You're only as healthy as your gut flora

How Gut Dysbiosis Impacts Digestion And Appetite

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Today I want to cover how gut pathogens can negatively impact the ability to digest food and regulate appetite. Here is an illustration of what should be, but oftentimes isn’t, absorbed in the digestive tract:


GI Tract

Courtesy: Advanced Nutrition and Human Metabolism, fifth edition.


Your ability to absorb nutrition is reliant on a healthy small intestine. If any part of the small intestine–duodenum, jejunum or ileum–is diseased, health and proper weight regulation are close to impossible.

Mouth and Esophagus

Once food is placed in the mouth and chewing begins, digestion starts. In the mouth, chewed food mixes with saliva secreted by the salivary glands. Saliva contains amylase, an enzyme that begins the breakdown of carbohydrate starches. A second enzyme called lingual lipase is released from glands in the tongue and back of the mouth. This enzyme begins the breakdown of fat. This mass of newly chewed food mixed with saliva is called a bolus.

Please note that any oral pathogens that may be present in the mouth will hitch a ride on this bolus as it’s swallowed. So too any other pathogens that populate your respiratory tract and happen to be in your mouth or throat at the time.

The bolus passes the pharynx and enters the esophagus. At the end of the esophagus, lies the lower esophageal sphincter.

Sphincters and various other muscles exist throughout your digestive tract, and their primary function is to allow swallowed food and its remnants to pass from one section of your intestinal tract to another. Ideally, partially digested food should continue in one direction. However, sometimes this process malfunctions.

For example, gastroesophageal reflux disease or GERD is caused when partially digested food mixed with gastric juice reenters the esophagus. I covered this disorder here. Be aware that pathogens and their toxic bacterial byproducts are quite capable of interfering with the normal function of these circular muscles.


Once past the lower esophageal sphincter, the swallowed bolus enters the stomach. Here it mixes with gastric juice to form a semiliquid substance called chyme. The stomach is lined with cells that contain millions of gastric glands producing this gastric juice, which is composed of water, electrolytes, hydrochloric acid, enzymes, mucus and intrinsic factor.

Hydrochloric acid has a very low pH of about 2, which is about the same pH as lemon juice. Hydrochloric acid has some extremely important functions:

  • It activates pepsinogen to pepsin. Pepsin is a protease enzyme that splits apart or hydrolyzes proteins into their amino acid building blocks.
  • It denatures protein. Proteins are quite complex structures so denaturing unfolds these structures allowing pepsin and other proteases secreted by the pancreas to begin the process of breaking them apart.
  • It releases nutrients from various organic complexes.
  • It is an important bactericidal substance meaning it kills bacteria ingested with food. All food contains bacteria, and as I just mentioned, any bacteria found in the mouth or throat will also be swallowed with it. The less acidic your stomach acid, the more likely your chances of developing a gastrointestinal infection.

Apart from pepsin, two other enzymes exist in gastric juice: amylase that was swallowed with the bolus and gastric lipase, an enzyme produced by cells of the stomach. Gastric lipase hydrolyzes short- and medium-chain fatty acids and is responsible for up to 20% of fat digestion in humans.

Intrinsic factor is also secreted by the same cells that secrete hydrochloric acid and is absolutely vital for the proper absorption of vitamin B12, also known as cobalamin.

Inhibiting the release of hydrochloric acid and intrinsic factor, either by binge drinking of alcohol or by taking proton-pump inhibitors like Prilosec®, Nexium®, or Prevacid® will inevitably lead to a number of negative health outcomes:

  • It will lead to the inability to properly digest protein which in turn causes protein deficiency. Undigested protein is now more likely to reach the colon where it will contribute to dysbiosis of the colon.
  • It will cause impaired digestion of up to 20% of fat. This will result in deficiencies in fat-soluble vitamins and minerals. Undigested fat that reaches the colon will also lead to colonic dysbiosis, further compromising the health of this part of the digestive tract.
  • It will sooner or later cause small intestinal bacterial overgrowth. This will displace beneficial lactobacillus species and inevitably cause leaky gut in the small intestine.
  • It will lead to B12 deficiencies. B12 deficiencies in turn cause:
  • anemia
  • skin pallor
  • fatigue
  • shortness of breath
  • palpitations
  • insomnia
  • tingling and numbness in extremities
  • abnormal gait
  • loss of concentration
  • memory loss
  • disorientation
  • swelling of nerve fibers
  • dementia

If this list of symptoms reminds you of those confused old people clogging the aisle of your local grocery store, this isn’t your imagination. Many of the elderly suffer from B12 deficiencies.

Unfortunately, due to their habit of eating gluten grains and high-fiber foods, many people, including the elderly, suffer from GERD and pop antacids and proton-pump inhibitors like Gummi Bears® at a movie matinée. The results are infection of the small intestine and B12 deficiencies.

Small Intestine

At the bottom of the stomach lies the pyloric sphincter where it opens every so often to allow chyme to enter the first part of the small intestine or the duodenum. Here again is an illustration of what the absorptive structures of the small intestine looks like:


Courtesy: Advanced Nutrition and Human Metabolism, fifth edition.

