PREBIOTICS 101 “Priming & dining the microbiota on a feast of fibre”

In this article I wanted to expand more into an area of my Functional Medicine (FM) work, and share some pearls of wisdom from almost a decade in FM, and Nutritional Therapy (NT), helping others restore functional wellness.

The average healthy human host carries microbes around with them that are equal to the weight of an average size newborn baby. Seven pounds to be precise which if in a good state of health, and if fed the right fuel, will do all the right things to help protect the body, and keep it functionally healthy. So what do these beneficial bugs like to see on the menu? Well, the simple answer to this question is fermentable fibre.

Allow me to plant a seed in your mind for a second… no pun intended…

Let’s say you want to grow a particular type of flower in your garden and plant the seed or bulb in the soil. For this process to be successful it requires more then just planting a seed in the ground in order to grow. If the conditions aren’t right such as the soil being devoid of key nutrients, or there is insufficient water, or sunlight required to grow, the seed will not produce a healthy flower. The same goes for the microbiome that resides within us all. If it doesn’t receive the right environmental signals & is not fed the right substrates, it won’t produce healthy diverse levels of beneficial flora.

The microbes themselves feast by fermenting various fibres that are present in the foods we eat, and cannot digest hence, why their food is referred to as fermentable fibre. All plant matter tends to contain fermentable fibre, with the only caveat being that they need to be in whole food form, meaning refined carbohydrates just don’t have the same effect I’m afraid. Sadly you are not going to get any fibre from your Pain au Chocolat that you have lined up to break your morning fast, which a substantial number of the worlds population select as their proverbial weapon of choice to go into battle and start their day. Eating a diet rich in whole plant foods such as whole grains, beans, nuts, seeds, vegetables, and fruits are the way to get your fermentable fibre in order to feed the favourable microbes that predominantly reside in the large bowel, or colon as it’s more commonly known.

The RDA recommended for fibre intake is around 30 grams per day, which most people don’t even get in their diet, but how come…?

Well, in most cases fibre is low in the typical diet as It’s not present in the types of foods in which the masses consume on a regular basis. Foods such as fats, oils, eggs, dairy products, meat and fish. When it comes to refined carbohydrates such as  breads, pastas, pancakes, pastries, cookies, and all things made from flour, these tend to contain little to no fibre in them at all.

Compared to traditional and ancestral cultures who used to easily eat, or ate, 50-200 grams of plant fiber per day, most people today hardly consume anywhere near the amount of plant matter in their daily diets. Now that’s not to say that 200g of fibre per day is optimal or the way forward, as too much of anything good can be detrimental in many ways, but getting in sufficient amounts of the right types can be beneficial in supporting functional wellness. Like with everything – the devil is always in the dose. After all, water which is absolutely essential for life can kill you if you drink too much of it at once.

As a general rule of thumb, I like to recommended my patients consume around 15g of fibre per 1000 calories of food eaten from a varied selection of different sources. Obviously, this suggestion is dependant on the context of the patients health situation which must be assessed at the start. Individuals with overgrowth or certain bacteria or pathogens need to avoid certain fibrous foods as bad bacteria also use these as a fuel source.

Some of the athletes who work with me in certain phases of their training where their calorie intake is anywhere up to 5000 calories a day, and consuming higher amounts of animal protein, sometimes require a little more than the RDA which is why I like to base fibre intake on total calories, taking into consideration the types of macronutrients the person is consuming. This is to ensure the fibrous matter assists in moving the additional animal protein through the GI tract for elimination, to nutritionally support vital nutrients lost during training to aid in recovery, to offset the metabolic acidity from the increased stress load, and to support the detoxification of increased metabolic waste – all this in addition to supporting a healthy immune system by-way-of keeping the internal eco-system happy & in-check. More fibre should always be accompanied by more water. Not at the same time, but throughout the day as some fibre absorbs water in the intestinal tract.

Hopefully most of you reading this article have heard of probiotics, but what are PREbiotics…?

Prebiotics are foods and supplements that feed the gut microbes. In addition to the fermentable fibre in all plants, your microbes also feed on polyphenols & sulfur from plants, and on other microbes. Polyphenols are antioxidant phyto (plant) nutrients that are rich in all berries, grape skin, red wine, dark chocolate, nuts, beans, flax seeds, cloves, peppermint, anise, spinach, artichoke, red onion, and cherries. Sulfur is high in foods such as garlic, all types of onions and shallots, and the brassica family of vegetables. Eggs and meat also contain high amounts of sulfur. What animal protein can feed the beneficial bacteria? Yes, even meat can feed microbes. It’s common for individuals with dysbiosis not to tolerate these kinds of foods too well, thinking they are allergic to the foods themselves, when it’s really their internal ecosystem that is imbalanced.

