Difference Between Prebiotics and Probiotics

Gut health is a hot topic these days. In particular, the difference between prebiotics and probiotics is discussed often. While you may have heard these terms, you might not know their different roles in maintaining a healthy digestive system.

An unhealthy gut can come from an imbalance of good and bad bacteria in your colon. Therefore, re-establishing the balance between both is key to good health.

Prebiotics and probiotics can help with that balance.

For this reason, let’s break down what are prebiotics and probiotics, what is the difference between both, why they’re key for your health, and how to include them in your diet.

What are probiotics and prebiotics?


Gut bacteria in the human microbiome

Simply defined, probiotics are good bacteria and yeasts. They live in the large intestine, mouth, vagina, urinary tract, skin, and lungs.

Because probiotics are good bacteria it is easy to see how they can be helpful to balance between good and bad bacteria.

For example, when you get an infection, you have more bad bacteria in the body than good bacteria. In that case, good bacteria help get rid of the bad bacteria and return our body to balance.

Probiotics can help add more good bacteria to your body (1) so you have enough to help the body have enough to recover the balance. 

When we take probiotic products, we consume products that are the same or similar to microorganisms that naturally live in our bodies (2).

While our large intestine hosts about 100 trillion microbes and 500 different species of bacteria (3), and your microbiome is as unique as a fingerprint, we all share common species of bacteria.

There are a few groups of common and beneficial bacteria. They belong to groups called lactobacillus and bifidobacterium specifically. Other common microorganisms include yeasts such as Saccharomyces boulardii.


Fiber from fruits, vegetables, whole grains, and legumes, are a great source of prebiotics.

Prebiotics are a form of dietary fiber that feeds good bacteria in our large intestine; and can be found in complex carbohydrates in fruits, vegetables, legumes, and whole grains.

When we eat prebiotic fiber, it goes undigested until it reaches the large intestine, where good gut bacteria then digest it.

As a result, good gut bacteria in our large intestine use prebiotic fiber as food, which helps nourish our good bacteria and helps them grow and thrive.

When good gut bacteria eat prebiotic fiber, short-chain fatty acids (SCFAs) are produced. These SCFAs are essential because they are the primary source of nutrition for the cells in your colon.

Therefore, prebiotic fiber is vital for a healthier digestive system (4).  

In summary, the difference between prebiotics and probiotics is that probiotics are good bacteria. In contrast, prebiotics is indigestible materials made of fiber. Both probiotics and prebiotics play a key role in creating a healthier digestive system. 

Registered dietitian Angela Lago makes easy to understand the difference with this analogy: think about probiotics like a beautiful plant and prebiotics as the water and fertilizer that help the plant thrive.

What are the benefits of consuming probiotics and prebiotics? 


It’s important to realize that the main job of probiotics is to maintain a healthy balance of bacteria in your body. When you are sick, bad bacteria enter the body and increase in number, knocking your body out of balance. However, good bacteria fights off the bad bacteria and restore the balance within your body, making you feel better.

Probiotics have a large number of potential health benefits (5,6):

  • Help your body digest food
  • Protect you from harmful bacteria and fungi
  • Aid in the immune system 
  • Create vitamins
  • Supports the gut lining to prevent bad bacteria from entering your blood
  • Breakdown and absorb medications
  • Improves symptoms of depression
  • Help address metabolic syndrome and obesity 

Probiotics may be used in the treatment or prevention of (7): 

  • Diarrhea from antibiotics
  • Diarrhea from C. difficile infection
  • Constipation
  • Irritable Bowel Syndrome (IBS)
  • Irritable Bowel Disease (IBD)
  • Yeast infections
  • Urinary Tract Infections
  • Gum Diseases
  • Lactose Intolerance
  • Eczema
  • Upper respiratory Infections
  • Sepsis

In conclusion, probiotics may be helpful for a large number of benefits. However, it’s important to note that research is still evolving in this area. 


The main benefit of prebiotics is that they produce SCFAs. Above all, SCFAs are the main source of nutrition for the cells in the colon.

The benefits of SCFAs include (8):

  • Help grow healthy bacteria in our gut
  • Communicate with our immune system
  • Prevent certain types of cancer
  • Lower cholesterol
  • Improve blood sugar
  • Prevent type 2 diabetes
  • Promote bowel regularity
  • Heal gut-barrier integrity 
  • Improve overall intestinal motility
  • Promotes overall digestive health

Prebiotics may be used in the treatment or prevention of (9,10): 

  • Diarrhea
  • Inflammatory Bowel Disease (IBD)
  • Colon Cancer

In conclusion, prebiotics may be helpful for many reasons. However, it’s important to note that research is still evolving in this area.

