Prebiotics vs probiotics (and how they keep your gut happy)

Prebiotics vs probiotics: what's the difference

This post contains affiliate links. Affiliate links means that sometimes if you click through to a website and register or purchase something, I may get a commission from that sale at no extra cost to you. For more information click here.

You’ve heard this countless times: probiotics and prebiotics are good for gut health. And it’s absolutely right! However, many people get confused by the terms, especially since it’s such a trendy topic in nutrition. In this post, I’m going to share the difference between prebiotics vs probiotics, what do pre and probiotics do, what are some good pre and probiotics food sources, and whether you need a pre or probiotic supplement. Keep reading to learn all about how to keep your gut happy and healthy.

Prebiotics vs probiotics
Pin Me!

What are probiotics?

Probiotics are the live bacteria and yeasts that make up what is known as the “good bacteria” in your digestive system. Our bodies are full of bacteria, most of it in the gut, and they’re necessary for optimal health.

In fact, it’s estimated that one hundred trillion microorganisms (bacteria making up about 1,000 different species represented by some 5,000 distinct bacterial strains), inhabit every healthy bowel.

What does a probiotic do?

what does a probiotic do?
Probiotics are the “good” microorganisms that live in our digestive tracts and are crucial for protecting our health

Probiotics help maintain our body’s balance of good and bad bacteria, and they can also help replace the body’s “good” bacteria when it’s been lost, such as when taking antibiotics.

Probiotics also aid with:

  • Digestion
  • Nutrient absorption
  • Fighting disease-causing bacteria
  • Supporting immune function
  • Producing vitamin K, which helps make blood-clotting proteins
  • Helping manufacture vitamins B12, B6, B5, B3, folate and biotin

Actually, an imbalance in the gut’s microorganism system can contribute to several health conditions, particularly gastrointestinal issues as well as infections and immune dysfunction (1). Which actually makes sense, given that these microorganisms make up more than 75% of the immune system.

Probiotics can seemingly promote gut health (2) via “direct interaction with the gut microbiota, interaction with the mucosal immune system and immune signaling to a variety of organs and systems”. 

The main strains of probiotic bacteria are Lactobacillus and Bifidobacterium. Yeasts such as Saccharomyces boulardii are also considered probiotics .

What are prebiotics?

Prebiotics are actually food for probiotics. They’re are a type of fiber that the human body cannot digest, but that bacteria can use as fuel to grow and function properly.

When gut bacteria use the prebiotics, this process produces (3) “short-chain fatty acids that are released into blood circulation, consequently, affecting not only the gastrointestinal tracts but also other distant organs”.

Thus, even though prebiotics are used in the digestive system, their by-products can benefit the central nervous system, the immune system, and the cardiovascular system, for example.

The following criteria are used to classify a compound as a prebiotic (4):

  • It should be resistant to the acidic pH of stomach
  • Cannot be hydrolyzed by mammalian enzymes
  • Should not be absorbed in the digestive tract
  • Can be fermented by intestinal microbiota
  • The growth and/or activity of the intestinal bacteria can be selectively stimulated by this compound and this process improves host’s health

The most common prebiotics are:

  • Fructo-oligosaccharides (FOS): Found naturally in plants such as onion, chicory, garlic, asparagus, banana, artichoke, among many others. Inulin is a common FOS.
  • Galacto-oligosaccharides (GOS): Foods such as dairy products, beans and legumes, and certain root vegetables are sources of GOS.
  • Resistant starch: This type of carbohydrate, as its name implies, is resistant to digestion, and functions like soluble, fermentable fiber. It feeds the friendly bacteria in your intestine, and has a positive effect on the type of bacteria as well as their number. Resistant starch is commonly found in whole grains, seeds and legumes.

What does a prebiotic do?

As we saw in the criterion factors above, prebiotics are able to modify the environment in the gut. For example, when prebiotics are fermented, this results in acid products, which decrease the gut pH.

It has been shown that one unit alteration in the gut pH (5) from 6.5 to 5.5 can contribute to a change in the composition and population of the gut microbiota. This change in gut pH can also inhibit the growth of certain harmful strains of bacteria.

Sometimes, a by-product of a prebiotic’s fermentation results in “food” for another microorganism. This process is known as cross-feeding.

For example, a particular bacteria can degrade resistant starches, and several other species of bacteria can use the fermentation products of this reaction as food. At the same time, some products may help prevent the growth harmful species.

The effects of these changes in the digestive tract can also protect us against certain types of cancer, vascular diseases, and even mental disorders, as we’ll see later on.

Prebiotics are defined as “a nondigestible compound that, through its metabolization by microorganisms in the gut, modulates composition and/or activity of the gut microbiota, thus conferring a beneficial physiologic effect on the host” (6)

How do prebiotics and probiotics interact?

As we’ve just seen, prebiotics serve as food for probiotics, and probiotics need access to prebiotics in order to work effectively.

Essentially, prebiotics and probiotics work together synergistically. In other words, prebiotics are the meals probiotics eat, which results in improved digestive health.

