A Probiotic’s Purpose: All About Gut Bacteria, Fiber, Histamine, IBS, FODMAPS, And More!

    Confession time!

    Despite my constant proclamations and evaluations of the importance of the gut microbiome, I've sort of had (er... have?) a slight fear of probiotics. Ya see, when you have a history of Small Intestinal Bacteria Overgrowth (see my blog post on the whole sticky matter!), you can become a bit, well, wary of bacteria. You enter this mode of KILL ALL THE BACTERIA ALL THE TIME, as you slam oregano, allicin, and berberine (to name just a few) down your throat, accompanied by well wishes of destruction. Things get real. You start to think that any sort of bacteria will immediately ferment and fester in your GI tract, creating more problems than they're supposed to solve.

    But in my journey (and boy, is it a journey!), I've started to see things a bit differently. As I've been healing my gut (and listening to basically every podcast provided by the wonderfully #onpoint Dr. Michael Ruscio), I've generated some new thoughts:

  1. We all harbor unique gut microbiomes, with our own personal "perfect" version of such. This means we shouldn't necessarily model ourselves after any certain person, study, or population.
  2. While prebiotics (more on those in a bit!) may not be the best thing to run to when you're suffering from gas and bloating, probiotics may be helpful. (Again, may.)
  3. The key (especially when it comes to things like histamine intolerance, intestinal permeability, and gut motility) likely involves choosing the right type of probiotic.
  4. While fiber may be awesome for many people's gut bacteria, that doesn't mean you should necessarily slam your system with veggies and psyllium husk. Low FODMAP and/or low fiber diets have been shown to be effective for the gut microbiome.
  5. While fasting may seem like it would starve bacteria, studies indicate it can actually generate a healthier gut microbiome, including one with increased diversity. (Yey!)
  6. The microbiome can change rather rapidly, so it's ok to experiment. In no way are you automatically committed for life in the things you try.


The word "probiotic" comes from the Greek word meaning "for life." It refers to the "good" gut bacteria which enter a symbiotic relationship with us. In fact, the amount of bacterial genes inside us actually outnumbers our own genes by 100-fold, and a typical human's intestines may play home to around a thousand various types of probiotics. If you lump together all the microbes in our system, including probiotics, viruses, fungi, and archaea (the last of which give us the methane-producers that those with SIBO/IBS-C may be familiar with), they would weigh around 3 lbs! 

When looking at the full spectrum, gut bacteria can be either gram positive or gram negative,  as discovered by Hans Christian Gram. The difference involves their cell walls. Long story short, gram negative bacteria feature a thin, but highly impenetrable membrane, whereas gram positive bacteria feature a thicker, yet less resilient wall. Gram negative bacteria tend to be more pathogenic, and are more resilient against antibiotics, whereas gram postive bacteria tend to be the more beneficial, "probiotic" sort.

The various probiotic species (more on the specific types in a bit!) provide a vast array of health- supporting benefits. For example, they can:

  • Stick to the mucous layer of our intestinal cells, so other "bad" bacteria can't.
  • Stimulate that mucous layer of the intestines, to help heal leaky gut.
  • Beneficially influence our immune system, including the innate (aka: preprogrammed) and acquired (aka: learned) systems, as well as antibody secretion and T cell activity.
  • Function as natural antimicrobials.
  • Generate short chain fatty acids which serve as fuel for our intestines.
  • Reduce the PH of the colonmaking it more acidic to thwart pathogens.
  • Produce lactate to also inhibit pathogens.
  • Beneficially influence phagocytosis (aka: preprogrammed cell death).
  • Calm inflammation.
  • Help heal leaky gut.
  • Actually influence our brains and cravings, and even treat depression! (Thanks to something called the gut-brain connection!)

And want to know something particularly fascinating? Even dead probiotics (killed by heat) have been shown to generate beneficial effects, from improving IBS symptoms to boosting the immune system to treating candida!  #Icanteven 


In addition to probiotics, we've also got prebiotics, "discovered" in 1995.  Prebiotics are food substrates (with crazy names like fructooligasaccharides (FOS), galacto-oligosaccharides (GOS), mannan oligosaccharides (MOS), and inulin) which aren't digestible by us, but do serve as food for the probiotics. Prebiotics appear in foods like artichokes, onion, garlic, leeks, and asparagus, as well as resistant starches, which include green bananas, raw potatoes, and cooked and cooled rice and potatoes.

