Probiotics & Prebiotics

Probiotics & Prebiotics

Meet the digestive powerhouse. In this post you will learn the difference between prebiotics and prebiotics, as well as how to incorporate both into your diet. 


Connecting gut bacteria to you in amazing ways.


Center for Genome Sciences, St. Louis, 2009 - Researchers seek out 154 twin pairs consisting of one lean individual and one obese individual. The fecal bacteria of each pair is then transplanted into the digestive system of specially-bred mice that do not have their own bacteria. As time passes, the mice transplanted with the lean twin’s fecal material remain a normal body weight, while their less fortunate counterparts begin to pack on the pounds, all other factors remaining constant.

Novartis Institute for BioMedical Research, Cambridge, 2003 - A private biomedical research firm links the signaling protein (cytokine) interleuken-6 to the immunological inflammatory response and development of insulin resistance in fat cells as a precursor to obesity, adding to a growing list of clearly identifiable warning signs for fat development.
Soukas, Cohen, Socci, Friedman, 2000 - Leptin, which has long been termed both the fat and satiety gene for it's abundance in obese individuals and animals, is studied in relation to gene expression in adipose (fat) tissue. Researchers discover that stress response gene concentrations move in coordination with leptin levels, and hold a strong positive correlation to obesity in both humans and animals, proving that stress is a strong factor in fat development.

The American Association for Laboratory Animal Sciences, Memphis, 1983 - A study conducted on sterile mice, which are specially bred to have no intestinal microorganisms, showed that those lacking digestive bacteria had to consume approximately 30% more food to extract the same amount of caloric value as those with normal bacterial colonies.

Merck Research Labs, New Jersey, 2011 - Production of acetate, propionate, and butyrate (the short chain fatty acids that our bodies metabolize for energy) within the colon are observed to diminish the correlation between diet and weight gain.

Department of Pathology, Emery University, Atlanta, 2010- Researchers identify gut borne protein receptors as regulators of weight and metabolism, finding their absence to cause low-grade inflammation and increased immune response (in the form of higher macrophage concentrations) from the vascular tissue surrounding fatty areas. This pattern of low-grade inflammation has long been accepted to be a near-universal trait among the obese. 


Kimmel Center for Biology and Medecine, New York University, New York, 2009 - T-Helper Cells (Th17), which are responsible for defending the body from opportunistic infections and are also linked to auto-immune disorders when in excess, are studied in relation to the Cytophaga-Flavobacter-Bacteroidetes (CFB) bacteria present in the intestine. A statistically significant, positive, relationship is found between the ability of the body to properly deploy Th17 cells when needed, and the presence of the CFB bacteria in the intestinal tract.

Amgen, Inc Labs, Thousand Oaks, CA, 2001 - Researchers identify extreme dietary conditions as the main factors dictating leptin concentrations, proving that low as well as high levels of the signaling protein create disorder within the body. Low-levels of leptin are linked to poor immune system response, leaving the body open to infection, while high levels are linked to overactive immune response, leading to excess macrophage activity, which ultimately leads to low-level, systemic inflammation, obesity, the metabolic syndrome, and increased risk of auto-immune disorders such as diabetes.


Department of Pathology and Molecular Medicine, MacMaster University, Ontario, 2007 - Mice babies are monitored after being separated from their mothers. Along with exhibiting behavior typical with anxiety, the alienated mice show consistent reductions in bacteria and hormones commonly found in the gastrointestinal tract. Interestingly, in another study in which mice were again separated from their mothers, but given supplemental dosages of the aforementioned bacterial strains, subjects displayed minimization of the effects typically associated with depression, as well as an increase in serotonin and tryptophan levels.

Mellor and Munn, 2000 - Tryptophan is discussed in relation to starvation and the suppression of the immunological response. They cite evidence which links decreased tryptophan catabolism (breakdown which facilitates utilization) to starvation and nutrient deprivation. The implications create a plausible link between dieting and depression, which has been studied extensively in relation to insufficient tryptophan levels, which are necessary for the synthesis of serotonin.

