The Ultimate Evidence Based Guide to Probiotics [**Updated 2021**]

Ultimate Guide to Probiotics

Probiotics have seen renewed interest as more and more researchers, consumers and product manufacturers learn about the potential health benefits these microorganisms can offer.

The first use of probiotics can be traced back to ancient times when physicians like Hippocrates recommended fermented dairy products to help alleviate gastrointestinal issues.

On the contrary, the modern outlook on probiotics,  which has been largely influenced by the theories proposed by Russian scientist Elie Metchnikoff, is that these microorganisms have the capability to modify the natural gut microbiota and replace harmful microbes with useful microbes. Although Metchnikoff recommended the use of fermented milk products to acquire these benefits, probiotics are currently consumed in a variety of different forms.

While some of the general concepts Elie Metchnikoff theorized about still remain true today, other ideas have been proven false. In this guide, we will bust those myths, while also providing you with the most current scientifically proven knowledge about probiotics so that you can select the perfect probiotic for your gut.



Probiotics are commonly referred to as “live microorganisms, which, when administered in adequate amounts, confer a health benefit on the host.” 1

There are a few key points in this definition:

  1. The microorganisms must be alive and not dead.
  2. The microorganisms must produce a health benefit to the host.
  3. There must be an adequate amount of these microbes, which is otherwise referred to as its therapeutic dose, to achieve these health benefits.

It is important to remember that a product should not be considered a “probiotic” unless it encompasses each of these criteria. Furthermore, the use of a specific strain(s) within the probiotic product must be supported by successful results that have been obtained during clinical trials.

Probiotics typically contain lyophilized (freeze-dried) or live bacteria/ yeast cultures, each of which can come in a variety of different preparations, some of which include:

  • Powders
  • Capsules
  • Medicinal Yogurts (Note that these differ from regular yogurts)
  • Oils
  • Drinks

Although there are many different fermented food products that contain live microorganisms, it is important to note that these products should not be defined as “probiotics,” since the health benefits and therapeutic dosage of the microorganisms within these products have not been determined. While these wild ferments may still be healthy and provide beneficial effects when consumed, they still do not fall under the “probiotic” classification.

Below are a few examples of these fermented non-probiotic products:

  • Non-medicinal yogurtsfermentedvegetables
  • Kombucha (without probiotic strains included, some include them)
  • Miso
  • Sauerkraut
  • Kimchi
  • Kefir
  • Fermented vegetables
  • Rejuvelac
  • Kvass

What Are Prebiotics?

You might have heard the term prebiotics mentioned alongside probiotics. This can make the discussion even more confusing if you are not familiar with what prebiotics are.

Prebiotics are simply a kind of fiber that the body cannot digest, thereby allowing this substance to serve as food for bacteria once it passes through your mouth to your gut. Common sources of prebiotics include fruits and vegetables such as artichokes, garlic, leeks, bananas, chicory root, oats, and apples.

Besides whole foods that contain prebiotics, there are also numerous prebiotic fiber supplements that can help feed beneficial microbes if someone is not able to get a range of prebiotic foods in their diet. You can learn more about the best prebiotic supplements here.

What Are Synbiotics?

One of the newest words being used in this area of gut health is synbiotics. Synbiotics are simply the combination of prebiotics and probiotics in a single product. Note that some probiotic supplements may be considered synbiotics if both prebiotics and probiotics have been incorporated into a single formula.

The theory behind synbiotic products is based on the assumption that prebiotics while working alongside probiotic bacteria, will help these highly valuable bacteria grow and flourish within the intestinal tract.

Common Classes of Probiotics


Probiotics are generally found in a few different genus classes where there are numerous species and strains in each class.


The most common species of Lactobacillus include:

  • Acidophilus
  • Plantarum
  • Rhamnosus
  • Casei
  • Reuteri
  • Crispatus
  • Fermentum


The most common species of Bifidobacterium include:

  • Bifidum
  • Infantis
  • Lactis
  • Animalis
  • Breve


This is a type of probiotic yeast. The most common species of Saccharomyces includes:

  • Cerevisiae variety boulardii (often referred to as boulardii)


Soil-Based Probiotics

Soil-based organisms are microbes that are naturally found in soil. Most soil-based organisms are spore-forming microbes; this means that these organisms have a small spore, which functions to protect them from heat, acid and antibiotics. As a result, soil-based organisms can better survive the harsh enzymatic environment of the small intestine. Several scientific studies have isolated these organisms and determined their ability to elicit various probiotic benefits. 3

Some of the most common Genus and Species of Soil Based Probiotics include:


  • Clausii
  • Coagulans
  • Subtilis


  • Faecium

What Are Probiotics Used For?

