If you’ve ever tried to “fix your gut” by buying a stack of supplements and hoping they’d magically reset your digestion, you already know the truth:

Gut healing is not something you take; It’s something you build.

Supplements can assist that process - sometimes dramatically - but they’re never the foundation. We can’t out-supplement a poor diet, lack of movement, or a circadian mismatch. 

Before we even talk about supplements, we need to be honest about something most people don’t realize:

You cannot heal the gut while living in a way that is constantly injuring the gut.

And that injury doesn’t just come from food.

It comes from light exposure, sleep timing, stress load, nervous system dysregulation, nutrition, poor stomach acid production, and the very common delusion that healing is just about “removing gluten & sugar and taking probiotics.”

Let’s reframe the entire conversation - and then we’ll get into the supplements I actually use clinically, why they work, and who they’re most effective for.

Why Gut Healing Isn’t About Taking a Supplement

Most people start with supplements because they’ve been trained by the wellness industry to think:

“I have gut issues → therefore I need a gut supplement.”

This approach is a recycling of the “pill for every ill” mentality we find so often in allopathic medicine. 

But the gut is not a tube you pour powders into until it behaves.

It is a living, immune-rich, hormone-regulated, electrically active tissue system that responds to signals long before it responds to supplements.

That means gut dysfunction isn’t random, nor is it genetic. 

It’s adaptive.

The bloating, the constipation, the reflux, the food intolerances - they are symptoms of a system that is dysregulated, not a single organ that is “broken.”

So yes, the supplements below are powerful. I use them with clients every single day.

But they only work long-term when the root physiology is supported.

And the most overlooked part of that physiology is circadian biology.

The Circadian Science of Gut Health (The Part Almost Everyone Misses)

The gut is not just a digestive organ — it is a clock-controlled organ.

Every part of digestion follows a circadian rhythm:

Research confirms that circadian disruption — late-night eating, blue light at night, irregular sleep schedules — increases intestinal permeability (leaky gut), alters microbiome composition, and slows motility (PMID: 33991175, 34807059).

This means people are trying to “heal leaky gut” while living in the exact rhythm that causes it.

That’s why one of the first interventions I give clients is not a supplement — it’s morning light exposure.

It turns on the vagus nerve.

It sets the bowel “clock”.

It signals safety to the body.

It costs nothing.

But it’s more foundational than any pill.

Once circadian rhythm is back online and nutrition is supplying the raw materials for repair, then supplements become powerful leverage — not crutches.

Nutrition: The Original Gut Supplement

Food is not just fuel.

Food is chemical information.

Every bite you eat programs gene expression, hormone signaling, neurotransmitter production, and immune activity in the gut.

That means there is no supplement that can undo:

– chronic under-eating, cycles of binging and restricting 

– excessive snacking

– low stomach acid from rushing through meals + years of plant based diets

– seed oils and ultra-processed foods

– lack of protein to rebuild tissue

– low salt and healthy fat intake causing constipation

– eating while in fight-or-flight

You cannot out-supplement missing minerals, missing amino acids, or missing sunlight.

Once nutrition stabilizes the terrain — real food, protein at breakfast, minerals, fat for motility, chewing to activate stomach acid — then supplementation becomes strategic support, not an act of desperation.

So When Are Supplements Actually Needed?

Supplements are most effective when they are used to:

✅ support healing while deeper root causes resolve

✅ temporarily replace something the body is not producing (ex: stomach acid, bile flow)

✅ provide concentrated levels of a nutrient/mineral required for repair

✅ protect the gut lining while inflammation is cleared

✅ regulate microbial balance after antibiotics, infection, travel, stress, or reactive food intake

THE SUPPLEMENTS I ACTUALLY USE FOR GUT HEALING

🌿 1. Slippery Elm

Category: Soother & Sealant

Best For: leaky gut, irritation, loose stool, cramping, post-antibiotic healing

Mechanism: mucilaginous polysaccharides coat and repair the mucosal lining

Why I love it: It’s safe for nearly everyone, extremely well tolerated, and it works. 

When the digestive mucosa is inflamed, frayed, or permeable, the enterocytes (gut lining cells) cannot absorb nutrients efficiently. Slippery Elm coats the lining and gives it the conditions to heal.

I often recommend it 15 minutes before meals to calm the tissue before food makes contact.