Lastly, we've got Symbiotics, which are combinations of probiotics and prebiotics.


So where do these bacteria actually come from in the first place? Are we just born with them? Actually... yes! Read on!


Children are first inoculated with their good gut bacteria (including the foundationary Bacteroides species, as well as Bifidobacterium, Lactobacillus, and many others) at birth. The main colonization (which sounds like a sci-fi movie) occurs through natural birth, as the baby makes his or her exciting exit through the mother's bacteria-rich birth canal! Recent 2014 research also indicates bacteria may enter the placenta from the bloodstream, since a baby's bacteria seems to mirror the bacteria in a mother's mouth, of all places! (And in fact, gum disease may be a risk factor for premature birth!)

A variety of key factors influence this initial bacterial set up. The state of the mother's gut bacteria is a major factor, and even her stress levels can affect things! Breastfeeding is notably key to further foster the baby's gut bacteria, as a mother's milk provides probiotic species, as well as oligosaccharides which feed these good bacteria. With this in mind, it's no wonder that the slew of C-section births, antibiotics, and formula (rather than breast) feeding can all negatively influence these initial populations, encouraging a slew of metabolic and immune disorders, including celiac disease, diabetes, and obesity. Talk about starting off on the wrong foot!


Influencing factors within the first few years of a child's life further mold his or her gut microbiome. In the good ol' days, we continued to foster beneficial probiotic colonies in a variety of ways. Think: children playing outside in the bacteria-rich dirt. Studies even indicate that children raised on farms tend to feature more robust gut microbiomes, as do children with pets. Exposure to probiotic species as a child has also been shown to discourage the development of allergies and skin conditions, while supporting the immune system. Today, however, children are encouraged to use hand sanitizers 24/7 in pristine sterilized environments, which can greatly dampen beneficial bacterial diversity in our GI tract, while also encouraging resistance of pathogenic species.

Beyond the differences in how children are raised, we also historically ate probiotic-rich unpasteurized fermented foods and raw dairy, as well as soil-covered, non sanitized produce. We'll look at all this more in a bit, and you can also check out my Fermentation Guide for DIY fermented food adventures!


While there may be up to 150,000 different species of bacteria on our dear planet (oh my!), a few common species tend to inhabit the human gastrointestinal tract. These include Bacteroides, Bifidobacteria, Lactobacilli, Streptococci, Enterobacteria, and Clostridia. We don't actively replenish all of these, and the commonly supplemented probiotics typically include the Lactobacilli and Bifidobacteria species. Soil Based Organisms, such as the Bacillus species, also inhabit the human GI, although in much smaller amounts.


The gram-positive lactobacillus species (of which there are 100+) produce lactic acid by fermenting carbohydrates.  Some also produce other gasses (like carbon dioxide) as well (which can potentially be problematic for those with GI distress like gas and bloating.) Lactobacilli are abundant in dairy products, especially less pasteurized versions. They can live in the presence of oxygen, which explains why you can find them in your open yogurt container (though don't hold your breath for the common additive-rich, pasteurized commercial versions.) While often abundant in the human gut, lactobacilli tend to be transient when supplemented, bestowing potential benefits as they pass through the system, rather than stick around for the long term. And while lactobacilli can live in the presence of oxygen, they still often require refrigeration. They also may be particularly beneficial to reinoculate the gut after a course of antibiotics.


The gram-positive, anaerobic bifdidobacteria (of which there are 30+) cannot live in the presence of oxygen, and utilize different metabolic pathways than lactobacilli. They produce both lactic acid from carb fermentation, but also acetic acid. Unlike lactobacilli, bifidobacteria are mostly just found in humans and animals, rather than foods and nature. But like lactobacilli, supplementing with bifidobacteria also tends to yield potentially beneficial, yet transient effects. Bifidobacteria are difficult to keep alive outside of us, and require refrigeration.