Courtesy: Advanced Nutrition and Human Metabolism, fifth edition.


You see that area labeled the brush border? This is where beneficial gut bacteria live and is also the site of most digestion. If this brush border is damaged, digestion will be compromised. And impaired digestion is just another way of saying nutrient deficiency and ill health. This is the area of the small intestine damaged by the autoimmune disorder known as celiac disease.

A healthy brush border produces appropriate levels of gut hormones. Conversely, an unhealthy brush border will produce fewer of these hormones. There are many hormones produced by a healthy small intestine. I could write a book on this subject but for today’s post, I want to concentrate on those most directly involved in proper digestion and satiety.


Secretin is produced by S-cells in the duodenum in the presence of chyme. This hormone tells the pancreas to release pancreatic juice rich in digestive enzymes to complete the breakdown of carbohydrate, protein and fat. Without these enzymes, there isn’t much hope for proper digestion.

Pancreatic juice also contains electrolytes that include sodium, potassium and calcium. Finally, it has bicarbonate, which is important because it raises the pH of the very acidic chyme entering the duodenum from the stomach. While low pH is what you want in the stomach, it is not what you want in the small intestine. Raising the pH of chyme is essential for the correct functioning of digestive enzymes released from the pancreas. S-cells damaged from pathogens or diet are not likely to release appropriate amounts of secretin to signal the pancreas to release its juice.

If pancreatic juice is not released, not only is digestion impeded and important electrolytes not secreted, but the small intestine and colon will experience inflammation from highly acidic chyme as it irritates the gastrointestinal mucosa and destroys beneficial bacterial populations in both locations. Many experience burning diarrhea as a result. This will encourage the growth of pathogenic bacterial species that thrive in inflamed conditions. A pancreas that does not release pancreatic juice is one that will become inflamed leading to pancreatitis, and in extreme cases, pancreatic cancer.


Cholecystokinin or CCK is a hormone secreted by L-cells in the duodenum that is also responsible for stimulating pancreatic secretion of digestive enzymes. It is also essential for proper gallbladder contraction and the release of bile into the small intestine. Bile, pancreatic lipase, and pancreatic colipase are responsible for 80% to 90% of proper fat digestion. If L-cells are not secreting CCK, or releasing it in insufficient quantities, the gallbladder will not contract as it should. Bile in a gallbladder that isn’t regularly expelled is going to harden into stones. Fat in stool or steatorrhea is a telltale sign that fat malabsorption is occurring.

The gallbladder is also an important route for bound toxins to be excreted from the liver and into the intestine for eventual elimination in feces. Therefore, if the cells that produce CCK are damaged from diet or dysbiosis, this very important detox pathway is not working properly. A liver that can’t dispose of toxins through proper bile excretion is a diseased liver; and a diseased liver means a diseased human.

Gallbladder disease is especially common in gluten-consuming societies and was one of the first manifestations of Western-type diseases when flour was introduced to the diet of cultures that had never eaten wheat. It is a very common finding in celiacs and gluten-sensitive people. (1) Knowing what you know about gluten’s promotion of intestinal inflammation and gut dysbiosis this should surprise none of you.

The inability to properly digest fat means improper digestion of fat-soluble vitamins A, D, E and K. And since many minerals also rely on these vitamins and proper fat absorption for transport across the gut wall, deficiencies in magnesium, zinc, calcium and other minerals are all but assured. As I wrote in the last post, deficiencies lead to food cravings.

CCK delays stomach emptying causing a feeling of fullness that curbs appetite. CCK receptors are abundant throughout the central nervous system, including the hypothalamus, site of weight control. CCK reduces appetite and food intake in both rodents and humans. (2) (3) So less secretion of CCK will lessen satiety signals sent to the brain and cause overeating.

Finally, in rodents CCK has been shown to trigger a gut-brain-liver neuronal circuit that directly reduces the production of glucose in the liver. (4) Type 2 diabetes is characterized by uncontrolled synthesis of glucose suggesting that dysregulation of CCK plays an important role in the development of this disorder.


Motilin is secreted by M-cells of the duodenum and jejunum. It stimulates stomach and small intestinal movement, pancreatic secretions, and like CCK, gallbladder contractions. Proper intestinal movement guards against small intestinal bacterial overgrowth so impairment of motilin secretion would increase the odds of gut infection.

Glucagon-like Peptides

Glucagon-like peptides (GLPs) are also released by healthy L-cells of the small intestine and colon, and the alpha cells of the pancreas. These hormones influence insulin and glucagon secretion and their dysregulation may be a contributing factor in insulin resistance. These hormones reduce appetite and the rate of stomach emptying making you feel full. So again, any damage to L-cells will impede the release of these insulin-regulating and satiety-enhancing hormones.

