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Probiotics are Only Half the Picture: Feed Your Microbiome With Prebiotics

What’s the difference between prebiotics vs. probiotics? What is a probiotic? Read on to find out! 

gut health

This is a guest post from Catherine Clinton, ND of WellFuture.

You have most likely heard a lot about the benefits of a healthy gut microbiome.

This community of microbes that makes up the gut microbiome has a foundational impact on our health. It can either promote health or, if out of balance, it can promote inflammation, mood and behavioral issues, chronic disease and obesity.

Probiotics and Prebiotics 

So how do we get and maintain a healthy balance in our gut microbiome?

Probiotics are strains of bacteria, and sometimes yeasts, that help push the balance in favor of beneficial rather than harmful bacteria in the gut.

RELATED: Getting your probiotics through food & the dangers of soil based probiotics.

Probiotic is probably not a new term to you, but there’s another necessary contributor to gut health. Prebiotics.

What are the best probiotics? I tested them and have the results for you! 

yogurt and blueberries

What are Prebiotics?

Prebiotics is a term used to describe the foods that help feed the gut microbiome.

Resistant starches are an example of prebiotics that ferment into the short-chain fatty acids that feed the cells that line the gut.

There is a wealth of research about the benefits of supplementing your diet with probiotics and there is a wealth of research about the benefits of getting enough prebiotics in your diet.

But which one is more important? 

Benefits of Prebiotics: The Ecosystem of our Gut Microbiome

The gut microbiome is an incredible ecosystem. I love to research and write about the ecosystem of the gut!

Like our ecosystems here on earth, there is no one healthy ecosystem, there are a variety of different healthy species and guilds.

Through our work with the gene sequencing of the gut microbiome, what we first thought was a system of bacteria, we now know is made up of bacteria, viruses, helminths or worms, and fungi/yeasts.

All of these microbes work together influencing our health for the better or the worse in a variety of ways.

Our gut microbiome produces molecules (MPMs) that create a range of effects on us from producing vitamins, short-chain fatty acids or amino acids to bioactive molecules that influence our developmental or regulatory networks and molecules that directly manipulate our cells. (1)


The production of these microbial metabolites depends on our diet and on the composition of our gut microbiota, again, pointing to the importance of probiotics and prebiotics in the diet.

RELATED: The care and feeding of your microbiome.

We need a diverse family of microbiota working together as different guilds to give us all the benefits of a healthy gut microbiome. (2)

Recent research into the diets of children shows that even vastly different strains and taxa of probiotics work together to either exclude each other or work together as guilds to create metabolites, substrates and promote health. (3)

“Here we need to take a step back and understand the ecology of the gut microbiota. What makes some microbes work together and form a guild? What is the relationship between guilds? Are some guilds more important than others?

The microbiome field has long advocated for the application of ecological concepts so that we can understand the gut microbiota as an ecosystem, but only recently, with our study as an example, has microbial ecology been used to interpret dietary effects.

Our data suggest that the availability of resources, for example, energy substrates from the host diet, creates a selective pressure on members of the microbial community; dominance of certain groups of microbes may then modify the environment that then impacts on other members.” (3)

What’s most interesting about this research is that we see bacteria from vastly different taxa working together to metabolize food or produce a metabolite, either co-creating with or co-excluding other species. These clusters or guilds of bacteria work collectively.

We need the entire guild or community to be working together.

In order to maintain these microbial guilds, we must have the fiber or prebiotics for them to thrive. Fiber or prebiotics can be thought of as key ancestral compounds that preserve the gut microbiota ecology. (4)

Are probiotics enough? Don't forget about prebiotics!

With the example of the ecosystem of a forest, if key species are missing from the forest the health of the forest will decline.

Adding back a missing species of wood sorrel to the forest will be helpful, but without the entire ecosystem in place, the health of the forest will still decline.

Much like a forest, if we are missing key microbiota in our gut, we’ll see a decline in health.

The gut microbiome is an amazing ecosystem that interacts intimately with our own ecosystem. Modern life has steadily marched us away from the life we need to have a healthy gut microbiome but, thankfully for us, the solution is waiting at the end of our forks.

