You're only as healthy as your gut flora

What Are Prebiotics And Why You Should Care

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Garlic, one of my favorite prebiotics


What Are Prebiotics?

Most people know what a probiotic is but what, exactly, is a prebiotic? Prebiotics are non-digestable but fermentable soluble fibers that stimulate the growth of beneficial gut flora or Bifidobacterium (bifidobacteria) in the colon. I like to think of prebiotics as fertilizer for your friendly colonic bacteria.

There are two types of prebiotics. Shorter-chain prebiotics like oligofructose that contain 2-8 links of saccharide per molecule. These are more apt to be fermented by colonic bacteria in the right side of the colon. Longer-chain molecules like inulin feed beneficial gut bacteria on the left side of the colon. A full-spectrum prebiotic like inulinFOS feeds both.

A number of foods contain prebiotic-soluble fibers. Good sources include raw chicory root, raw Jerusalem artichoke, dandelion greens, raw garlic, raw leek and raw onion. While cooking will reduce the availability of these fibers for fermentation, I nevertheless highly recommend you include these foods in your diet. Just be aware that if gas or bloating is an issue for you, the fermentation of these foods by your colonic bacteria can cause a lot of discomfort and potential embarrassment if you know what I mean. And if you suffer from small-intestinal dysbiosis or fructose malabsorption, these foods can add to your discomfort so be careful. If this is a problem for you, cut back on the amount you eat or consider supplementing instead with a prebiotic powder. This allows you more control over the amount of FOS inulin you ingest as you heal your gut.

The following has been briefly covered in my post “The many vital functions of healthy gut flora” but this is a more in-depth coverage of the subject.

Prebiotics and Intestinal Function

Many of us at one time or another have struggled with constipation. For those with IBS or other gut disorders, it can be a constant companion. Inulin-type fructans have been demonstrated to offer relief from this problem.

In one study done in Germany, 35 elderly and hospitalized female patients suffering from constipation had their hospital food supplemented for 19 days either with the milk sugar lactose or the prebiotic inulin to see if there would be any change in bowel movement frequency. Before the study began all patients had only one or two bowel movements per week so we’re talking serious constipation here.

Those treated with lactose had results that varied widely. Some reported more frequent bowel movements while others experienced even worse constipation along with increased gas. In the inulin group, however, 7 out of 10 experienced improvements between weeks eight and nine. Stools were softer and easier to pass. Not only was stool frequency improved but an increase in friendly Bifidobacterium was noted from collected stool samples as well as decreases in potentially pathogenic Enterococci bacteria. (1)

In a randomized, placebo-controlled study conducted in France on elderly volunteers, supplementing with 15 grams of inulin daily for 28 days led to a significant increase in friendly bifidobacteria as well as increased frequency in bowel movements. (2)

In yet another study conducted in an elderly population suffering from constipation, supplementing with both a probiotic and prebiotic resulted in an increase in stool frequency and increased measures of well-being and quality of life. (3)

Another randomized, placebo-controlled study was performed in five French hospitals to study the effects of prebiotics on patients reporting minor bowel disorders. 105 patients were randomized into two groups. One group received 5 grams of prebiotic daily while the other group received a placebo. The study lasted six weeks. On day 43 of the trial, those receiving prebiotics experienced a 43.6% reduction in their symptoms as opposed to an increase of 13.8% in reported symptoms in the placebo group. 75% of the subjects in the treatment group reported improvements in their symptoms as opposed to 53.8% of the placebo group that saw no change. A quality of life questionnaire showed an increase in satisfaction in the prebiotic group and either no change or worsening quality of life scores in the placebo group. (4)

Increases in Bifidobacterium have been seen in infants after supplementing with prebiotics as well as in children, adults and the elderly with or without supplementation with a probiotic. (1 – 9)

Prebiotics and Short-Chain Fatty Acids

Apart from encouraging the growth of friendly colonic gut flora, there are a number of short-chain fatty-acid substances produced during their fermentation. Short-chain fatty acids (SCFA) are organic fatty acids of one to six carbon atoms in length. They are water-soluble and easily absorbed by the body. SCFAs are also found naturally in fruits, vegetables and milk fat.

The three main SCFAs produced are acetate, propionate and butyrate.