Probiotics have been widely studied and used to assist in the treatment of many health conditions including both gastrointestinal conditions and non-intestinal conditions.

Some of the most common health conditions in which probiotics have shown positive effects include:

  • Irritable Bowel Syndrome (IBS)
  • Inflammatory Bowel Disease (IBD)
  • Constipation
  • Gut infections
  • Dysbiosis
  • Lactose intolerance
  • Leaky Gut
  • With or post antibiotics
  • Vaginal thrush
  • Eczema
  • Obesity
  • Diabetes
  • Endometriosis
  • Anxiety
  • Depression
  • Gastroesophageal reflux disease (GERD; acid reflux)
  • Food allergies
  • Low immunity

How Do Probiotics Work?


There are several different mechanisms of action in which probiotics elicit their beneficial health effects within the gastrointestinal tract, some of which include:

  1. Probiotic microorganisms can compete with pathogenic bacteria and fungi present within the gastrointestinal tract to take up any available space.
    • This mechanism of action is particularly useful when the gut is experiencing a direct attack on its natural microbiota, such as that which can occur during antibiotic or chemotherapy treatment.
  2. Probiotic microorganisms can be hostile towards pathogenic microorganisms by secreting antimicrobial compounds to help inhibit the toxic effects of pathogenic microorganisms
  3. Probiotic microorganisms can be used to train and balance the immune system of the entire body.
    • For example, the use of probiotics is associated with reducing the occurrence of allergic reactions and inflammation, as well as improve certain food tolerances and increase the secretion of immunoglobulin A (IgA).
  4. Probiotic microorganisms can also produce compounds that provide direct benefits to the gut.
    • These beneficial compounds can include short-chain fatty acids, which help maintain a healthy colon pH, which describes the ideal acidity levels required within this part of the large intestine.
    • Certain species of probiotic microorganisms are also associated with releasing polyamines, which function to help restore normal intestinal structure 5, 6
  5. Probiotic microorganisms can have anti-inflammatory activity.
  6. Probiotic microorganisms can assist in maintaining an ideal gut transit time.
    • Certain probiotic strains are associated with accelerating colon transit time, whereas others can slow down colon transit time. As a result, patients with conditions like IBS-C and IBS-D can selectively use certain probiotic strains to experience these benefits, respectively.
  7. Probiotics can decrease intestinal sensitivity; a condition otherwise referred to as visceral hypersensitivity, by reducing the response of overly sensitive nerves present within the gut.
  8. Probiotics can strengthen the intestinal barrier against foreign invasion.
  9. Probiotics can alter brain chemistry and balance mood.
  10. Probiotics can alter metabolism.

Side Effects From Probiotics

probiotic side effects

Although the use of probiotics is associated with various health benefits, it may be possible for certain individuals to experience unwanted side effects from the ingestion of these microorganisms. The severity and extent to which an individual experience unwanted side effects from using probiotics is largely determined by their state of health.

For example, people who are generally healthy will most likely tolerate probiotics well, aside from occasionally experiencing mild digestive symptoms, such as gas.

Other mild side effects associated with probiotic use include:

  • Headaches
  • Excess histamine release in the GI tract, which can lead to:
    • Itching
    • Watery eyes
    • Runny nose
    • Trouble breathing
    • Redness
    • Swelling
  • Allergic reactions
  • Increased risk of infection (1 in 1 million) 7

Even so, there remains a lack of research that has been made on creating a full safety profile of all probiotic strains to determine whether even healthy people can experience more severe side effects.

Individuals with underlying health problems may experience more severe side effects, such as infections, following the use of probiotics. The groups of people who are at most risks of experiencing this type of severe reaction include those who are immune-compromised, such as infants, the elderly, and those with severe illnesses 8.