Food with Prebiotics 

How can we get prebiotics through diet? There are many foods rich in prebiotic fibers. Some of these include:

Leeks and onions are a good dietary source of prebiotics to feed your gut microbiome.

Note from Katie: 

There are many ways to get both probiotics and prebiotics from your food, but if you do decide to use a supplement here are my recommendations prebiotic supplements.

Some Quality Probiotics

Some of these I’ve used, some I’m planning to use, and some have been recommended by friends and professionals alike. It’s good to remember a few things about probiotics: 1. People should get different colonies of probiotics, so switching brands/strains every so often (6 weeks?) is good practice. 2. What works great for one person’s needs doesn’t always work for another. I’ve personally tried:
  • Just Thrive Probiotics – this one can be taken during antibiotics and not be rendered ineffective, which almost all other probiotics are! It’s the top-recommended probiotic overall by Paleo Mom Sarah Ballantyne. 😮 (Be sure to use the code Katie15 for 15% off; also found on Amazon and from Perfect Supplements where you can use the coupon KS10 for 10% off!)
  • Seed Daily Synbiotic – the new player in the field but recommended by superstars like Chris Kresser for its unique probiotic/prebiotic synergy. Here’s my full review including a number of surprises for my thinking and a 15% off code!
  • Note: If you’re struggling with digestion, especially constipation, or you feel like you really need to populate your gut with healthy probiotics, I would recommend Saccharomyces Boulardii in addition to any other you choose (except any above which include this strain). Saccharomyces Boulardii is research-proven to get through the digestive tract without being killed, which is rare. 
  • Balance One probiotics with a unique time-release formula (use the code KITCHENS15 at either Balance One’s site or even Amazon to save 15% either place! Wow! Use the code at checkout on Amazon btw.)

For Little Ones (we use all of these):

  • Mary Ruth’s liquid probiotic is a liquid probiotic that doesn’t need to be refrigerated and tastes like…nothing! It’s my new favorite for administering to kids! (Use code KCRF15 for 15% off!)
  • WellBelly by WellFuture (9 strains of probiotics in apple and banana carrier – it’s a powder)
  • Buddies in my Belly probiotic powder (2 strains of probiotics + potato starch carrier and prebiotics) or chewable tablets
Recommended by experts I trust:

Probiotic vs Prebiotic

So which is more important? Probiotic or prebiotic?


Your gut microbiome, and by extension your entire body, just can’t function well without a variety of healthy gut bacteria and the food it needs to thrive.

Adding probiotics in the diet can help, but without tending to the overall health of the microbiome with food, water, exercise, and stress relief, a probiotic supplement can only go so far.

What do you do to maintain a healthy microbiome?


  1. Mark N. Read and Andrew J. Holmes. Towards an Integrative Understanding of Diet–Host–Gut Microbiome Interactions. Front. Immunol., 08 May 2017
  2. Larsen, O.F.A., Claassen, E. The mechanistic link between health and gut microbiota diversity. Sci Rep 8, 2183 (2018)
  3. Lam, Y.Y., Zhang, C. & Zhao, L. Causality in dietary interventions—building a case for gut microbiota. Genome Med 10, 62 (2018)
  4. Kassem Makki, Edward C. Deehan, Jens Walter, Fredrik Bäckhed. The Impact of Dietary Fiber on Gut Microbiota in Host Health and Disease. Cell Host Microbe. VOLUME 23, ISSUE 6, P705-715, JUNE 13, 2018.

Dr. Catherine ClintonCatherine Clinton ND is a licensed naturopathic physician with a focus on gut health, autoimmunity and psychoneuroimmunology. Author, speaker, pediatric health advocate, Dr. Catherine Clinton ND practices in Eugene, Oregon.

When in medical school Catherine was diagnosed with an autoimmune disease that affects the gastrointestinal tract, leaving her with a special interest in autoimmune diseases and how the gut microbiome impacts immune and overall health.

With the birth of her own children, Catherine Clinton became passionate about the prevention of these chronic diseases and conditions by addressing the psychoneuroimmune system and gut health of children. She has multiple peer-reviewed medical journal publications as well as guest writing for several publications. Her blog can be found here and you can follow Dr. Catherine Clinton ND on Instagram and Facebook.

Unless otherwise credited, photos are owned by the author or used with a license from Canva or Deposit Photos.

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