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  • Siri DeMarche

Gut Health, The Difference Between Prebiotics & Probiotics, and The Importance of Having Both

Updated: Jan 28, 2021

Both prebiotics and probiotics play important, and different, roles in your health. Both are vital to the health of your gut microbiota and to the health of the human body as a whole. Simply put, probiotics are beneficial bacteria and prebiotics are food for that bacteria. Probiotics are live bacteria found in certain foods and supplements that grow the bacteria in your gut (good or bad). Prebiotics are types of fiber that feed the friendly bacteria in the digestive system. Having a balanced intake of both prebiotics and probiotics is essential for a healthy gut microbiome.

Having a healthy and balanced gut microbiome is essential to performing optimally, and plays a significant role in everything from your mood to your immune function. Your body houses trillions of microscopic organisms. Bacteria, fungi, viruses, and other microbes inhabit nearly every part of you. This ecosystem of microorganisms is your gut microbiome. Most of your microbes live in your gut and over one thousand species of bacteria have been discovered in the gut. These bacteria digest your food, keep your immune system strong, protect your intestines, remove environmental toxins from the body, produce B vitamins, and generate vitamin K (helps your blood clot).

While particular diverse combinations of microbes are similar among those with a healthy gut, everyone's gut microbiome is unique to them and their experiences. Everyone's gut flora also contains varying amount of "bad" bacteria. The presence of these "bad" bacteria is normal in small amounts, but become detrimental to your health in large amounts. It is important to keep a healthy balance between the good and bad bacteria. You want the good bacteria to thrive, while keeping the bad bacteria in check. This is why it is so important to consume both prebiotics and probiotics.

When your gut bacteria is out of balance, your body is not able to digest food very well and you are likely to experience food sensitives or allergies, digestive problems (like gas and bloating), weight fluctuations, skin issues, fatigue, mood swings, and difficulty concentrating. Research shows that gut health heavily impacts metabolic health, so it is vital to keep your gut balanced and healthy.

Your gut flora, your diet, and the strength of your intestinal lining determine the health of your gut, and by extension your health overall. Gut health starts young. When you pass through your mother's birth canal, you get your first dose of microbes as you are being born (unless you were delivered via C-section). Your microbiome changes during the first few years of your life as influenced by microbes in breast milk, your first solid foods, and antibiotics. Your microbiota begins to stabilize around the age of three. This early development of intestinal flora sets the tone for your gut health for life.

The gut microbiome is connected to nearly every aspect of the body. An imbalanced gut leads to all kinds of health challenges. Virtually all conditions are connected to gut health in some way because of its impact on everything from your weight to your well-being. Keeping your gut bacteria in balance can be a challenge because there are many things that can easily shift it in the wrong direction. Some of these things include eating processed foods, getting sick, drinking alcohol or taking drugs, experiencing stress, losing/gaining weight, getting older, traveling overseas or to new environments, and taking medications.

Improving your gut health begins with your eating habits because it is the most natural way to support good gut bacteria. Your good bacteria eat what you eat. A few ways to support good bacteria are, cutting back on sugar, eating more whole foods, and upping your fiber intake from specific sources. Bad bacteria feed off of sugar, so cutting back on sugar (including the fructose from fruit), low-nutrient carbohydrates, alcohol, and conventional dairy is necessary. Eating more whole foods supports a thriving digestive system by helping to balance the gut microbiome and its diverse species of bacteria. When looking for sources of fiber, choose sources like leafy greens, nuts, root vegetables, avocados, and other prebiotic sources. While grains and legumes are technically sources fiber, they are also sources of antinutrients that can contribute to inflammation and impede nutrient absorption.

Another way to support the balance between good and bad bacteria in your gut is with supplementation. Understanding where prebiotics and probiotics come into play is essential to a healthy and thriving gut microbiome and it is necessary to understand the role of each. Unfortunately this is where a lot of folks mess things up because they do not consume a balance of both prebiotics and probiotics, and consequently grow more of the bad bacteria unintentionally.

What's the difference?


Probiotic supplements help support gut health by adding beneficial bacteria to your gut microbiome. They are the good bacteria that are normally found in your intestines and help digest food, produce vitamins, and destroy harmful microorganisms.