Soil Based Organisms (SBOs)

Soil-based probiotics refer to an altogether different species of bacteria: little guys found in the air, water, and dirt! In addition to popping up in animal and even insect guts, the popular strain found in the human GI tract includes the Bacillus species. SBOs are sort of like the plant world's alternative to our own probiotics, like the previously discussed lactobacillus and bifidobacteria. They live in a symbiotic relationship with plants, breaking down nutrients (like phosphorus and nitrogen), providing hydration, and also combating pathogens and serving as antifungals.

Unfortunaelty, in a devastating symmetry to the attack on our own gut bacteria, our planet's soil microbiome has also been greatly injured and depleted of nutrients, thanks to the antibiotic equivalent of fertilizers and pesticides. While we historically often ingested SBO's in the pre-industrialzied world by eating dirt-covered fruit and veggies, we don't so much anymore. (Although Asian populations may get some via other means, since bacillus subtitles is actually the bacteria responsible for the fermented Japanese soybean-based food known as natto.)

Due to their spore-like nature, SBO's can be stored at room temperature indefinitely, with no worries of dying. While lactobacilli and bifidobacteria tend to be transient when we ingest them, in a "we're just passing through and bestowing some benefits" type-way, SBOs can be more resilient, forming endospores and potentially colonizing the small intestine (though studies debate to what extent). Interestingly, SBOs may also interact with and affect our populations of  bacteroides and lactobacillus as well.

When we ingest SBOs, we can reap some of the benefits. Though clinical trials on SBOS are sparse, some have found they may reduce cholesterol, and mitigate diarrhea from antibiotics. They can also stimulate the immune system, prompting IgG responses. (Depending on the personal state of your immune system, this may or may not be beneficial.) The aforementioned bacillus-based natto, for example, has been shown to provide vitamin K2, support the immune system, and yield anti-cancer effects.

And remember their pathogen-fighting powers in plants? SBO's also have antibacterial effects. Studies have found the bacillus species produce potent antibiotic-like substances capable of fighting many intense bacterial strains, including  Staphylococcus aureus and Heliobacter pylori. They've got anti-fungal effects as well, and may be able to outcompete and inhibit candida - yippee! In fact, I think these antimicrobial powers may be one of the reasons SBOs tend to work well in those with overgrowths of problematic bacteria populations. SBOs also may be able to take compounds which are damaging to our genes, and convert them into inert substances. Pretty nifty. 


Saccharomyces-Boulardii is is actually not a bacteria, but rather a beneficial yeast,  first isolated from the lychee fruit in 1923. It can be particularly beneficial for restoring gut homeostasis, and combatting the candida yeast responsible for common fungal overgrowths (which can yield symptoms like a white and fuzzy tongue, itchiness, brain fog, digestive distress, and a myriad of other factors). Studies indicate saccharomyces-boulardii supplementation may also fight pathogens, treat gastroenteritis, and calm diarrhea.  It may be constipating for some, so that's something to keep in mind. That said, I currently believe its benefits likely outshine this potential negative.


A common reason certain probiotics may make  some people feel worse rather than better, may involve histamine production. Histamines are a chemical released in response to certain foods, as well as allergic and immune reactions to many other dietary and environmental triggers. Histamine is broken down by the DAO (diamine oxidase) enzyme in the intestine, although many people (including those with digestion distress) often feature less than adequate DAO production. Too much histamine can result in a myriad of symptoms, including fatigue, skin rashes and itchiness, anxiety, and a myriad of other unpleasant things.  

Certain probiotic strains can generate excessive amounts of histamine, while others may be neutral, or even degrade histamine. In general, lactobacillus strains (quite common in fermented dairy products) are often histamine raising, while bifidobacteria are often lowering. See the next section for more info regarding specific strains!


Okie dokie, if your head isn't already swirling with all the crazy bacteria names, let's get even more real, shall we? Here's a brief overview of specific strains common in probiotic supplements, to help guide your decisions of probiotic supplementation. I've listed how the various strains affect histamine, as well as any relevant studies I've come across involving their effects on digestion and gut health.