Peptide YY

This hormone is secreted by cells in the ileum and is the focus of quite a bit of research for its appetite-suppressing effect in rodents, primates and humans. (5) (6) (7) Supplementation of probiotics and prebiotics in rats has been shown to increase levels of this hormone. (8)

Small intestinal bacterial overgrowth due to impaired intestinal peristalsis affects the ileum first and would have the most profound adverse impact on this hormone’s production. Speaking from my experience, nothing has suppressed my intake of food more than clearing up my intestinal dysbiosis and supplementing with prebiotics and probiotics. I believe it’s due to increases in peptide YY and reduction in endotoxemia which will be the subject of the next post.


This hormone is secreted along with GLPs and peptide YY by healthy intestinal L-cells. In both rodents and humans it reduces food intake. (9) (10) Like the other satiety hormones, its production will be enhanced by the presence of healthy gut flora but inhibited in the presence of gut dysbiosis.


Ghrelin does not suppress appetite. On the contrary, it is termed the “hunger hormone” because it acts on the arcuate nucleas (ARC) region of the hypothalamus to increase food intake. It is synthesized mainly in the stomach. Ghrelin acts in opposition to peptide YY, oxyntomodulin, glucagon-like peptides, CCK and other satiety hormones. As it is produced in the stomach, it is the least likely of the appetite-regulatory hormones to be impacted by small gut dysbiosis.

Other gut hormones that depend on a healthy, non-damaged gut, are glucose-dependant insulinotropic peptide (GIP), enterogastrone, amylin, somatostatin, and substance P. Proper digestion and appropriate short-term hunger-suppressing signals are all reliant on a healthy small intestine. A healthy small intestine, in turn, is reliant on healthy gut flora. You can’t have the one without the other.

The Colon

After transiting the last section of the small intestine or ileum, chyme empties through the ileocecal valve into the right-hand side of the colon known as the cecum. Here, contractions mix the mainly liquid contents of undigested food so that sodium, chloride and water are absorbed. Approximately 90% to 95% of the water and sodium entering the colon daily are absorbed here.

The colon contains the most gut bacteria of any part of the digestive tract. It is here that any undigested food is typically fermented by bacteria. However, in the case of small intestinal bacterial overgrowth, some food will also be fermented there.

In the colon, soluble fiber is fermented by friendly bifidobacteria into short-chain saturated fatty acids that are transported to the liver and other cells. However, bifidobacteria-produced butyrate serves as “food” for the cells lining the colon. Butyrate strengthens these cells and makes the colon wall impervious to translocating gram-negative endotoxins and their highly inflammatory lipopolysaccharide cell-wall remnants. In other words, if you want to reduce endotoxemia from the colon, you want plenty of butyrate.

While colonic bacteria mainly ferment carbohydrates (fiber and undigested starches), other substrates that can feed bacteria in a healthy colon are glycoproteins (mainly from mucin), sugar alcohols (sorbitol and xylitol), fructose, pectins, gums and some proteins and amino acids. If you have trouble digesting milk sugar or lactose, it will end up in the colon where bacteria will produce plenty of gas as they ferment it.

However, large quantities of undigested carbohydrate, fat or protein should never reach the colon. If they do, something is amiss in the small intestine. You can rest assured that this will cause bacterial blooms in the colon that specialize in fermenting these substrates, many of them pathogenic.

These bacterial species will crowd out friendly species like bifidobacteria. The entry of highly acidic chyme that was not properly neutralized by pancreatic juice in the duodenum will also affect beneficial species for the worse.

Excess fermentation in the colon will cause lots of gas and discomfort. This will cause the colon to expand like a balloon which can lead to diverticulitis as pouches form along the colonic wall with some becoming infected as bacteria and undigested food become trapped within them. And yes, this also includes indigestible fiber that everyone keeps telling you is great for your health. For more on the destructive role of indigestible fiber on GI health, I again refer you to Fiber Menace: The Truth About the Leading Role of Fiber in Diet Failure, Constipation, Hemorrhoids, Irritable Bowel Syndrome, Ulcerative Colitis, Crohn’s Disease, and Colon Cancer.

A colon is only as healthy as the digestive tract that precedes it. If the stomach or small intestine is not functioning properly or diseased, the colon will reflect that, always. Any treatment that concentrates solely on the health of the colon risks being short-lived if low stomach acid or small gut dysbiosis is not also resolved.

To recap, gut dysbiosis will interfere with proper digestion and appetite control by:

  • inhibiting the release of brush-border hormones necessary for proper pancreatic and gallbladder function.
  • impair the proper digestion and absorption of fat and fat-soluble vitamins and minerals.
  • impair the proper digestion of protein.
  • impair the proper digestion of carbohydrate.
  • inhibit the pH neutralization of acidic chyme from the stomach.
  • inhibit secretion of hormones that regulate intestinal motility.
  • inhibit secretion of hormones that play a leading role in short-term appetite control.
  • inhibit secretion of hormones that play a role in regulating insulin and blood glucose levels.
  • increase inflammation throughout the gastrointestinal tract and the occurrence of endotoxemia.
  • displace beneficial bacteria in the small intestine and colon that would otherwise keep these areas of your digestive tract and you healthy.

In the next post, I’ll detail how gastrointestinal dysbiosis, endotoxemia and inflammation impacts metabolism for the worse.



