Upstream: The Complete Gut Health Guide

A free guide from Luna Lab

Upstream

The Complete Gut Health Guide

Fix the source, not just the symptoms.

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Introduction

Your gut is like a stream.

If the water downstream is muddy, you can keep scooping it out. Or you can walk upstream and find out what is getting in.

Most people treat their gut issues downstream. A pill for the bloating, a cream for the skin, an elimination diet for the food reactions. Sometimes it helps for a while. Then the symptoms come back, because the source was never touched.

This guide walks upstream first. It is written to be read in order, like a short book.

Chapter 1 · The source

The six systems your body uses to protect your gut, and what happens when they break down.

Chapter 2 · Protect them

The everyday things wearing them down, and the habits that help them work again.

Chapter 3 · Further downstream

How damaged protection systems show up as the symptoms you feel, and the protocol to clear each one.

Chapter 4 · Repair

Rebuilding the gut lining once the cleanup is done.

Your roadmap

All of it on one page: what to do, in what order, and for how long.

Bonus · The high-dose probiotic gut remedy

Restocking the good bacteria with a 36-hour homemade yogurt.

Fix the source first. Everything downstream gets easier.
Chapter 1

Your six protection systems

Every cause has a cause. But almost every gut issue runs through the same six systems.

"Root cause" is an endless cycle.

You feel bloated after almost every meal.

↑ because

Bacteria have overgrown in your small intestine.

↑ because

Your stomach acid is too low to keep them in check.

↑ because

You have been on acid reducers for a year.

↑ because

They were prescribed for heartburn.

↑ because

The heartburn started during months of stress.

↑ because

It was busy season at work.

↑ because

Your team was two people short.

↑ because

The company had just lost its biggest client…

…and on, and on.

You could chase the root cause forever. That is why, instead of root causes, we focus on your body's six protection systems.

Your body has six systems whose whole job is to keep your gut clean, sealed and balanced. When one of them is damaged, problems start to appear downstream: bloating, cravings, food reactions, skin flare-ups, irregular digestion. Protect these systems, and you stop the cycle much closer to the source.

  1. Stomach acid, the gatekeeper
  2. Bile and digestive enzymes, the digestion crew
  3. The cleaning wave, your gut's housekeeper
  4. The gut lining, the wall
  5. Microbe diversity, strength in numbers
  6. The nervous system, the master switch
Protection system 1 of 6

Stomach acid: the gatekeeper.

Most people think stomach acid is the enemy. It is actually your first line of defense. It kills most of the bacteria, yeast and parasites that come in with your food, starts breaking down protein, and signals the rest of your gut to get to work.

When it breaks down

Bugs survive the trip and can overgrow further down. Heavy meals sit like a brick, and you absorb less B12, iron, zinc and magnesium. Heartburn is not always too much acid; it is usually the valve at the top of the stomach. Long-term acid reducers lower your defense, so talk to your doctor before changing them.

What wears it down: long-term acid reducers · chronic stress · eating in a rush · H. pylori · age

Protection system 2 of 6

Bile and enzymes: the digestion crew.

Stomach acid starts digestion; bile and enzymes finish it. Your liver makes bile and your gallbladder releases it to break fat into tiny droplets. Bile also helps keep the small intestine clean. Your pancreas adds enzymes that break down fat, protein and carbs.

When it breaks down

Food reaches your gut bacteria half digested, and they ferment it into gas. Fatty meals leave you heavy, stools may be pale or float, and vitamins A, D, E and K are absorbed less well. Pain under your right ribs after fatty meals needs a doctor.

What wears it down: low stomach acid · skipping meals then overeating · very low-fat diets · gallbladder problems

Protection system 3 of 6

The cleaning wave: your gut's housekeeper.

The one almost nobody has heard of. Between meals, your small intestine runs a sweeping wave called the migrating motor complex. About every 90 to 120 minutes while you are not eating, it pushes leftover food and bacteria down to the large intestine. Every time you eat, it pauses.

When it breaks down

Bacteria are not swept away. They settle in the small intestine, multiply and ferment your food early. Bloating builds through the day, and overgrowth tends to come back even after it is cleared.

What wears it down: snacking all day · food poisoning · stress · sitting all day · low thyroid

Protection system 4 of 6

The gut lining: one cell thick.