You can get probiotics in fermented foods like kimchi, sauerkraut, kefir, and probiotic supplements. However, not all probiotics are the same. Some strains can increase your levels of histamine (the chemical that your body produces during an allergic reaction), which causes inflammation in the body. This is largely dependent on your unique biology. Many people tolerate fermented foods like tempeh and miso just fine, while others feel bloated, sluggish, and foggy after eating histamine-rich foods.

Because the human gut biome contains 100trillion or so bacteria cells (10x the number of human cells in your body), consider your gut biome a significant organ in your body. Your gut bacteria control everything from your mind, your appetite, and your stress levels. Research shows that an unhealthy gut contributes to obesity, diabetes, rheumatoid arthritis, autism, depression, and chronic fatigue. As such, it is vital to keep it balanced and healthy to reduce your risk of disease. Because modern life is chalk full of factors that destroy your good gut bacteria (i.e. antibiotic use, a diet high in processed foods, foods containing inflammatory histamines...), it is important to replenish and add good gut bacteria to your microbiota. When your gut bacteria become imbalanced, you can develop a histamine intolerance. This leads to increased inflammation, congestion, hives, migraines, and more.

If you are not already supporting your gut with a diet full of fibrous vegetables, grass-fed and wild-caught meats, avoiding industrial meats, and managing your stress levels, supplementing with probiotics will not get you very far.

Not all probiotics are equally beneficial to your gut microbiota, and some actually might do more harm than good. Depending on the specific bacteria that you're supplementing, some probiotics will help those bacteria flourish, while others will do the opposite. This is why it's important to be aware of which bacteria produce histamines, which degrade them, and which might not affect them at all.

Because you want to decrease histamine intolerance while repairing a potentially unhealthy gut, in addition to eating an anti-inflammatory diet, you need to minimize histamine-producing bacteria and maximize histamine degrading bacteria.

Here is a quick rundown of what that means for your probiotic strains:

  • Histamine Producing: Lactobacillus casei, Lactobacillus reuteri, & Lactobacillus bulgaricus. These are found in many yogurts and fermented foods. Although yogurt is marketed as a "gut-friendly" food, most manufactured probiotics are minimally effective at repopulating the gut biome because not all strains interact with the gut in the same way. In addition, if that yogurt or kombucha is loaded with refined sugar, it is not a good pick.

  • Neutral (test & see how you feel): Streptococcus thermophilus and Lactobacillus rhamnosus. If your body handles them well, these strains may help degrade histamines. Streptococcus thermophilus is found in yogurt and fermented milks. Lactobacillus rhamnosus is a probiotic supplement and a yogurt starter.

  • Histamine Degrading: Bifidobacterium infantis, Bifidobacterium longum, Lactobacillus plantarum, and some soil-based organisms. You can find these guys in fresh, organic, local meats and vegetables. You can also get these guys into your system by walking barefoot in the soil (grounding).

Here is a quick rundown of which probiotic-rich foods will make you feel great and which ones you may want to avoid, depending on your unique tolerance (even though they may be marketed as "gut-friendly" and "healthy"):

  • Eat more of: antioxidant-rich foods (blueberries, dark chocolate, quality coffee, green tea...) that boost populations of beneficial gut bacteria, grass-fed and organic dairy (if you tolerate dairy, things like quality yogurt and kefir are good options here), and prebiotic fiber (more on this below).

  • *Eat less of: matured and fermented foods (dependent on the bacteria yeasts that are involved in the process, i.e. soy sauce, some soy products, kombucha, fish sauce, pickles, fermented low quality coffee, kombucha, sauerkraut...), microbiologically produced foods (most yogurt, buttermilk, kefir, mature cheese, red wine, sauerkraut), processed, smoked, & fermented meats (low quality bacon, lunchmeat, sausage...), alcohol (red wine, white wine, champagne, beer), yeasty foods (especially breads made with yeast), certain vegetables, fruits, and nuts (tomato, peanuts, cashews, kiwi, pineapple...).