Bailey and Coe, 1999 - Researchers discover a link between emotional stress in mothers and susceptibility to disease in their infant due to altered gut bacteria colonization during early life stages. The study, which was conducted using rhesus monkeys, presented a possible causal link between mood and microbiome composition, which laid a foundation for further work exploring the link between the microbiome, gut, and brain, known as the MGB axis.   


School of Pharmacy, Texas Tech University, Lubville, 2008 - For three months, two groups of young mice (five weeks old) are fed either a standard rat chow, or a biologically diverse (and therefore bacterially diverse) food, and then tested for cognition and memory changes. The mice that were fed the diversified food showed significant improvement in both working and long-term memory over the group of “non-diverse” rats.


American Academy of Pediatrics, New York, 2012 - Infants born to mothers with a history of asthma are monitored for 6 years and have their asthma symptoms tested every 6 months along with a sample of their gut bacteria (ascertained from fecal samples). The results show a strong inverse relationship between the diversity among microbiota (gut bacteria) and positive indications of allergic rhinitisallergic sensitization, and peripheral blood eosinophil countall of which hold strong predictive power to the presence of allergies in children.


Department of Microbiology and Cell Science, University of Florida, Gainesville, 2010 - The stool samples of 16 Finnish children, 8 with type I diabetes, 8 without, are collected with the intention of studying the relationship between the disease and bacterial microbes. The study shows a strong inverse relationship between the diversity of intestinal bacteria and the presence of autoimmune disorders in children.


Gail and Gerald Oppenheimer Family Center for the Neurobiology of Stress, Los Angeles, 2012 - A UCLA study of 36 women draws connections between brain health and supplementation of bacterial cultures ascertained from supermarket-bought yoghurt. The study found that “…the women consuming probiotics showed greater connectivity between a key brainstem region known as the periaqueductal grey and cognition-associated areas of the prefrontal cortex. The women who ate no product at all, on the other hand, showed greater connectivity of the periaqueductal grey to emotion- and sensation-related regions, while the group consuming the non-probiotic dairy product showed results in between.” This study builds on suggestions from previous research that gut bacteria and the brain form a sophisticated communication network that can affect nearly every aspect of our body’s performance.

Fighting Histamine Intolerance

Fighting Histamine Intolerance

Food Intolerance & Histamine

First thing’s first, what is histamine? Besides being recognized by most people as the second word in anti-histamine, histamine is a chemical that is released within our bodies either as a neurotransmitter, which helps regulate various functions in our body including regulating our sleep patterns, or as a signal to our immune system to create a response that alerts us to, and protects us from foreign invaders and disease causing pathogens. If this process is working properly, when we come in contact with something like a bee sting or poison ivy, histamines are released, it does it’s job to send protective agents to that specific area, and then it’s deactivated by enzymes that degrade it’s molecular structure. However, when our body doesn’t produce enough of the deactivators, or we eat too many foods containing histamine, our body is bombarded by signals to protect itself when there is really no need.  We then experience a physiological response that feels and looks similar to a flu or allergic reaction, i.e. inflammation, dizziness, skin irritation, hives, throat tightening, increased heart rate, nasal congestion, migraines, fatigue, heartburn, acid reflux, flushing of the face and hands, and even narcolepsy.  Your body is basically in panic mode by this point because histamine is signaling to it that we are in danger, so the response is to create a physical response that serves to protect us from that danger, and signal to your conscious self that something is wrong, it’s both a subconscious and conscious warning system. Chronic experience of the symptoms described above, or extreme anaphylactic reactions to foods and beverages like red wine and fermented foods is called histamine resistance, and can be life threatening if left untreated. Most people experience only mild versions of these symptoms, so it’s difficult to diagnose in a clinical setting, but the CDC estimates that about 1% of all Americans suffer from full-blown histamine resistance, with most of those people being middle aged. Regardless of whether your body produces and deals with histamine in the correct way, eating too many foods that either produce, enable, or contain histamine will cause some form of the symptoms listed above. 

