Feeding Your Microbiome: A Fiber Primer

Read the related posts All About Your Amazing Microbiome and Your Microbiome: Diversity, Diversity, Diversity!

You have about seven pounds of microbes in your GI tract, and when you feed them the right fuel, they will do all the right things for you. What do they like to eat?

liver cleanse detox

Fermentable fiber for your microbes

Your microbes eat by fermenting various fibers that you cannot digest. Hence, their food is called fermentable fiber. All plants contain fermentable fiber. The caveat is that plants need to be in whole food form, so refined carbohydrates don’t work – you are not going to get fiber from your chocolate croissant, sorry. Eat whole plant foods such as whole grains, beans, nuts, seeds, vegetables, and fruits to get fermentable fiber.

The RDA recommends about 30 grams per day of fiber, which most people don’t get. Why not?

  • Fiber is low in the typical diet. It’s not in fats, oils, eggs, dairy products, meat and fish (except crustacean shells and insects – not the main fare in our diets).
  • There’s no fiber in refined carbohydrates like bread, pancakes, pasta, cookies, and all things made from flour, which is the main type of carbohydrate in the American diet.
  • Our diets are super low in whole plants, compared to traditional and ancestral cultures who easily eat, or ate, 50-200 grams of plant fiber per day!

Feed your superhero microbes with PREbiotics

PREbiotics are foods and supplements that feed your gut microbes. In addition to the fermentable fiber in all plants, your microbes also feed on polypheonols and sulfur from plants,* and on other microbes. We have some knowledge of what substances feed which microbial strains, however the preferred menu of all beneficial gut microbes is still mostly unknown. So, your best bet now is to go with a diversity of PREbiotics.

*Polypheonols are antioxidant phyto (plant) nutrients that are rich in all berries, red wine, dark chocolate, nuts, beans, flax seeds, soy, cloves, peppermint, anise, spinach, artichoke, red onion, and cherries). Sulfur is high in garlic, all onions and shallots, and the brassica family of vegetables. Also, eggs and meat have sulfur. So, even meat can feed microbes.

So, how to properly feed your superhero microbes? Simply eat a diverse array of whole plant foods rich in polypheonols, sulfur, and fermentable fiber!

In addition, you can take powdered prebiotic fibers, which also lower cholesterol, bind with toxins and harmful estrogens, and regulate bowel motility for constipation AND loose stools.

To get highly specific about feeding your microbiome superheroes, you can do Functional Medicine stool and breath tests to determine what you have, and what you don’t have. Afterwards, you can gear your fermentable fiber protocol towards adjusting your individual microbiome. This is useful if you discover “bad” microbial colonies to reduce, or “good” colonies to build.

A fiber primer

If this is too much detail, simply cut to the take-home points at the end.

When you see any of these terms, think fermentable fiber:

  • Prebiotic
  • Oligosaccharide
  • Soluble
  • Fructooligosaccharide (FOS)
  • Galactooligosaccharide (GOS)
  • Polyoligosaccharide
  • Inulin
  • Mucilage
  • Resistant Starch

Fructans: Inulin and fructo-oligosaccharides (FOS)

Fructans have strong PREbiotic effects. They increase superhero bifidobacteria, which increases the short-chain fatty acid (SCFA) butyrate – a byproduct of fermentation in the colon. Butyrate does all sorts of good things for you, including reducing inflammation. You want lots of bifidobacteria and butyrate!

Artichokes, asparagus, dandelion leaves and roots, chicory roots, sunchoke or Jerusalem artichokes, chicory or dandelion beverages, onions, leeks, garlic, chives, and cactus.

Inulin and FOS powders to put in water, mushy foods, smoothies, etc.

These are FODMAPS and many people with SIBO (small intestine bacterial overgrowth) and IBS (irritable bowel syndrome) cannot tolerate FODMAPS. You may find you can tolerate a small amount, or some of these foods, but not all.

Galacto-oligosaccharides (GOS)

This combination of lactose and glucose is in breast milk. Baby formulas have added GOS, from hydrolyzed cow’s milk. GOS increase lactobacillus and bifidobacteria, * * and limit the growth of opportunistic bacteria, including E. coli, Klebsiella, Prevotella, Salmonella typhimurium, and Clostridia. * *

Breast milk, lentils, chickpeas, lima, and kidney beans.

GOS is supplemented in baby formulas, and is in some prebiotic fiber formulas, such as Galactomimmune.

GOS increases SCFA in the colon by increasing beneficial bacteria. GOS is not a FODMAP.


These are polysaccharide-protein molecules that feed lactobacillus and bifidus, and increase short chain fatty acids (SCFA) in the colon, especially butyrate and propionate. *

Carrots, kiwi, radishes, pears, tomatoes, red wine, and the bark of the larch tree. Larch arabinogalactan is in foods as a thickener, binder, and sweetener.

Powder that tastes slightly sweet.

Increases lactobacillus and bifidobacteria, and is very well tolerated.

Galactomannons (gums)

These are viscous polysaccharides that make up cell walls of certain legumes. Gums are thickening and gelling agents.

Over 100 varieties of legumes contain gum fibers, including guar, xanthan, acacia, tara, carob, and fenugreek. Not all legume sources are edible.

Partially hydrolyzed guar gum (PHGG) and acacia powder are both promising supplemental prebiotic fibers. Konjac root is another source.

Research shows that PHGG improves SIBO, IBS, and increases bifidobacteria. * * *  Acacia gum has been shown to improve IBS. * There’s a well-known study that PHGG improves SIBO outcomes in combination with xifaxan. *


Beta-glucans are closely related to gums and are also soluble (a minority are insoluble), viscous, and fermentable.

