Doctor Answers: Prebiotics vs Probiotics: What’s the Difference?

The concept of prebiotics was introduced in 1995 by Glenn Gibson and Marcel Roberfroid at Clinical Nutrition Centre in Cambridge, UK. They described prebiotics as a non-digestible food ingredient that beneficially affects the host by stimulating bacteria in the colon. This definition is still relatively unchanged.

Indeed, prebiotics are foods, usually high-fiber foods, our body can’t digest. They act as food for gut flora.

When discussing prebiotics, it’s also helpful to mention resistant starch. Resistant starch is a type of carbohydrate that resists digestion in the small intestine and ferments in the large intestine.

A compound is prebiotic when it’s:

• Resistant to acidic pH in the stomach
• Fermented by intestinal microbiota
• Able to stimulate growth and/or activity of the intestinal bacteria, thereby improving the host’s health

To provide expert insights, we spoke with  Dr. Hamad Shafqat, a clinical nutrition specialist, who shared research-backed guidance on the roles of prebiotics and probiotics. Throughout this article, you’ll find expert-reviewed content and credible resources to help you make informed decisions for your gut health.

Q: How do prebiotics work?

Dr. Hamad answers: As mentioned above, prebiotics are a source of food for bacteria in your gut. They are carbohydrates the body is unable to digest. Prebiotics are soluble fiber. Insoluble fiber, on the other hand, is not fermented by bacteria in the gut.

Prebiotics go down to the lower digestive tract. There, they act like food that helps the healthy bacteria grow.

An important mechanism of action for prebiotic fiber is fermentation in the colon and changes in gut microflora.

Your large intestine is one of the most diversely colonized and metabolically active organs. In fact, up to 1000 different species of bacteria reside in the colon. What makes the colonic environment favorable for bacterial growth is:

• Slow transit time
  
• Readily available nutrients
  
• Favorable pH
  

The most significant advantage of prebiotics is the growth of target healthy gut bacteria. These microorganisms compete species considered dangerous to energy sources. Then, they exclude those species by protecting or promoting the production of favorable fermentation substances with immunomodulatory properties.

It’s also useful to mention bacteria in the gut turn prebiotics into butyrate. Butyrate is a type of short-chain fatty acid. Production of butyrate in the colon would be impossible without prebiotics. Why is this important? It matters because butyric acid can aid the management of Crohn’s disease and irritable bowel disease, among other health benefits.

Q: Which foods are prebiotic?

Dr. Hamad answers: Since prebiotics are fibers present in plant foods such as fruits, vegetables, and legumes, you can obtain enough from your diet.

Some of the best types of prebiotic food to include in your menu:

• Bananas
  
• Oats
  
• Legumes, peas, and beans
  
• Onions
  
• Leeks
  
• Garlic
  
• Dandelion greens
  
• Asparagus
  
• Jerusalem artichokes
  
• Berries
  
• Chicory root
  

Many people also take inulin prebiotic supplements. Make sure to choose a high-quality product, though.

Q: How are prebiotics beneficial?

Dr. Hamad answers: Prebiotics are incredibly beneficial for our health and wellbeing.

Some of their most significant health benefits:

• Decreased prevalence and duration of infectious and antibiotic-associated diarrhea
  
• Improved satiety and weight loss; obesity prevention
  
• Lower risk of cardiovascular disease
  
• Reduced inflammation and symptoms linked with inflammatory bowel disease
  
• Enhanced bioavailability and uptake of minerals such as magnesium, calcium, and iron
  
• Protective effects against colon cancer
  

Q: What are probiotics?

Dr. Hamad answers: Probiotics are live microorganism that exerts health benefits to the host upon digestion. In other words, probiotics are good bacteria that support gut microbiota, improve digestive health, and provide many other health benefits. You can obtain them through diet, but many people also take probiotics in supplement form.

The definition of probiotics was developed in 2001 at the request of the Food and Agriculture Organization of the United Nations. Since then, scientific investigation of these live bacteria has grown substantially.

Also, demand for probiotics-containing foods expanded globally thanks to the incredible health potential of these microorganisms. Without them, you wouldn’t be able to have or get a good microbe in your gut.

Q: How do probiotics work?

Dr. Hamad answers: Probiotics have a wide range of effects on the body. Each strain of these living bacteria may have its unique mechanism of action.

However, probiotics may work by helping the body maintain a healthy community of microorganisms in your GI tract. Or, probiotics may help the body’s community of microorganisms return to a healthy condition after being disturbed.

Additionally, probiotics may produce substances that exhibit favorable effects on gut health. These helpful bacteria also work by influencing the body’s immune response. After all, a great deal of the immune system resides in your gut.

Q: Which foods are probiotic?

 Dr. Hamad answers: It’s entirely possible to obtain enough probiotic bacteria through diet. Some foods are natural sources of good bacteria, such as yogurt and kefir. However, not all yogurts are a good option for you.