Replacing Histamine Producing Bacteria

In addition from ingesting histamine from the food that we eat, excess histamine can also come from the bacteria living in our own digestive tracts. Certain strains of bacteria, especially Lactobacillus bulgaricus and casei (the responsible parties for fermented milk products) are known to be histamine promoting in the colon, meaning that histamine is a byproduct of their digestive activities. Normally, the resulting histamine is deactivated and broken down in our large intestine by the enzyme DAO (diamine oxidase) before a noticeable effect can take place. Occasionally, when the proportion of histamine to DAO increases enough, or your body isn’t producing enough of the enzyme, our bodies can’t effectively get rid of the excess histamine and we are hit with a headache, feel dizzy, or start showing signs of a cold or flu, like sneezing and coughing. Lucky for us, we can help eliminate the symptoms of a histamine overload by taking a few steps to even out the balance of DAO to Histamine in our guts. 

L. Plantarum: Lactobacillus Plantarum is a unique bacteria because it naturally reduces our sensitivity to histamine in two ways by 1) regulating the brain-blood barrier, which controls the rate at which our body recognizes histamine, which gives us more time to break it down naturally, and 2) producing DAO enzymes, which neutralize histamine altogether by deactivating it’s reactive components. There are three strains of bacteria that have been clinically observed to be histamine reducing in our guts. Those are bifidobacterium infants (from breast milk), bifidobacterium longus (in yogurt and other fermented foods alongside it’s histamine producing friends), and lactobacillus plantarum. L. Plantarum is a particularly interesting strain because it has been observed to be effective at reducing our reactivity to histamine when supplemented through food by improving the blood-brain barrier described before. In addition to it’s ability to reduce histamine production, L. Plantarum has also been observed to alleviate the symptoms typically associated with antibiotic treatment,  remaining in the digestive system long after other probiotic strains have been killed off.  You can find L. Plantarum in fermented foods like kimchi, sauerkraut, and rye bread, but unfortunately, these foods also contain high levels of histamine producing bacteria. For that reason I can’t really suggest one over the other if you are trying to fix a histamine intolerance, eating those foods can exacerbate the problem just as much as they could help it. There are a few products that have managed to synthesize L. Plantarum and are effective at restoring the DAO-histamine balance in our large intestines. This drink, which is made with a regard to histamine intolerance and contains all three of the aforementioned histamine neutralizing bacterial strains and is made with natural, organic ingredients. ADD L. PLANTARUM SUPPLEMENTS.

It may be advisable to follow The Hard Reset (page blah blah) plan if you believe that your bacterial colonies are far out of wack or if you’re having frequent reactions to fiber-rich foods. The reset will break up the entrenched bacteria living in your gut and give you a chance to more predictably recolonize with beneficial, or probiotic, bacteria.

Limiting Histamine Rich Foods

Our body’s response to histamine has evolved over thousands of years to protect us from potentially harmful pathogens (bacteria and other microorganisms). It makes sense then that the foods which have the highest concentrations of histamine are those that utilize bacteria to be made. Foods such as saurkraut, aged cheeses, wine, and salted-cured fish and meat products are a few histamine-containing examples that are pretty common in most people’s diets either because of cultural significance or due to the fact that they are damn delicious. For most people it would be unimaginable to eliminate these foods entirely, and it would take a lot of joy out of many people’s diets if they had to be cut out entirely, so I suggest simply being aware of the foods that contain the most histamine, and using that knowledge to make smart choices when you want to feel your best. That being said, if you have severe histamine resistance, it may be necessary to completely eliminate these types of foods from your diet in order to live a healthy and happy life. 

Below is a list of common foods that contain histamine or tyramine, both of which will cause an allergic-like reaction if eaten in excess or if DAO is not present in the digestive system.

Aged Cheeses

Alcohol (Beer, Wine, Sake, Soju)





Fermented Meats and Veggies (pickled or smoked meats, sauerkraut, kimchi, etc.)



Processed Meat and Byproducts (sausages, hot dogs, salami, bologna)

Pumpernickel and Other Yeasty Breads


Sour Cream



Vinegar and Vinegar-Rich Sauces (mayonnaise, salad dressing, ketchup, pickled vegetables)


Eliminating Histamine Triggers

Besides foods that contain histamine, some of the things we eat can trigger a histamine response in our bodies. The signaling agents are found most commonly in foods that are either spoiled or near-spoiling, although other foods and beverages can trigger the release of histamine as well. 