A single layer of cells stands between what you eat and your bloodstream. Tight seals hold the cells together, and a layer of mucus keeps bacteria at a distance. The good news: these cells replace themselves every few days, so the lining can recover quickly.

When it breaks down

The seals loosen and particles slip through. This is often called "leaky gut." Your immune system reacts, and that can show up far from your gut: food sensitivities, skin flare-ups, brain fog, achy joints.

What wears it down: pain relievers · alcohol · gluten · emulsifiers · sugar · stress · overgrowth

Protection system 5 of 6

Microbe diversity: strength in numbers.

You carry roughly as many bacterial cells as human cells. Hundreds of species help digest fiber, make vitamins, feed your gut lining and train your immune system. The wider the mix, the harder it is for any one troublemaker to take over.

When it breaks down

A few types take over. This is called dysbiosis. It can mean more bloating, irregular digestion, stronger sugar cravings and more food reactions.

What wears it down: antibiotics · the same few foods every day · low fiber · sugar · artificial sweeteners

Protection system 6 of 6

The nervous system: the master switch.

Your gut is wired to your brain through the vagus nerve. When you are calm, your body is in "rest and digest" mode, and acid, bile, enzymes and the cleaning wave all switch on. Under stress, your body pulls resources away from digestion. It cannot tell the difference between a bear and an inbox.

When it breaks down

Every other protection system is turned down at once. This is why one stressful season can set off the whole chain from the start of this chapter. Symptoms flare on stressful days.

What wears it down: chronic stress · poor sleep · eating on the go or while scrolling

Chapter 1 · Review

What your body has in place to protect you.

1

Stomach acid. stops bugs at the door

2

Bile and enzymes. finish digestion

3

The cleaning wave. sweeps the small intestine clean

4

The gut lining. keeps the wrong things out

5

Microbe diversity. keeps troublemakers outnumbered

6

The nervous system. switches them all on

Chances are, your gut issues started with one or more of these systems out of balance.

They lean on each other. Low stomach acid weakens bile and enzymes. Stress slows the cleaning wave. Overgrowth wears down the lining. So the fix is not one magic pill. It is protecting all six at once.

The good news: each one responds to a few simple changes. Let's dive into the key things that fix them.

Chapter 2

Protect your protection systems

First, remove what is wearing them down. Then build in the habits that help them do their job.

The 9 things wearing down your protection systems.

Most people do several of these every single day without realizing it. Limit or remove them as much as you can, especially while you are healing.

  1. Pain relievers, used often. Ibuprofen, naproxen and aspirin can wear down the gut lining with regular use.
  2. Long-term acid reducers. They lower your first line of defense. Talk to your doctor before changing anything.
  3. Alcohol. It loosens the gut lining and shifts your bacteria, especially most nights of the week.
  4. Gluten, every day. It triggers zonulin, the signal that opens the seals between gut cells.
  5. Emulsifiers. Polysorbate 80, carrageenan and cellulose gum can thin the protective mucus layer.
  6. Processed sugar and artificial sweeteners. Both can shift the mix of bacteria in your gut.
  7. Fried and fast food. Reused, overheated oils are hard on the gut lining.
  8. Glyphosate. Sprayed on conventional wheat, oats and beans. Choose organic grains and legumes.
  9. Antibiotics you do not need. Sometimes essential, but every round affects diversity. Ask if it is necessary.

For the full breakdown, with label names to look for and the research behind each, read our free guide 8 Things Breaking Down Your Gut Lining.

What to implement.

Simple, free habits. Each one supports one or more of your protection systems.

Apple cider vinegar or a digestive enzyme with mealsStomach acid · Bile and enzymes

A teaspoon of apple cider vinegar in water before eating, or a digestive enzyme with your meal, helps break food down before it reaches your gut bacteria. Evidence for vinegar is mostly anecdotal; skip it if you have reflux or ulcers.

Sit down, slow down, breathe firstStomach acid · Nervous system

Digestion starts before your first bite. Five slow breaths and a calm, seated meal put your body in "rest and digest" mode.

Stop snacking: 3 to 4 hours between mealsThe cleaning wave

The cleaning wave only runs when you are not eating, and every snack pauses it. Add a 12-hour overnight fast and a 10-minute walk after meals.

Start meals with something bitterBile and enzymes

Arugula, dandelion greens, artichoke or radicchio. Bitter taste is a natural signal for bile release.

