The Simple Health Total Gut Reboot: How to Restore Flora Diversity with Probiotics and Prebiotics

You get it. Fixing your gut is of supreme importance to whole body health.

As you may be acutely aware, the gut is one tricky little devil.

Try this diet, try this probiotic, try this prebiotic.

Which one? What order? What diet should I eat?

Few articles actually put together a plan of action that you can follow to give the gut a total reboot.  This is my attempt to do just that.

Specific protocols work for specific people, and that specific person may or may not be you.

What I mean is that you need to have flexibility built into your gut reboot.

So how do you build a flexible plan to repair your gut once and for all?

While many protocols look at “Stage 1, Stage 2, Stage 3”, instead it is best to view the stages of gut repair as dynamic & overlapping steps that shift back and forth based on your needs.

Musical compositions are often broken up into “movements”. The movements are played in succession. The movements tie and blend to create a complete work.

I use the same approach when healing the gut.

Treat it like a musical composition – take each movement in stride.

When all of the movements are played in the right succession – the body steps in and does the rest.

All you need to do then is give it a few tweaks to keep it playing good music – to maintain good gut composition, if you will.

When the gut composition is out of balance, it is no different than an orchestra playing out of rhythm.

Sometimes, you need a total reboot – going back to fundamentals and tying the pieces back in one at a time.

Other times, a few instruments just need to be tuned.

I’m going to lay out the order of importance – which movements and instruments to look to first when recreating your gut composition.

Natural antibiotics, anti-inflammatory herbs, enzymes, motility support, micro-nutrients, probiotics, prebiotics, and gut lining support all have their places in the symphony.

These are the instruments of the gut, our job is to get them to play music again.

Let’s start with a few rules.

RULE #1: Generally, the more severe your gastrointestinal or immune symptoms, the earlier the “movement” you should focus on. Go back to the fundamentals. “Clean the Slate”, and start fresh.

RULE #2: If you seem to be getting worse or plateauing, go back a movement or two until symptoms lessen, and you feel better. Further master the basics, and proceed more slowly. Professional musicians, athletes, and yes, top health professionals do this too!

RULE #3: Some aspects of Movements #1 and #2 contradict later movements. This is why the movements are played in succession. If you jump too far ahead, or combine too many movements at once, your symphony becomes disjointed, and you may be forced to jump back to the beginning.

Rule #4: Gut healing takes time. It requires the testing out approaches. Even highly-recognized experts like Chris Kresser will let you know that it can take 3 months to 12+ months to reboot your gut once and for all. Put some pieces together, see how the “music” sounds, and make some tweaks.

Below, I give you the superstructure of which to base those decisions. There are many ways to move between each movement, but it gives you a path to follow so that you’re attempts feel less scattered, and you can move forward with less guesswork.

If it sounds difficult, I promise you…

  • that living with chronic gut and immune problems is more difficult.
  • traveling to specialist after specialist and trying to find practitioners who are not cookie-cutter, and, who think through your case and personalize recommendations, is more difficult.
  • having to do it all over again from scratch because you became impatient and jumped ahead a movement too soon is more difficult.
  • getting partial results, and still experiencing discomfort and a decreased quality of life is more difficult.

I am going to teach you the ropes and offer specific ideas for each step along the way.

Sound like a plan?

Let’s go!

“Movements” of Healthy Gut Composition







Think in “movements” that flow back and forth without distinct borders.

We are looking to reboot the gut by reducing or ridding the body of overgrown bacteria, replenishing and adding diversity of the good guys, and then maintaining that diversity long-term. The lists are not meant to be followed exactly – these are groups of tools.

Seek standard medical evaluation and screening as needed.


Elimination Diet and/or Allergy/Sensitivity Testing: IgG, IgA
Expanded Wheat/Gluten Testing: Cyrex Labs
Candida antibodies (IgA, IgG, IgM)
Lactulose Breath Testing (SIBO Testing)
Parasite Testing
C. diff Testing
Fecal calprotectin
Fecal blood
Fecal fat
Leaky Gut Testing
Micronutrient Testing
CBC with immune differential, Complete Metabolic Panel, 25-OH vitamin D, ESR, hsCRP, Lipid Panel, Thyroid Panel
Organic Acid Testing (many)
Autoimmune Markers (many)

Others: Anemia panel, Lyme testing, Histamine Intolerance, Mold/Mycotoxins, Genetic analysis (HLA, FUT2, detoxification pathways, antioxidant protection systems, and more), Gall Bladder Testing, Abdominal CT Scan, Endoscopy, Intestinal Biopsy

While these are not inclusive of all strategies and tests available to you. This list is a great start to identify what is going on functionally in your body, shore up micronutrient deficiencies, and get an overall picture of health.