Capsules or powder both work — this is one of my most universal gut supports.

2. Digestive Bitters

Category: Digestive Fire & Flow

Best For: low stomach acid, reflux, bloating after meals, constipation, sluggish bile

Mechanism: bitter taste receptors → vagus nerve → HCl, enzymes, bile release

Bitters do something enzymes cannot:

They restore the body’s ability to digest on its own.

Dandelion (leaf, root, tincture, decoction, or even in salad form) is one of my go-tos because it supports both liver and bile flow — a missing piece for people who bloat after fat or feel nauseous after meals.

Burdock root is another wonderful bitter that supports the liver, alkalizes the blood and assist with bile flow and digestive enzyme secretion. Start small with burdock root, it packs a powerful punch in the form of liver detox. 

📌 Tip: If you don’t want alcohol in your tincture, add hot water — it evaporates.

3. Colostrum

Category: Sealant + Immune Buffer

Best For: acute gut inflammation, post-infection, post-food poisoning, permeability, immune rebuilding

Mechanism: immunoglobulins, lactoferrin, growth factors repair lining + train immune system

Colostrum is baby’s first food for a reason — it seals and protects the gut.

But it’s not meant as a forever supplement.

I typically use it for ~8–12 weeks while deeper root causes are being addressed, then cycle off.

Look for low/no heat, clean-sourced colostrum so the active compounds are intact.

4. L-Glutamine

Category: Sealant + Fuel Source

Best For: leaky gut, intestinal permeability, post-antibiotics, post-infection, over-exercisers

Mechanism: primary fuel for enterocytes → literally rebuilds gut lining

Glutamine can help “knit” tight junctions back together — but it works best when inflammation is already being lowered.

I do not recommend it for people with mold toxicity or active cancer (due to metabolic pathways), but it is extremely effective in many gut-healing protocols.

5. Zinc

Category: Digestive Support + Immune Repair

Best For: low stomach acid, poor protein digestion, recurrent infections, hair loss, slow healing

Mechanism: required for stomach acid production, brush-border enzymes, immune signaling

People don’t realize this:

You need bioavailable zinc to extract nutrients from your food.

So even if you’re eating red meat, oysters, etc… If stomach acid is low, you can’t liberate the zinc inside it, which means you stay deficient and digestion stays weak.

Supplemental zinc is often necessary in early repair phases, especially with low appetite, hair loss, white spots on nails, or chronic loose stool.

6. Vitamin C

Category: Immune + Motility Support, Foundational Nutrient Repletion

Best For: GUT REPAIR, constipation, histamine/mcas, post-illness symptoms, collagen-building

Mechanism: antioxidant, strengthens epithelial tissue, increases bowel motility at higher doses

Most people think of Vitamin C as an immune supplement.

But in gut healing, it’s a motility agent, a collagen builder, and a mast cell stabilizer.

It is also one of the few gut-friendly supplements that is safe in very high doses for most people — and can be titrated to “bowel tolerance” for constipation relief.

The form which is the true gut healer is pure ascorbic acid - not liposomal or whole food vitamin c supplements. 

I have seen enormous value in reviewing and applying the methods used by Dr. Robert Cathcart and Linus Pauling. You can determine you level of bowel tolerance by taking 3-5grams of pure ascorbic acid every 15-30 minutes until a loose watery stool is produced. Record the total dosage, and then calculate about 80-90% of that amount as a daily dosage, which you can split up throughout your day. This method is called titrating to bowel tolerance, it is the most effective way to saturate your tissues in vitamin c. 

7. Saccharomyces boulardii

Category: Microbiome Defense

Best For: diarrhea, post-antibiotics, candida overgrowth, traveler’s gut, C. diff history

Mechanism: beneficial yeast that crowds out pathogens + increases secretory IgA

This is one of the only probiotics that can be taken during antibiotics, and it’s often one of the first I bring in for gut dysbiosis.

It’s not a forever supplement — it’s a targeted clinical tool.

8. Probiotics

Category: Microbiome Reset

Best For: gas, bloating, post-antibiotic recovery, IBS, slow motility, SIBO support

Mechanism: spores survive stomach acid, recondition terrain rather than “adding bacteria”

I don’t use generic probiotics. 

I use strain-specific probiotics based on the person’s symptoms.