Add fermented foods and as many plants as you canMicrobe diversity · Gut lining

Sauerkraut, kimchi, kefir or homemade yogurt (the bonus chapter), plus every different vegetable, fruit, herb and spice you can fit in.

The one most people skip

Calm your nervous system.

This is far more important than most people think. You can eat perfectly and take every supplement, and a stressed nervous system will still turn your digestion down.

Remember: stress switches off stomach acid, bile, enzymes and the cleaning wave all at once. That is why so many people notice their gut is worst during their hardest seasons. Calming your nervous system is not a "nice to have." It is the switch that lets everything else work.

Breathe before you eat

4-7-8 breathing: in for 4, hold for 7, out for 8. Three rounds before each meal.

Protect 7 to 9 hours of sleep

Sleep is when your gut lining does most of its repair. Keep a regular bedtime.

Get morning sunlight

Five to ten minutes outside soon after waking helps set your body clock, which your gut follows too.

Put your phone away while you eat

Eating while scrolling or working keeps your body in "go" mode.

Chapter 3

Further downstream

What damaged protection systems turn into, and why you feel the symptoms you do.


Turning off the faucet doesn't dry the floor.

Imagine coming home to a flooded house because someone left the faucet running. The first thing you do is turn it off.

That is what Chapter 2 does. It stops the damage at the source. But the water is still on the floor, and if you walk away now, it soaks into the walls.

The overgrowth, the parasites and the inflamed lining that built up while the faucet was running do not leave on their own. This chapter is the cleanup. Chapter 4 repairs the damage it left behind.

Protect the source first. Then clear what is already downstream.

Which one sounds like you?

Find the box with the most symptoms you recognize, then skip to its protocol. Many people see themselves in more than one; start with the one that bothers you most.

01
I'm bloated
  • Bloated within an hour of eating
  • Flat in the morning, bloated by night
  • Gas, burping or pressure
  • Worse with fiber, probiotics, onion or garlic
  • Constipated, loose, or both
02
My body reacts
  • A growing list of food sensitivities
  • Breakouts, eczema or redness
  • Flushing, hives or a stuffy nose after wine, aged cheese or leftovers
  • Brain fog after eating, achy joints
  • An autoimmune condition
03
It comes and goes
  • Bloating with no clear food pattern
  • Sugar cravings that feel like a command
  • Itching, often at night
  • Grinding teeth in your sleep
  • Started after travel, new water or pets
04
I'm tired and foggy
  • Tired even after a full night of sleep
  • Brain fog and headaches
  • Sensitive to smells or chemicals
  • Past mold exposure, or a water-damaged home
  • Feel worse in certain buildings
Not sure? Take the free 3-minute Gut Health Quiz.

It matches your answers to the most likely root causes and gives you a plan. lunalab.shop/pages/gut-health-guide

Protocol 1 of 4

I'm bloated.

What is happening

Bacteria (and sometimes yeast) have overgrown in your small intestine, where there should be very few. They ferment your food early, in a narrow tube that cannot stretch. That is the bloat. When the microbes make methane, everything also slows down, so you feel bloated and backed up.

Protection systems involved: stomach acid (lets bugs through) and the cleaning wave (fails to sweep them out).

Protocol 1 of 4 · The plan

I'm bloated.

Step 1Restart the cleaning wave

Stop snacking, keep 3 to 4 hours between meals and walk after eating (Chapter 2). This is what keeps overgrowth from coming back.

Step 2Clear the overgrowth

Use the most studied ingredients for a balanced small intestine for 1 month (next page). Still bloated after that? Do a second month before moving on.*

Step 3Ease up on trigger foods for 2 to 4 weeks

Go lighter on onion, garlic, beans, wheat and apples while you clear, then add them back one at a time.

Step 4Repair the lining as you go, then after

This formula already includes gut lining support. Once the bloating has settled, finish with the repair step in Chapter 4.*

Go deeper: The SIBO Reset Guide and the Flat Belly Guide, free at lunalab.shop

Protocol 1 of 4 · What to take

The most studied ingredients for overgrowth.

These are the ingredients with the strongest research behind clearing, restarting and repairing.