Gropper, S. R., Smith, J. L., Groff, J. L. (2009). Advanced Nutrition and Human Metabolism. Belmont, CA: Wadsworth Cengage Learning.

17 Responses to How Gut Dysbiosis Impacts Digestion And Appetite

  • HT says:

    Thank you Ray for this super explanation of digestion. It will be something I refer to more than once. I’m interested in what you have to say about the colon because I actually have ulcerative colitis. I don’t have any of the gas or bloating symptoms which I’m happy about, but makes it difficult for me to know what the root of my problem is. I have chronic diarrhea with blood and urgency which completely disrupts my life as you can imagine.

    I don’t even know where to start to start fixing my digestion. As you expertly point out, this is a really big tangle of a problem With my inability to get my symptoms under control, it’s next to impossible to experiment.

    Have any ideas? Decreasing starches? Taking digestive aids?

    Thanks again

    • Ray Medina says:

      Hi HT,

      Thanks for commenting and telling me about your digestive issues. Ulcerative colitis (UC) is a tough one as I don’t need to tell you. Like Crohn’s disease, it is quite likely that your small intestine is also diseased. As I don’t know your particular situation, what follows are some general recommendations I think should help:

      You should be on a daily probiotic and also taking a prebiotic supplement powder twice daily. Whether you choose to go with Syontix products or not, these need to be part of your daily regimen. Start or increase your consumption of fermented dairy like yogurt or kefir, homemade being better than store bought. Just be aware that fermented foods act slowly and will not quickly resolve your issue.

      Under no circumstances whatsoever should gluten pass your lips. And yes, even if you tested negative for celiac, this still applies. As far as I’m concerned, gluten is good for no one, especially those experiencing GI issues. That means nothing made from wheat, barley or rye. This is not optional and eating any amount of it after you have stopped for a while can undo months of work. There are many hidden sources of gluten in food and medicine. This article is a good place to start for learning about hidden gluten sources:

      Banish vegetable oils from you diet. No safflower, soybean, corn, canola, peanut, etc. oils. This only adds fuel to the fire. Natural saturated fats from whole foods, beef tallow, lard from pastured pigs, coconut oil, olive oil and palm oil are acceptable. No hydrogenated fats. Read those labels carefully. Refrigerated lard is fine, shelf-stable lard is not. Butter is encouraged as it contains butyric acid as does Parmesan cheese, and goat’s milk. This will help strengthen and heal the colonic gut wall.

      Indigestible fiber is not your friend. This has been one of the most destructive dietary recommendations of all time which is saying a lot. Indigestible fiber is just that, indigestible. It is the only dietary substance that swells four to five times its normal size when mixed with gastric juice. This fiber-laden, acidic chyme, when not neutralized (and I bet that’s part of a UC sufferer’s problem), will scrape along the inside of your small intestine and colon adding to inflammation. Like rubbing a Brillo Pad on an open wound.

      What this means is no high-fiber foods like beans, whole grains, dried fruit, nuts and seeds. Fruit should be peeled before eating. Better yet, eat tropical fruits like banana, mango, pineapple, papaya. Eat low-fiber vegetables or peel off their fibrous parts. No added psyllium husks for constipation. I again refer you to the book Fiber Menace for more info.

      All legumes should be avoided for possible lectin contamination. No dried beans, peanuts or soy anything. If you drink soy milk, stop. The only soy safe to eat is when it is fermented into natto, tempeh or soy sauce. Many soy sauces contain gluten so if you eat sushi, bring your own bottle of gluten-free soy sauce. I do it all the time.

      Alcohol should be drunk sparingly or not at all until you get this under control. Beer must be avoided because it contains gluten unless you drink some of the new gluten-free beers on the market.

      Iron-rich foods need to be limited. Pathogens love, love, love iron and need it to grow. That means cutting back on red meats, foods like cereals that contain added iron and iron-rich vegetables. Here is a web page that talks about these foods: Red meat, shellfish and eggs are all very healthful foods that you want to re-add to the diet once you get your UC under control. I would concentrate on eating wild-caught fish, pastured poultry, and pastured pork for your protein sources most days of the week until your UC gets better.

      Dairy should be limited to cream, butter, goat’s milk, 100% Jersey Cow milk, and cheese. If you have known casein allergies then dairy should be limited to cream and butter. Likewise if you are lactose intolerant. Consume the best quality butter and cream you can afford.

      Candida yeast overgrowth is part of inflammatory bowel disease as it is in small bowel disease. Candida degrades the protective mucus layer in the digestive tract opening up the epithelial layer to bacteria. Yeast can feed on alcohol and ketones and will overgrow in the absence of beneficial bacteria. I do not recommend a very-low carb diet that produces lots of ketones. I experienced a bad yeast overgrowth on such a diet as have many others. You need to make sure you are eating enough glucose daily in the form of safe starches. That would include white rice, taro, yucca, yam, sweet potato (note it’s high iron content, however). I would include potato but it is a nightshade that may irritate an already inflamed mucosa. For other nightshade vegetables that you should probably stay away from for now see the glossary.