Products that combine these together are called synbiotics. For example, adding bananas to your yogurt smoothie, is a delicious way to take care of your gut health, since both components are present.

Thus, incorporating health-promoting functional foods, such as those containing prebiotics and probiotics, can help to create a healthier you.

Benefits of prebiotics vs probiotics

As you can already deduct, it’s not a question of prebiotics vs probiotics; both are crucial to keeping your gut happy and healthy. Both components can help maintain good health and protect against diseases.

And, since most of the products of prebiotic fermentation are molecules are small enough to diffuse through the gut and enter blood circulation (7), prebiotics “not only have protective effects on the gastrointestinal system but also on other parts of the body, such as the central nervous system, immune system, and cardiovascular system”. Let’s check it out.

Prebiotics vs probiotics and digestive health

It appears that the symbiotic relationship between prebiotics and probiotics can help with the treatment and management of:

  • Crohn’s Disease and Irritable Bowel Syndrome: It has been reported that in both IBS and Crohn’s disease, beneficial bacteria may be reduced in the digestive tract. According to certain research studies, intake of FOS (8) and GOS (9) has suggested improvements in symptoms of IBS.
  • Colorectal Cancer: According to this paper (10), “It has been demonstrated that prebiotics fermentation products, such as butyrate, could have protective effects against the risk of colorectal cancer, as well as its progression, via inducing apoptosis [the death of cells–in this case, cancer cells]. In addition, several clinical trials (11) have demonstrated that symbiotic therapy…could reduce the risk of colorectal cancer by reducing the proliferation rate in colorectal, inducing colonic cells necrosis [cell injury which results in death], which leads to improving the integrity and function of epithelial barrier”.

Probiotics vs prebiotics and the immune system

Pro- and prebiotics can improve immune function by increasing the population of protective microorganisms. Animal and human studies have shown that prebiotics can decrease the population of harmful bacteria by the “good bacteria” Lactobacilli and Bifidobacteria.

Prebiotics can also induce the expression of immunity molecules, especially cytokines (small proteins important in cell signaling ). Prebiotics also help:

  • Improve antibody responses toward viral vaccines
  • Reduce the side effects of viral vaccines
  • Improve the function of natural killer cells
  • Reduce the risk of some immune diseases in infants, such as atopic dermatitis

Probiotics vs prebiotics and the nervous system

The gut microbiome can influence the gut-brain axis (the connection between the digestive and nervous systems), which can alter minds and behaviors through the central nervous system (12). Probiotics may directly alter chemicals in the nervous system, such as:

  • γ-aminobutyric acid (GABA): A neurotransmitter that blocks certain brain signals and decreases activity in your nervous system.
  • Serotonin: Another neurotransmitter that’s responsible for controlling mood, attention, sleep, and pain.
  • Dopamine: A neurotransmitter involved in motor control, motivation, arousal, reinforcement, and reward through signaling cascades.

Likewise, the stress response has been shown to be reduced by probiotics by decreasing corticosteroid levels. And, since probiotics also influence the immune system by limiting inflammation, this in turn can also benefit the endocrine and nervous systems.

An improved gut microbiota also changes the products of fermentation, such as short-chain fatty acids and tryptophan, which can indirectly improve nervous system functions.

Prebiotics and the cardiovascular system

Prebiotics are able to reduce the risk of heart disease by reducing the inflammation through changes in the intestinal barrier and altering the bacterial colonies present as well as the gut associated lymphoid tissue (GALT). They can help:

  • Improve lipid profile
  • Reduce the formation of blood lipids (13) in healthy individuals
  • Decrease LDL (or “bad”) cholesterol levels

Foods with prebiotics and probiotics

As a registered dietitian, I always advise to improve your intake of prebiotics and probiotics through food sources versus supplements. These foods are not only rich in these components, they also provide essential vitamins, minerals, fiber, phytochemicals and other health promoting antioxidants.

Although probiotics are already present in our digestive system, eating foods that contain them can help enhance your gut health by increasing your levels and variety of strains of good bacteria. Likewise, when it comes to prebiotics, the human diet is the chief source of energy for probiotics. 

Probiotics foods

Probiotic food sources
Some common food sources of probiotics

The main types of foods that provide probiotics are fermented foods. Fermentation is the process where microbes convert carbohydrates into alcohols and acids. This method has been used for centuries in many cultures to preserve food and enhance health properties.  Food sources rich in probiotics include:

  • Plain live yogurt (look for the words “live, active culture”)
  • Kefir (or coconut kefir, for a vegan option), a fermented milk drink similar to yogurt
  • Fermented soybean products such as tofu, tempeh, natto and miso
  • Sauerkraut and kimchi, made by fermenting cabbage and other vegetables
  • Kombucha, a slightly fizzy drink made by fermenting black or green tea
  • Kvass, a traditional fermented Slavic and Baltic beverage commonly made from rye bread
  • Fermented pickles, which are not the same as regular, brined pickles (look for brands that have no vinegar and no sugar added)