The difference between prebiotics and probiotics is that prebiotics aid the colon while probiotics improve the microbiome. Both impact our immune, gastrointestinal, and metabolic health.

Why should we care about increasing our probiotics and prebiotics?

Eating foods that naturally contain prebiotics and probiotics can improve digestive health, reduce inflammation, and prevent metabolic syndrome and obesity. In recent years, we have also seen a connection between gut health and brain health. fascinating!


Americans often eat the “Standard American Diet,” high in sugar, fat, and processed foods, a practice that is expanding to many other areas of the world.

Sadly, 58% of Americans consume ultra-processed foods (UPFs) rather than whole, unprocessed foods. UPFs contain few nutrients as well as many food additives and pathogen-associated molecular patterns (PAMPs). As a result, a diet high in UPFs can change gut microbiota and create inflammation in the body (11).

Overall, the Standard American Diet negatively impacts gut bacteria by lowering gut diversity.

In contrast, a diet high in fruits, vegetables, legumes, whole grains, and fermented foods, naturally high in prebiotics and probiotics, support a healthy microbiome.


A less diverse gut means we can develop the following issues:

  • Systemic inflammation
  • Intestinal inflammation 
  • Reduced gut barrier integrity 
  • Insulin resistance
  • Metabolic syndrome

More research is needed to better understand the full impact of the lack of prebiotics and probiotics in the diet.

While there is a difference between prebiotics and probiotics, both serve the same purpose in reducing inflammation and preventing metabolic syndrome.

Examples of foods that contain probiotics and prebiotics

Get the PDF version of the probiotic food list here


To increase your intake of probiotic foods, then focus on eating fermented foods with live cultures. 

Best sources of probiotic foods:

  • Yogurt
  • Kefir
  • Sauerkraut
  • Tempeh
  • Natto
  • Kimchi
  • Miso
  • Kombucha
  • Pickles
  • Traditional buttermilk
  • Fermented cheeses: swiss, provolone, gouda, cheddar, edam, gruyere, cottage cheese 
  • Sourdough bread 


To increase your intake of prebiotic foods, focus on eating 25-35 grams of fiber per day. To clarify, fiber is in vegetables, fruits, whole grains, nuts, seeds, and legumes. After all, by eating enough fiber and eating fiber from various sources, you will naturally eat some prebiotic foods.

Get the PDF version of the prebiotic food list here.

To eat the best sources of prebiotic foods, include foods from the following list.

Best sources of prebiotic foods: 

  • Chicory root
  • Dandelion greens
  • Jerusalem artichoke
  • Garlic
  • Onions
  • Leeks
  • Asparagus
  • Bananas (green, unripe)
  • Barley
  • Oats
  • Apples
  • Potatoes (cooked and cooled) 
  • Cocoa
  • Konjac Root
  • Burdock Root
  • Flaxseeds
  • Yacon Root
  • Jicama Root
  • Wheat Bran
  • Seaweed 

In summary, the difference between prebiotics and probiotics is that prebiotics are found in dietary fiber while probiotics are in fermented foods. To optimize your health and improve your balance of good gut bacteria overall, eat a diet that contains both.

Should I take a probiotic supplement?

Taking a supplement can be beneficial, however, is based on personal needs and health background. As always, a registered dietitian provider can help with the decision and the best for you.


Taking a probiotic supplement may be helpful to:

  • Prevent diarrhea after a round of antibiotics
  • Reduce the number of colds 
  • Reduce gastrointestinal symptoms not due to an acute illness, such as gas, bloating, or constipation.

However, more research is needed to understand the full scope of the benefits of probiotic supplements (12).  


There are risks associated with taking probiotic supplements. First, probiotic supplements are dietary supplements; therefore, the FDA does not monitor the making of probiotics. Therefore, some probiotic supplements may not contain the bacteria or amount listed on the label. 

Some probiotics may not survive while sitting on the grocery store shelf or when passing through the intestinal tract. 

