What Are Probiotics & Prebiotics?

Gut Health
Probiotics

What Are Probiotics & Prebiotics?

Probiotics are living bacteria and yeast that function to enhance the gut microbiome ...

What are probiotics?

The term “probiotic” was first used by Lilley and Stillwell in 1965 to describe substances secreted by one microbe that stimulated the growth of another (1). In 2001, the Food and Agriculture Organization of the United Nations redefined probiotics as “live microorganisms which, when administered in adequate amounts, confer a health benefit on the host” (2). In other words, probiotics are living beneficial bacteria and yeast designed to enhance the gut microbiome. Through DNA sequencing, the Human Microbiome Project has discovered more than 40,000 different microorganism species living within the colon. Today research is being conducted to learn more about these individual microorganisms, and the role they play in our overall health. The abundance and diversity of these species are greatly dependent upon a variety of factors. These following factors negatively affect the microbiome:

    • Poor diet: Too much sugar, carbohydrates, and processed foods. Not enough fiber.
    • Stress: People are overworked and under rested.
    • Sleep: Most people don’t get a full 8 hrs of sleep, and the sleep they do get isn’t refreshing.
    • Hydration: If you aren’t drinking at least half your body weight in ounces of water per day, you are dehydrated.
    • Exercise: With an increase in stress and decrease in time, more and more Americans are becoming increasingly sedentary.
    • Environment: Do you have access to clean air, water, and food?
    • Toxin exposure: Toxic chemicals are found in the food you eat, the water you drink, the air you breathe, and the products you use on your body and around your home.
    • Antibiotics: Antibiotics decrease the healthy population of bacteria found in your gut.
    • Cigarettes, alcohol, drugs, medications: Increased use of these substances increases the toxic burden on your body.
  • Antibacterial products: Like antibiotics, the overuse of these products are leading to a decrease in a healthy, abundant gut flora.


Unfortunately, in today’s society, the average American lifestyle is not designed to support the proliferation of the microbiome. As technology increases, and our population continues to grow, the quality of our food steadily declines, and environmental pollution increases. People are consuming fewer whole organic foods, and more sugar and processed items. The American Dream has turned into a never ending rat race that brings with it increased chronic stress and fatigue. Antibiotics are over prescribed by doctors, and used in mass quantities by the agriculture industry. As a result, the microbiome is becoming less abundant and diverse, and we are seeing an increase in many illnesses.

Health benefits of probiotics

In the not too distant past, scientists discovered that the microorganisms (microbiota, microbes, flora) found inside of our digestive system played an important role in our overall health. The functions of the microbiota that we are certain of today include (3):

  • Salvaging calories – helping us to get nutrition from the food we eat.
  • Producing short chain fatty acids (SCFA) – fatty acids produced in the gut when bacteria ferment the fiber we eat. Butyrate is one example, which possesses both anti-inflammatory and antioxidant properties.
  • Producing arginine and glutamine – 2 important amino acids involved in gut barrier function, inflammation modulation, and protection from oxidative stress.
  • Synthesis of Vitamin K and folic acid.
  • Participation in drug metabolism.
  • Deconjugation of bile acids – an important process allowing for the reabsorption of bile salts for future use in digestion and absorption of fat and vitamins A, E, D, and K.
  • Preventing the colonization of pathogenic (harmful) microbes.
  • Stimulating immunoglobulin A (IgA) production – and important protein of the immune system designed to prevent illness.
  • Regulating inflammation.
  • Inducing regulatory T cells – these cells help your body distinguish between itself and everything else. This is important for the prevention of autoimmunity where the body starts attacking itself.

Additional research is looking at the link between the health of the microbiome and the development of autoimmunity, obesity, cancer, mood disorders, hormone imbalances, cardiovascular disease, and other metabolic conditions. We now believe that microbes have the ability to even alter how our genes are expressed. With all of these benefits, you can see why efforts are being made to support the microbes in our gut. This is where probiotics come into play. By consuming probiotics via food or supplements, you are helping to enhance the good bacteria and yeast in your digestive system. This is very important today due to how many factors are currently contributing to the depletion of a healthy abundance and diversity of flora. Most research to date has focused on using probiotics in the treatment of diarrhea, constipation, H. pylori, C. diff, Candida, allergies, irritable bowel syndrome (IBS), and inflammatory bowel disease (IBD) (4).