      Caffeine should be avoided. Drink non-decaf coffee is this appeals to you. Stay away from high-caffeine teas and soft drinks, which should be avoided anyway due to their high sugar content. The safest drink is water.

      I would recommend a digestive enzyme and an HCI betaine supplement with each meal. Cod liver oil should also be part of your healing regimen and you can find a good one here:

      Make and consume bone broths. These are very easy on your GI tract and are great for healing it. For more info see here: If you don’t see yourself making bone broths, then find a local Vietnamese restaurant that serves Pho. This soup is a beef stock with rice noodles. Order it with gelatinous connective tissue and eat it at least once a week. Skip adding any peppers or hot sauce to the pho. Conversely, you can try a product like this but it’s more costly and not nearly as helpful.

      Finally, there is the procedure known as fecal transplant that has helped many. My only concern, apart from cost, is that the problem may reoccur if nothing is done about problems further up in the GI tract. Chriss Kresser recently blogged about it here:

      Please keep in touch and let me know how you are doing.

  • dyamik says:

    Hi Ray,

    You’ve got some awesome information on your site!

    I was hoping maybe you can help me out with my specific issue.

    I’ve been Paleo for a year trying to fix my acne. I was low carb in the beginning since it was the only thing that worked. I added bone broths and probiotics and now I’m able to eat more veggies and white rice as a starch.

    I still have some really frustrating symptoms. Intolerance to fructose, some relief and then worse from probiotics, white coating on my tongue, and sorry for being graphic, balanitis(which I believe is a fungus or yeast problem).

    I’m very very very strict with my diet, with the exception of alcohol, which I’m now ready to eliminate. I ended up consuming a little too much and the next day I had my symptoms flare up.

    I believe I have SIBO because of my fructose intolerance and probiotic intolerance and the tongue coating, acne, and balanitis as a result of a yeast/fungal infection.

    I can’t afford a ND in my area so I was hoping you could recommend some kind of protocol. I was thinking about doing the garlic protocol you did and after 3 days adding your prebiotics and probiotics. What do you think about this?

    I’m getting desperate at this point since these problems have been with me for a couple of months now and I can’t seem to find a cure.

    If I don’t get better I was hoping to fork out the $ for the MetaMetrix DNA Stool Analysis, would this help me find out the root cause of my issues?

    Thanks for the info on SIBO and hopefully a reply :)


    • dyamik says:

      I just read your reply to someone suffering from digestive issues above and I noticed you said to avoid high iron foods.

      I noticed that whenever I eat meat, I’ve only been eating beef for a while now and some fish, my tongue coating gets thicker. Is the iron feeding the pathogens?

      Also as far as ketones go, I have grass fed pastured lard in my fridge but I’ve been using coconut oil for my cooking needs instead. Should I switch to the lard since coconut oil promotes ketones which could potentially feed the bad guys?

      Thanks again!

    • Ray Medina says:

      Thanks for visiting the website and commenting.

      I’m always hesitant to give advise as everyone is unique when it comes to dealing with gut dysbiosis. That said, I too battled yeast overgrowth as part of my dysbiosis so I have a lot of experience with this very vexing problem. Judging by what you have described in both your comments, I would hazard a guess that you are suffering from gut dysbiosis due to both an overgrowth of pathogenic bacteria and yeast. In fact, I don’t believe SIBO exists without yeast being a problem as well. That probably explains why the relapse rate is so high for those who are only prescribed an antibiotic.

      I would like to tell you that if you eliminated this or that from your diet, it would clear up your problem. When I had these issues I tried everything but it wasn’t until I took the raw, organic garlic that my issues began clearing up.

      As you read from my last post on SIBO, this is not side-effect free, but no effective treatment is including prescription antibiotics and antifungals. Until then, I would recommend reducing your intake of iron-rich food like red meat. You don’t want to provide whatever pathogens are populating your small intestine or colon with more fuel to grow. I would recommend fish for the anti-inflammatory effects of omega-3s.

      Yeast loves alcohol as you’ve already found out so you will really need to cut that out entirely to get on top of this. It also increases intestinal permeability which is not what you want if you already have a leaky gut.

      Whatever you do, don’t go low-carb to the point of glucose deficiency or you risk an increase in endotoxemia. If your extremities are cold all the time and your nasal passages very dry, that’s a good indication you need to up your consumption of glucose by consuming safe starches as recommended by Paul Jaminet. Too many low-carbers out there are giving themselves euythroid sick syndrome caused by endotoxemia and increased IL-1 and IL-6 cytokine levels. Don’t be one of them.

      Coconut oil has proven antibacterial, antiviral and antifungal properties. It is also protective of your liver in the case of translocationg gut pathogens. However, as you mentioned, it promotes ketone production so I wouldn’t go too crazy using it. While I did find it effective at keeping my oral thrush under control, it didn’t do a thing for my gut dysbiosis. Neither did home-made kefir or yogurt for that matter.

