In 1906, while serving as the deputy director of the Pasteur Institute Laboratory in Paris, Elie Metchnikoff made a landmark observation while studying the dietary habits of Bulgarian peasants. In his book, The prolongation of life, he draws a connection between high concentrations of centenarians (people of 100+ years of age) and countries that have culturally engrained practices for the fermentation of dairy products. The same bacterial cultures found in the yogurt products those peasants were eating 100 years ago are only now being recognized by mainstream medicine for their incredible effects on the human digestive system.

A number of products have already taken advantage of the recent popularity of live cultures and probiotics. With such a massive expansion in a short period of time, as so often happens in the diet and nutrition industry, it presents the need for an objective review of the science behind the flood of miraculous claims. You’ve probably heard of probiotics and prebiotics already, presumably while perusing the supplement section at your local grocery store, or during an hour long TV special produced by suspiciously tan medical professionals.  As the colorful packaging and doctors touted the miraculous effects of their unconfirmed contents, your head swells with thoughts of you playing beach volleyball, joining pickup games of “b-ball”, and any number of other activities that allow one to gratuitously rip off their shirt begin to commandeer your good judgement. I implore you, at this point, before spending money on products cashing in on the popularity of probiotics and prebiotics, strive to understand the definition of each, where they can be found, and what their observed effects are. This information will serve as an 

indispensable base of knowledge when faced with a barrage of sensational advertisements by Jamie Lee Curtis claiming to present the secret to health and happiness in a cup of yogurt. 

From the last graphic we now understand the basic difference between pro- and pre- biotics. Probiotics are the actual bacteria living in your gut, and any live culture fits this definition so long as it has a positive effect on your health. Unfortunately, there are over 1000 strains of bacteria living in the average human colon, and we understand the functions of only a small percentage of these, so choosing a “probiotic” is not as simple as picking the most colorful bottle off of the shelf of your local Super Supplements. 

However, Metchnikoff, along with a slough of recent studies utilizing the most advanced techniques in genetic mapping, have allowed us powerful insights into which broad categories of bacteria can a) be used effectively as a supplement, and b) contribute to the overall function of our microbiome. 

Choosing a Probiotic

When choosing a probiotic to incorporate into your diet, it is important to first identify the end goal of your microbiome therapy. For most people, this will sway in one of two directions, weight loss, or increasing your energy level. 

For General Health

Increasing your energy level, in terms of probiotics, means increasing the amount of energy, or calories, that our bodies can extract from our food. Using logic, we can see that a possible implication of this would be gaining weight if you were to let that excess caloric load be converted into fat. Therefore, we can see where there may be a problem with those that are sensitive about their weight. For athletes, lifters, and the generally active, however, this increased efficiency is a welcome respite from the groggy afternoons and sluggish mornings that coax many into a second cup of coffee or snickers bar before lunch. To this end, the category of ‘lactic acid bacteria’ will fit the bill when supplementing live cultures into a healthy diet. Lactic acid producing bacteria (LAB) are the easiest and most commonly available form of probiotic. LAB can be found in most fermented dairy products, yogurt and kefir being those most commonly available, and are effective as supplements due to their ability to survive the harsh, acidic environment of the upper GI tract. In other words, they are the most likely to survive your stomach and small intestines and therefore be available to be added to the composition of your gut bacteria.

For the Weight Conscious

If your goal is weight loss, you will want to tread lightly when picking out probiotics at the grocery store, and hold off on adding fermented dairy to your diet. Many strains of lactobacillus have been shown to produce high levels of histamine when present in the digestive tract. Histamine causes an immunological response within the body characterized by low-level, systemic inflammation, which has been linked to weight gain and obesity. However, there is one strain of lactobacillus that actually works to reduce the amount of histamine present in the body, called lactobacillus plantarum. This particular probiotic, which can be found here, is found in prevalence in lean individuals, and may represent a causal link between histamine reduction and weight loss. When concocting the synbiotic (probiotic + prebiotic = synbiotic) smoothie that I will teach you to make later on, mix in one capsule of L. Plantarum bacteria with each serving. 

Culture(s) In America

Americans are at a bit of a disadvantage when it comes to buying fermented and preserved foods from the grocery store, due to strict, blanket regulation by the FDA in regards to the heat treatment of fermented and acidified foods, a process that kills approximately 99% of the live cultures which would otherwise be present in foods like yogurt and sour cream. The European Union has passed regulation allowing for the incorporation of live cultures into food made for purchase [without heat treatment], by classifying foods that do not have a significant history of being consumed, or that incorporate new or synthetic ingredients as “novel” food, laying down a procedure for responsible labeling and marketing of foods that have yet to be proven entirely safe.

Health and food organizations from all over the world have spoken out in recent years about the importance of allowing live cultures in food products. The National Yogurt Association in particular has been successful in their fight against FDA blanket regulations by creating a universal labeling standard for products containing minimum, viable concentrations of lactic acid bacteria. A full list of yogurt products that carry the “Live Active Culture” seal is available here.

Unfortunately, antiquated pasteurization procedures still apply to all other naturally fermenting food products. However, the FDA now maintains a list of clinically proven and effective probiotic strains that can be added to specifically identified food products after pasteurization. 