To get probiotics, you should opt for high-quality, plain yogurt with live cultures. When in the store next time, you may want to check the label. There you will find the information regarding friendly bacteria present in that specific yogurt. In most cases, it’s a probiotic strain called Bifidobacterium.

Besides yogurt, you may also want to consume fermented foods. These foods contain beneficial bacteria that thrive on the naturally occurring fiber or sugar in the food.

Some of the best examples of probiotic food you may want to include in your diet:

• Sauerkraut
  
• Kombucha tea
  
• Kimchi
  
• Kefir (both dairy and nondairy)
  
• Unpasteurized pickles
  
• Unpasteurized pickled vegetables
  

Why unpasteurized? It’s simple – the process of pasteurization kills these beneficial bacteria.

If you don’t eat fermented foods and other sources of probiotics, you may want to take a dietary probiotic supplement.

However, you should keep in mind not all supplements are equal.

Consult your doctor regarding the best options for you or go for a high-quality product.

Q: How are probiotics important?

Dr. Hamad answers: Probiotics have a significant impact on your health and wellbeing.

Benefits of probiotics:

• Treating antibiotic-resistant diarrhea
  
• Aiding management of irritable bowel syndrome and leaky gut
  
• Improving overall digestive health
  
• Promoting weight loss
  
• Anti-inflammatory properties
  
• Reducing symptoms of anxiety and depression
  
• Lowering total and LDL (bad) cholesterol
  
• Providing modest reductions in blood pressure
  
• Enhanced immune function
  
• Reduced risk of infections
  

Q: What is the difference between prebiotics and probiotics?

Dr. Hamad answers: Throughout this post, you’ve probably noticed subtle differences in probiotics vs prebiotics. They have similar names, and both are crucial for a healthy gut. But, at the same time, they are entirely different.

The difference in probiotics vs prebiotics is this: Probiotics are good gut bacteria that eat prebiotics (a form of dietary fiber). In other words, prebiotics are foods for probiotics in your digestive system. While prebiotics are in fruits, vegetables, and legumes, probiotics are present in fermented food and yogurt.

Q: How is gut bacteria beneficial?

Dr. Hamad answers: Your but contains good and bad bacteria. The balance between the two is necessary for our digestive health and overall wellbeing. It’s not uncommon for different factors that affect the delicate balance between these bacteria. An unhealthy diet is one of those factors.

It is best to consume both probiotics and prebiotics because they are beneficial for good bacteria in the gut. The central role of good bacteria is to protect you from fungi and harmful bacteria.

Evidence shows good bacteria in the gut can strengthen the function of your immune system, relieve symptoms of depression, addresses obesity, and exhibit many other health effects.

Additionally, your gut microbiota can metabolize nutrients from food and certain medications. It served as a protective barrier against intestinal infections and produced vitamin K. This micronutrient helps make various proteins necessary for blood clotting and the building of bones.

Besides healthy microbiome, the gut microbiota is also necessary for preventing or contributing to the treatment of certain health conditions.

For example, some bacterium strains can lessen the severity and frequency of symptoms and decrease inflammatory conditions associated with rheumatoid arthritis.

Additionally, good bacteria could prevent inflammation that leads to a buildup of fatty plaque in the arteries.

For your reference, the buildup of plaque in blood vessels leads to atherosclerosis. Atherosclerosis is a major risk factor for cardiovascular diseases and events such as heart attack and stroke.

Q: How does food affect gut microbiota?

Dr. Hamad answers: The food you eat has a direct influence on gut microbiota. This is yet another reason to adopt healthy eating habits and avoid unhealthy foods. For instance, high-fat and high-sugar diets are harmful to gut bacteria. As a result, this may lead to insulin resistance and other conditions.

Studies also show high-fat diet can enhance gut permeability and inflammation. High-fat diet-induced changes in the gut microbiome have been linked to increased disease risk.

So, if you feed the bad bacteria regularly, you put your health at risk of various complications.

Bad bacteria have the outstanding potential to grow faster and colonize more easily. They become stronger and make you more susceptible to weight gain, weak immune system, cardiovascular diseases, and other problems. But, at the same time, the gut doesn’t have enough good bacteria to fight the “bad guys.”

Your diet is the most important factor in maintaining delicate gut microbiota. For that reason, you need to enrich your menu with both prebiotics and probiotics. Foods rich in these organisms can add more variety to your diet and do wonders for your gut health, digestion, and overall well-being.

Key FAQs on Prebiotics vs Probiotics

Q: Can I take prebiotics and probiotics together?

Dr. Hamad answers: Yes, you can – and in a few instances, you should. Taking prebiotics and probiotics at the same time is known as microbiome therapy, and studies indicate it can boost the survival and effectiveness of the probiotics in the gut. Prebiotics are the fiber that remains undigested and feeds the good gut bacteria (probiotics). The prebiotics are the fuel, and the probiotics are the beneficial workers.