Probiotic safety and side effects

According to the National Center for Complementary and Integrative Health (NCCIH), probiotics are considered relatively safe for individuals in generally good health (5). This is because most of the research conducted up to this point has resulted in minimal adverse side effects. However, caution should be used with individuals who have compromised immune systems, and who are battling with multiple health concerns. Some research has demonstrated the possibility of probiotics causing various infections in these individuals (6). Additional areas of worry, requiring further research, surround the possibility of undesirable gene alterations, excess immune stimulation in susceptible individuals, and adverse metabolic activity. In general, it is always a good idea to consult your healthcare professional before starting the use of a potent probiotic supplement.

Common probiotic side effects include various digestive symptoms. People often report gas, bloating, abdominal cramping, and changes in bowel habits. This can either imply that the probiotic isn’t of good quality, isn’t right for you, or that your body just needs time to adjust to it. Most people with a poor diet and lifestyle will experience side effects from taking probiotics due to the transitional phase of creating a new microbial colony. I always recommend taking things slow. If you experience symptoms, back down on your dose. If symptoms remain persistent, you might want to switch to a different probiotic source.

Food sources of probiotics

When you think about probiotics today, you most likely think about yogurt. Did you know that fermented milk products date all the way back to the Ancient Egyptians, and that Tibetans have been using fermented yak milk for hundreds of years to stay nourished during long journeys (4)? Long before the awareness of probiotic microorganisms, fermented foods such as wine, beer, bread, kefir, and cheese where being used for nutritional purposes. In 1905, scientist Elie Metchnikoff associated the longevity of Bulgarians, not to the yogurt they consumed, but to the Lactobacilli used to ferment their yogurt (4). The following foods are good sources of probiotics, and safe to consume regularly.

1. Sauerkraut – is finely chopped cabbage, or other vegetables, that gets naturally fermented by the Lactobacilli living on the surface of the cabbage.

2. Kimchi – is very similar to sauerkraut, and a traditional favorite in Korea. With Kimchi, the main difference is the addition of a variety of spices and fish sauce.

3. Kefir – is the process of fermenting milk by adding in kefir grains (a starter for yeast and bacteria). You can find goat kefir, sheep kefir, cow kefir, and even coconut kefir. The coconut version doesn’t possess as many probiotics as the dairy version, because coconut isn’t as much of a preferred food source as the lactose found in dairy. When consuming dairy products, I always recommend buying raw dairy. This means it has not been pasteurized (heated), and still contains important enzymes, probiotics, and nutrients.

4. Yogurt – is live cultured milk, and one of the best sources of probiotics you can find. However, not all yogurt is created equally. Most of the commercial yogurt found in stores is pasteurized, non-organic, and contains way too much sugar and other chemical fillers. If you’re going to eat something for its health benefits, make sure you are consuming the purest version. Always buy organic, sugar-free, grass-fed, and preferably raw. It is easier to find organic raw milk than it is to find organic raw yogurt, so I suggest buying the milk and making yogurt yourself.

5. Natto – is fermented soybeans, and a traditional food of Japan. It is a rich source of the probiotic Bacillus subtilis. When it comes to soy, always make sure you are buying non-GMO and organic.

6. Miso –  is also fermented soybeans. It is most widely used in soup form, and I am sure you have gotten a bowl of it from your favorite sushi restaurant at one point or another. It is extremely easy to make at home by dissolving a spoonful of the miso in warm water. Once again, make sure it is non-GMO and organic.

7. Kombucha – is the fermentation of black tea by the use of a scoby. A scoby is a pancake/disk like structure that is a symbiotic culture of bacteria and yeast. Sugar is added to the black tea, which feeds the bacteria and yeast, resulting in the final fermented product. Kombucha has become very popular today, and is commonly seen with the addition of various fruit and herb flavors.

Best probiotic supplements

The topic of quality probiotic supplements is a challenging one, because so much research still needs to develop in this area. The most important thing to note is that everyone is unique, and that what works for one person won’t necessarily work for others. When working with my patients, it always took a lot of trial and error to find the right probiotic for them. In addition, probiotic supplements are not created equally. People often have the poor assumption that all probiotics have the same effect regardless of the type or quantity of probiotics used. This is simply untrue. Science has discovered that each and every strain of probiotic has a different effect in our body. There are thousands of different strains of Lactobacillus, each with their own unique effects. For example Lactobacillus gasseri BNR17 is being studied for its benefits in preventing obesity and type II diabetes. On the other hand, Lactobacillus gasseri SBT2055 is being studied for similar effects, but with the addition of its ability to boost the immune response of it’s host.

Factors that determine a quality probiotic supplement

  1. Ability to survive the digestive process and make it to the large intestine. This means that the delivery system must allow for resistance against gastric and bile acidity.
  2. Ability to adhere to the mucosal surfaces and colonize within the large intestine.
  3. Ability to inhibit or interfere with pathogenic organisms, and thus decrease the chances of them causing an infection.
  4. Ability to maintain potency outside of the manufacturer.

