The How When & Why of Probiotics

Last updated on August 3rd, 2021 at 04:10 pm

What Are Probiotics?

Simply put, ‘probiotics’ are live bacteria or yeasts that can be taken as supplements to improve digestive health. People usually think of bacteria as being bad or pathogenic and causing disease but your body is full of bacteria that are healthy and good for you. Probiotics are made up of good bacteria that helps keep your body healthy and working well. This good bacteria helps you in many ways, including fighting off bad bacteria when you have too much of it, helping you feel better.

Can I Get Probiotics From Food?

You can increase beneficial microbes in your body from the foods you eat. Certain foods have probiotics (good bacteria) in them and can benefit the health of your microbiome. These foods can be introduced into your diet at any point of the day. You may even be regularly eating them now and not realize that they contain probiotics. You will want to check the food label for “live and active cultures.”

In the digestive tract good bacteria help to break down nutrients in food coming from the stomach so they can be absorbed by the body. There are two ways that you can get these ‘good bacteria’ into your gut. You can either eat more probiotic rich foods or take probiotic dietary supplements. No guideline states how many probiotic foods that you need to eat every day, so it is not easy to know if you are getting enough probiotics in your food intake alone. Here are some foods you can eat to put good bacteria in your gut:

For breakfast, try:

  • Yogurt.
  • Buttermilk.
  • Sourdough bread.
  • Kefir.

For lunch, try:

Cottage cheese.

For a snack, try: Fermented pickles.

For dinner, try:

  • Fermented sauerkraut.
  • Kimchi.
  • Miso soup.

The general rule of thumb is to include as many fermented foods in your diet as possible.

The downside to natural sources of probiotics is that not everyone enjoys eating them or can stand the strong smell that comes with most of them. Also, not all fermented foods contain probiotics so you may be deficient even while including probiotic foods in your diet. Lastly stomach acid kills pretty much everything including good food based bacteria. You can counter all the above by taking specially formulated probiotic supplements. These have specifically isolated bacteria and yeast which support good digestive health.

What Types of Probiotics Are There?

Lactic acid bacteria probiotics

Lactic acid probiotics include strains you may have heard about, such as bifidobacterium and lactobacillus, which is the most common strain found in fermented foods like yogurt. These are bacteria that produce lactic acid by eating lactose, sugar, and carbohydrates. They eat these foods through a process of fermentation, which lowers the pH of the gut and, therefore, limits the growth of pathogens and Candida.

The challenge with lactic acid strains of probiotics is that the live bacteria they contain are highly sensitive to light and heat making them hard to successfully deliver to you. Under these conditions, they die easily. While manufacturers have gone to great precautions to prevent this death before you receive a bottle (refrigeration and dark glass, for example), the stomach acid of your stomach may kill many of these probiotic bugs before they have a chance to reach their target location in your intestines. They aren’t very helpful if they can’t make it to the intestines where they are needed. The good news is some very clever medical folks have figured out how to package lactic based probiotics in a capsule that breaks down in the intestines and not the stomach therefore getting the lactic bacteria to the right spot.

Lactic acid bacteria are also transient, meaning they don’t hang around in the gut after they’re consumed. Instead, they move through quickly, doing their work as they pass by. That’s somewhat helpful but it would be more helpful if they stuck around and did more good work.

Soil-based probiotics

Soil Based Probiotics

A second class of probiotics are soil-based probiotics, or SBOs. These are bacteria that are naturally found in the dirt, not in the human body. Most have a hard shell around them so they’re able to withstand the demands of Mother Nature. SBOs enrich the soil so that plants and food have the nutrients to grow well. These bacteria are naturally on our food, so we would naturally consume them and they’d help enhance our immune system.

Today, few of us are harvesting our own food from the ground and even fewer are eating foods without washing away the dirt. This distance and food cleanliness has decimated the number of soil-based probiotics we ingest. Proponents of soil-based probiotics point to this as one of the main reasons we’re experiencing such collective digestive distress.

Certain strains of SBOs have been found to be highly effective in balancing GI issues, improving regularity and stimulating the immune system. Some soil-based probiotics are transitory while others have the ability to colonize.

Spore Based Probiotics

The third class of probiotics are spore probiotics. It’s important to understand that spore-forming probiotics can be a type of soil-based probiotic, meaning that some spore-forming bacteria are from the soil. This explains why only some soil-based bacteria have the ability to colonize the gut, whereas all spore-forming probiotics have it. There is no crossover with lactic acid probiotics.