I've also noted if these probiotics are included in VSL - a highly clinically-studied probiotic formulation featuring 8 strains, and up to 900 billion colony-forming units, depending on the strength you use. (By comparison, typical probiotic formulations typically contain more like 5-25 billion or so.)  The double strength VSL formulation is by prescription only,  while the less (though still highly) potent versions are available at Costco and Amazon.  I recently got a prescription for VSL, and probably took a *bit* too much. While bloating seemed to dissipate a bit, the increase in, shall we say, bowel matter was nothing less than shocking. To the point that I was like, "K bye." (It's still sitting in my fridge, and I may try it again in the future in smaller amounts.) 

The Bifidobacteria Class

Bifidobacterium bifidum: This strain is histamine lowering.

Bifidobacterium breve: This strain is histamine lowering. It is found in VSL.  

Bifidobacterium infantis: This strain is histamine lowering. It has been shown to aid constipation. It is found in VSLand is also the strain making up the popular Allign

Bifidobacterium longum: This strain is histamine lowering. It is found in VSL.

Bifidobacterium longum: This strain is histamine lowering. It is found in VSL.

The Lactobacillus Class

L. Acidophilus: While debated, studies have shown it may be histamine raising. It is found in VSLIt has been shown to attach to the intestinal cells and thus discourage other bad bacteria from doing so. It may aid abdominal pain by creating opioid-like effects in the guts. (That said, opioids can slow gut motility, so this makes me a smidge nervous.) 

Lactobacillus bulgaricus: This strain is histamine raising.

Lactobacillus casei: This strain is histamine raising. A 2008 study of found it reduced hydrogen production in 14 out of 18 SIBO patients. 

Lactobacillus delbrueckii: This strain is histamine raising.

Lactobacillus plantarum: This strain is histamine lowering. It is found in VSLStudies have found it may help heal leaky gut by affecting the tight junctions in intestinal cells. It is naturally found in kimchi, sauerkraut, and cultured veggies.  In fact, a 2017 study found it degraded 100% of the histamine in a broth with  50 ppm of histamine!

Lactobacillus rhombus: I'm not sure about the histamine on this one. It has been shown to benefit eczema.

Lactobacillus reuteri: This one has an interesting relationship to histamine. While it is histamine raising, it also increases something called cAMP which calms the inflammation response. Studies have found it may benefit constipation, and yield antibacterial effects.

The Others

S. thermophilus: This strain is likely either histamine raising or neutral. It is found in VSL. It produces lactic acid, and may help those with lactose intolerance. 

Bacillus coagulan: This one does not produce histamine.​​​​ In a 2014 study, this SBO probiotic resulted in a negative breath tests in 93% of the participants. 


It is estimated that up to a whopping 80% of patients who have IBS actually have small intestinal bacteria overgrowth, also known as the dreaded "SIBO." SIBO refers to an overgrowth of bacteria (both potentially good and bad, though likely more often the later) in the small intestine, which should be relatively sterile compared to the large intestine/colon. While the colon typically harbors around 100,000,000,000,000 bacteria, the small intestine features more like 100,000. 

Though a myriad of factors can encourage or exacerbate SIBO, here are a few potential causes:

  • Exposure to pathogenic bacteria (often in the form of food poisoning), which leads to gut dysbiosis. An increasingly popular theory proposed by Dr. Pimental at Cedars Sinai, is that this inciting incidence leads to an autoimmune response which then damages intestinal motility, leading to a further buildup of bad bacteria.
  •  A disfunction in the migrating motor complex (MMC) - the intestinal waves which keep things moving through the intestines and discourage bacteria from building up. When the MMC doesn’t function correctly, stuff can build-up in the small intestine, including bacteria.
  • Hypothyroidism, which slows motility/ digestion/etc, leading to bacteria buildup.
  • Digestive problems, such as inadequate stomach acid, bile, and/or digestive enzyme generation.
  • Chronic stress.
  • Dysfunction in the vagal nerve.
  • And, unfortunately, a ton of other things. (Check out my post Is Your IBS Caused By SIBO? Get ALL The Info! for more!)