Histamine Triggering Foods -




High-Citrus Fruits (Lemons, Oranges, Grapefruit)









Note - The longer a food remains in your fridge or on your counter, the more of these chemicals will be present, and the more severe the histamine reaction will be. It should be common sense not to eat spoiled food, but further than that, it needs to become a priority to either eat the food that you have immediately, or prepare it for long-term storage. 

How to reduce histamine production in food -

There are two ways for preparing food for long-term storage that are natural and don’t involve adding harmful preservatives to your edibles: marination and freezing. 

Marination: Besides being delicious, garlic, ginger, and various other spices, also have antimicrobial and anti-putrificative traits. When you store meats in a marinade that contains these spices you can slow down the formation of histamine, and histamine enabling chemicals. 

Freezing: Freezing food has been shown to significantly reduce the formation of histamine over time compared to refrigeration or dry-storage techniques. The main concern for most people when they are freezing foods is whether they are losing any nutritive value through the process, the answer….

Promoting DAO Activity

Vitamins C and B6 have both been shown to promote histamine degradation by promoting DAO enzyme activity. Relatively, a deficiency of either of these vitamins can lead to histamine intolerance. You can find B6 in fresh fish, such as tuna, which contains 70% of your recommended daily value in each serving, as well as in fresh turkey, and fresh beef, with 55% and 44% respectively of the recommended daily intake. Foods rich in vitamin C include, papaya, with 0ver 200% of your recommended daily intake in each serving, as well as bell peppers, broccoli, brussel sprouts, and strawberries, each containing over 100% of your recommended daily value in each serving. 


Taking DAOsin or other DAO supplements

DAO Blockers

Some foods can actually block the release of DAO in our body, which will lead to an excess of histamine in our digestive system. For the most part, you will want to limit these in your diet if histamine is a problem for you.


Energy drinks

Black tea

Mate tea

Green tea

Eat Fresh

Besides eliminating histamine-rich foods, the key to avoiding histamine and the resultant symptoms is buying fresh foods and eating them immediately, or storing them at either freezing temperature, or in an antibacterial mixture such as the marinades I mentioned before. A good place to start would be a farmer’s market or co-op. Avoid pre-packaged foods that could have been sitting out for prolonged periods of time, and grow what you can. Also remember, spices are your friends, especially garlic, ginger, and oregano, so there shouldn't be any enjoyment taken out of your dietary experience just because you need to avoid histamine. 

Interested in learning more about gut health?

Identifying and Treating Small Intestinal Bacterial Overgrowth (SIBO)

Traveling often changes the way you eat and throws your normal routines out of whack.  While on an extended trip through East Asia and India, my carbohydrate consumption increased dramatically and I noticed bloating and gas on a daily basis, to the point that eating became a major stress. Seemingly after every meal, my stomach felt as if it were going to burst, uncomfortably bloated, even though my stomach would be relatively flat again when I woke up the next morning. I had noticed this pattern before, but I had always written it off as the side effects of a big meal. While spending a month in South Korea, I took advice from the locals and started smoking cigarettes after I would eat in order to get relief from the gas and bloating. Proof that folk remedies are often misguided. 

As my suspicions about the origins of my nightly bloat grew, so did my curiosity, so I decided to do some research. During a late night google search, I stumbled across a disorder called SIBO (small intestinal bacterial overgrowth) and was immediately intrigued by the symptoms that it described - dizziness, fatigue, nausea, flatulence,  and bloating. With bloating and gut discomfort starting to derail the enjoyment of my trip, I decided to take action. Being overseas, and thousands of miles from the closest healthcare provider covered by my insurance, I decided to self-diagnose based on my past experiences and see how my body responded to treatment. I would suggest that you consult a physician before undertaking any major dietary changes, and I stress that my experience is simply a single case study of success with this method.