Like soil-based probiotics, spore probiotics are highly resistant to harsh conditions, which means they can survive and grow in any environment.

A significant benefit is that they can even resist antibiotics, whereas other types will likely be killed by antibiotics. This means they are much more likely to stay and colonize the gut, living there and helping to sweep out bad bacteria. They can also remain dormant in the gut for a long time, and then revive themselves when nutrients are present making a good diet and a great source or prebiotics like Microbiome Labs Mega Pre even more important for realizing the most potential from spore based probiotics.

How do probiotics work?

Probiotics work in many ways. When you lose the ‘good’ bacteria in your body after taking broad-spectrum antibiotics, for example, taking probiotic supplements can replace them. They can also help to counter the bad bacteria in your body with good bacteria. Lactobacillus, Bifidobacterium are types of bacteria that are probiotic. They help with diarrhea and can aid those that are lactose intolerant.

Probiotics have also been found to help in digestion and immune regulation. It has been shown that they secrete protective substances that activate the immune system. When this happens, pathogens are prevented from taking hold and causing disease. They also improve common gastric issues like gas, bloating, and constipation. The challenge with probiotics is making sure that they survive the stomach’s digestion process with its associated acid and make it successfully to the right places in the intestines in order to do their job. More on that in a bit.   

How Safe Are Probiotics?

Microbes used as probiotics already exist naturally in your body so probiotic foods and supplements are generally considered safe. They may cause mild stomach upset, diarrhea, or flatulence (passing gas) and bloating for the first few days after starting to take them. In rare cases they can cause allergic reactions.

People who may have the following need to use caution when using probiotic supplements:

  • A weakened immune system (those going through chemotherapy for example).
  • A critical illness.
  • Recently had surgery.
  • Caution should also be used when giving probiotics to very sick infants.

Always talk to your healthcare provider before starting a probiotic supplement.

Who should take probiotics?

Probiotics can be taken by virtually any person but if you are immunosuppressed it is recommended that you talk to your doctor before starting to take them. It’s a good idea to talk with your doctor before taking any supplement to make sure you’re taking something that will benefit you and won’t cause any unexpected side effects. If you have one of the symptoms listed below you should consider taking probiotics:

Leaky Gut
Parasitic Infection
Autoimmune DisordersSeasonal Allergies
Recent Antibiotic UseHepatic EncephalopathyKidney Disease
Parkinson’s DiseaseAlzheimer’s DiseaseLiver Disease
Cardiovascular DiseaseMetabolic SyndromePolycystic Ovarian Syndrome
Helicobacter pylori InfectionEczemaDiabetes
InfertilityClostridium difficile InfectionSmall Intestinal Fungal Overgrowth (SIBO)
Food SensitivitiesFood AllergiesSmall Intestinal Overgrowth (SIFO)
Candida OvergrowthCeliac DiseaseDiverticulitis
Ulcerative ColitisCrohn’s DiseaseIrritable Bowel Syndrome

What Is The Best Probiotic To Use?

There are many probiotics that may be beneficial for you and we encourage you to consult your doctor or nutritionist about what might be right for your specific situation but today we’re going to highlight four of the most popular based on purchases. These four also cover multiple categories of probiotics including lactic and spore based. If you have questions please don’t hesitate to contact us.

1. MegaSporeBiotic by Microbiome Labs

Microbiome Labs MegaSporeBiotic is a spore-based, broad-spectrum probiotic that has been clinically shown to maintain a healthy gut barrier function. It reconditions the gut by promoting microbial diversity and maintaining key health-promoting, commensal gut bacteria.

MegaSporeBiotic is part of a three part total gut restoration protocol and you can read more about that here with the Recondition, Reinforce and Rebuild summary.

It has a 5-year shelf life which makes it convenient to keep in the house. You do not need to refrigerate it and it still works even when you are taking antibiotics. MegaSporeBiotic is a blend of 5 Bacillus spores. Spores can survive the harsh digestive conditions until they reach the large intestine where they can change into their active vegetative forms which recondition the gut. MegaSporeBiotic is highly favored by health practitioners and consumers as well.