In any case, since SIBO and IBS often involve too much bacteria, does that mean probiotics should be avoided? The debate surrounding this can get quite intense. I originally was hardcore #teamavoid, but increasingly more research has caused me to re-evalute things a bit (and then re-evaluate my re-evaluations: it never ends!)


On the one hand,  supplementing beneficial bacteria can potentially aid bowel movements in a variety of ways. Quite a few studies have shown probiotics can benefit IBS and bowel movements, even in comparison to pharmaceuticals, which is super nifty! (Anytime we can reduce those, I'm totally down!) And because probiotics tend to be transient,  you can make the argument that you're unlikely to create long-term problems with supplementation, if bacterial build-up is a problem.

The beneficial effects of probiotics could be due to a myriad of reasons. Though transient, probiotics can yield a highly antibacterial effect against pathogenic species. This can in turn reduce inflammation and overgrowths which injure the gut and slow motility. Some can also produce lactic acid and short chain fatty acids which stimulate movement of the intestine, and increase acidity, which in turn enoucrages muscle contractions. Some probiotics also convert bile salts into free bile salts, which increases hydration in the colon. And on the too-much-movement (AKA: diarrhea) side of things, some probiotic can do the reverse and actually block receptors for motility, helping that whole runny issue.

So yes, some people do, indeed, find great relief and resolution of symptoms with probiotic supplementation.  

But things are still tricky….


Ok, here comes my real (controversial) musings on the matter. While I have no doubt that a highly populous, bacteria-rich microbiome is a crucial feature of many (if not most) healthy digestive systems, does that mean it's the only way to have a healthy digestive system? I don't think so. It's sort of like comparing a Mercedes (representative of an awesome gut with a high bacteria count) to the much less common - though arguably equally pristine - Tesla (comparative to an also awesome, yet more sterile gut). And appropriately enough, a Tesla uses a completely different fuel substrate: love how perfect this analogy is!

Let's take a moment and explore the proposed foundational benefits of gut bacteria: inhibiting pathogenic bacteria, generating short chain fatty acids which serves as fuel for the colon,  and regulating immunity and inflammation. 

Bacteria Battles

Probiotics are often advocated for their ability to take up "real estate," so the bad guys can't. But think about this: if you don't overfeed any of the bacteria in the first place, and maintain a less populated gut, perhaps there would be less gut bacteria to de-place?  It's sort of like the difference between living in a highly populated city  (oh hi Los Angeles!) filled with good and bad guys, versus, oh I dunno.... living in the middle of an empty field somewhere. (Oh hi Kansas!) The former needs neighborhood watches and police to keep an eye on things (aka: probiotics), while the later doesn’t really (horror movies which take place in creepy rural environments aside). Also, living in either city is not "right" or "wrong," but rather a matter of personal suitability. 

To this point, while we often think a healthy colon will be teaming with wonderful bacteria, studies show that those with intestinal inflammation (like celiac patients) actually often feature more microbes in their intestines (including the presumably “healthy” bifidobacteria), indicating more may not always be better. The same also often goes for obese patients. 

Additionally, studies have found that that those with intestinal dysbiosis who go on low carb and/or low FODMAP diets which effectively reduce bacterial load, tend to experience great improvement in symptoms, such as reduced inflammation, bloating, and gas. Furthermore, after adhering to a low FODMAP diet for a bit, these patients often - ironically enough - can experience more microbial diversity, despite an overall reduced bacteria population. So it may be that less bacteria overall, but with adequate (or even more) diversity, may be key for those struggling with intestinal distress due to excess and/or the wrong type of bacteria.  Think of it like the difference between a raging college party filled with tons of just a few "types" of people, compared to an exclusive dinner party with just a few, unique and different, guests. So rather than shoving the system with bacteria, relief and restoration of health may more easily come from seemingly “starving” said bacteria overall, which will then allow the “good” bacteria to naturally flourish, even if in smaller amounts. 

