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Gut Health 101

Hi all,

This post is intended to help you understand the protocol used for any form of gut dysbiosis whether that be SIBO (Small Intestinal Bacterial Overgrowth) SIFO (Small Intestinal Fungal Overgrowth) or Candida. You do not need to be overweight or with significant health problems in order to have this - in fact it is very common with our modern diets + lifestyles to have dysbiosis. This protocol, while quite strict, follows very healthy guidelines, helping to get the microbiome back in balance.

Lil disclaimer: I am not a health professional - just someone who cares - a lot. I’ve done a ton of independent research and am finding new things out every day. I am well aware of how overwhelming the medical / functional medicine communities can be, as well as the internet, so this is the process of me having distilled some things down. If it works for you, then great, if not - that’s ok too, as we are all different.

Also, please bear in mind that this protocol requires eating meat + fish. I was vegan + vegetarian for two years, which led to my own dysbiosis. This protocol is not a moralization / condemnation of veganism or vegetarianism in any way, but simply approaching from the perspective of total health and homeostasis.


First, we need a few key terms.

Microbiota: ecological communities of commensal, symbiotic and pathogenic microorganisms found in and on all multicellular organisms studied to date from plants to animals. Microbiota includes bacteria, archaea, protists, fungi and viruses.

Microbiome: the collection of all the genetic material / microbiota, including the places in which the microbiota reside (gut, skin etc).

Metabolome: the biologically active molecules produced by the microbiota, also called postbiotics.

Prebiotics: dietary fiber that feeds healthy bacteria in the gut. Needed for short chain fatty acid production (SCFAs).

Probiotics: live bacteria and yeasts.

Postbiotics: see above - bioactive compounds that are created by the microbiota as a result of fermentation.

“An estimated 30-100 trillion bacteria comprise the microbiota, collectively weighing around 4.5 pounds! These bacteria include a mixture of commensal (neutrally existing), probiotic (mutually beneficial, also called symbiotic), and pathogenic (harmful to us) organisms, and can consist of any of 35,000 species known to inhabit the human gut. Every person’s gut contains approximately 400 to 1,500 different bacterial species of the possible 35,000 that are well adapted to survive in the human gastrointestinal tract, although thirty to forty species of bacteria will dominate an individual’s gut microbiota, accounting for about 99% of the microorganisms present in our gut.” ~ The Gut Health Guidebook, by Dr. Sarah Ballantyne, PhD

So given this amazing biodiversity, it is easy to see how, when in dysbiosis, so much of our health can go awry.

Dysbiosis occurs when a) too many pathogenic bacteria / fungi populate the gut (think Candida or E-Coli, or b) when bacteria / fungi overpopulate places they shouldn’t, i.e. the small intestine. The small intestine is naturally home to some bacteria, but it should not be overpopulated. SIBO and SIFO occur when too many bacterial colonies (they do not have to be pathogenic) invade this area. This occurs due to the pyloric sphincter between the stomach and small intestine, and the ileocecal sphincter between the small and large intestine, remaining too open and allowing bacteria to pass through (and inevitably take up residence).

The cause of this is yet mostly unknown - but a lot of anecdotal evidence suggests that low stomach acid is the cause, as when we don’t have enough of this, it does not kill off “bad” bacteria. It also, of course, leads to improper digestion of foods, which means that the lower digestive tract must pick up the slack. More on what to do about this later on.

Please research the symptoms of SIBO, SIFO and Candida to see if they apply to you. I will include links at the bottom of this document.

Unfortunately, gut dysbiosis is a fairly new topic of study. Which means, more unfortunately still, that a) when we go to doctors about this, they will often not know what to do and b) untreated dysbiosis can lead to a whole whack of autoimmune illnesses, including MS, Lupus, etc.

Hippocrates believed that all illnesses begin (and end) in the gut. When we consider that the microbiome is a host of other living organisms inside of us that perform tasks and have their own gene expressions, it makes sense. The gut can literally help our genes express themselves and change how they do.

Leaky gut occurs when the SIBO / SIFO begin eating away at the epithelial cells (cells that act as barriers) in your small intestine. Proteins begin to “leak” out into your bloodstream, which your immune system picks up as something to fight. If you have a steady stream of “leakage” and therefore a steady stream of immune system red flags, you develop inflammation and autoimmunity.

This diet is geared towards reversing all of this, and for me, it has been working. I’m only a month in, but have been seeing great results - so I hope this helps you, too.


Diet(s) - (these are what I am doing, other diets / variations are possible as well).

1. Autoimmune Protocol Diet (AIP):

Diet that essentially removes, for at least 6 weeks, ALL known "general" allergen producing foods (barring unique allergies we may have). The idea is to wean them back in one by one after at least this period of time, but some people (for example those who have MS) will be on the diet for much longer. Immensely helpful for identifying inflammatory responses in the body, and beginning to heal the gut.