If taken together, they can reinforce each other, synergistically multiplying their effects, boosting gut health, digestion, and even immunity. Timing and pill form are everything. Some supplements in the market combine both of them in one single capsule, while others are best taken separately. If taking them in separate products, just don’t have them with hot drinks or just before antibiotics. Otherwise, yes – together they make a great team.

Q: Do prebiotics or probiotics help with skin conditions like acne or eczema?

Dr. Hamad answers: There’s growing evidence to point to a strong gut-skin connection – and yes, in certain instances, prebiotics and probiotics can assist. Probiotics can potentially soothe inflammation and balance the immune system, which underlies acne and eczema. Specifics such as Lactobacillus rhamnosus and Bifidobacterium breve have yielded promise in early studies.

Prebiotics can also assist with this effect by cultivating those beneficial bacteria. That is not to say, however, that they’re magic pills. Effects can be extremely unpredictable from person to person, strain to strain, and dose to dose. Prebiotics can also help by contributing to a well- supporting a balanced gut environment, which indirectly influences skin health. So, we can say that while more research is needed, for many people, probiotics are a gentle, science-backed addition worth considering.

Q: Is it better to take probiotics in the morning or at night?

Dr. Hamad answers: There’s no hard-and-fast rule, but many experts recommend taking probiotics on an empty stomach first thing in the morning before eating breakfast or at bedtime. It is to provide the best chance for bacteria to make it past stomach acid and into your gut. It is to bypass harsh digestive enzymes that will destroy the probiotic strains.

Some studies suggest that eating before breakfast works slightly better, while others argue bedtime is ideal because digestion slows down, reducing acid exposure. That said, the most important thing is consistency – taking them regularly matters more than the exact hour. If taking it at 7 am every day works for you, do that. If 9 pm feels more natural, stick with that. It’s not about perfection – it’s about giving those little good bacteria a fighting chance, every day.

Q: Can prebiotics or probiotics help with food allergies or intolerances?

Dr. Hamad answers: Yes, intolerances and food allergies can be managed by prebiotics and probiotics because, according to some evidence, probiotics can modulate the immune system and suppress inflammatory responses associated with food allergy, particularly in children. For instance, certain species of Lactobacillus and Bifidobacterium have been shown to be promising in decreasing cow’s milk allergy as well as decreasing eczema related to food sensitivities.

With intolerances (like lactose), the evidence is stronger. Some probiotics contain enzymes that can split lactose and therefore make milk more easily absorbed in mild intolerance. Prebiotics may be beneficial as well, by improving the general gut environment and feeding the right microbes, but they can bloat sensitive individuals. So yes, there’s hope here, but it’s not a replacement for proper diagnosis or advice from an allergist.

Q: Are refrigerated probiotics more effective than shelf-stable ones?

Dr. Hamad answers: Not necessarily. Refrigeration was the default, but with improved technology, numerous shelf-stable probiotics are equally effective, if not more so. Most important is whether the bacteria were still alive when they arrived in your gut — and that’s a function of strain stability, packaging, manufacturing integrity, and how the product was handled before it arrived in your fridge or on-shelf.

Some strains (e.g., Lactobacillus rhamnosus GG or Bacillus coagulans) are extremely stable and require no refrigeration whatsoever. These are slightly more delicate and do benefit from being stored cool, however.

Always check the CFU (colony forming units) count on the expiry date, not the manufacture date, and for clinical-grade or strain-specific labelling. And always check if it requires refrigeration after opening, particularly if purchasing online or in warm climates.

Conclusion 

Prebiotics vs probiotics are not two terms depicting the same thing. As seen in this post, prebiotics are food for probiotics.

You need both for proper gut health, a robust immune system, and better quality of life. Strive to obtain them through diet or take supplements if necessary.

Our Medical Review Process

At Ben’s Natural Health, we prioritize accuracy, transparency, and scientific integrity. All health content is written by qualified medical professionals and undergoes review every 12 to 24 months to ensure it stays current and evidence-based. We cite only peer-reviewed research from reputable medical journals and provide full references and direct links to support our commitment to credibility. Learn more about our medical review process and research standards.

Our Editorial Guidelines

For more than 25 years, Ben’s Natural Health has been a reliable source of science-backed natural health information. Our editorial process is designed to uphold the highest standards of accuracy and trustworthiness. Every article is written by certified experts—doctors, nutritionists, dietitians, fitness professionals, and surgeons—and independently reviewed for accuracy. Contributor bios and credentials are clearly listed at the top of each article to ensure full transparency. Read more about our editorial standards.

Medical Disclaimer

The content on this website is intended for informational and educational purposes only and should not be taken as medical advice, diagnosis, or treatment. While our articles are developed and reviewed by licensed healthcare professionals, they may not reflect your unique health circumstances. Always consult a qualified medical professional with any questions or concerns. Do not delay or avoid seeking professional care based on information you’ve read here. Your use of this content is at your own risk.