Probiotic species and researched health benefits (7)

Lactobacillus Genus

  • Lactobacillus acidophilus – treats diarrhea, yeast overgrowth, bacterial vaginosis, urinary tract infections, C. diff, IBS
  • Lactobacillus casei – treats constipation, C. diff, bacterial vaginosis, rheumatoid arthritis, IBS, immune deficiency, Salmonella infection
  • Lactobacillus rhamnosus – treats viral lung infections, atopic dermatitis, allergies, diabetes, obesity, bacterial vaginosis, gastroenteritis.
  • Lactobacillus delbrueckii (bulgaricus) – treats antibiotic resistance, E. coli infection, modulates brain activity, increases immune function in the elderly
  • Lactobacillus brevis – protective role in bile salt tolerance
  • Lactobacillus johnsonii – increases respiratory immunity, treats gastritis, H. pylori, allergic rhinitis
  • Lactobacillus plantarum – treats yeast overgrowth, IBS
  • Lactobacillus fermentum – treats bacterial vaginosis, insulin resistance, high cholesterol
  • Lactobacillus reuteri – lowers LDL cholesterol, treats gastroenteritis, diarrhea, colic

Bifidobacterium Genus

  • Bifidobacterium infantis – treats IBS, enterocolitis in infants
  • Bifidobacterium animalis (lactis) – treats constipation, urinary tract infections, respiratory infections, reduces total cholesterol, modulation of brain activity
  • Bifidobacterium bifidum – treats diarrhea, enterocolitis in infants, reduces total cholesterol
  • Bifidobacterium longum – treats enterocolitis in infants, diarrhea, IBS
  • Bifidobacterium breve – reduces cholesterol, treats enterocolitis in infants

Bacillus Genus

  • Bacillus subtilis – treats diarrhea, H. pylori, produces nitrous oxide
  • Bacillus coagulans – treats diarrhea, bacterial vaginosis, prevents cavities,
    provides immune support

Misc Genus

  • Lactococcus lactis – treats diarrhea, bacterial vaginosis, C. diff., modulates brain activity
  • Enterococcus durans – anti-inflammatory activity
  • Streptococcus thermophilus – treats IBS, enterocolitis in infants
  • Saccharomyces cerevisiae (boulardii) – treats diarrhea, IBS, ulcerative colitis, C. diff.

Probiotic Supplements I recommend

The following are probiotic supplements that I have used myself or with my patients. They are all trusted brands for quality assurance. My general rule of thumb is to use a probiotic that has many different strains, and is above 10 billion CFU. It is also a good idea to rotate probiotic strains in order to increase the diversity in your gut.

Probiotic 50B by Pure Encapsulations

Probiotic 100B by Ayush Herbs

MegaSporeBiotic

Bio-Kult Probiotic

Multi-Strain Probiotic 40 Billion by Douglas Labs

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What about prebiotics?

The term prebiotic was defined in 1995 by Gibson and Roberfroid as “a non-digestible food ingredient that beneficially affects the host by selectively stimulating the growth and/or activity of one or a limited number of bacteria in the colon, and thus improving host health.” (8) In other words, prebiotics are non-digestible fiber that pass through the digestive system to the colon where they are fermented by our gut microbes providing them with fuel so that they can in turn provide us with overall health. The lack of sufficient dietary intake of fiber for most people is a big part of the reason for a decrease in microbial abundance and diversity. So if you don’t feed your good gut bacteria, then they won’t be able to flourish and keep you healthy. Oligofructose, inulin, and beta-glucan are examples of prebiotics.

Since the average American diet lacks many of the plants that contain prebiotics, many companies have created inulin powder products. The most common ones on the market come from jerusalem artichokes, chicory root, and blue agave. It comes as a fine white powder that can easily be added into smoothies, mixed in beverages, or added into just about anything. It dissolves very easily, and tastes like a very mild sweetener. The brands that I use personally are Jetsu Chicory Root Inulin, Opportuniteas Blue Agave Inulin, and Erbology Sunchoke Powder. The last one isn’t an inulin extract, it is the entire jerusalem artichoke dried and turned into a powder. I add it into my smoothies, because I believe that the constituents of a plant work better when the entire plant and all of its constituents are included. All 3 products are organic of course, and I have been very pleased with them. The following infographic shows the main foods that are an excellent source of prebiotics.

Affiliate Disclosure: In the spirit of full disclosure, there are affiliate links in this article, which means that I may get a commission if you decide to purchase any such product. I only recommend products and services that I use and love myself.