Here is the working list of strains which can be added to food:

  1. Bifidobacterium longum BB536, for use as a food ingredient and in infant formula
  2. Lactobacillus casei subsp. rhamnosus GG, for use in infant formula
  3. Lactobacillus reuteri DSM 17938, for use in food
  4. Bifidobacterium lactis Bb12 + Streptococcus thermophilus Th4, for use in infant formula
  5. Lactobacillus rhamnosus HN001, for use in infant formula
  6. Bifidobacterium animalis ssp. lactis Bf-6, for use as a food ingredient

The strains injected into supplemented foods are listed visibly on their packaging, although shelf time and lack of oxygen may create inconsistencies in the amount of live cultures actually begin delivered.

Weight Gain

When incorporating fermented dairy products into your diet, slight weight gain is normal for the first few weeks. Your body is not used to the increased availability of nutrients and will therefore be intaking more calories than before, if your intake remains equal. The key to cresting that hill and beginning to approach a healthy, ideal body weight is portion control. The gut will begin burning like a furnace, hot and efficient, taking in the food that you eat and immediately converting it into energy for you. The implication of this is that, if you are paying attention, you will begin to feel full and satisfied more quickly when you eat. Many people, myself included, don’t know when to say no, and instead opt for the “when my plate is empty, I am full” method of portion control. This will always lead you to gain weight, healthy gut or not. 

Portion Control

In order to acknowledge your body’s natural satiation signals, you have to turn your intention inward. That is an ambiguous statement, so let me clarify- when you eat, do you need a distraction? Do you sometimes look down at your plate and not remember where the food has gone? That means you were ignoring your body and resting your attention on something other than the task at hand. We need to change this if it is your intention to reach a healthy weight. The tactic that is most effective in this endeavor is known by many names (i.e. presence, being in the moment, mindfulness, giving a shit, things my buddhist parents talk about a lot, etc.) but all refer to the same thing- focus. The next time you eat, take away all of your normal distractions, whether that’s your cell phone, the TV,  your computer, a book, anything other than food, just set it aside for a few minutes and focus on the task at hand. As you are chewing, pay attention to each bite and bring your focus into what is happening directly in front of you.  Listen to the sound of the food as you eat it, the smell emanating from your plate, the colors of your vegetables, count the chews you take with each bite, pay attention to that food as if it were your junior high crush and they just asked you for a pencil. Continue like this for the entire meal, and I guarantee you, at a certain point you will feel a fullness unrelated to the amount of food left. If you continue practicing this, you will eventually stop yourself once you are full automatically, but in the beginning, you will have to work at it. On a side note, this practice can enhance many other areas of your life, and can bring both joy and fulfillment to an otherwise flustered and anxious mind. If you want to learn more, I suggest reading “The Power of Now” by Eckhart Tolle, it’s a quick read, but revolutionary in the concepts it discusses.

Fecal Transplants

Supplementation with probiotic strains has proven effective in promoting some aspects of digestive health, such as suppressing diarrhea and increasing immune response. However, fecal transplants have proven consistently more effective, and less costly, in recolonizing gut bacteria from a state of disorder. 

The gist is this: although foods containing probiotics are great for improving and maintaining digestive health, fecal transplants are substantially more effective at repairing your gut biome from a state of drastic disorder.

The prevalence of antibiotic use in chemical-based medicine has created a war-like environment within the gut’s of some already suffering individuals. Antibiotics, which are designed to destroy unwanted pathogenic bacteria in the body, often lack the discretion necessary to discern the good from the bad within our bodies, creating a genocidal environment for our microbiome, if used in excess. The reduction of gut bacteria witnessed in cases of antibiotic use creates a less competitive environment for the remaining strains, allowing for easier colonization of the large intestine by hazardous bacteria, while the few remaining probiotic bacteria struggle to convert food into the fuel our bodies run on. Sometimes, this takeover is too severe to be corrected through nutrition, and so the fecal transplant was developed to replace the gut biome altogether.

The idea for fecal transplants, or fecal bacteriotherapy, can be traced to 4th century China, where patients suffering from various maladies would drink “yellow soup”, or a mixture of healthy feces and water in an effort to introduce healthy organisms into their digestive system. The treatment has progressed somewhat from it’s gag-inducing origins, with informal experimentation preceding it’s prevalent adoption among digestive health professionals. The data backs up the nearly unanimous, positive reactions from treated patients, with observed success rates above 90% for treating chronic bowel diseases. Additional applications of fecal transplant are currently being explored, with research emerging which support the transplants effectiveness in treating irritable bowel syndrome, severe constipation, multiple sclerosis, Parkinson’s disease, autoimmune disorders, obesity, and diabetes. With the average cost of a fecal transplant around $1000, it’s growing list of uses, and it’s near 100% rate of effectiveness, it is emerging as the main treatment of major gastrointestinal disorders and diseases.