Testing gives you benchmarks of success and failure.

You can still “feel” poorly, but your functional health may start showing signs of improvement much earlier and help to keep your momentum going. Testing can help keep your momentum moving forward.

You’ll just do a few of these to get started and revert to others if you get “stuck”. The list above is to  trigger ideas, that’s all.

Sometimes you have had the right tests performed, but your health professional did not fully review the results with you, or may have ignored findings that a functional health professional may not.

Worse yet, not all health professionals “check their work” by re-performing a test to check progress.

You’re the consumer. You have control. Speak up, ask questions, and lobby for your health.

Zinc Carnosine
Vitamin D3
Bromelain, Papain, Proteases, Serratiopeptidase, and other enzymes.

Inflammation has a mind of its own and creates vicious cycles. Inflammation causes inflammation, which then contributes to more inflammation…

Sometimes, you need to step in and change the pattern. Soothe things before repairing and rebuilding so that your system is more open to the healthy changes.

The good news is that many of the options play direct roles in healing the gut, soaking up oxidative stress, and fueling/balancing the immune system.

Elemental Diet
Specific Carbohydrate Diet
Low FodMAP diet
GAPS diet
Digestive Enzymes
Motility Support
Intermittent Fasting


Overgrowth refers to an imbalance of gut microbiota. Microbiota is a broad term to describe the diverse balance of healthy bacteria, yeast and fungi in the body. You’ll also see me switch around and call it the gut flora, or, the “microbiome”.

Health professional refer to imbalance in the gut microbiota as “dysbiosis”. You may also have overgrowth, which is technically an infection of a specific organism. You can have a specific clinical manifestation of overgrowth like Helicobacteri pylori, Clostridium difficile, Small Intestinal Bowel Overgrowth, or intestinal Candida.

Stealth infections can be systemic in and outside of the gut. Epstein-Barr virus, Herpes zoster, Herpes Simplex I and II, Cytomegalovirus can all become activated and affect the gut and other tissues. Mycoplasma, Staphylococcus, Streptococcus, and others can also create local and systemic issues.

These infections can be acute, or “stealth” in that they may not be full-blown but still contributing to stress on the body.

Monolaurin (Lauricidin)
soil based microbes (Megasporebiotic, HU58, RestorFlora)
S. boulardii (a probiotic yeast; RestorFlora).
Lactobacilli and Bifidobacteria strains may also be added (TruFlora, TruBifido, Theralac), but sometimes may aggravate with small intestinal bowel overgrowth, or just being too immune-stimulating to start.

They will be essential later on, but it is a case-by-case decision to add them here. This is because you can have healthy strains of bacteria that are just off-kilter, or in the wrong place (Small Intestinal Bowel Overgrowth).

Sometimes, it is best to “clean the slate” and kill off the bad guys and restore proper motility before adding these.

Generally add these slowly, and one at a time! When microbes starve or die, they release toxins and wastes that can make you feel flu-like. So if you’re getting body aches, headache, loose stools, fatigue, or other symptoms, it is a sign that your protocol is working, just too much too soon!


Colloidal Silver
Berberine herbs and extracts
Oregano Oil
Garlic – Allicin extracts
Olive leaf
Vitamin D3
Elemental Diet Protocol (used for rest, but also starves bad bacteria)


Microbes are smart. They have learned how to hide from our immune system and outside agents by “cloaking” themselves in biofilm.

Biofilm is a matrix-like living environment of sugars, proteins, and fats that microbes produce and are suspended in which prevents outside agents from being able to act on all of the individual cells at once.