Berberine 500 mg, AM + PM In a published study, herbal formulas including berberine cleared overgrowth about as often as the standard antibiotic.*
NAC 600 mg Helps break down the protective biofilms bacteria hide behind, in lab studies.*
Organic ginger root 1,000 mg Speeds stomach emptying and supports the cleaning wave, in a randomized trial.*
8-strain probiotic + FOS 10B CFU Across 18 studies, probiotics were linked with clearing overgrowth more often.*
L-glutamine 750 mg Fuel for the gut-lining cells while you clear.*
Quercetin + zinc 500 mg / 25 mg Support the tight seals of the gut lining.*
Aloe, marshmallow, slippery elm Soothing blend Coat and calm an irritated lining.*

We included everything you need for this in the Microbiome Balance Formula.

All of the above, pre-dosed into daily packs for 30 days. Nothing to measure, nothing to mix.*

View the Microbiome Balance Formula →

Then: once the bloating settles, repair the gut lining (Chapter 4). Full timeline on the roadmap.

Protocol 2 of 4

My body reacts.

What is happening

When the seals in your gut lining loosen, particles slip through and your immune system reacts. About 70% of your immune tissue sits along your gut, so the reaction can show up anywhere: in your skin, your joints, your energy, or as a growing list of foods you cannot handle. When the lining is irritated it also makes less of the enzyme that breaks down histamine, so histamine can build up.

Protection systems involved: the gut lining, plus microbe diversity and the nervous system.

Protocol 2 of 4 · The plan

My body reacts.

Step 1Remove the 9

Cut back on the 9 things in Chapter 2, especially alcohol, frequent pain relievers, gluten and emulsifiers.

Step 2Feed the lining, starting with 1 month

Use the most studied gut lining nutrients (next page).*

Step 3If histamine is part of it

Flushing, hives or headaches after wine, aged cheese or leftovers? Try 2 to 4 weeks of fresh, low-histamine foods, and hold off on fermented foods (including the bonus yogurt) until things calm down.

Step 4Calm your nervous system

Stress loosens the gut lining directly. The habits on the nervous system page matter here more than anywhere.

Living with an autoimmune condition? Research has linked a leaky gut barrier with several autoimmune conditions, which makes the gut lining a sensible place to start. Use this alongside your doctor's care, never instead of it, and keep taking any prescribed treatment.

Go deeper: The Gut Lining Repair Guide and the Clear Skin Guide, free at lunalab.shop

Protocol 2 of 4 · What to take

The most studied ingredients for the gut lining.

Your protocol is the Gut Lining Reset. Chapter 4 explains each nutrient in detail.

L-glutamine 1,500 mg The main fuel for gut-lining cells; lowered gut permeability in a 2019 randomized trial.*
Quercetin 500 mg Supports the tight seals and a calm histamine response.*
Aloe vera (200:1) 300 mg Soothing gel that coats an irritated lining.*
Marshmallow root + slippery elm Soothing blend Mucilage-rich herbs that form a protective layer.*
Organic triphala 500 mg Supports digestion and gentle daily elimination.*
10-strain probiotic + inulin 10B CFU Reseeds and feeds friendly bacteria.*

We included everything you need for this in the Gut Lining Reset.

All of the above, pre-dosed into daily packs for 30 days. Nothing to measure, nothing to mix.*

View the Gut Lining Reset →

Start with 1 month, then check in. Most people keep going for 1 to 2 more months as their repair step, then move to maintenance on the roadmap.

Protocol 3 of 4

It comes and goes.

What is happening

Symptoms that seem random and cycle on and off, especially after travel, untreated water, undercooked food or time with pets, are often linked to parasites. They are more common than most people think. They compete for your nutrients and irritate the gut lining. Yeast can overgrow the same way, and often brings the same mix of sugar cravings, itching and random bloating.

Protection systems involved: stomach acid (your first defense against what comes in with food) and the gut lining.

Protocol 3 of 4 · The plan

It comes and goes.

Step 1Cleanse for 1 month

Use the herbs with the longest traditional use and the most research behind them (next page).*

Step 2Use a binder

Chlorella helps carry out what is released along the way, so it leaves your body instead of lingering.*

Step 3Keep things moving

Aim for a daily bowel movement: water, fiber and movement. Elimination is how a cleanse leaves.

Step 4Then repair the lining

After the month, move on to the gut lining repair in Chapter 4.