It is, therefore, important for anyone, particularly people with underlying health issues, to always consult with a doctor before starting any new therapy.

Probiotics are Strain-Specific

It is important to understand that probiotics are highly strain-specific. What this means is that different strains from the same species of bacteria can have different therapeutic effects.

While it may appear to be sufficient to just know what genus and species your probiotic microorganism originates from, it is also crucial to be aware of the specific strain, as this often determines the ability of the microbe to adhere to intestinal cells, colonize the gut and produce antimicrobial compounds.

For example:

  • This is a label containing the strain: Lactobacillus plantarum 299v
  • This is a label that does not contain the strain: Lactobacillus plantarum

A good example of this in a real-life scenario is the different breeds of dogs. Dogs are all of the same species, but there are many different strains or types of dogs.

dog breeds

For example, a bulldog has a much different personality, physical characteristics, and traits as compared to a small little Jack Russel.

This is the same as different strains of probiotics!


Common Probiotic Myths to Be Aware Of

Myth #1: There Is No Difference Between Strains of The Same Species

Why this isn’t true: Research has shown over and over again that the strain determines the therapeutic effect of the probiotic and that different strains within the same species can have totally different effects. 9

Myth #2: You Shouldn’t Use Probiotics During Antibiotic Treatment

Why this isn’t true: The research has shown that using probiotics alongside antibiotics can help prevent antibiotic-associated diarrhea and any potential destruction to the microbiome that can occur as a result of antibiotic use. 10, 11

Myth #3: Bacterial Strains Will Permanently Colonize or Reseed The Gut

Why this isn’t true: Most of the current probiotic strains only temporarily colonize the gut after oral ingestion. The majority of probiotic strains will only survive from a few days to a maximum of one to two weeks after cessation. 12

Myth #4: You can “reseed” your gut after taking antibiotics by eating fermented foods or taking probiotic supplements

Why this isn’t true: Fermented foods like Kombucha and Kefir do not contain most of the same species of microorganisms that comprise normal human gut bacteria.

Furthermore,  both fermented foods and probiotic supplements will typically only colonize the gut for a few days, during which they can have therapeutic effects; they do not function by “reseeding” the gut. Time, diet and prebiotics are a much more effective way to reestablish gut microbes.

Myth #5: Taking probiotic supplements is better than taking probiotics in food form (medicinal yogurts, drinks, oils)

Why this isn’t true: There are several medicinal yogurts, such as Activia, Yakult, and Vaalia that contain multiple well-researched strains of bacteria. Also, the dairy base of yogurt acts as a more effective transport mechanism to allow a larger amount of bacteria to survive the environment of the upper portion of the intestinal tract as compared to supplements.


A Few Beneficial Probiotic Strains


Below are just a few of the well-researched probiotic strains that have been shown to provide a wide range of health benefits:

  1. Lactobacillus rhamnosus GG– One of the most widely researched probiotic strains showing a wide range of benefits in preventing intestinal infections, helping with gastrointestinal disorders, respiratory disorders, and more. Source
  2. Lactobacillus casei Shirota– Another widely researched probiotic strain commonly seen in the product known as Yakult. This strain has shown numerous health benefits including helping with chronic fatigue, intestinal dysbiosis, SIBO, lactose intolerance, anxiety and more. Source
  3. Saccharomyces cerevisiae variety boulardii– This widely researched strain of yeast has been proven to help with traveler’s diarrhea, antibiotic side effects, giardia, candida, small intestinal damage and more. Source
  4. Bifidobacterium lactis Bb12– This widely researched probiotic strain has been shown to help with viral gastroenteritis, constipation in the elderly, H pylori infection, intestinal dysbiosis and more. Source
  5. Lactobacillus plantarum 299v– This well-researched strain has been shown to help with irritable bowel syndrome, antibiotic-associated diarrhea, Ulcerative Colitis, coronary artery disease and more. Source


What Disrupts Friendly Probiotic Bacteria

The gut microbiome is a delicate and complex ecosystem that provides many health benefits. It’s important to remember that taking a probiotic supplement or eating fermented foods can certainly help, but our lifestyle, environment, diet, and medications have the biggest impact on our microbiome. Sometimes they can even have a negative impact on our gut microbes.