      Lard is high in monounstaurated fat and is not as protective of your liver as beef tallow or medium-chain saturated fats like coconut oil. That said, I would use added fats sparingly until you get this infection under control. All fat is effective at causing bacterial translocation for the same reason it’s effective for absorbing fat-soluble vitamins and minerals. Omega-6 vegetable oils are the worse because they also increase intestinal permeability and liver inflammation. But from what you’ve told me, that doesn’t appear to be an issue for you. I would, however, recommend using butter for its butyric acid content to strengthen gut barrier function. Parmesan and goat cheese, by the way, are also high in butyric acid. You should also be on a prebiotic like inulin/FOS to raise levels of bifidobacteria in the colon. Bifidobacteria will reduce endotoxin translocation by also strengthening the gut wall. Increasing levels of beneficial bacteria helps crowd out gut pathogens of all types, including yeast.

      A stool analysis can tell you a lot about what pathogens may be causing problems and whether you are digesting your food properly. I know because I had one. Unfortunately, the practitioner who ordered the test still failed to give me the right solution to clear up my dysbiosis even though they were both an MD and an ND. I was instructed to take expensive probiotics, digestive enzymes, aloe vera, glutamine, DGL, a liver-detox formula, and expensive vitamins. All lovely things but totally ineffective. However, my wallet was noticeably lighter and able to wear a size 0 after the experience;)

      At the end of the day, this infection has to be dealt with either naturally by the anti-bacterial and anti-fungal actions of raw, non-irradiated garlic or with a doctor’s antibiotic/antifungal prescription. Even then, it can take a while to overcome. Once you get this under control, you’ll find that probiotics and fermented foods will be far more effective at clearing up remaining gut dysbiosis and nagging symptoms like skin issues.

      • dyamik says:

        Hi Ray,
        I appreciate the response very much!

        I’m more than willing to deal with side-effects if it means well being in the future. I’m all to familiar with eliminating foods hoping it will be the magical cure, which is really what led me to finally find a real solution.

        I’ve been following Paul Jaminet’s recommendation of avoiding glucose deficiency and it has definitely been helping.

        Good thing the coconut oil isn’t as bad as I thought, I really like the taste of cooking in it!

        I went ahead and ordered your prebiotic powder and probiotics, do you have a specific recommendation on how and when I should take them when dealing with my specific issue? Should I start right when I start the garlic or should I wait a few days?

        If the stool analysis wasn’t so expensive I would have had one by now, but this is basically my last attempt at healing myself before forking over the $ to get one done and maybe find a competent ND, who hopefully doesn’t try to lead me into a money pit like you.

        I will definitely be doing the garlic, would organic garlic at Whole Foods be non-irradiated? I’m not sure how I would be able to know. I don’t believe NDs are allowed to prescribe anything in NY where I live so I would have to visit my conventional doctor who just likes to throw antibiotics out unfortunately.

        Do you have any idea if Oregano Oil might be helpful too? I have some in my cabinet and have read that some people have had good success with it.

        Thank you once again for your response!


        • Ray Medina says:

          Hi Dyamik,

          Yes, I would start the prebiotics and probiotics with the garlic. However, I would take the probiotic away from the garlic. Not sure if garlic harms beneficial gut flora like antibiotics, but to be safe, I would treat the garlic as an antibiotic and take the probiotic at a different time. You can take the prebiotics whenever. I would take the prebiotic and probiotic together first thing in the morning. While you can take the probiotic with food, I rather take them on an empty stomach to avoid a delay in transiting the stomach. I would begin with once a day and work yourself up to twice a day for both depending on reactions you may have. If die-off occurs or it makes your digestion worse, back off but don’t stop. Unlike other probiotics, ours can be split in half. Remember to put your prebiotic powder in a dry glass before adding water or liquid or you risk it clumping. Wish I had put that on the label.

          Garlic at Whole Foods is fine and what I used. As long as it’s labeled organic it should not be irradiated. Start with only 1 crushed clove. It can be powerful stuff especially when you first start. Remember to add water and wait a minimum of 15 minutes before drinking it down.

          I have been communicating with another person who has tried oregano oil to no avail. It did nothing for me either. As for peppermint oil, it can work for some. I found peppermint tea far more effective at relieving gas and bloating than the pills, but your experience may vary. If gas is an issue, it’s because improperly digested food is being fermented by colonic bacteria. I suggest a good digestive enzyme to prevent this from happening. I’ve had good luck with this brand: You would take a pill with each meal.

          • dyamik says:

            Hi again Ray,

            I started the garlic today along with peppermint tea. So far I’ve had some discomfort, maybe a little bit of a headache and more frequent bathroom visits. I noticed that my tongue coating flared up and it is yellowish and furry. Do you know what this could mean?

            I’ll keep you updated on my progress.


  • dynamik says:

    Hi Ray,

    Great thanks for the reply, for some reason however I wasn’t able to see it on the website rather I was able to read it through my email. Not sure why this is the case, I tried it on two different computers and the same problem occurred.

    It is now day 3 1/2 and I’ve only gone to the bathroom once through this whole ordeal and it was very loose and a feeling of having to go immediately.

    I don’t have much die off or as far as I can tell at this point, no gas, I do sometimes wake with a soar back and throat. My tongue seems to be less yellow and more whitish now however the same consistency. Acne is a little bit worse and my yeast problems seem to be the same.