*Certain foods have higher histamine contents or help to release stored histamine. Some people tolerate histamines better than others. Test out to see if these foods make you feel tired, weak, foggy, and bloated. Not everyone tolerates fermented foods the same. Fermented foods do not work for everyone. It's a lot of trial and error to figure out what works best for your body. Just because something is touted as a "healthy" or "gut-friendly" food, does not mean that it is for you. Everyone is different. Some probiotics will make you feel amazing and some will leave you feeling inflamed, tired, and weak. When in doubt, get rid of pre-packaged, processed, low-nutrient dense, and sugary foods. Consume low-toxin and nutrient-dense foods to heal your gut. After eating, you should feel focused, energized, and light. Not bogged down, foggy, or tired.


Prebiotics are what the probiotics eat. They are the food for the good bacteria. The best source of prebiotics comes in the form of resistant starch. Resistant starch is a carbohydrate that resists digestion in the small intestine and ferments in the large intestine. As the fibers ferment, thy act as a prebiotic and feed the good bacteria in the gut. When resistant starch arrives in the colon intact, good bacteria feeds on it and produces beneficial short-chain fatty acids. Resistant starch strengthens the gut, burns fat, and protects against colon cancer, diabetes, and heart disease. As with fermented foods, it's important to experiment with resistant starch because not everyone can tolerate it well.

Once the resistant starch arrives in the colon, your good bacteria feeds on it. This produces butyrate (butyric acid), a short-chain fatty acid that is an energy source for your enterocytes (cells that line the GI tract). For example, one of the reasons that grass-fed butter is a better alternative to conventional butter or butter substitutes is because it is high in butyrate.

There are four types of resistant starch, and not all are beneficial to growing the good bacteria in your body;

  • RS1: embedded in the coating of seeds, nuts, grains, and legumes.

  • RS2: the resistant granules in green bananas and raw potatoes.

  • RS3: transforms into resistant starch when cooked and then cooled (ex. cooked and cooled potatoes and white rice)

  • RS4: man-made resistant starch found in processed food like breads and cakes. The food label might say "modified starch" or "polydextrin." Note: While most man-made starches are harmful to the bacteria of your gut, not all are. For example, resistant dextrin is a type of soluble fiber that may improve insulin resistance in women with type 2 diabetes.

In addition to feeding the probiotics in your gut, research shows that beneficial resistant starch could protect against colon cancer by killing precancerous cells in the gut and shrinking cancerous lesions in the bowel. Quality resistant starch also reduces insulin resistance. Because resistant starch is not digested, your insulin does not rise like it does when you consume other starches that consequently cause blood sugar problems. In addition, resistant starch is beneficial to weight control (through curbing hunger and helping to burn fat) and improving sleep.

It is important to note that not everyone handles resistant starch the same way. Some folks respond super well from the get go, while others need six weeks for their body to get used to it. If you are experimenting with resistant starch, it is important to pay attention to how your body is responding. If you're still experiencing bloating and gas after several weeks of experimenting with resistant starch, it is worth getting your gut checked out because you likely have an imbalance in gut bacteria. If you've taken antibiotics or eaten industrially-produced meat in the past year, this is likely to be the case. You can get a gastrointestinal pathogen panel or have genetic sequencing of your gut bacteria done, and likely you will need very specific strains of probiotics to fix the issue.

Some of the best sources of resistant starch include raw potato starch, cooked and cooled white rice, cooked and cooled sweet potatoes, green bananas, and raw plantains. It is incredibly important to pay attention to how you feel when experimenting with sources of resistant starch because some sources work really well for some and horribly for others, even with a balanced gut. For example with potato starch, some folks have trouble with the potato lectins and develop joint issues and rashes.

Consuming both probiotics and prebiotics is necessary to maintaining a diverse and heathy gut microbiome to perform optimally. To do so, it is necessary to understand which probiotic strains are beneficial for a diverse microbiota, which ones are harmful, and which ones you need to experiment with. Everyone is different with different experiences that determine how they handle certain probiotic foods, and how these foods affect their health. The same goes for prebiotics and consuming various sources of resistant starch. Everyone is different and experimentation is necessary to understand what your body needs to perform optimally. When in doubt, the best thing you can do to repair a healthy gut is to feed its good bacteria with nutrient dense and anti-inflammatory foods, while killing its bad bacteria by limiting your exposure to harmful foods.


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