Acetate is produced in the colon by bacterial fermentation but quickly departs the colon to be used by the liver, muscles and other tissues throughout the body. In pigs, acetate has been found to stimulate sodium uptake. If this is true for humans, its presence may help to curb recurrent diarrhea. (10)

Propionate is largely used to fuel liver function. Propionate may also reduce hunger in humans by increasing satiety signals. (11)

Butyrate is a major source of energy for the cells lining the colon providing up to 60-70% of the energy requirements for these cells. Simultaneously, it can provide the body with between 7-10% of its energy needs. (12) Butyrate has been shown to prevent carcinogenic activity in rats by inhibiting mammary tumor progression. (13) Finally, it has been proposed that the inability of utilizing butyrate properly could be a predisposing factor in ulcerative colitis. (14)

Prebiotics and Conjugated Linoleic Acid

Bifidobacterium was first reported as also producing conjugated linoleic acid (CLA). (15) B. breve was the particular strain most likely to produce this important substance.

CLA is found naturally in the milk and tissue fat of ruminant animals and in the highest concentrations in grass-fed cows. CLA has been shown to have a number of positive physiological activities such as reducing weight gain, and having anti-diabetic, anti-carcinogenic and anti-atherosclerotic properties. (16)

In the pre-diabetic Zucker fatty rat, CLA was shown to normalize glucose levels. (17) CLA has also been shown to regulate the leptin hormone in rats and mice. (18) Leptin is a hormone produced in fat tissue that regulates long-term weight homeostasis.

Finally, CLA has been positively shown to influence calcium and bone metabolism. (19 – 21) Could gut dysbiosis be part of the reason so many suffer from osteopenia and osteoporosis?

Prebiotics and Health

First, I want to cover some animal studies before I discuss studies in humans. As always, keep in mind that these studies may or may not be relevant to us but their results are intriguing nonetheless.

In quails that were purposely infected with various species of Clostridium and E. coli pathogens in order to study the progression of necrotizing enterocolitis, encouraging the growth of bifidobacteria by including prebiotics in their feed prevented the overgrowth of these harmful organisms. (22) (23) Necrotizing enterocolitis is death of intestinal tissue often seen in very sick or premature babies, although it may also afflict the elderly.

In two pig studies, supplementing with prebiotics protected the pigs from colonization with pathogenic bacteria including the cholera toxin. (24) (25)

In mice, supplementing with prebiotics reduced Candida albicans populations and increased survival rates. Moreover, supplementing with a probiotic and prebiotic showed improved intestinal motility, increased intestinal barrier function and decreased pathogenic translocation.  In mice infected with Salmonella and Listeria, supplementation with prebiotics significantly reduced mortality from these infections. (26) (27) Finally, supplementing with inulin either alone or with probiotics has demonstrated an anti-colon cancer effect in mice. Both pre-cancerous lesions and tumors were reduced after supplementing with prebiotics. (28) (29)

Human clinical trials have shown that supplementing with prebiotics can protect against colonization by harmful bacteria. In a study of critically ill patients at risk of sepsis in an intensive care unit, supplementing with oligofructose reduced the number of pathogens sampled from their nasogastric fluid. (30)

In patients suffering from Clostridium difficile diarrhea, prebiotics suppressed further C. difficile colonization and increased Bifidobacterium resulting in less diarrhea and a shorter hospital stay. (31)

In those suffering from ulcerative colitis, bifidobacteria populations are 30-times lower than in healthy controls. In one study, supplementing with both a probiotic and prebiotic for one month resulted in 42-fold increase in bifidobacteria. Decreases in chronic inflammation and regeneration of colonic tissue was also seen. (32) (33) In Crohn’s disease, supplementing with prebiotics also increased bifidobacteria and reduced levels of inflammation. (34)

 Other Health Benefits

Either supplementing with bifidobacteria or encouraging its growth has been shown to increase HDL levels in a small group of women, reduce lactose intolerance, have a modest effect in preventing infectious diarrhea, reduce triglycerides levels, improve glucose control and reduce inflammation and intestinal permeability. (35 -42)


The take home message from all these studies is that fermentable-soluble fibers should be part of a healthy diet. Feed your friendly gut flora so that they in turn can protect and nourish you.


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10 Responses to What Are Prebiotics And Why You Should Care

  • Hi Ray, some people argue that prebiotics, like soluble fiber, will also feed pathogenic bacteria so they should be avoided at first, but apparently that’s not the case?
    And by the way, even though bacteria can process protein they mainly feed on carbs. Parasites can feed on fat. And fungus? Carbs too?

    • Ray Medina says:

      Hi Gonçalo,

      Sorry for the delay in getting back to you. I was traveling and visiting with family today.

      …some people argue that prebiotics, like soluble fiber, will also feed pathogenic bacteria so they should be avoided at first, but apparently that’s not the case?

