transplant, it will not take.

• Medical ozone administered rectally before a transplant breaks down biofilm, hyperoxygenates the colon, and stimulates mitochondria in the columnar stem cells of the gut wall, giving the new microbial community a cleaner surface to colonize.

• The reason human FMT protocols historically used vancomycin and metronidazole before transplant was to clear the gut. Ozone achieves a similar result without destroying the beneficial bacteria that take the longest to come back.

• A nine-month-old husky puppy arrived unconscious, white as a sheet, with blood pouring from its rear end from parvo. After rectal ozone, FMT, nutraceuticals, and subQ saline, it was sitting up and wanting to eat within an hour and a half. The only dog in that outbreak that died did not receive ozone or FMT.

• Dr. Roman's donor dogs have never received antibiotics across 30 years and seven generations. They are rated among the highest in microbial diversity in the country. Her MBRT-7G capsule blends material from four generations of donors in a single dose.

• Fresh donor material consistently outperforms frozen in clinical results. Metabolites, bile acids, and live anaerobes that do not survive freeze-drying appear to play a meaningful role in engraftment success.

• Antimicrobial resistance is now responsible for 1.2 million human deaths per year globally. Veterinarians are part of that conversation whether they choose to be or not, and terrain-based medicine is one of the most direct answers available.

RESOURCES

MASH Veterinary Clinic: https://www.mashvet.com

MBRT Life: https://www.mbrt.life

The Miracle of the Microbiome by Dr. Margo Roman: https://atouchoflifembrt.square.site/

AHVMA (American Holistic Veterinary Medical Association) https://www.ahvma.org

CIVT (College of Integrative Veterinary Therapies) https://www.civtedu.org

Chi University https://chiu.edu

IVAS (International Veterinary Acupuncture Society)

CONNECT WITH DR. MARGO ROMAN

Facebook: Margo Roman

Instagram: @Drmargoroman

CONNECT WITH DR. LILY CHEN

Instagram: @dr.lilychen @the.unicorn.vet

Threads: @the.unicorn.vet

LinkedIn: Lily Checn DVM

INTEGRATIVE PET WELLNESS CENTER: https://integrativepet.com

UNICORN ACADEMY: https://theunicorn.academy

LinkedIn: The Unicorn Vet

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Real science. Real cases. And a little magic.

How the science behind the Dysbiosis Index is reshaping how we diagnose, treat, and think about chronic GI disease in companion animals.

If you have spent any time in the veterinary microbiome space, you already know the name. Dr. Jan Suchodolski is a professor and head of Microbiome Sciences at the Gastrointestinal Laboratory at Texas A&M University, one of the most influential veterinary microbiome research centers in the world. A lot of the foundational science clinicians reference every day came out of his lab.

In this episode, Dr. Lily Chen sits down with Dr. Suchodolski to talk about how the Dysbiosis Index was built, what it is actually measuring, and why a single number can tell you more about a patient than a long list of bacterial species. They dig into chronic GI disease as a spectrum, the two major drivers of severe dysbiosis, and why some patients can be restored while others cannot. They also get into where microbiome medicine is headed next, including emerging mucosal damage markers, early diagnostic testing in puppies, the role of steroids alongside FMT, and what a truly multimodal approach to GI disease looks like in practice.

Real science, real cases, and a little magic.

KEY INSIGHTS:
✨ The Dysbiosis Index is a machine learning tool built from hundreds of validated qPCR studies across thousands of animals. It measures total microbiome shift, not just individual bacterial changes, and a score above zero indicates dysbiosis, with higher numbers reflecting increasingly severe disruption.

✨ There are two major drivers of severe dysbiosis: broad-spectrum antibiotic use and chronic GI disease with mucosal remodeling. Antibiotic-induced dysbiosis often recovers on its own or with FMT. Chronic mucosal damage is a different challenge entirely.

✨ Not every animal with chronic GI disease has dysbiosis, and not every dysbiotic animal has the same underlying disease. Treating them as the same population is a clinical mistake.

✨ Twenty years ago, the treatment recommendation for dysbiosis was antibiotics. Understanding why that was both clinically effective and fundamentally wrong is one of the most important paradigm shifts in veterinary GI medicine.

✨ FMT is not a one-session fix for chronic GI disease. If there is partial improvement followed by relapse, that is a reason to keep going, not to stop. The severity of the dysbiosis should set the expectation for how long and how often treatment is needed.