We now understand that the term ‘probiotic’ simply refers to the helpful bacteria already living inside your gut. We can infer that they have done at least a decent job up until this point because you’re still sitting there, reading this book, metabolizing, and generally being alive. The main function of this gang of helper organisms living inside our digestive system is to prevent attack by way of the intestines and stomach, and act as a power plant for the rest of the body. If your gut microbiome is doing it’s job, you shouldn’t even notice it, a reflection of how integral it is to our continued existence. The word “prebiotic” refers to the food that nourishes our gut bacteria, they have to eat too! Prebiotic foods are defined by the fact that they make it to your colon, where your microbiome lives, works, and feeds. When we eat prebiotic/fibrous foods, we are essentially compensating the microscopic workers living inside out intestines, making their jobs easier, which, in turn increases the amount of energy available to our bodies through their increased efficiency. In addition to aiding in the digestion process, certain prebiotics have been shown to lower the metabolic availability of certain foods, namely fats and carbohydrates, in turn decreasing the amount of calories from fat and carbs that can be converted into fat. The results of this are an increase in lean body mass, with decreased adipose (fat) storage, providing evidence that consumption of particular prebiotics can shift one’s body composition away from obesity, holding all other factors constant. This section will show you which prebiotics are the most effective at feeding your microbiome and increasing the power hidden in the gut.


In it’s broadest form, the word fiber applies to any indigestible portions of the food that we eat. The body deals with fiber in two ways, depending on whether it’s soluble or insoluble. Soluble fiber is broken down by the bacteria present in our large intestine, fermenting food particles and turning them into gases that are absorbed by our microbiome. Insoluble fiber collects other indigestible material, along with toxins and water as it passes through the digestive system, resisting being broken down by the acidic milieu of acid, bacteria, and pressure present at the different stages of the digestive tract. At the end of it’s pungent trek, this resilient little ball of water, toxins, bile, and insoluble material is excreted, finally, to relish on it’s journey, in the bowels of your local sewer system. 

Super Fiber (Resistant Starch)

Within the definitions of soluble and insoluble fiber, there is a third type of semi-indigestible material that satisfies the definition of both, called resistant starch (RS). Resistant starch is unique from other starches in that the glucose units that it is made of, which would normally be broken down in the small intestine and stomach, resist digestion until arriving at the bacterially-rich large intestine. The effects of incorporating this type of starch into a healthy diet have been linked to increased colonic health, reduction of the glycemic index of other foods, reduction of diet as a factor in predicting obesity, as well as many other effects as far reaching as preventing the effects of aging

I feel that I need to clarify when I say “reduction of diet as a factor in predicting obesity”. I don’t mean that it makes diet an unpredictable factor in obesity, but that it works to remove it from the equation entirely. Obesity from inactivity is still a very real factor, but this takes a bit of the pressure off come meal time. 

FYI - What Is The Glycemic Response?

The glycemic response is the scientific  term for how our bodies respond to sugar. More specifically, it is our body’s response, in blood sugar levels, to the rates of conversion of  carbohydrates into glucose. The quicker a carb is digested (in general), the higher that food’s glycemic index (GI) will be. The amount of sugar in our blood will tell our bodies how much insulin to produce, which will in turn signal our energy storage centers (fatty deposits) to store the glucose extracted from carbohydrates and metabolize it when needed. Foods with a relatively low GI are intended to trigger a lower insulin response, are thought to be beneficial in weight management, and may have many other positive health implications

Picking Your RS

Recent evidence has suggested (inconclusively) that constant variation of nutrient sources can reduce the overall diversity of your gut bacteria, warranting a loose focus on consistency when starting a diet intended to promote digestive health. Practicality also suggests that we should choose a readily available, easy to prepare source of resistant starches to incorporate into our diets, so as to promote sustainability. To narrow down the bank of RS foods that we can choose from, let’s first look at the effectiveness of the various types of resistant starches in achieving regularity, a by-product of colonic health. 

A note about the diagram above: the maize product used in the study cited is a retrograded grain, which gelatinizes when mixed with heat and water (aka it’s corn flour). 

Something to note from this study is that 26% of participants couldn’t digest one or two of the four types of resistant starches, so, if one of the foods mentioned above doesn’t seem to be having a beneficial effect, try another one!

We can see from this simplified visualization that there is a significant difference in our body’s ability to utilize different types of resistant starches. Since we get more usefulness (in terms of RS) out of wheat and maize, and since many of the foods they are found in are are denser in calories, we can use slightly less of them in relation to plants and tubers when incorporating resistant starch into our diet. Next, we can look at which foods pack the most resistant starches into each serving. From the table linked in the last sentence, we can see that their are a few outliers among the group that deserve out attention because

  1. they are more densely packed with resistant starches, and
  2. they are all commonly found in your local supermarket in their raw, unprocessed form. 

plantain/green banana four (35 to 68 grams)

cassava starch (44.6 to 80.8 grams)

potato starch, raw (66.7 to 79.3 grams)

a note on gas

A not-so-pleasant byproduct of high fiber intake can be an increase in flatulence caused by the bacterial activity taking place in the gut. What does this mean? Farts and Burps. Those gifted few among you who prefer the company of people to computer screens may find this objectionable, so i’ve included a brief guide to minimize the amount of lies you will have to make up about squeaky leather chairs while you increase your resistant starch intake.