Great Gut Blog

Everything You Need To Know About Prebiotics

Posted by Brad Dennis, Ph.D. on

Everything You Need To Know About Prebiotics

It’s no secret that the body is a complicated place. But even when you just focus on small parts of the body, the complexity is still there. And the gut is no different. Regardless of if you’re well-versed in prebiotics or if you’ve heard the term once or twice, they can still be a complicated subject. Prebiotics are the leading-edge of gut health research and although there is still a lot of research to be done, we know a lot about them already. The important thing to understand is that our microbiome is wonderfully diverse with each person having about 150 different species of bacteria that live in different parts of the digestive tract.  A lot of this bacteria is good, some are pathogenic, and each has their own nutritional needs. This is why it is important to know just a little bit more about the different types of prebiotics, where they come from, and how they nourish the bacteria in your gut.

Prebiotics are defined as functional foods that allow the gut to work better by selectively promoting the growth of good bacteria and producing some health benefit. Prebiotics generally aren’t digested in the digestive tract–places like the stomach–making them useful because they can travel through your gut providing much-needed nutrients to the bacteria that live in its different parts. Additionally, some prebiotics can even discourage the growth or effectiveness of bad bacteria. Without the consumption of prebiotics, the good bacteria can’t thrive and the bad bacteria can grow unchecked.

But it’s not as simple as just eating a prebiotic food or taking the first prebiotic supplement you find. Think of your gut as a 30 foot long hollow tube. Some bacteria live at the start of the tube,  (e.g. your mouth), others along the middle (the stomach and small intestines), and the bulk of them towards the end of that tube (your colon). Not only do you need diverse prebiotics to provide for the different nutrient needs of your gut bacteria, you also need prebiotics with different digestibility characteristics to reach different parts of your digestive tract. To further complicate matters, some recent studies have suggested that the same prebiotic can even have different effects based on the source it was derived from. In short, In order for your microbiome to flourish, you need a broad spectrum of prebiotic sources.

The majority of beneficial prebiotics identified so far are oligosaccharides, which are very complex sugars. They are difficult to digest due to their large size, which means that they don’t break down until they’ve reached the gut. In the gut, microbes can break them down and use them as fuel. Now, we will walk through the major prebiotic compounds that are the hot topics in the gut research world. We’ll cover where they come from, where they are typically fermented and the benefits that have been linked to them through research. It should be noted that I am deliberately not including inulin in this list. Inulin was one of the first identified prebiotics and has been studied for a long time. This is probably why so many commercial supplements use it: old, easily accessible research. I generally avoid it since it can often cause flatulence, bloating, or constipation.

Isomaltooligosaccharides (IMO)

  • Sources: These are short-chained carbohydrates generally derived from the starch of rice, tapioca, and other starchy vegetables.  It can also be found in some fermented foods like authentic soy sauce.
  • Where they primarily break down: Small intestines
  • Key good bacteria it nourishes: B. infantis, B. adolescentis, B. breve
  • Key bad bacteria it suppresses: C.perfringens, Salmonella, E.Coli
  • Benefits: Decreased constipation, flatulence, enhanced blood lipid levels, and reduced dental caries

Fructooligosaccharides (FOS)

  • Sources: These are typically medium-chained carbs found in and derived from foods like Jerusalem Artichoke, chicory root, blue agave, and garlic. FOS is the shorter-chained, better tolerated cousin to inulin.
  • Where they primarily break down: Ileum, colon
  • Key good bacteria it nourishes: B. longum, B. infantis, Lactobacillus
  • Key bad bacteria it suppresses: C.perfringens, Clostridium leptum, E.Coli
  • Benefits: Improves dysbiosis, allergy and appetite suppression, improves calcium absorption

Xylooligosaccharides (XOS)

  • Sources: Food-grade XOS is usually produced by applying enzymes to corn cobs.
  • Where they primarily break down: Colon
  • Key good bacteria it nourishes: Bifidobacterium catenulatum, Bifidobacterium bifidum, Bifidobacterium pseudolongum, Bacteroidetes
  • Key bad bacteria it suppresses: None have been identified yet.
  • Benefits: Improved cholesterol, enhance blood lipids levels, and create more butyrate (which is needed for cell health in the colon)

Galactooligosaccharides (GOS)

  • Sources: Cow’s milk, peas. Structurally, GOS is similar to the oligosaccharides found in a human mother’s milk(HMO) that nourish a newborn’s gut microbiota. This makes it a very exciting area of research and has shown a lot of promise.
  • Where they break down: Colon
  • Key good bacteria it nourishes: Bifidobacterium
  • Key bad bacteria it suppresses: C.perfringens
  • Benefits: Increase calcium absorption, reduce infant intestinal and respiratory infections, decrease duration of flu and gastrointestinal distress


  • Sources: A micronutrient found in a wide variety of fruits and vegetables. I like the polyphenols from cocoa as some studies have shown them to have a unique prebiotic effect.
  • Where they break down: Oral cavity, stomach, small intestine
  • Key good bacteria it nourishes: Lactobacillus helveticus, Lactobacillus, Enterococcus
  • Key bad bacteria it suppresses: Streptococcus, Clostridium hystoliticum
  • Benefits: Decreased susceptibility to blood clot formation, decreased inflammation, improved circulation, and possibly aid weight loss


  • Sources: Pectin is the fiber found in many plants and is used as the gelling agent in many foods like jams and jellies. I like kiwi pectin as it’s been shown very high prebiotic activity.
  • Where it breaks down: Colon
  • Key good bacteria it nourishes: Lactobacillus casei, Lactobacillus acidophilus, Bifidobacterium lactis
  • Key bad bacteria it suppresses: Salmonella typhimurium, E. Coli
  • Benefits: Possible role in DNA repair, increases adhesion of good bacteria and decreases adhesion of bad bacteria

Resistant starch

  • Sources: Resistant starch is a particular kind of starch found in or derived from potatoes, bananas and some whole grains. It’s called resistant starch because it resists digestion.
  • Where it breaks down: Colon
  • Key good bacteria it nourishes: Bacteroides, Lactobacilli, Bifidobacteria
  • Key bad bacteria it suppresses: Enterobacteria, Clostridia, E. coli
  • Benefits: Mild laxative, improves quality and frequency of bowel movements, increases insulin resistance, lowers cholesterol levels, and early research also shows it can help decrease obesity-related sleep apnea

Guar fiber (PHGG/Sunfiber)

  • Sources: Guar fiber is an amazing dietary fiber that comes from the guar bean.  
  • Where it breaks down: Colon
  • Key good bacteria it nourishes: B. longum, B.  infantis, B. breve, B.  adolescentis
  • Key bad bacteria it suppresses: Salmonella enteritidis
  • Benefits: Relieves constipation, it’s approved in Canada for treatment of irritable bowel syndrome (IBS), and lowers cholesterol

This list is by no means exhaustive, but as you can see, prebiotics are a very diverse set of functional foods. If you’re looking into prebiotics to improve your gut health, balance your microbiome or just to enhance your diet, you need to be armed with the right knowledge to make the right decisions. I hope this list empowers you to make good choices about how you integrate prebiotics into your life. If you’re interested in learning even more about prebiotics, check out my white paper on prebiotic diversity where most of the research for this article was put together.


Leave a comment

Please note, comments must be approved before they are published