Identifying SIBO - The Symptoms

Excessive Gas - Does your significant other complain about your flatulence? Do you sit in leather chairs so you can have something to blame your uncontrollable farts on? It might not be your fault...

Uncomfortable Bloating - After eating a large meal, do you often need to lie down because your stomach feels too full or bloated? Does it return to it's normal state after a few hours? This could be the result of overactive bacteria residing in your small intestine.

Fatigue - Find yourself napping on the job after a big lunch? Have trouble concentrating within an hour of eating? Your gut may be in a state of disorder due to bacterial overgrowth. 

Stomach Pain - If you have chronic stomach pain after meals, often resulting in loose stools and diarrhea, you may have a "leaky gut", a result of excess gas in the small intestine, and another sign of SIBO.

Understanding SIBO (Small Intestinal Bacterial Overgrowth)

Small intestinal bacterial overgrowth is a disorder of the small intestine in which the bacteria that resides in the colon starts to migrate up the digestive tract and colonize the small intestines. In order to understand why this is a problem, we should first look at the composition of a healthy small intestine. Our small intestine is generally a sterile environment, in which our carbs and simple sugars are broken down using a mixture of enzymatic digestion and the contractions of the sphincters which transport partially digested food to the colon. The microscopic particles which are released through these processes are then passed through the epithelial (intestinal) lining, which has tiny holes made up of tightly woven protein membranes which allow the passage of enzymes, hormones, and fatty acids to our liver, which will eventually be distributed throughout the body via the bloodstream. Generally, fibers, plant matter, and complex sugars are unaffected by the milieu of digestive enzymes residing within this portion of our tract, and are passed onto the colon, where our gut bacteria can finish the digestive process using fermentation. In cases where the small intestine has been invaded by fermentative bacteria, the final stage of digestive process is initiated early, releasing gases and other chemicals that were previously foreign to this portion of our guts. The gases build up in the upper GI tract, which damage the walls of the small intestines, as well as creating uncomfortable pressure in and around your gut that can be seen clearly when large amounts of fermentable materials (starches, uncooked fruits and veggies, nuts) are ingested at once. The results of the excess gas is a dilation of the epithelial membranes that comprise our intestinal wall, creating dysfunction between that wall and the protein gatekeepers that generally dictate the transfer of our vitamins, fatty acids, and enzymes into our bloodstream. With these larger holes, the barrier between our nutritional inputs and the compounds that reach our bloodstream is put under excess strain, allowing toxins, non-nutrients, and all kinds of foreign substances to enter our bloodstream. This can cause a variety of problems including allergies, diarrhea, stomach pain, dizziness, fainting, fatigue, and of course, bloating and gas. Since these are maladies that many people all over the world experience everyday, they are often written off as simply the after effects of a big meal.  The results of that notion were acceptance of a life filled with discomfort, and the need to cater my activities around two hours of forced sedation after eating a bowl of rice. I found freedom from that life using the methods described below. 

Treating SIBO

Here’s what I’ve found to be most effective at restoring the digestive work assignments that are so pertinent to proper digestion. 

I broke my SIBO treatment into 3 distinct stages -

  1. Lowering the defenses of small intestinal bacteria.
  2. Eliminating the bacterial overgrowth, without creating an environment of dysbiosis (digestive disfunction resulting from killing too many helpful bacteria).
  3. Repairing the intestinal lining. 

What not to do. What you need to understand going into this is that, for a little while at least, we must starve our gut bacteria so that we can give our digestive systems a fresh start.  First, eliminate all starchy carbohydrates (rice, potatoes, green bananas, and anything else listed in the section entitled “Resistant Starches”) and significantly reduce your sugar intake (one apple per day, or the equivalent, is acceptable, preferably in a smoothie) while doing the Hard Reset, since they act as nourishment to both the good and bad bacteria in our small intestines. Another tenant of the diet is lowering your caloric consumption per meal, accomplished by eating small, protein and fat-rich meals every 2-3 hours, or whenever you feel hungry, but this will continue on throughout the GUT diet, so you should just start to adjust to it now. The last limitation during the Hard Reset is temporarily eliminating live cultures of any kind from your diet. This includes probiotic supplements, fermented and acidified foods like yogurt, kombucha, kefir, sauerkraut, and anything else that utilizes bacteria in it’s production. Don’t worry, it’s only temporary, I love my kefir and kimchi. 