Some grains (mainly oats and barley, but also rye, triticale, sorghum, maize, and wheat), yeast and mushrooms (shiitake and maitake) and some types of seaweed like algae. Some microbes also make beta-glucans.

Available as a concentrated powder, often mixed with other prebiotic fibers.

Helps superhero microbes attach to your intestinal lining, including lactobacillus plantarum. * *


These diverse and complex polysaccharides are highly fermentable. They are found in citrus fruit peels and apple pomace. The food industries use pectins as gelling substances in jam, and as food thickeners. Pectin is in industrial yogurt, cakes, ketchup, and fruit jelly.

Present in all plants but the content and composition varies. 60 – 70 % of the fiber in citrus fruits is pectin. Apple, grapefruit, orange and apricot have high levels. Also, other sources include banana, beets, cabbage, and carrots.

Common in powder formulas, because of its strong prebiotic effect. Modified citrus pectin (MCP) is as a detoxification

Increases bifidobacteria and Eubacterium rectale numbers with a subsequent increase in butyrate. * It’s very well tolerated.


Mucilages are similar to gums, since they are soluble and viscous, form a thick gluey substance, and nearly all plants (and some microorganisms) produce them. They are soluble but not highly fermentable, unlike gums which are very fermentable.

Concentrated in cacti and other succulents (like aloe), many types of seaweed (like agar agar and algae), and seeds (flax, chia and psyllium).

This type of fiber is not highly fermentable, and is used primarily for other health purposes.

Flax is shown to increase microbial diversity, and aloe vera increases SCFA. Swelling occurs when these mucilages absorb water, so they can improve constipation for some people, and cause more bloating for others, especially if they push against hard stool in the colon. The swelling can cause pain. With SIBO, colonic swelling is not a good idea because it can increase bacterial translocation up to the small intestine.

Resistant Starch

This starch is “resistant” because amylase, the enzyme that breaks starch into individual glucose units, doesn’t work on this type of starch. So, in theory that resistant starch doesn’t feed bacteria until it reaches the colon. Resistant starch is insoluble yet highly fermentable in your large intestine.

Green bananas, green plantains, potatoes, tiger nuts (an ancient nut) and legumes are all sources of resistant starch (particularly when eaten raw). Also, cooked and then cooled white potatoes and white rice are good sources (think sushi and potato salad).

Resistant starch powders have become popular in recent years. These include potato starch and plantain flour, among others.

Resistant starch, by definition, is resistant to fermentation in the small intestine and therefore reaches the large intestine where it can be fermented.

Chitin and Chitosan (COS)

Chitin is insoluble fiber and very weakly fermentable. It’s found in the exoskeletons of insects, the shells of crustaceans, and cell walls of algae and fungi. Chitin-Glucan, from mushrooms, raises Clostridial Cluster XIVa gut bacteria Roseburia, associated with being lean.

Chitosan is also found naturally in the cell walls of fungi. Also, it is produced  from chemically treated chitin. Chitosan Oligosaccharides (COS) grow a greater variety of lactobacillus and bifidobacteria strains than FOS! However, chitosan needs an acidic environment to be soluble (like your large intestine). Therefore, it’s NOT soluble in alkaline environments, such as your small intestine. Nowadays, you can get probiotic strains with chitosan coatings, to help the probiotics reach your large intestine!

These are in soft insect skeletons and soft crustacean shells like shrimp, and in fungi and mushrooms.

Chitosan is widely found as a prebiotic supplement.

Both show promising results as prebiotics. In our culture, these are in supplements more than in foods.

Take Home Points

Eat from each of these categories to rock your microbiome diversity:

  • Lots of varied plants in whole (unrefined) forms.
  • Artichokes, asparagus, dandelion leaves and roots, jicama, sunchoke or Jerusalem artichokes, onions, leeks, garlic, chives, and chicory root beverages.
  • Lentils, chickpeas, lima beans, and kidney beans.
  • Carrots, kiwi, radishes, pears, tomatoes, turmeric.
  • Oats, shiitake and maitake mushrooms.
  • Apples, grapefruit, oranges, apricots, bananas, beets, cabbage, and carrots.
  • Green (under-ripe) bananas and plantains, green banana or plantain flours, tiger nuts, lentils, cooked and cooled potatoes and white rice.
  • Supplemental powders like arabinogalactan, pectin, GOS, fresh ground flax or chia or hemp hearts, acacia, PHGG (partially hydrolyzed guar gum), FOS, inulin, beta-glucans, and green plantain flour.

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One Comment

  1. Hello Dr. Paris; Feeding Your Microbiome: A Fiber Primer, Is the best introduction to fiber and prebiotics, and one of the most comprehensive overviews of fiber and prebiotics available on the internet.

    I have a few questions.

    Do the yeast and mushroom Beta-Glucans provide the same prebiotic benefit as the oat and barley Beta-Glucans?

    Do the mucilages such as psyllium support the prebiotics and can mucilage supplements be taken at the same time as other prebiotic supplements?

    There are two relatively new (I think) prebiotic supplements available to consumers: XOS, xylooligosaccharides, which are oligomers of a type of sugar, xylose, PreticX® is the best example, AND Bacteriophages, which are submicroscopic bundles of DNA or RNA surrounded by a protein shell that target and break down the unwanted bacteria in the gut, PreforPro® is the best example. Have you had a chance to review and evaluate XOS or Bacteriophages?

    Thanks again for this primer.

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