      Pathogens in the colon can most certainly feed on soluble fiber but it’s an issue of who is more adapted to utilize them: your bifidobacteria or the pathogens. From the results of numerous studies in both rodents and humans, soluble fiber leads to a blooming of beneficial bifidobacteria. If it were pathogens we wouldn’t see this consistent result. I suppose if you were so devoid of bifidobacteria, pathogens might bloom at first but I suspect this would be short-lived especially in the presence of bifidobacteria probiotic supplementation. I always recommend supplementing both together to help establish bifidobacteria colonies in the colon.

      And by the way, even though bacteria can process protein they mainly feed on carbs. Parasites can feed on fat. And fungus? Carbs too?

      Fungus can feed on carbs and ketones which is why some people on ketogenic diets suffer from yeast infections even when total carbs eaten is low. Yeast also seems to enjoy alcohol as well.


  • I always recommend supplementing both together to help establish bifidobacteria colonies in the colon. – a think that must make it safe

    So, in that case, a ketogenic diet might promote yeast overgrowth in some cases, because there’s less glucose to feed the bacteria and so yeast has more room to grow. I wonder if in the case of an elemental diet, in which all nutrients are ready to be absorbed, any of these categories of infectious organisms (yeast, bacteria, parasites…) have any advantage. Do you have any ideas on that? I’m thinking about doing that to extinguish pathogenic organisms and ingest probiotics and prebiotics to reinoculate the gut (i’m not sure if I should do it simultaneously or sequentially but maybe simultaneously is safer),in addition to EDTA and Ferritin to destroy biofilms and activated Charcoal to remove toxins.

  • Ray Medina says:

    I like the elemental diet because it gives your gut a chance to heal without the added stress of a long fast. However, I would supplement with both prebiotics/probiotics during the regimen to help displace pathogens quicker than would normally be the case. As you suggest, any of the elemental diet nutrients can end up feeding pathogens as well which is why I’m a bit leery of any “diet only” cures for dysbiosis.

    Keep us posted!

  • Thanks for the answer!

    I’m also thinking about adding garlic to the mix for one week, as you described. I think it’s a good option since it is anti-biotic, anti-fungic and anti-parasitic simultaneously. I think because of that it might prevent an overgrowth of one of these pathogens…

    • Ray Medina says:


      As I wrote, make sure it’s organic and crushed or diced. I do not recommend it on an empty stomach, however, or it can make you throw up. Start slow as it’s very powerful stuff.


    • Ray Medina says:

      Hello Jeff,

      Thanks for the link but whenever I see a tagline that reads: “blending science with the natural healing arts” and advertises a “healthy detoxification program”, I instinctively grab my wallet lest it be made lighter by another “alternative” quack preying on the desperate.

      But OK, let’s play along shall we?

      What is FOS and Inulin? 
      Fructo-oligosaccharides (FOS) and inulin are types of fructo-polysaccharides, comprised of -(glucose-fructose)-  subunits. The only difference between FOS and inulin is polymer chain length. Inulin/FOS also goes by the name of Neosugar, Alant Starch, Atlanta Starch, Alantin, Dahlin, Helenin, and Diabetic Sugar. Inulin tastes sweet, cannot be digested by humans, and is soluble (unlike cellulose). 

      True, although not all Inulin/FOS tastes sweet.

      What does Inulin/FOS do? 
      Since Inulin/FOS is indigestible by our bodies, it gets transported to the large intestine where it feeds microbes and promotes fermentation. Inulin/FOS has been dubbed a “prebiotic”, essentially serving as fertilizer for the bacteria in your colon. Certain lactobacillus species of bacteria have been shown to preferentially ferment Inulin/FOS. For this reason, it is being promoted as a supplement to feed the good bacteria in our guts. 

      I don’t know why it’s a prebiotic when in natural food, but when derived from the same natural food with absolutely no additives as ours is, it’s somehow “dubbed” a prebiotic. And no, it does not feed lactobacillus bacteria, it feeds bifidobacteria that most people are woefully lacking. These bifidobacteria use it to grow and outcompete other pathogens in the colon producing short-chain saturated fatty acids that strengthen the gut wall.

      Inulin/FOS feeds only good bacteria, right? Wrong. 
      Manufacturers claim that Inulin/FOS specifically feeds only good bacteria. The reality of the situation is much different. If you examine the scientific literature about Inulin/FOS, you will find that this is untrue. The best example is concerning Klebsiella. Recent studies have shown that Inulin/FOS encourages the growth of Klebsiella, a bacterium implicated in Ankylosing Spondylitis and increased intestinal permeability. Inulin/FOS may indeed promote the growth of lactobacillus bacteria, but what other potentially harmful bacteria are we feeding as well?  Furthermore, we have not even addressed the issue of yeast. Many different species of yeast are able to utilize Inulin/FOS for energy. 