    I’m going to keep up with the garlic and peppermint tea as maybe the reactions are delayed.

    Is there any possibility of the starch, in my case white rice, causing any sort of flora imbalances?



    • Ray Medina says:

      Hi Dynamik,

      First let me say that the rice should be of no concern. You need a source of dietary glucose if you are fighting a Candida infection. I know there are those who would disagree with me on this but I have yet to see how eating a food that breaks down into glucose molecules feeds Candida any more than eating a carbohydrate that breaks down into both glucose and fructose. Just make sure you stay away from gluten grains, refined sugar or high fructose corn syrup, alcohol, and omega-6 vegetable oils, including canola oil.

      It’s not clear to me how much garlic you’re taking. I assume one-crushed clove in water three times a day after eating. If you are tolerating that well, then I would increase the dose to two-crushed cloves three times a day after eating and see what happens.

      The peppermint tea is only useful if you have bloating, otherwise I see no reason to continue with it.

      You should be drinking plenty of water throughout this process as well as taking your probiotics and prebiotics. If you are not eating yogurt or drinking kefir, I would recommend adding those foods to your diet. I’m partial to plain Greek yogurt. You can add fruit like berries if you like.

      The garlic will help kill an overgrowth of yeast but will never eliminate it entirely. That’s impossible as Candida is a normal constituent of the human gut and will accompany you to the grave. What keeps it under control for the long-term is beneficial bacteria. This is why antibiotic use causes Candida problems for so many people.

      • dyamik says:

        Hi again Ray,

        I decided to stop the garlic a day later, I don’t think following through for another 2 days would do much since I wasn’t getting better but rather worse. Thick yellow coating on tongue, same balanitis(it’s not very serious, a little redness) as always.

        I have some raw sauerkraut with garlic that I tried to eat today. Within an hour my balanitis flared up and I had a thicker coating on my tongue. What the heck can this mean?

        I’m on the verge of getting a stool test done because I simply don’t want to guess anymore.

        -I eat fruit, I breakout, my tongue gets yellow and furry, and my balanitis flares up.
        -Alcohol does the same.
        -Starch = tired after eating the meal, thick white coating and furry instead of yellow, no breakouts, balanitis = neutral.
        -Probiotic ginger carrots, neutral effect, sometimes good sometimes bad. I seem to sneeze more often
        -Probiotic fermented garlic and cabbage sauerkraut, symptoms flare up.
        -When I don’t eat enough starch a couple hours later I get cold hands/feet. (I supplement 12.5mg iodine and 200mcg selenium per day) I also get a dry mouth and get thirsty.
        -Yellow palms, which I believe is from eating lots of the probiotic ginger carrots.
        -Sometimes hesitation to urinate

        Someone suggested diabetes… I mean I have some symptoms but can a 18 year old who’s been skinny his entire life really have diabetes? Wouldn’t I have more serious complications? The only thing really affecting my quality of life is this balanitis/acne..

        Would you recommend the Stool Test? I read that SIBO can be effectively diagnosed through an organic acids test, so should I get that done?

        The only thing I can imagine that the garlic helped is when I stopped it I started eating a lot more of the fermented ginger carrots and my tongue coating receded , but I ran out of the carrots within two days so I went about 3 days without any probiotics and my tongue coating came back. Sorry for so many questions, I’m just frustrated with this since I’ve been pretty strict Paleo with broths and probiotics(fermented foods, coconut kefir, and probiotic capsules) to no avail.

        • Ray Medina says:


          I would really recommend you see a physician for a full medical checkup. Yes, diabetes can and does occur in skinny people all the time which is why I wrote my series on weight dysregulation. Weight is a terrible indicator of health status as I explained here:

          If you have diabetes or prediabetes then that will need to be dealt with. If not, then I would suspect an infection. If you doctor suspects it’s fungal in origin, there are antifungal medications that he can prescribed. If it is bacterial, then antibiotics are the way to go. The only herbal that I know that is both is garlic, but if that is not working for you, then you will need prescription meds.

          Your mention of cold hands and feet suggests euthyroid sick syndrome (ESS) and therefore low metabolic function. My latest post covers that disorder. This is very common in people who go too low carb as many in the Paleo community unfortunately do. It can make a Candida overgrowth worse as fungus can and does feed on ketones to promote their growth. That includes going overboard on coconut oil as that increases serum ketones. Vegetables should never count against your glucose calories as many of these calories are fermented into fatty acids by colonic bacteria.

          As always, I would continue with your probiotics and prebiotics whether from Syontix or elsewhere. You’ll need them if you are put on antibiotics. As for this organic acids stool test, that’s news to me. All I can say is that it is not a medically recognized method for detecting SIBO.

          One question, how much red meat are you eating? If you do have a bacterial infection in your GI tract, be aware that iron-rich foods like red meat can really feed those critters.

          I too used to make and eat sauerkraut and had horrible gas pains and bloating as a result. Rather than make me feel better, it always made me feel worse. Sounds like it isn’t working for you either so you may want to cut that out. In fact, you may want to go easy on the veggies (fermented or not) and stick to rice and starchy tubers until you get a handle on this.