Lauricidin (monolaurin) – also dirupts biofilm
Proteolytic enzymes: can include Protease, Serrepeptase, Bromelain, Papain, Nattokinase, Lumbrokinase, and Cellulases for Candida spp.
N-acetyl cysteine (also supports Glutathione – your body’s main antioxidant)
Colloidal Silver
Stevia Leaf extract (yes, the sugar replacer also disrupts biofilm and helps provide support against microbes like Lyme)



Motility support is important at any stage. If my concern is just to get rid of some overgrowth, I may wait to add it after a month or two of natural support. Motility will keep foods from fermenting too early in the gut (like in SIBO). One of the biggest causes of SIBO is lack of motility – foods particles stay in the small intestine too long and microbes from the large intestine are able to migrate to the small intestine and start fermenting them.

I use MotilPro by Pure Encapsulations, others may use an herbal formulation known as Iberogast, ginger extracts, or other motility formulas.

Gentian root, ginger root and others are also used as digestive stimulants and motility aids.

An elemental diet also promotes motility, starves bad bacteria, deflames, and helps replenish micronutrients.

Part of fermentation is making sure that foods are fully digested before entering the gut in the first place.


I like Critical Digestion by Enzyme Science. Their Complete Digestion formula is less potent but may be sufficient and more affordable. Enzalase from Master Supplements is effective as well, especially for food later in the gut as it works preferentially past the stomach.

A Betaine HCl supplement can also be helpful for protein digestion. If you suffer from reflux, Betaine HCl may help reduce symptoms.

Intolerance Complex from Enzyme Science or Gluten Manager from Integrative Therapeutics may be on hand when eating outside of the home or to mitigate impact of occasionally eating allergic/sensitive foods. These will minimize the impact of eating sensitive foods or micro-exposures to sensitive foods.

Take your support to the level you think you need.



I will later add Bifidobacteria (predominate in Large intestine), followed by diverse Lactobacilli (predominate in small intestine).

-You do not to add Bifidobacteria and Lactobacilli too early as they may be what is overgrown in the small intestine in the first place (even the healthy ones). You need to crowd these out and improve gut motility before adding these guys.

I then generally like to switch or rotate with a broad-based probiotic such as Theralac by Master Supplements alongside the soil-based microbes.

It may be month(s) between these shifts. You may need to back-track, they can overlap. Of course, working with a professional can help guide these decisions.

Soil-based organisms naturally make it past the stomach acid. I use the industry leader, Microbiome Labs, although some copy-cat products are popping up due to their success and growth.

I also use Master Supplements, Inc. for my Bifidobacteria and Lactobacilli-based blends as they have a patented means of ensuring delivery of non-spore probiotics through the gut.  I also love that Master Supplements boasts a 100% money back guarantee on their products.


I add prebiotic starches like Partially Hydrolyzed Guar Gum to the mix LAST alongside the broad based probiotic and spore probiotic. Prebiotics are used to sustain flora once they have been re-established. It acts like fertilizer to keep the bugs happy, diverse, and healthy.

PHGG is well-tolerated by both constipation and diarrhea-dominant individuals. If I want to expand from there I will go to a bend of inulin, larch arabinogalactan, and beta-glucan to add diversity – but this is usually a wellness step when they are maintaining changes alongside a normal diet.

Once they can handle a prebiotic supplement, it’s a sign they can also shift away from starch limiting diets (like Low-FODMAP, GAPS, Specific Carbohydrate Diet) and start re-integrating a whole food, Paleo-style diet.


Dietary prebiotics are found in a Paleo-style diet rich in diverse, multi-colored vegetables. 

To supplement a prebiotic-rich diet, I rotate supplemental prebiotics like PHGG and blends of inulin, beta-glucan, & larch arabinogalactan to promote biodiversity in the gut further. Measured amounts of potato starch from the grocery store can also feed healthy probiotics in the gut. The best source is and always will be food. The supplements are particularly helpful in Movement #4 when adding prebiotics back in measured, controlled doses.

For Movement #5, prebiotic supplements are useful on days where your diet lacks diversity and/or overall volume of vegetables. If you are like me and are genetically prone to low levels of Bifidobacteria in the gut (specifically, I carry two slow-functioning “FUT2” gene copies identified via testing and reports from Promethase and Livewello), you might choose to take them more regularly.