✨ Steroids do not significantly disrupt the microbiome at anti-inflammatory doses and can actually support mucosal recovery through bile acid transporter pathways. A multimodal approach combining FMT, diet, and targeted anti-inflammatory therapy is increasingly where the evidence is pointing.

✨ The Dysbiosis Index normalizes around eight weeks of age in puppies. Testing after that window gives clinicians a genuine early intervention opportunity before subclinical dysfunction progresses.

✨ Emerging fecal markers of mucosal cell shedding, including arachidonic acid, nervonic acid, and ceramides, may open a new diagnostic layer for understanding epithelial damage independently of microbiome shifts. This is where Dr. Suchodolski's lab is focused next.

RESOURCES:
Texas A&M Gastrointestinal Laboratory: https://vetmed.tamu.edu/gilab

FOLLOW:
Integrative Pet Wellness Center: https://integrativepet.com

Unicorn Academy: https://theunicorn.academy

Dr. Lily Chen:

Instagram: @dr.lilychen @the.unicorn.vet

Threads: @the.unicorn.vet

LinkedIn: Lily Chen, DVM, CVA & The Unicorn Vet

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A practical guide to reading the microbiome report, choosing FMT, and resolving the cases that don't respond to conventional tools.

The gut microbiome has gone from buzzword to bedside, but what is it actually telling you in practice? In this episode of The Veterinary Microbiome Project, Dr. Lily Chen sits down with Dr. Holly Ganz, microbial ecologist and Co-Founder and Chief Science Officer of AnimalBiome, to turn microbiome science into clinical decisions.

Together they unpack how to read a companion animal microbiome report without drowning in it: 16S rRNA sequencing versus the Dysbiosis Index, relative versus absolute abundance, and a simple three-part framework for spotting missing core bacteria, pathobiont overgrowth, and low diversity. They get practical on fecal microbiota transplantation (FMT): what goes into an oral FMT capsule, why consistency matters, donor screening, and when a case needs more support. Plus the gut-organ axes (gut-skin, gut-brain, gut-kidney), supplements and fermented foods, autologous self-FMT banking before antibiotics, and where microbiome-informed medicine is headed next.

A must-listen for veterinarians, specialists, and integrative practitioners ready to look one layer deeper. Real science, real cases, and a little magic.

KEY INSIGHTS:

✨ Dr. Ganz developed the first oral FMT capsules for dogs and cats after her own herding dog, Yuki, was cured of recurring hemorrhagic gastroenteritis once the missing gut bacteria were restored.

✨ A simple three-part framework for reading a report: check whether core beneficial bacteria are missing, whether pathobionts like E. coli or C. perfringens are overgrown, and what overall diversity and richness look like.

✨ 16S rRNA sequencing maps the whole bacterial ecosystem, while targeted panels like the Dysbiosis Index are built for known pathogens. Each has its place depending on what the clinician needs to know.

✨ Oral FMT capsules showed improvement in about 80 percent of cases within 30 days in AnimalBiome's data, though some animals need a slower, more gradual approach to tolerate them.

✨ Intolerance to a first FMT session is not a reason to stop. It can signal the microbiome needs more support, not less, since the immune system has to learn which bacteria are friend rather than foe.

✨ Donor screening is central to safety. AnimalBiome runs IDEXX and Antech panels on every donation to rule out parasites and pathogens before freeze-drying.

✨ A recent pilot study with Dr. Curtis Dewey linked FMT capsules to improvement in canine cognitive dysfunction, one of many emerging gut-organ axis findings spanning skin, kidney, and brain health.

✨ Autologous self-FMT, banking a healthy pet's own stool before a course of antibiotics so it can be transplanted back afterward, is an emerging option for protecting an already-balanced microbiome.

RESOURCES:

AnimalBiome: https://animalbiome.com

AnimalBiome Veterinary Hub: https://animalbiome.vet

Email: [email protected]

LinkedIn: https://www.linkedin.com/company/animalbiome

Facebook: @animalbiomeveterinary

Instagram: @animal.biome

FOLLOW:

Integrative Pet Wellness Center: https://integrativepet.com

Unicorn Academy: https://theunicorn.academy

Dr. Lily Chen:

Instagram: @dr.lilychen @the.unicorn.vet

Threads: @the.unicorn.vet

LinkedIn: Lily Chen, DVM, CVA & The Unicorn Vet

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Why the Microbiome, and Why Now? With Dr. Lily Chen

Eight years ago, Dr. Lily Chen was seeing a German Shepherd named Klaus every couple of weeks for chronic diarrhea that would not resolve. She had prescribed everything and run every diagnostic. Nothing worked. Then Klaus's mom asked a question that changed the direction of Dr. Lily's career: why don't we try a fecal transplant?