Short Chain Fatty Acids

Gut bacteria are also often indicated as key for generating short chain fatty acids (SCFAs) - specifically a version called butyrate - which then serve as fuel for the colon. That said, excess butyrate production from excess bacteria may not always be a good thing. Studies have found that obese and celiac patients often feature excess SCFA production, which indicates an excess of bacteria. Furthermore, those with gut dysbiosis in general also may generate excess butyrate. So depending on the situation, too much energy from SCFA a-brewin' in the intestines may be indicative of distress, fueling the bacteria (be it the bad guys, good guys, or good guys in the wrong place), rather than fueling you.

Let’s also take a moment and look at the function and sourcing of butrate. Fermentation of this colonic fuel is key in herbivores featuring a long large intestine, who rely primary on bacterial fermentation as a fuel substrate. In fact, this generation of fat from fiber makes them ultimately function on a higher "fat" diet than their plant-based food meals may appear, as such plants are transformed into fatty acids by gut bacteria. The western lowland gorilla, for example, generates around 57.3% of its energy from fatty acids, despite its seemingly “low fat” diet. This requires quite a change in perspective, but I find it fascinating! Think of it like the difference between using cash to buy something (eating fat), versus being given a “credit” for cash, which you then go and exchange for cash.

Omnivorous humans, on the other hand, feature a longer large intestine and rely less on bacterial fermentation for such energy. Furthermore, our elongated small intestine allows us to absorb energy directly from fats, including already-formed butyrate found in foods like butter. While a higher carb, low-fat diet rich in fiber may not supply such an immediate fuel source, a low carb diet rich in short chain fatty acids may supply abundant energy, bypassing the need for supplemental bacterial fuel substrates. 

Inflammation & Immunity

As a final note, probiotics are often advocated for their ability to regulate inflammation and immunity. On the one hand, this is quite likely a pivotal factor in gut health, as well as chronic and autoimmune disease situations. Probiotics can definitely be highly beneficial for disease states. On the other hand, certain probiotics may actually exacerbate inflammation or immune conditions, either by encouraging bacterial overgrowth, or unnecessarily motivating an overactive immune system. As often reiterated in Michael Ruscio's Healthy Gut, Healthy You , eating to reduce inflammation is key. For some, that may mean more probiotics, for others, it may mean less.  


Let’s zoom in for a moment on fiber's relation to the gut microbiome. Fiber serves as a prebiotic in the gut, feeding gut bacteria and presumably leading to a healthier gut state. Yet many IBS sufferers find that reducing fiber actually massively improves their GI distress symptoms.  So while some may easily benefit from feeding their gut bacteria with ample fuel substrates such as fiber, for others, this may just make things worse. 

Consider a shocking 2012 study, "Stopping or reducing dietary fiber intake reduces constipation and its associated symptoms.” (Note: This is the only study I can find testing this concept, which is quite telling re: the public perception of fiber.) The study looked at the effects of a zero fiber diet (gasp!) for 2 weeks in 63 individuals with constipation. After the first 2 weeks, the participants self-selected "acceptable" amounts of fiber for 6 months. The diet excluded all veggies, whole fruits, cereals, and whole grains (strained fruit and vegetable juices were allowed.) Despite what you may expect, here's what happened:

  • Those who followed a zero fiber diet, went from having a bowel movement every 3.75 days, to once daily! They also experienced a complete relief of straining, abdominal pain, and bloating.
  • Those who followed a low fiber diet, went from an average of having a bowel movement every 4.19 days, to once every 1.9 days. Almost half experienced no straining, and 31% experienced reduced bloating.
  • Those who maintained a high fiber intake, experienced no change in their bowel movements, which occurred every 6.83 days, with no resolution of bloating or ab pain.

After the study, 41 of the patients maintained the zero fiber diet, 16 went on a low fiber diet, and only 6 chose to go back to their fibrous ways. In other words, fiber made matters progressively worse for those with constipation, while no fiber completely resolved it! Of course, we don’t know what the root cause of the consitpation was in these individuals, but I imagine gut dysbiois was likely key in many, if not most, if not all of them. To reiterate: reducing the fuel substrates for bacteria (fiber), actually resolved symptoms. 


If you are indeed struggling in the gas and bloating department, there are a few dietary approaches you can try. They've got some overlap, and it can be difficult to find what's best for you, but you just gotta try things, ya know? I like a Low FODMAP Diet for starters. You can also get my IBS Food Comparison Guide, for a color coded chart of every food I could think of, comparing these diets!