2. Low FODMAP Diet (Fermentable, Oligo, Di, Mono-saccharides, Polyols):

Much different variety of foods than AIP, but can be added on (or subtracted, as it were) from AIP to ensure that things like SIBO, SIFO and Candida are being taken care of. In our modern diet, we often combine the wrong foods together, which can lead to fermentation in the gut. When we have SIB/FO + Candida, the fermentation is highly problematic, as it becomes 'food' for the overgrowth of bacteria / fungus.

The following protocol is keeping both AIP and FODMAP in mind:


~ Meat, shellfish, fish (emphasis on fatty fish, lean meats, with some saturated fats, more on that later).

~ All veggies barring beans (green beans, snap peas etc), white potatoes and the entire nightshade family (tomatoes, eggplant, bell peppers, hot peppers, goji berries etc)

(note: for FODMAP, be mindful of the stalks of broccoli, garlic, onion, shallots, cauliflower, beets, mushrooms, artichokes, asparagus - see how your system does with these). High FODMAP veggies may be able to be taken in moderation, but you may want to eliminate them completely for a while to give yourself the best chance.

~ All fruits in very strict moderation - see how you tolerate them. High fructose fruits are more likely to "feed" SIBO and Candida, so be mindful and keep track of your symptoms when you eat them, you should be able to tell what is ok and what isn't. Certain fruits are really high in fiber, though, which is very important (more on that later).

~ Fats: MCT oil, olive oil, avocado oil, tallow, duck fat, coconut oil.

~ Green herbs and spices, salt (no pepper + avoid all "red" spices, barring cinnamon and turmeric, both are fine).

~ Apple cider vinegar for salad dressings and potentially before meals to help stimulate bile (more below).

~ WATER WATER WATER WATER WATER. Cannot emphasize this enough. Stay hydrated. Once you begin shedding these toxins (die-off) you will want them to exit! You do not want these re-circulating through your bloodstream, making you feel extra ill. Water and fiber are essential.


~ Get a good bone broth protein, plus collagen and peptides. I get mine here. Bone broth is SUPER helpful in healing + soothing the gut

~ MCT oil - trendy and therefore expensive but also SUPER important. I put 1 tbsp into my morning protein shake (more on its benefits below)

~ Omega 3 supplement (we get too many omega 6's in our diet, so a supplement that says 3,6,9 is often unnecessary)

~ a solid multivitamin, not all are created equal. This is a good one. If you are female, getting an iron supplement (or a multi that contains iron) is important. If you have low stomach acid, iron is harder to absorb.

~ Oregano oil - antiviral, antibacterial and antifungal. Trifecta of amazingness. Absolutely essential!

~ CoEnzyme Q10 - antioxidant, helps remove any free radicals / endotoxins from the body

~ Psyllium Husk - an insoluble fibre, helps bind toxins and excrete them - take in moderation as it can also feed SIBO / Candida if taken too much (so maybe 2x / week, 2 tbsp mixed with hot water to form a paste, I add a little cinnamon for flavour)


Carbs: Ketosis - under 50g/day || "Regular" diet - 50-100+g/day

The AIP / FODMAP diet is naturally lower in carbs, which may cause you to lose weight. For some this is desirable, but if it isn't, and for balance's sake, you may want to up your carb intake. The reason I say balance is because the gut is home to trillions of bacteria and up to 1,500 different strains. At first I thought that being entirely ketogenic was desirable, because the complete lack of carbs and fruit sugars would inevitably starve the SIBO etc, right? While this is possible, no extensive human studies have yet been done on how keto affects the gut microbiome. The preliminary ones that have been conducted on rats + mice show that ketosis leads to the decline of certain helpful bacterial colonies and less gut biodiversity overall. What we want is diversity. It may seem counterintuitive to eat in such a restrictive fashion if what we ultimately want is diversity, but this restriction is only ever supposed to be temporary, in order to help restore variety in the colonies (starving the overgrowth). Similar to the planet's ecosystem, these colonies work in harmony with one another. Which is why, in my belief, carbohydrates in moderation are important during this healing process.

Since carb sources are so limited (sweet potato, squash, lower quantities in other veg), and protein ends up becoming a larger nutritional source, it is very important to up your fiber intake to ensure waste is being excreted.

Fiber: as much as feels ok, but make sure to chew, a LOT.

Three types - soluble, insoluble, resistant

You will want to get the same amount of all three if possible, and the more the better. Hunter / gatherer diets in different regions used to get between 100-250g of fiber per day. The Standard American Diet (SAD) is as low as 25g/day, sometimes not even that much.