Prebiotics foods

Food sources high in prebiotics

Prebiotics are found in high fiber food sources such as fruits and vegetables (another reason to eat those veggies!). While eating a wide variety of fruits and vegetables can definitely help keep your gut healthy, here are some of the best food sources of prebiotics to include in your diet:

  • Onions: Onions are rich in inulin (a non-digestible, prebiotic fiber) and Fructo-oligosaccharides (FOS), which can strengthen gut flora, helps with fat breakdown and supports the immune system (14) by increasing nitric oxide production in cells
  • Soybeans: Soybean oligosaccharides (15) may benefit immune function by stimulating the growth and metabolism of protective commensal intestinal bacteria, which are part of the first line of defense in the digestive tract 
  • Asparagus: Due to its high inulin content, asparagus can promote the growth of gut-friendly lactobacilli and bifidobacteria (16)
  • Bananas: High in fiber, bananas (especially green bananas) also provide resistant starch, which acts as a prebiotic
  • Leeks: From the same family as onions and garlic, leeks offer similar health benefits. They’re also high in inulin, which, as this paper (17) investigates, could improve cognitive performance and may be “associated with greater accuracy on a recognition memory task, and improved recall performance”.
  • Whole wheat bread: Wheat bran has been shown to boost healthy Bifidobacteria in the gut, as well as promoting gut microbiota diversity (18)
  • Jerusalem artichokes: Up to 76% of this vegetable’s fiber comes from inulin, making it an excellent prebiotic food source. The fibers in Jerusalem artichokes may help lower (19) “plasma glucose and intestinal pH level, which results in higher calcium bioavailability…has a positive impact on the plasma lipid profile, acts as an immunomodulator, affecting digestive systems’ lymphatic tissue”. 
  • Garlic: Garlic not only promotes the growth of beneficial Bifidobacteria in the gut, it also prevents disease-promoting bacteria (20) from growing, such as Clostridia.
  • Apples:  The main type of fiber in apples is pectin, which increases butyrate, a short-chain fatty acid that feeds the beneficial gut bacteria and decreases the population of harmful bacteria
  • Chicory root: Mostly used as a caffeine free substitute for coffee, chicory root has 47% of fiber that comes from inulin.

Prebiotics and probiotics supplements

OK, so now you may be wondering: “What about all those pre and probiotics supplements that are promoted everywhere with miraculous properties?”. It seems like a good idea to take a supplement that can effortlessly improve your gut health, right? Well, not so fast.

First of all, no standard safety guidelines currently exist regarding the oral administration of probiotics and prebiotics (21) in human cases. Therefore, individual probiotics and prebiotics supplements should be carefully evaluated in order to determine potential adverse reactions.

Second, as this article (22) very well explains it: “Different types of probiotics may have different effects. For example, if a specific kind of Lactobacillus helps prevent an illness, that doesn’t necessarily mean that another kind of Lactobacillus or any of the Bifidobacterium probiotics would do the same thing”.

Finally, research is still ongoing into the relationship of the gut microflora to disease. The health benefits of currently available probiotics and prebiotics have not been conclusively proven.

Probiotic safety

Probiotics are apparently safe to use, particularly in healthy people. However, only a few studies have looked at the safety of probiotics in detail, so there’s a lack of solid information on the frequency and severity of side effects.

In addition, people with severe illnesses or compromised immune systems should consult with a healthcare professional before taking probiotics.

The National Institutes of Health (NIH) states that: “Possible harmful effects of probiotics include infections, production of harmful substances by the probiotic microorganisms, and transfer of antibiotic resistance genes from probiotic microorganisms to other microorganisms in the digestive tract”.

Some probiotic products have been reported to contain microorganisms other than those listed on the label. In some instances, these contaminants may pose serious health risks.

Do you need a probiotic supplement?

As with all things health related, there are no one-size-fits-all recommendations. If you’re considering taking a nutritional supplement, remember to always consult with a healthcare professional. They can help you determine:

  • If you actually need a probiotic supplement
  • Which probiotic do you particularly need
  • Which dosage is right for you
  • How long should you take it for
  • What you can and can’t take it together with

Only take pre or probiotic supplements if prescribed by your doctor.


In short, we’ve learned through this post that it doesn’t come down to prebiotics vs probiotics for improving gut health, since both have a synergistic relationship that can help keep you healthy.

And what better way than to eat your way to better gut health? There is a wide variety of foods you can choose from to improve your digestive health, and combining both probiotics and prebiotics can result in a double whammy of nutrients for your gut.

Don’t know where to start incorporating gut healthy foods into your diet? Try a refreshing smoothie! Sign up for free to the Fad Free Nutrition Blog email list and receive a FREE downloadable recipe book of fruit and vegetable smoothies chock full of prebiotic and probiotic rich foods. What are you waiting for? Your health will thank you!

Free Smoothie ebook

Like what you’re reading? Subscribe to the Fad Free Nutrition email list and stay up to date in all things Intuitive Eating, Gentle Nutrition and Health at Every Size!

* indicates required