The Low Fodmap Diet

Developed by researchers at Monash University, the Low FODMAP diet stands for “Fermentable Oligosaccharides, Disaccharides, Monosaccharides, and Polyols.” FODMAPS are short-chained carbohydrates which are not easily absorbed in the small intestine, and are easily fermented by bacteria, causing gas and bloating. The clinical trials on Low FODMAP diets are pretty impressive when it comes to reducing IBS symptoms. 

The Specific Carbohydrate (SCD) Diet

The Specific Carbohydrate Diet was developed by Dr. Sidney Valentine Haas and has been popularized by Elaine Gottschall. The SCD diet aims to heal damaged gut linings. It allows easily digestible monosaccharide carbohydrates (dubbed "Legal" foods), and forbids disaccharide and polysaccharide complex carbohydrates (dubbed "Illegal" foods). For the full details on the SCD protocol, please read Breaking the Vicious Cycle: Intestinal Health Through Diet .

The Gaps Diet

The Gut and Psychology Syndrome (GAPS) Diet is a regimented tangent from the SCD diet. It is a progressive protocol broken into an Introduction of 6 stages (progressively implemented for 3-6 weeks) followed by the Full GAPs diet. The GAPS diet aims to completely heal and seal the gut lining, while starving bacterial overgrowth and slowly reintroducing good bacteria via fermented foods. For the full details on the protocol, please read Gut and Psychology Syndrome: Natural Treatment for Autism, Dyspraxia, A.D.D., Dyslexia, A.D.H.D., Depression, Schizophrenia by Natasha Campbell-McBride. (I heart that book so much!)

The Cedars-Sinai Diet

Developed by Mark Pimentel, the Low Residue Diet seeks to minimize foods which slow down digestion and hinder the cleansing waves of the small intestine. It deviates from many of the other diets by discouraging most veggies, and actually encouraging many fruits and easily digestible carbohydrates (including some processed grains.) Probiotics are discouraged.


It would seem that there's more to the gut health story than simply popping probiotic pills or even feeding the gut microbiome. Indeed, the root cause of any potential inflammation in the intestines must be addressed, and that will likely entail different diets and/or probiotics for different people. While probiotics are all the rage in our modern world, available in an almost overwhelming number of brands and formulations, here are some key things to keep in mind:

  • Historically healthy populations have featured a diverse array of probiotic populations.
  • We weren't always popping probiotics via pills: rather we supplemented our natural food populations via fermented foods and dairy, and supported our natural populations via prebiotic foods.
  • Diet likely plays a key - if not larger - role in the composition of the gut micriobome than a probiotic pill.
  • People react differently to different probiotics. What works for your friend may not work for you.
  • Probiotic supplements tend to be transient, so you can likely supplement without too much worry of long term colonization, if SIBO is indeed your issue.
  • Many probiotics contain unnecessary additives and fillers which may cause adverse reactions and spike inflammation. Always read the back label, and choose brands wisely. (I like brands like Thorne and Pure Encapsulations.)

The ultimate takeaway? Supporting an anti-inflammatory state in the gut, as well as appropriate energy generation, is vital. How that plays out for you is, well, up to you! Don't fear experimenting with your gut micriobime, feeding it less or more at different times. Try different things, and respond appropriately. Remember the gut microbiome can change rather rapidly, so forward progress is always an option! And if you want to consider not eating #alltheprebioticthings for a spiel, don't worry about any raised eyebrows from fiber-chugging friends.

In any case, I encourage you to keep in mind the bigger picture. Overall health and reducing inflammation is the main issue to address, and other lifestyle factors - particularly chronic stress, sleep, and environmental toxin exposure - can greatly influence this. If the answer for all gut problems were in a probiotic pill, I'm sure everyone would be taking that pill by now! But alas, such is not the case. So be kind to yourself, and nourish your microbiome through anti-inflammatory, stress-relieving, nourishing lifestyle practices which support overall health.  See any gut bacteria (be them more or less) as working in your favor.  You got this!


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