Spore-based forms can be incredibly useful because they train the microbiome instead of just adding bacteria that may not colonize. For severe gut issues I like to go with at least 8 different strains and at least 25 Billion CFU. Certain stronger strain combos can be used for a short duration, like 3-6 months to assist with deeper gut work. 

9. Collagen 

Category: Structural Repair + Barrier Support

Best For: leaky gut, post-antibiotic gut lining repair, skin issues, joint weakness, post-surgery healing, aging digestion

Mechanism: supplies glycine, proline, and hydroxyproline — the amino acids required to rebuild epithelial tissue and collagen matrix in the gut wall

Collagen is not just a “beauty supplement.”

It’s a gut lining raw-material supplement.

The gut is made of connective tissue.

When that tissue breaks down — from stress, processed foods, alcohol, infections, low stomach acid, or chronic inflammation — the body needs glycine and proline to rebuild it.

Most people do not get enough glycine from diet alone, especially if they only eat muscle meat and not bones, skin, or slow-cooked cuts.

Collagen (and gelatin!) can be a game-changer when combined with:

✅ real protein (not shakes alone)

✅ stomach acid support

✅ minerals (especially sodium + potassium)

✅ Vitamin C (required for collagen synthesis)

10. Beef Liver (Desiccated or Fresh)

Category: Foundational Nutrient Repletion

Best For: fatigue, constipation, slow wound repair, hormonal imbalance, low stomach acid, low iron, poor detox capacity, hair loss

Mechanism: nature’s multivitamin — rich in retinol, B12, folate, iron, choline, copper, zinc, and amino acids

I don’t consider beef liver a “gut supplement.”

I consider it the nutrient insurance policy required for the gut to have the materials to heal.

The gut lining cannot rebuild itself without:

– Vitamin A (retinol — not beta carotene)

– Zinc

– Copper

– B vitamins (especially B12 and folate)

– Iron

– Choline

– Amino acids

Most people with gut issues are severely under-nourished at the micronutrient level — especially women eating “clean but low-calorie” diets.

Beef liver delivers a dense nutrient payload that supports:

✅ stomach acid formation (zinc + B12)

✅ epithelial repair (retinol + amino acids)

✅ better energy production (B vitamins + copper)

✅ improved motility + detox (choline)

✅ thyroid hormone conversion (iron, selenium synergy)

Capsules work for people who won’t eat fresh liver — the key is consistency.

11. Manuka Honey (Medicinal-Grade)

Category: Antimicrobial + Mucosal Repair

Best For: H. pylori, ulcerations, sore throats, post-antibiotic gut irritation, immune support, SIBO recovery

Mechanism: high methylglyoxal (MGO) rating → antibacterial, anti-inflammatory, pro-healing

Manuka honey is not the same as regular honey.

It has measurable antibacterial activity, can inhibit pathogenic bacteria in the gut, and supports mucosal healing.

I only recommend authentic, lab-tested Manuka honey — not “Manuka-flavored” honey with no verified MGO content.

📌 Brand preference clarification for transparency:

I personally use Manukora because it’s one of the only companies that is fully traceable from hive to jar and now offers honey in glass, not plastic — which is important when using something this medicinal.

✅ best used: ½–1 tsp on empty stomach a.m. or before meals for gut soothing

✅ also useful during gut flares, post-food poisoning, or after travel

12. Magnesium (Multiple Forms Matter)

Category: Motility + Nervous System + Enzyme Support

Best For: constipation, tension, sleep issues, low stomach acid, stress-driven gut issues

Mechanism: relaxes smooth muscle tissue, increases peristalsis, regulates electrolyte balance, modulates stress response

Most people are magnesium deficient, and if you have gut issues, stress, or constipation — you are using up magnesium faster than you’re replacing it.

Not all magnesium is the same. 

I often use combinations of forms — not just one.

✅ liquid ionic magnesium: 10x more absorbable 

✅ citrate: moves the bowels

✅ glycinate: calms stress-driven gut dysfunction, assists with sleep 

✅ threonate: supports brain-gut axis

✅ malate: helps motility by restoring cellular energy

🛠️ Troubleshooting Diarrhea: What I Do First

When a client suddenly develops diarrhea — whether from food poisoning, travel, stress, or a sudden flare — I immediately do two things:

1. Increase Saccharomyces boulardii (often double the dose short-term)

2. Increase targeted probiotics based on symptoms

S. boulardii is one of the fastest microbiome stabilizers we have — it binds pathogens, increases secretory IgA, and protects electrolyte balance.