Okay, now that I’ve covered the no-no’s, here’s how to actually fix SIBO. 

Lowering their Defenses

The bacteria in your small intestines sometimes form what is called a “biofilm matrix” which is a membrane that a collective of bacteria live in, where they can share resources and even DNA in order to maximize their chance at survival. In order to effectively eliminate these bacteria we have to disrupt that biofilm using disrupting agents that break down this protective shell.

Lactoferrin and N-Acetyl-Cystein - Both of these nutrients are effective at destroying the protective layer covering bacterial deposits in our gut. There is a good supplement offered by Klaire Labs, called Interfase Plus, which is available at for a pretty reasonable price (~30 bucks for 120 caps). Open up the caps and take it with water or food to ensure it is absorbed by the bacteria in your small intestines. I like to just shotgun it in water before breakfast.

Clearing the Small Intestine (Natural and Synthetic Methods)

Synthetic Anti-Microbial Agents-

 Monolaurin capsules - Available at the vitamin shoppe for about $20 bucks for all that you will need. This is an antimicrobial agent that will help destroy the bacteria living in your upper GI. Again, when you take the supplement, you want to open up the capsule and just swallow the powder with food or some water. This ensures that the monolaurin is activated before it reaches the colon, where it’s affects would be misdirected on your normal gut colonies. Repeat this process once per day for a month.

Rifaximin - This is a selective antibiotic that will target the bacterial overgrowth in your upper GI tract. You will need a prescription for this and it can sometimes be costly, so consider your options carefully and pursue testing before jumping into an antibiotic regimen. That being said, this is the most effective treatment for SIBO, and should be utilized if you have a serious case of bacterial overgrowth that severely effects your life on a daily basis. You will want at least a ten-day supply of the drug, with 21 days being optimal. 

Natural - Anti-Microbial Agents

Freshly Grated Garlic and Ginger - Both have been known for a long time to help with digestive problems and have been widely used as folk remedies for weight loss and any number of other maladies. The downside? They are hard for some people to palette and a little bit burdensome to freshly grate each morning. Be aware that garlic will make your breath, skin, hair, poop, everything, smell like garlic, so if you’re not a garlic enthusiast like I am, take your time deciding which method to pursue. Eat a tablespoon of whichever you choose with every meal for about 30 days.

Oregano Extract Oil- This one is a little bit unpredictable. According to health personality Chris Kresser, oregano extracts are used commercially as an antimicrobial agent. That should give you some indication on how strong it is. There are plenty of synthetic antimicrobial agents out there, but many food processing companies still use oregano oil as their substance of choice for sterilization. It is effective, undoubtedly, but the danger you run is destroying too much of your bacteria, making recolonization of the colon more difficult after, and creating the risk of developing diseases such as IBS and Crohn’s disease. If you are going to use oregano extract oil, consult your doctor and continue to work with them to monitor your health throughout the process. 

Repairing the Epithelium

This one is pretty simple, the cells that repair our intestinal lining require glutamine to operate properly. In order to help the repair of our gut walls, we want to increase our glutamine intake. Glutamine is abundant in beef, fish, and other protein rich foods. So go eat a steak. You can also take glutamine powder, but that’s not as fun as eating steak. Try to ingest 50-60% of your daily caloric value from protein, 20% from healthy fats, 20% from vegetables, and the remaining 10% from fruits and anything else the fat kid living in your stomach can’t resist. Also, try not to blacken the meat too much or else you run the risk of depleting the nutritive value contained within it.

Remember, this diet is temporary, and serves a very specific purpose, and will be confined to a month long timeframe, not the rest of your life. The goal is to reset your gut, so that, when we begin to recharge our metabolism, our efforts are directed to the colon, where they belong, instead of the small intestine, where bacteria can lead to a whole slough of disorders. 

Interested in learning more about gut health?