Typically, you want to add as much diversity as you can in your diet. Try new vegetables, new colors, new varieties. It’s all diverse fuel for your friendly bugs in your gut. Prebiotic fibers should be added back slowly in Movement #4, and Movement #5 is about sustaining intake and tolerance.

Supplementally, I use spore probiotics like Megasporebiotic and rotate various blends from Master Supplements, Inc. with Theralac being my go-to for large and small intestine support.

To best ease into Master Supplements products, start with TruBifido, then Theralac, and rotate TruFlora last.

If at any point symptoms bloom, it’s a sign that overgrowth still exists or that you’re adding things back too fast! Reverse your steps by first reducing the dose of what you’re doing currently, but gradually back-tracking until the symptoms disappear again. Excessive bloating and gas may still indicate that overgrowth exists.

Generally, digestive enzymes and motility support are important throughout any overgrowth protocol. Don’t overlook their impact.

Enzymes help to fully digest food to ease the digestive tract and provide fuel in the right forms to our healthy bugs. Motility support keeps things moving along so that overgrowth is less likely to occur.


Long-term, other strategies still need to be implemented for to maintain the changes and prevent relapse.

Strategies to prevent re-occurrence can include a partial elemental diet, and continued diversification of your whole-food diet.

If you take antibiotics in the future, you may need to repeat some of these steps as well. I’ve written on the Use of Probiotics During and After Antibiotic Therapy

“Success” is measured most importantly by how you feel. It may also be measured using inflammatory markers like ESR, CRP, and fecal calprotectin, breath testing (such as lactulose breath test), and other markers that you may have identified in the “Identify” portion of Movement #1.

Urine organic acid testing may also be useful as it gives you some insight on the gut, but also tells you how your whole system is doing metabolically.

If you’re wondering, Now what?, organic acid testing offers a great roadmap to refining old goals, and identifying new goals. It can be useful to repeat organic acid testing once a year to identify metabolic areas you can improve.

Stool testing can be useful for inflammatory markers, or for identifying fat or blood in the stool, parasitic infections and more – yet as I mentioned in Movement #1, I trust it less for dysbiosis and SIBO at this time.

When first reintroducing food from a restricted food plan,  a Specific Carbohydrate Diet (SCD) or Low-FODMAPS diet are often recommended to prevent the blooming of unwanted organisms in the short-term.

Starch-restrictive diets (SCD; low-FODMAPS) are not life-long changes – you NEED these starches eventually as they serve valuable prebiotic & motility functions. Add them back when your system is ready, and always re-introduce them slowly in a measured fashion!

While an SCD or low-FODMAP diet may be necessary when reintegrating a diet, they are NOT intended as long-term solutions.

It is not unusual for a gut restoration program like this to last anywhere from 3-12+ months depending on the initial severity of symptoms. Some may respond to removing gluten out of their diet, and that’s all they need to do. Others may require more comprehensive support.

My rule of thumb is that the more severe the symptoms, the more comprehensive the support needed.

The Plant Analogy

A plant needs three things to grow properly.

It needs water, soil, and sunlight.

If you just give it two out of the three, the plant can still wilt or die.

The point being – if you’re not getting the results with your protocol, you could just be one small piece away from seeing results!

Your gut is a garden. It needs certain things to grow properly. What’s the missing link to your garden? Motility? Adding prebiotic starches and fibers too early? Not killing overgrowth? Eating foods that you are sensitive or allergic to? Acute inflammation? Are you giving the gut at least a 12-hour break between your last meal or snack and your first meal or snack of the day?

The answers are slightly different per person. If we’re honest with ourselves, we often know the answer, but are looking for a short-cut.

I handle my urge for a shortcut with one simple mantra: The long way is often the short way.

I see this time and time again, where clients design a protocol through their own research, or through a separate health professional, and remark that “nothing seems to help” or “everything seems to make it worse”.

In these cases, usually they:
1.) Took or combined a movement too early.
2.) Are just one minor tweak or missing piece away from seeing results.

What piece is missing for you?

My hope is that thinking of the steps in terms of “Movements” and finding that personalized composition that works for you is that missing link to a total gut reboot.

Use this discussion as a template to reboot and cultivate the garden of the gut.

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