MegaSporeBiotic is made up of 5 Bacillus spores. These are Bacillus Licheniformis, Bacillus Indicus HU36, Bacillus Subtilis HU58, Bacillus Clausii, and Bacillus Coagulans. Bacillus Licheniformis produces proteases that are important in protein digestion. It also produces all the B vitamins. Bacillus Indicans produces the recommended daily allowance levels of carotenoids, lutein, astaxanthin, and beta-carotene. It also produces quinols and other vitamins. Bacillus Subtilis HU58 produces nattokinase and vitamin K2. It also supports the development of the gut-associated lymphoid tissue. Bacillus Clausii and Bacillus Coagulans support immune function and produce lactic acid respectively. It’s one of the most popular probiotics and we consistently see positive reviews from those taking it.

2. Probiotic Sufficiency by Innate Choice

Probiotic Sufficiency is the world’s only probiotic formula based on those species found most commonly in the food of our ancestors and in the intestinal tracts of healthy human beings. We know from research that our ancestors consumed healthier diets and had superior health and less chronic illness compared to modern, Industrial humans.

In consideration of this fact, Probiotic Sufficiency™ has been created from the “ground-up” to model the types and amounts of bacteria ingested by our ancestors – the types and amounts we genetically require. The most prevalent species in Probiotic Sufficiency™ is Lactobacillus plantarum, which was the most common bacteria in the food of our ancestors and is still the most common bacteria in fermented foods in Africa. Lactobacillus plantarum was also the dominant species isolated from the GI tracts of healthy subjects in a recent study in the United States.2 Not surprisingly, it is also one of the species most commonly shown by research to have health-promoting effects. Every one of the nine different species of probiotic bacteria in Probiotic Sufficiency™ was chosen using these scientific criteria.

The human normal flora was determined thousands of years before humans ever consumed dairy, goat’s milk, or grains. For this reason, Probiotic Sufficiency™ is derived from 100% vegetarian culture and contains no dairy, soy, goat or grain products. It is provided in a 100% vegetarian gel capsule and is entirely wheat free. Probiotic Sufficiency™ contains over 30 billion viable organisms per serving, one of the highest amounts available! It comes in individual bottles or buy in bulk and save with a 3 pack or a case of 12.

3. Ortho Biotic by OrthoMolecular

OrthoMolecular Ortho Biotic is a unique probiotic formula designed to deliver active organisms shown to promote healthy gut microflora, protect intestinal integrity and boost immune function. Included in this formula is Saccharomyces boulardii, an extensively researched microorganism shown to help restore microflora balance by enhancing commensal organism function. Each Ortho Biotic capsule provides seven proven probiotic strains chosen for their ability to withstand the harsh gastrointestinal environment and adhere to the intestinal tract to deliver superior results.

The secret sauce if you will for OrthoBiotic is the capsule that holds the bacteria is designed to withstand harsh stomach acid and open up in the right area of the intestines in order to get the bacteria to the place in the digestive tract where they are most needed.

4. Spore Probio by TonicSea

TonicSea Spore Probio with Phage technology is a complete probiotic containing powerful digestive enzymes with a synergistic bacteriophage formula that promotes immune function and digestive health. Bacteriophages are submicroscopic packages of DNA or RNA that have the ability to attach to unique strains of unwanted bacteria in the intestines. 

Unlike traditional probiotics, bacteriophages selectively target specific unwanted bacteria while leaving beneficial “good” bacteria to thrive in your gut. They also colonize better and are not heat sensitive. Phages are considered an intelligent bug, meaning they multiply at the site of interest to support healthy immune function. When used in conjunction with digestive enzymes as well as pre and probiotics, the effectiveness of bacteriophages are multiplied.

Supplementing with Spore Probio is recommended to support a healthy gut microbiome and promote the health properties of probiotics.


  1. Should you take probiotics?
  2. MegaSporeBiotic
  3. What are probiotics?
  4. How to get more probiotics


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    Greetings! Very useful advice within this article! It is the little changes that will make the biggest changes. Thanks for sharing! Dona Will Kimmie

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Medically reviewed by Dr. Jamy Antoine, D.C. — by Chris Bowman — On October 19, 2020


Chris Bowman

Chris Bowman is the CEO and Co-Founder of and has over 15 years of experience in nutritional sciences and wellness. Simply Nutrients is a part of Dr. Jamy Antoine's Select Health Practice in Edina, Minnesota. Chris is passionate about helping people live healthier lives by using the best practices of nature, nutrition, and medicine.