Go deeper: The Parasite Cleanse Guide, free at lunalab.shop

Protocol 3 of 4 · What to take

The most studied herbs for a full intestinal cleanse: parasites and yeast.

Centuries of traditional use, plus modern lab research.

Wormwood Core herb Documented in the Ebers Papyrus; traditionally used against roundworms and pinworms.*
Black walnut Core herb A Native American remedy; studied against Candida yeast in the lab.*
Clove Core herb Traditionally used against parasite eggs and larvae.*
Garlic Supporting herb Allicin has been studied against Giardia in the lab.*
Pumpkin seed + pomegranate Supporting herbs Traditional remedies for intestinal worms.*
Turmeric Supporting herb Supports healthy fungal balance and a calm gut.*
Quassia, rhubarb + more 14 botanicals total Support elimination and digestion.*
Organic chlorella The binder Binds what is released so it can leave the body.*

We included everything you need for this in the Herbal Cleanse Formula.

All of the above, pre-dosed into daily packs for 30 days. Nothing to measure, nothing to mix.*

View the Herbal Cleanse Formula →

Optional add-on: our L-Glutamine powder daily during the cleanse.* Then: repair the lining (Chapter 4).

Protocol 4 of 4

I'm tired and foggy.

What is happening

Mold, heavy metals and everyday chemicals add to the load your liver and gut have to clear. Your liver packages them into bile and sends them out through your gut. If bile is sluggish, or nothing binds them on the way out, they can be reabsorbed. The result is often fatigue and fog that sleep does not fix.

Protection systems involved: bile and enzymes (the exit route) and the gut lining.

Protocol 4 of 4 · The plan

I'm tired and foggy.

Step 1Lower your exposure

Filter your drinking water, air out your home, and check for water damage or mold. You cannot clear faster than you are taking in.

Step 2Support bile flow

Bitter foods, healthy fats and regular meals (Chapter 2) keep the exit route open.

Step 3Mobilize, bind and exit

Use the most studied clearing nutrients plus a binder (next page).*

Step 4Keep things moving, then repair

A daily bowel movement is how it all leaves. After the month, move on to the gut lining repair in Chapter 4.

Go deeper: The Environmental Detox Guide, free at lunalab.shop

Protocol 4 of 4 · What to take

The most studied ingredients for clearing.

Each one supports a step of your body's natural clearing process: mobilize, protect, bind and replenish.

NAC 600 mg Supports your body's production of glutathione, its master antioxidant.*
Alpha-lipoic acid 500 mg Pairs with NAC to support glutathione and antioxidant defense.*
Milk thistle 80% silymarin Clinical-strength support for the liver, your main filter.*
Methylated B-complex 5-MTHF + methyl B12 Active forms that support healthy methylation.*
Chlorella The binder Gentle binding support so what is released does not get reabsorbed.*

We included everything you need for this in the Complete Environmental Cleanse.

All of the above, pre-dosed into daily packs for 30 days. Nothing to measure, nothing to mix.*

View the Complete Environmental Cleanse →

Optional add-on: our L-Glutamine powder daily during the cleanse to keep the gut lining fed.* Then: after the month, repair the gut lining (Chapter 4).

Chapter 4

Repair the gut lining

The water is cleared. Now repair the floor and the walls. Almost everyone with gut issues has a gut lining that is not working at its best.

Why repair comes next.

Think back to the 9 things wearing down your protection systems, and to whatever your protocol just cleared. Almost all of it pressed on the same thin wall: the gut lining.

The cleanup removes what was causing the damage. Repair rebuilds what was damaged, so the gut can hold its ground once you stop.

Three steps

  1. Remove what damages it (Chapter 2).
  2. Protect it with daily habits (Chapter 2).
  3. Rebuild it by giving it the nutrients it uses to repair.

If "My body reacts" was your box in Chapter 3, this is your Step 1: start with 1 month. For everyone else, this is your Step 2, right after your protocol.

The 5 most studied nutrients for your gut lining.