Below are a few of the common ways the microbiota can become disrupted:

  1. Antibiotics both prescription and natural
  2. Food poisoning or traveler’s diarrhea
  3. Stress
  4. Unhealthy diet and excess sugar
  5. Medicines
  6. Lack of exercise
  7. Alcohol
  8. Smoking
  9. Poor sleep
  10. Overly excessive sanitation

Microbiome disruptors


How to Choose a Probiotic Supplement

Due to the increasing amount of research on probiotic strains, we now have enough scientific data to effectively match a specific probiotic strain to a specific health condition where it may be beneficial.

Let’s go over the basics of choosing the right probiotic supplement.

1. Make Sure it Has Characteristics of a Good Probiotic Supplement

The following table from Dr. Jason Hawrelak (probiotic researcher) shows the desirable characteristics of probiotics.

Desirable Probiotic Characteristics
Human Origin
Can Survive Gastric Acid and Bile Salts Reaching the Lower Bowel
Adherence to Intestinal Mucosa
Ability to Colonize the Intestinal Tract
Able to Produce Antimicrobial Compounds
Antagonism Against Pathogenic Organisms
Safety in Food and Clinical Safety
Clinically Documented Health Effects
Adequate shelf life and stability maintaining therapeutic effects through processing


Out of the mentioned characteristics, the most essential ones that should be considered when choosing a probiotic supplement should include:

  1. The ability of the probiotic to survive the upper part of the intestinal tract (gastric acid and bile salt stability)
  2. The ability of the probiotic to adhere to intestinal cells
  3. The ability of the probiotic to temporarily colonize the gut
  4. Any scientifically proven health effects for strains contained in the product at the necessary amount

When choosing a probiotic product, make sure that the product meets the essential requirements listed above, contains a strain that has been proven effective for your health issue, and is alive and viable until its labeled expiration date.

2. Make Sure it is a Researched Strain


It’s also very important to understand that the strain of bacteria determines the therapeutic effect it has. This is why when choosing a probiotic product a reputable company will label the genus, species, and specific strain that is in the product.

For example, Lactobacillus plantarum 299v not Lactobacillus plantarum

In order to choose the best probiotic for your situation make sure that the strain is labeled on the product and that the strain has been clinically proven to help with the condition you have.

You can simply type in a google search like “probiotics studied in IBS” or “probiotics studied in IBD” to browse through the scientific studies or check the labeled strains on the product you are considering then search that strain in google to see what the studies have shown on it.

If you want an even better way to find the correct probiotic for your condition, check out Probiotic Advisor, which is a searchable probiotic database that matches probiotic strains and brands to health conditions they have shown positive benefits in clinical trials.

3. Stay Clear From Red Flags

bad probiotic products

Below are the most common red flags to steer clear from when choosing a probiotic product:

  1. When a company does not specifically list the strains on the label
  2. When the company uses research results from similar strains or species for their strain
  3. When strains are not in the adequate amount (usually at least 109 CFU/dose)
  4. When the product viability is not maintained through processing and guaranteed until expiration
  5. When the company has negative consumer reviews or trust signals

Remember, most companies who go the extra mile to select well-researched strains of probiotic bacteria and label them clearly on their products will provide the best products.

In summary, to select the right probiotic supplement make sure it has the most essential probiotic characteristics, make sure it is a well researched and clinically proven strain for the health issue you are treating, and make sure the company does not have any red flags associated with it.


In summary, probiotics are amazing microorganisms that can offer health benefits to humans if used the right way. As more and more research is being done to understand how the use of probiotics can improve different health issues, consumers like you and me will be able to better match which strains will be best suited to help with specific health conditions.

As previously mentioned, it is crucial to recognize which probiotic strain is most appropriate for your given health concerns.

Remember, the notion that a probiotic supplement or food can “reseed” the gut after a disruption occurs in the microbiota is outdated. It is better to view probiotic supplements as therapeutic tools that can help with certain issues. For example, someone looking for the best probiotics for SIBO or IBS should look for strains that have been researched in those specific conditions. 

Also Read: Probiotics Detox Symptops: Everything You Need to Know

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