There’s a lot of buzz recently about the microbiome – the vast assortment of microorganisms (bacteria, fungi, viruses, and more) that live in and on our bodies. Although we have long understood the microbiome’s importance in various areas of health (like the gut), research has recently been exploding, leading us to realize the microbiome is more complex and more important than previously appreciated. 

Accompanying this new knowledge is growing interest in how to influence and leverage the microbiome to support and improve health. Much of the initial focus has been on probiotics – specific strains of bacteria similar to those naturally found in the body – as a way to supplement or augment the existing microbiome, much like giving higher levels of a specific vitamin or mineral to boost its level.

But research now points to other ways to influence the microbiome that are potentially of equal or greater value depending on the health goal being targeted. Perhaps having the most important influence on a healthy microbiome are the substances known as prebiotics. In reality, they all work together.

Prebiotics are often defined as substances that act as food for probiotics or for the microorganisms of the microbiome. Perhaps a more useful analogy is that of a garden. If you think about your body as a garden, then:

  1. The microbiome consists of healthy vegetables.
  2. Probiotics are helpful plants you grow with the vegetables to support their growth (like planting marigolds to keep away pests).
  3. Dysbiotic (unhealthy) organisms are the weeds that sprout up and crowd out the vegetables.
  4. Prebiotics are the nutrient-rich soil and fertilizer you mix into the soil to be sure the vegetables grow big and healthy.

Without good soil, even the best plants will grow weak or not produce because they lack the right food. Similarly, you can take the best and most expensive probiotics in the world and not benefit because you aren’t providing the right nutrition (prebiotics) for them to flourish.

Prebiotics are found naturally throughout the diet, although often in small quantities. Most commonly, they are carbohydrates,1 like fructans (found in onions, asparagus, and artichokes, or as inulin) and oligosaccharides (found in beans, grains, bananas, and some vegetables, as well as in supplements and foods as fructooligosaccharides or FOS).

There are also non-carbohydrate components of some foods, like specific polyphenols and flavones2 that act as prebiotics. Finally, specialized nutrients called bacteriophages3 (microscopic proteins that interact with bacteria in the gut) can act both as prebiotics and as inhibitors of dysbiotic organisms (the weeds in the garden). 

What do I take? Do I need both?

Although probiotics can target specific areas of health like gut health or immune health, many individuals often only take a probiotic to replenish their microbiome after being sick or taking a microbiome-unfriendly medication, or if they are seeking a very targeted health benefit.

Prebiotics more generally allow a healthy microbiome to flourish by providing the specific nutrition that encourages the good organisms to thrive while discouraging the non-beneficial ones. Although this combination is great for supporting better outcomes, prebiotics can also be used alone to simply optimize your natural microbiome, in the same way you take a multi-vitamin to support the general nutrition of your cells.

If you are primarily looking to support the health of your gut and enjoy the many benefits of a well-nourished microbiome, then adding a prebiotic to your health routine is a great place to start. 


  1. Davani-Davari D, Negahdaripour M, Karimzadeh I, et al. Prebiotics: Definition, types, sources, mechanisms, and clinical applications. Foods 2019;8(3):92. 
  2. Cardona F, Andrés-Lacueva C, Tulipani S, et al. Benefits of polyphenols on gut microbiota and implications in human health. J Nutr Biochem 2013;24(8):1415-1422. 
  3. Febvre H, Rao S, Gindin M, et al. PHAGE Study: Effects of supplemental bacteriophage intake on inflammation and gut microbiota in healthy adults. Nutrients 2019;11(3):666.