Nutrient 1L-glutamine

The main fuel for your gut-lining cells. Your intestinal cells use glutamine as their preferred fuel, and it helps them build the proteins that hold the tight seals together. In a randomized, placebo-controlled trial published in the journal Gut (2019), people with IBS and a leaky gut barrier who took glutamine for 8 weeks had lower intestinal permeability and fewer symptoms than those on placebo.*

Nutrient 2Quercetin

Supports the seals and a calm histamine response. A plant flavonoid found in onions, apples and capers. In lab studies, quercetin increases the proteins that seal the gaps between gut cells, and it helps stabilize mast cells, the immune cells that release histamine.*

Nutrient 3Soothing herbs: aloe, marshmallow root, slippery elm

A protective coating. All three are rich in mucilage, natural plant fibers that form a soft gel when they meet water. That gel coats and soothes an irritated lining, much like your own mucus layer does. They have centuries of traditional use for digestive comfort.*

Nutrient 4Triphala

Digestion and gentle daily elimination. A traditional Ayurvedic blend of three fruits (amla, bibhitaki and haritaki), rich in polyphenols. Small clinical studies support its use for regularity, and lab studies suggest it feeds beneficial bacteria.*

Nutrient 5A probiotic with prebiotic fiber

Reseeding and feeding the good bacteria. Lactobacillus and Bifidobacterium strains, plus inulin, a fiber that feeds them. When good bacteria ferment fiber, they make butyrate, the main fuel for the cells lining your colon.*

These five are the reason we made our Gut Lining Reset, which combines them in one daily pouch. You can also take them on their own.

Your next 1 to 3 months

We combined all of these into the Gut Lining Reset.

All five nutrients in one pre-dosed daily pouch: L-glutamine, quercetin, 200:1 aloe, marshmallow root, slippery elm, organic triphala and a 10-strain probiotic with prebiotic fiber.*

Nothing to measure, nothing to mix. 30-day supply, free US shipping, and our 30-Day Reset Guarantee.

View the Gut Lining Reset →

A word on probiotics.

Remember protection system 1? Stomach acid is built to kill bacteria. That includes many of the ones in a probiotic capsule.

A good share of most probiotic strains do not survive the trip through the stomach. Some do, and taking them with or just before a meal, when food buffers the acid, helps more get through. We include one in our gut lining formula because the doctors we work with recommended it, and we want you to have every advantage. We would still rather be honest about its limits than oversell it.

If you want probiotics that reach your gut

Spore-based probiotics. Bacillus strains, like B. coagulans and B. subtilis, live inside a tough protective shell, a bit like a seed. That shell helps them survive stomach acid far better than most strains.

Fermented foods. Food carries bacteria through the stomach in a protective package, and you get far more of them per serving. The strongest version is homemade, long-fermented yogurt. That is the bonus chapter at the end of this guide.

Probiotics work best when the source is protected. Fix upstream first, then reseed.
The most important page

Your roadmap

Everything in this guide, in order, on one page. Find your box. Follow your row.

Your roadmap

Start with one thing.

Find your box (see the four boxes). Right now you only need your Step 1. Everything else can wait until you see how you feel.


Step 1 · NowClear
Microbiome Balance Formula1 month. Still bloated? Do a second.Start here →
Herbal Cleanse Formula1 month. Optional: add L-glutamine powder daily.Start here →
Complete Environmental Cleanse1 month. Optional: add L-glutamine powder daily.Start here →

↓ We'll email you a check-in
↓ We'll email you a check-in
↓ We'll email you a check-in
↓ We'll email you a check-in
Step 2 · LaterRepair
Gut Lining Reset1 to 3 months. Already includes L-glutamine.
Keep going with the Gut Lining Reset1 to 2 more months.
Gut Lining Reset1 to 3 months. Already includes L-glutamine.
Gut Lining Reset1 to 3 months. Already includes L-glutamine.
↓
↓
↓
↓
↓
Step 3 · LaterMaintain
L-glutamine powder daily, plus colostrum if you want extra support for the gut barrier,* plus the 36-hour yogurt (bonus).For as long as you like.
What it can look like. Bloated? Start with the Microbiome Balance Formula. → About 3 weeks in, we'll check in: still bloated, do a second month; feeling better, we'll walk you through Step 2.
One thing at a time. Finish a step before you start the next.
More than one box? Start with the one that bothers you most.
Symptoms come back? Go back to your column and run it again.
Why it takes time. Your gut lining renews every few days, but what wore it down built up over years.
Bonus

The high-dose probiotic gut remedy

A 36-hour homemade yogurt that may be one of the most powerful things you can do for your gut. It costs a few dollars and sits in your fridge.