In this first episode, Dr. Lily shares the case that pulled her into microbiome medicine, why the original sedated FMT protocol had real limitations for pet families, and how that led her to develop the BiomeBalance™ method: sedation free, fast, and gentle. She also lays out why she believes every veterinary professional needs to understand this work, and what listeners can expect from the podcast going forward.

KEY INSIGHTS:

✨ Klaus's case was the turning point. After one sedated FMT session his chronic diarrhea improved dramatically. After a second, it resolved completely with no further prescriptions needed.✨ The original sedated FMT protocol worked, but anesthesia was a deal breaker for many pet families. It added risk and cost, and many parents simply said no.✨ The BiomeBalance™ method took roughly five years to develop into a system that runs smoothly in a real, busy practice. It is sedation free, takes only a couple of minutes, and pet parents can stay in the room.✨ The microbiome connects to far more than GI disease: the gut-immune axis, the gut-skin axis, chronic allergies and itch, and even oncology and immune-mediated cases.✨ Tools like the Dysbiosis Index and microbiome testing now let clinicians measure what used to only be guessed at, including how habits like reflexive metronidazole use affect the gut long term.✨ Pet parents are already researching root cause options. If clinicians are not equipped to have that conversation, someone else will have it for them, not always accurately.✨ Future episodes will cover how to test and interpret microbiome reports, how to select donor material, how to support chronic GI, skin, and cancer cases through the gut, and how to bring clients along toward root cause care.

FOLLOW:Integrative Pet Wellness Center: https://integrativepet.comUnicorn Academy: https://theunicorn.academy

Dr. Lily Chen:

Instagram: @dr.lilychen @the.unicorn.vetThreads: @the.unicorn.vetLinkedIn: Lily Chen, DVM, CVA & The Unicorn Vet

Join our newsletter to get more clinical microbiome insights 🐶🐈‍⬛

Welcome to The Veterinary Microbiome Project: Gut Health, FMT & Root Cause Medicine with Dr. Lily Chen

The dog whose diarrhea comes back the moment they look at a blueberry wrong. The cat with IBD who has tried every diet trial and is still vomiting and losing weight. The patient on every allergy drug and injection who is still itching. If you have sat with a case like this and thought there has to be more I can do, this podcast is for you.

Dr. Lily Chen is an integrative veterinarian, practice owner, and creator of the BiomeBalance™ sedation free fecal microbiota transplant method. The Veterinary Microbiome Project brings the gut microbiome out of the research papers and into the exam room, through real conversations with the researchers, specialists, and FMT pioneers redefining what is possible in clinical practice.

Each episode covers dysbiosis, fecal microbiota transplant, the gut immune and gut skin axes, antibiotic stewardship, and the chronic and complex cases that keep clinicians up at night. No fluff. Just the science, the cases, and protocols you can actually use in a busy practice, because suppressing symptoms was never why we became vets.

KEY INSIGHTS:
✨ Chronic GI disease, relentless IBD, and allergy cases that fail every standard protocol often point back to the same root: dysbiosis.
✨ The existing toolbox of symptom management is not keeping pace with how sick our patients are getting. Microbiome medicine is a shift that has already started.
✨ Every conversation is built to leave clinicians with something practical: how to test, how to interpret results, how to bring clients along, and how to integrate root cause medicine into daily practice.
✨ This podcast exists because veterinary professionals deserve a seat at the table with colleagues who refuse to settle for managing symptoms.

FOLLOW:Integrative Pet Wellness Center: https://integrativepet.com

Dr. Lily Chen:

Instagram: @dr.lilychen @the.unicorn.vet
Threads: @the.unicorn.vet
LinkedIn: Lily Chen, DVM, CVA & The Unicorn Vet

Join our newsletter to get more clinical microbiome insights

👉 https://theunicornvet.kit.com/vetsignup