👉 This is almost always my first response before using anti-diarrheal drugs.

Then we assess:

• • Was it triggered by food?
  • Did it follow alcohol or restaurant eating?
  • Was there a stress surge before it started?
  • Has there been poor sleep or travel dysregulation?

Tracking patterns is crucial.

The bowels are responsive, not random — and a simple food/symptom log can reveal the trigger.

🔒 Troubleshooting Constipation: What Works in the Real World

Most people think constipation means they need more fiber.

But in clinical practice, I repeatedly see the opposite — fiber often worsens stool bulk, bloating, and cramping when the gut lining is already irritated. 

My first-line constipation interventions are:

✅ Add fat (tallow, butter, ghee, coconut oil -  fat lubricates the bowels)

✅ Add salt (constipation is often dehydration + electrolyte imbalance)

✅ Add magnesium (citrate form, not oxide which is way too harsh)

✅ Add Vitamin C (bowel-tolerance dosing moves the colon reliably and safely)

And a quick note — hydration matters, but water alone does not solve constipation.

You need minerals and fat for motility.

Fiber can help once the gut is healed, but when the mucosa is raw and inflamed, adding fiber is like rubbing sandpaper on a sunburn. 

When Supplements Don’t Work (And What That Tells Us)

If someone is taking:

– probiotics, but still bloated

– enzymes, but still constipated

– L-glutamine, but still inflamed

– magnesium, but still not pooping

– zinc, but still low in stomach acid

It’s not because the supplements “failed.”

It’s because the root conditions have not been corrected.

Supplements don’t override:

❌ sympathetic dominance (stress state)

❌ eating while multitasking and not chewing your food properly

❌ low stomach acid from chronically low protein intake

❌ circadian misalignment

❌ blue light at night suppressing melatonin-driven gut repair

❌ under-mineralized hydration

❌ fear of salt, fat, or calories

There is no such thing as a supplement strong enough to fix a lifestyle that’s still creating the problem.

🚫 Supplements I Rarely Recommend — And Why

❌ Generic probiotics

→ Too random, often worsen symptoms, rarely colonize

❌ Fiber powders for constipation

→ Gas, bloating, dependence; constipation is usually poor food choices and poor motility, not lack of fiber

❌ Enzymes as a long-term crutch

→ If you’re always taking enzymes, you’re not fixing the stomach acid signal that triggers enzyme release

❌ A supplement-only gut protocol

→ Always fails, always leads to relapse

Closing Reminder: Supplements Are Tools — Not Foundations

The right supplements can accelerate healing.

They can calm inflammation, restore lining integrity, improve motility, and recondition the microbiome.

But supplements only work when paired with:

✅ circadian rhythm repair

✅ real food and good quality protein + fat 

✅ stomach acid activation

✅ nervous system regulation

✅ mineralized hydration

✅ light before screens

✅ chewing + slow eating

✅ elimination of processed seed oils + food chemicals, plastics, and other toxins

If you want to explore any of the supplements mentioned above, you’ll find versions of them in the Dr. Clark Store catalog — just make sure you’re rebuilding the terrain, not trying to outsource healing to a handful of capsules. 

And if you need help customizing a protocol for your specific situation, reach out to me and I would be happy to see how I can help. 

Because there are no “magic pills”. And real gut healing isn’t passive. 

It’s a collaboration between your biology, your environment, and your choices.

About the Author:

Davida Syne is a Naturopath specializing in hormone and gut health for women. She integrates evidence-based nutrition, herbal medicine, circadian biology, and the science of habit formation to address root causes and support the body’s natural healing abilities. With a background in the arts, yoga, breath, and movement. Davida takes a holistic approach to healing, weaving together structural, chemical, emotional, and energetic health. She believes that true healing begins with understanding the body’s innate wisdom and working in coherence with it. Through her work, Davida inspires others to reconnect with themselves, embrace nourishing practices, and reclaim their health as a pathway to liberation and personal sovereignty.

You can connect with her on Instagram @davida.light or via her website www.vidahealingarts.com