Not the yogurt from the store.

Most store-bought yogurt is fermented for a few hours, with whatever strains the brand chose, and is often sweetened or thickened. Homemade yogurt fermented for about 36 hours, with a strain you choose, ends up far more concentrated. Estimates put a well-fermented half cup in the hundreds of billions of bacteria, many times what a typical capsule holds.

And because the bacteria travel inside food, more of them make it through your stomach alive, along with the vitamins and compounds they have already made.

Read this first: the yogurt is the finish, not the start.

If you are bloated (Protocol 1) or have histamine symptoms (Protocol 2), adding a high dose of bacteria and the fiber that feeds them can make things worse at first. Work your protocol for at least a month, let symptoms settle, then start fermenting. The yogurt will land in a gut that is ready for it.

"But I can't have dairy."

During a long ferment, the bacteria use up much of the lactose, the milk sugar most people react to, so many people who do not tolerate regular dairy do well with it. Start small. If you have a true milk allergy, rather than an intolerance, skip this.

Choosing your strain.

Three strains have enough research behind them to be worth a 36-hour ferment. Our founder ferments L. reuteri about half the time and rotates the other two.

L. reuteriThe ancestral strain

A bacterium that lived in the human gut for most of history and is now missing from most modern guts. The best-studied versions are DSM 17938 and ATCC PTA 6475.

L. gasseriThe second native strain

Another native gut bacterium with a strong research base, and a common partner to reuteri.

B. coagulansThe spore-former

A spore-based strain that survives stomach acid well, with research on digestive comfort. Often combined with the other two.

Watch it made: the step-by-step video of our founder making a batch.

How to make it.

You need

  • 1 quart organic half-and-half (the fat helps; whole milk works but turns out thinner)
  • 2 tablespoons inulin (a prebiotic fiber that feeds the bacteria)
  • Your starter culture, or ½ cup of your last batch
  • A yogurt maker that holds exactly 100°F (38°C), and a clean glass jar

Steps

  1. Whisk 3 tablespoons of the half-and-half with the inulin and your starter until smooth.
  2. Pour the rest of the half-and-half into the jar, add the mixture and stir gently.
  3. Set the temperature to 100°F. Not 105, not 110. This matters more than anything else.
  4. Ferment for 36 hours, and do not open the lid.
  5. Refrigerate. It will be thick and tangy and may separate. Stir it back in. Save ½ cup to start your next batch.

Start with a tablespoon or two a day and build up to about half a cup.

Safety. Use very clean jars and spoons. Throw it out if it smells rotten or shows mold or pink, orange or black spots. Keep it refrigerated and eat it within about two weeks. Check with your doctor first if you are pregnant, immunocompromised or seriously ill.

When to see a doctor.

Most gut symptoms are functional, but some need a proper workup first.

See a doctor promptly if you have:

  • Blood in your stool, or black stools
  • Unexplained weight loss
  • Persistent vomiting or trouble swallowing
  • Fever, or pain that wakes you at night
  • Severe pain under your right ribs after fatty meals
  • New symptoms after age 50, or a family history of colon cancer, celiac or inflammatory bowel disease
  • Signs of anemia, like unusual tiredness or paleness

Worth testing

Ask about celiac screening (before you cut out gluten), H. pylori, a breath test for overgrowth, and a stool test.

Medications

Do not stop acid reducers, pain medication or any prescription without your doctor. Some supplements interact with medications, so check with your doctor or pharmacist.

Where to go next

Protect. Repair. Target.

Start upstream with the free habits in Chapter 2. Give it a few weeks. Then, if you want more support, we have built a pre-dosed protocol for each focus.

Gut Lining Reset · the gut lining, where most people start
Microbiome Balance Formula · bloating and overgrowth
Herbal Cleanse Formula · parasite cleanse
Complete Environmental Cleanse · toxic load

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*These statements have not been evaluated by the Food and Drug Administration. These products are not intended to diagnose, treat, cure, or prevent any disease. This guide is for education only and is not medical advice. Consult a healthcare professional before starting any supplement, especially if you are pregnant, nursing, take medication or have a medical condition.

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Targeted Protocols Rooted in the Gut Microbiome

Pre-dosed, doctor-formulated protocols designed to support your body's natural cleansing processes — safely, effectively, naturally.