Discuss the use of probiotics with your health care provider if you have (13):

  • Immune system deficiency 
  • Undergoing cancer treatment
  • Critical Illness
  • Recent surgery 
  • Sick infants
  • Small intestinal bacterial overgrowth (SIBO)

How to choose a supplement (14)

  • Choose probiotic products with at least 1 billion colony forming units (CFUs)
  • Select probiotics containing Lactobacillus, Bifidobacterium or Saccharomyces boulardii because these are some of the most researched strains
  • Stay away from store brands and pay for name brands because these have better testing procedures and studies to show their efficacy
  • Try out various probiotics: if you don’t see an improvement in a few weeks from one probiotic product, try a different product with a new strain of bacteria
  • Introducing probiotics may cause mild bloating, gas, and changes to stool patterns, indicating the product is working

Should I take a prebiotic supplement? 

Prebiotic supplements can be an excellent way to get in prebiotic fiber. However, taking a prebiotic supplement is dependent on personal needs and health background. 


Taking a prebiotic supplement may increase and drive the growth of good bacteria in your gut. In addition, prebiotic supplements are easy to add to food and drink.


When starting a prebiotic regimen, individuals may see an increase in gas, constipation, loose stools, loss of appetite, bloating, and acid reflux. Individuals with small intestinal bacterial overgrowth (SIBO) or FODMAP intolerances may want to avoid specific types of prebiotic fibers or avoid them altogether. 

How to choose a supplement

Below are tips on choosing a prebiotic supplement:

  • Start with 3g and work your way up to 5g of prebiotic fiber. 
  • Start with a low serving size of prebiotic fiber and gradually increase your dose to avoid mild gastrointestinal symptoms. 
  • Look for ingredients like acacia, psyllium husk, partially hydrolyzed guar gum, chicory root, inulin, fructooligosaccharides (FOS), oligofructose, or galactooligosaccharides (GOS).
  • Individuals with Irritable Bowel Syndrome (IBS) may do better on low-FODMAP prebiotic supplements like psyllium husk, acacia, or guar gum. 
  • Individuals with Irritable Bowel Syndrome (IBS) should avoid high-FODMAP prebiotics like inulin, FOS, and chicory root.

Please consult your doctor before starting a prebiotic supplement.

The difference between prebiotics and probiotics in supplement form is that prebiotics are from dietary fiber and probiotics are from live strains of bacteria. Both can be found in supplement form and may or may not be right for you, given your health background and specific needs. 

Tips for getting the most out of your gut health plan

Adding more prebiotic and probiotic foods into your diet is as easy as a few simple additions or swaps:


  • Smoothie with yogurt, banana, flaxseed
  • Oatmeal with chopped bananas and cocoa
  • Swapping regular bread for sourdough bread
  • Cottage cheese


  • Salad with dandelion greens or warm barley and a spoonful of sauerkraut 
  • Cooled potato salad 


  • Kombucha
  • Cheddar cheese on wheat bran crackers with apples
  • Jicama sticks 
  • Pickles


  • Garlic and onion as flavor enhancers 
  • Tempeh miso stir fry
  • Roasted asparagus or Jerusalem artichokes 
  • Kimchi

The difference between prebiotics and probiotics is the probiotics come from fermented foods, and prebiotics come from dietary fiber found in vegetables, fruits, whole grains, and seeds. Both prebiotics and probiotics can be found in your local grocery store and added to meals and snacks. 

Difference between Prebiotics and Probiotics in Menopause

During menopause, the decline in hormones estrogen and progesterone can cause women to experience digestive problems like constipation or diarrhea.

If you’re experiencing constipation, focus on eating more high-fiber, prebiotic foods. If you are experiencing diarrhea, both prebiotic and probiotic foods can help. Soluble, prebiotic fibers can aid in diarrhea in addition to probiotic foods. Supplemental prebiotics and probiotics are also great to add.

The bottom line

In summary, prebiotics and probiotics are a great addition to improving gut, immune, and metabolic health. You can eat prebiotic and probiotic foods every day through fibrous fruits, vegetables, whole grains, legumes, seeds, and fermented foods. Prebiotics and probiotics can also be taken in supplement form, however, it is always best to consult a doctor before taking any new supplements. 

The difference between prebiotics and probiotics is that probiotics are the actual good bacteria that we need, while prebiotics can help create the perfect environment for these bacteria to thrive.

“The Difference Between Prebiotics and Probiotics” was written by soon-to-be Registered Dietitian Rebeca Davis. Reviewed/edited by Su-Nui Escobar, DCN, RDN, FAND.

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