So, how do you properly feed your superhero microbes? Well, eating a diverse array of whole plant foods rich in polyphenols, sulfur, and fermentable fibre is a solid start. In addition to whole-foods, you can take powdered prebiotic fibers, which also aid lower bad cholesterol, bind with toxins and harmful estrogens, and regulate bowel motility for constipation AND loose stools.

The types of fibres & prebiotic foods that an individual can consume that will improve their condition or make matters worse is completely dependent on their current state of health which would need to be comprehensively assessed by a FM Practitioner such as myself in advance. For example, take the trusty banana. A nutrient dense powerhouse that can be amazing if used in the right context & application to feed & support the growth of the microbiome in the large bowel – however, if the person has an infection such as any of the Klebsiella family of bacterium, which based on the literature, and my own clinical experience is a common trigger or mechanism of autoimmunity by way of provoking antibodies the react with joints of spine, and other joints that can lead to rheumatoid arthritis (RA) – then eating bananas will end up making the patients condition worse by encouraging this bacteria to grow in numbers and take a greater foothold in the body. Even foods classed as superfoods, or healthy foods can make a patients condition worse if applied or wrongly recommended in certain circumstances.

When I carry out the initial comprehensive FM assessment with every new patient; which involves a series of highly advanced, evidence-based laboratory testing, we can get specific about the approach, to determine what needs to be fed, if at all, and when; and what doesn’t, or not yet. Probiotics & Prebiotics definitely aren’t for every patient’s condition, or a one-size-fits-all approach. Some areas of consideration are targeting them strains & types of bacteria in specific locations, the types & amounts of Prebiotics, dosing, timing, all need to be carefully considered once the FM assessment has been carried out. As I’ve said many times before – randomly taking anything can make a patient’s condition worse.

A take-home is when you see any of these terms, think fermentable fibre:

• Prebiotic

• Oligosaccharide

• Soluble

• Fructooligosaccharide (FOS)

• Galactooligosaccharide (GOS)

• Polyoligosaccharide

• Inulin

• Mucilage

• Resistant Starch (RS)

Below I have broken down & expanded on a list of Prebiotic’s that I often use in Functional Medicine & Nutritional Therapy practice. I’ve gone into greater detail to add context & offer an understanding around my clinical decisions in a live application with a patient.


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 & supporting a healthy immune system. The goal is to have 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 are all forms of FOS. Inulin and FOS powders are also useful to put in water, mushy foods, & smoothies, etc.

Now FOS are FODMAPS. 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. These feed both good & bad bacteria.


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 can limit the growth of opportunistic bacteria, including E. coli, Klebsiella, Prevotella, Salmonella typhimurium, and Clostridia. Breast milk, lentils, chickpeas, lima, and kidney beans are all forms of GOS. GOS is also supplemented in baby formulas, and is in some prebiotic fibre formulas, such as Galactomimmune. GOS increases SCFA in the colon by increasing beneficial bacteria. GOS is not a FODMAP.


These are polysaccharide-protein molecules which are generally well tolerated by most which feed lactobacillus and bifidus, and increase short chain fatty acids (SCFA) in the colon, especially butyrate and propionate. These probiotics can be found in carrots, kiwi, radishes, pears, tomatoes, red wine, and the bark of the larch tree. Larch arabinogalactan is used in foods as a thickener, binder, and sweetener.


These are viscous polysaccharides that make up cell walls of certain legumes. Gums are thickening and gelling agents. Over 100 different varieties of legumes contain gum fibres, including guar, xanthan, acacia, tara, carob, and fenugreek, although not all legume sources are edible. Partially hydrolyzed guar gum (PHGG) and acacia powder are both effective supplemental prebiotic fibres. Based on my own clinical experience & which is backed up by the literature – PHGG improves SIBO, IBS, and increases bifidobacteria. Acacia gum can also be used with IBS patients. Even though my philosophy & my approach is strictly Naturopathic using only plant-based/naturally derived products, botanicals, and nutraceuticals, and I don’t prescribe or use pharmaceutical interventions – there’s a well-known study that PHGG improves SIBO outcomes in combination with xifaxan – one of a select number of antibiotics used to treat some individuals with SIBO.


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 binding agent. Pectins are in Chinese medicinal herbs, such as panax ginseng, and may be responsible for their therapeutic effects. 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 fibre 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.


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 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 is insoluble fibre 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.

To wrap up this weeks informative article, I’d like to get you thinking of yourselves as biological farmers of beneficial flora, and the food choices you select to consume are fertiliser for your crop. In order to yield a healthy crop, you must first get the environment and conditions right, and then feed & nurture the crop in order to achieve a healthy harvest.

If you are suffering with poor health, and looking for a well-rounded & experienced Functional Medicine Practitioner that specialises in the all aspects of hormonal, gastrointestinal, metabolic, and immune system restoration in order to help you feel well again, working with you on a 1-2-1 basis, then feel free to book a free 30 minute consultation to see if we are the right fit to go on that journey together.

Thanks for your attention

*Steve Hawes