      Historically, microbes have demonstrated the innate ability to adapt to almost any condition and fuel source. If bacteria can adapt to break down industrial solvents in our soil and use them for energy, it would be irresponible to think that they will not adapt to utilize Inulin/FOS, a high energy carbohydrate. There are hundreds of different species of bacteria and several yeast strains living in our GI tracts. Studies have only looked at the effects of Inulin/FOS on a handful of these microbes. 

      I have news for the “leaf lady”. When you have gut dysbiosis, ANYTHING, and I mean ANYTHING you eat or drink can feed pathogens, period. According to this reasoning, we should stop eating entirely lest we feed the wrong bacteria. Klebsiella, like Clostridium and a whole host of other potentially problematic pathogens, are normal constituents of our guts. They will be with us until the day we die. The only hope we have is to have abundant colonies of beneficial bacteria like bifidobacteria to keep them in check and the only way to ensure that is to feed them.

      Oh, and last time I checked, human breast milk also has oligosaccharides so maybe we should encourage mothers to stop breast feeding. You wouldn’t want to encourage Klebsiella now would you?

      Is Inulin/FOS found naturally anywhere? 
      Yes. It is found naturally in asparagus, garlic, Jerusalem Artichokes, chicory root, and others. 

      You see, when it’s found in its natural form (our inulin comes from GMO-free chicory root) it somehow has a magical ability to be good for you because apparently it comes with a dash of “sprites and fairies” that ensure no bad bacteria can utilize it.

      Since Inulin/FOS is found in natural foods it must be okay, right?
      Wrong. Sucrose (table sugar) is naturally found in beets, sugar cane, oranges, and other plants. Humans have perverted this naturally occurring substance into a refined chemical. Sucrose is arguably one of the most unhealthy food additives in human history. We should learn from our experiences with sucrose and apply them to Inulin/FOS. Instead of adding refined, super concentrated Inulin/FOS to your food, eat the foods that naturally contain Inulin/FOS. 

      More anti-scientific rubbish. Sucrose occurs naturally in fruit and honey. While it is far better to get your sugar from these sources than from processed sugar, because at least it’s packaged with other nutrients, the oxidative effects on the intestine and liver are the same if you eat too much of it. Many “health” practitioners wax on and on about the dangers of sugar in processed food but have absolutely no problem recommending ridiculous quantities of organic apple juice when prescribing their “colon cleanse” or other such quackery.

      But what the hell does sugar and Inulin/FOS have to do with each other? Last time I checked, there were no documented studies crediting sugar with increasing beneficial bifidobacteria in the colon. This line of argument, however, is typical of those who question all modern medicine as suspect because it isn’t “natural”. Botulism and aflatoxin are natural. Does that make them good?

      Is it possible to be allergic to Inulin/FOS? 
      Yes. In one documented case, inulin caused an anaphylactic reaction. As the use of Inulin/FOS as an additive in the food industry increases, reports of allergic responses will probably increase. “Inulin may be the culprit behind more food allergies than is currently recognized.” 

      Wow, in one documented case? Really? Bar the door folks! “Leaf Lady” does know we’re talking about soluble fiber here, right?

      Milk, wheat, nuts, corn, shellfish, fish, mushrooms, peppers – can I possibly count the ways people can have a reaction to food? But that also condemns garlic, chicory and Jerusalem Artichokes too or do those natural “sprites and fairies” protect you somehow from possible Inlulin/FOS allergies when the allergen occurs in its natural form?

      What are the recognized side effects of ingesting Inulin/FOS?
      Assuming one is not allergic to Inulin/FOS, the typical side effects will vary depending on one’s level of tolerance. The list of known side effects include: flatulence, bloating,  cramps, abdominal pain, and diarrhea. As Inluin/FOS permeates our food supply, the list of side effects is expected to grow.

      Earth to “Leaf Lady”, these are the exact same side-effects when eating raw garlic, chicory or Jersusalem Artichokes. How do I know? Because I experienced them myself. It is very easy to overeat Inulin/FOS in natural foods when you have absolutely no hope of knowing how much of it you are getting. Variations in soluble fiber between one bulb of garlic to the next or one Jerusalem artichoke to the next can be great. That’s why the safest way for someone with gut dysbiosis to get their Inulin/FOS is in powder form so at least they can control the side effects. And yes, any medicine, whether natural or not, has side effects otherwise it might as well be homeopathy.


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