          You will need to find someone in your area you can work with to resolve these issues. I wish I could recommend someone but I can’t. At a minimum they should know your family and medical history to help determine the right protocol to follow.

          Good luck!

  • Alyssa says:

    I have a feeling I’m going to be comment-bombing almost all of your posts, so I apologize in advance. I just found your site and already commented on another post, but after reading this one and the comments, I just have to comment here as well! You’re mentioning all these things that I’d heard bits and pieces of while I was trying to deal with my UC, but I never got the whole story because I could never find good resources for information. Specifically, I find your take on safe starches and on iron fascinating. I was on the Specific Carbohydrate Diet for quite a while, and often went VLC because I suspected yeast. Most people in my support group and other sources online agreed that any carbs were bad when dealing with candida, but I remember that somebody once mentioned that going VLC can actually aggravate the problem…now that I’m reading your more thorough explanation, it makes sense. Although I’m still a bit baffled, because the only time I can experience no digestive symptoms (other than diarrhea, which never goes away due to not having a colon) is when I eat no carbs. But I do get cold hands and feet, and logically, I know I need glucose. Too bad I seem to be unable to digest it.

    Also, your mention of iron. I always knew that pathogens love iron, and taking iron supplements just makes their biofilms stronger, but I’ve been anemic for over 4 years (since I was diagnosed with UC) so my doctors always tried to make me take iron supplements. I knew a little bit about the bacteria thing back then, but they never acknowledged that there was any merit to my resistance. Currently, I’m still anemic, and still bleeding even though they took my colon out. I’ve done iron infusions in the past, but clearly they didn’t help long-term. I haven’t taken a full strength iron supplement in years because in addition to the bacteria thing, it hurt my stomach, but I have been emphasizing red meat, hoping to get iron that way. I never knew that even iron from real food could cause a problem. If I do have a bacterial overgrowth or infection in my small intestine (which I’m almost positive I do, not that that narrows my issue down much!), I should probably not be eating any iron, but I’m worried I’ll get even more anemic. On the other hand, maybe I’m so anemic because I’m not absorbing any iron at all, because the pathogens get it first, so not eating any iron wouldn’t make any difference.

    Also, I’ve never even heard of secretin before now, but I’m highly intrigued because it seems like a plausible mechanism for my problems. No secretin > impaired digestion + acidic environment > pathogens + gas + inflammation. But it’s all so interconnected, and I still feel so uneducated, that I really don’t know.

    Sorry to just dump my whole medical history on you, but this is literally the first place I’ve found with detailed, seemingly science-based information about digestion and digestive troubleshooting. Other sources tend to give broad recommendations (like ‘eat Paleo’) without the mechanisms of what’s actually going on in the gut, so when things I try don’t solve my problems I really don’t know where to go from there. This is going to sound dumb, but where do you learn all of this? What area of study is this even classified under? Is it biochemistry? Physiology? I wish I knew some of this four years ago. And I wonder if GI doctors know about it. It seems like they would, but then why wouldn’t they tell me?

    • Ray Medina says:


      No worries. I like comments, really I do:)

      Digestion is very complicated in and of itself. Now throw in countless beneficial and pathogenic microbes, yeasts, parasites, and viruses and the complexity just explodes as does my head at points;)

      In addressing iron, I only recommend reducing its intake when an active bacterial infection is present. Withholding it from the diet has obvious disadvantages, namely anemia, so this should only be a short-term “fix” for symptom relief. I had a gentlemen email me on his intestinal discomfort and when I asked him what he was eating, he confided that he was eating lots of red meat as he was “Paleo”. After I suggested he cut back on his red meat intake, he experienced some symptom relief so I feel it necessary to warn people about overdoing iron-rich foods when fighting an active bacterial infection.

      My knowledge comes from reading the literature which requires trips to my local medical library and lots and lots of reading. The research is there if you look for it. Unfortunately, most of this information never makes it to primary care practitioners. Partly because they don’t have the time and partly because they are practicing to “standard of care”. I’m sure some of this will eventually filter down to doctors on the front line but it certainly wasn’t true for me when I had my gut issues which is what started me on this quest. It’s always a good idea to explore the research literature before undertaking a medical procedure. In your case, probiotics, prebiotics and/or a fecal transplant would have saved your colon. I posted a link to an article on the Syontix Facebook page about this today. You can read about it here:

      • Alyssa says:

        I’m glad you like comments (: Yes, I’m disappointed that I didn’t try a fecal transplant. I can’t remember if I knew about it then or not, but I guess it doesn’t really matter now! I tried to heal my UC through diet for 3 years before the colectomy, but even with the SCD and Paleo I could never get it to go into remission. I think the piece I was missing was more intensive antibacterials/antifungals. It’s disappointing that the research isn’t more readily available to the public. I feel privileged now to be attending a research university where I have access to huge amounts of research, but as a 14 year old all I had was Google! Thanks for replying to my comments, and I will definitely read your SIBO series.

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