Prebiotics: Details on Building Your Gut

prebiotic to treat bacterial infections klebsiella gut health expert byron herbalist todd mansfield

I have been delving into the world of prebiotics lately and wanted to update my thinking on this subject from the last article.

Previously I was concerned with the idea of feeding potentially pathogenic or less than friendly microorganisms with the use of prebiotic foods and supplements but after looking into the subject more extensively I am less concerned.

The question – Do prebiotics, including fermentable oligosaccharides, galactooligosaccharides and lactulose increase intestinal dysregulation for those who already have dysbiosis is one that I have been thinking on for quite some time. The answer becomes clearer when we actually drill down to what a prebiotic is actually defined as. A number of different researchers have had a go at defining it. One that stands out to me is as follows

“A prebiotic is a non-digestible food ingredient that beneficially affects the host by selectively stimulating the growth and/or activity of one or a limited number of bacteria in the colon, and thus improves host health (2)”

The same paper goes on to list the four key points that a food must have to be considered a prebiotic

  1. It cannot be digestible or absorbed in the small intestine. Basically it must completely escape digestion.
  2. It must very selectively feed a small number of beneficial bacteria that inhabit our large intestine.
  3. As a result of the selective feeding prebiotics shift the colonic flora in a healthy way. Basically feeding the beneficial microflora to the detriment of the pathogenic microbes
  4. As a result of the beneficial shift in the microbiomes residents, consumption of prebiotics are responsible for beneficial for the host

All are valuable points on the subject of prebiotics and gut health. For me the third point is the most important and brings me to a point that I hadn’t fully understood in the last article.

What is the difference between colonic foods and prebiotics.

Prebiotics selectively feed a small number of beneficial microbes in the gut whereas colonic foods feed whatever is there.

A Range of Prebiotics

There are two very popular prebiotics, fructooligosaccharides and galactooligosaccharides, and a third one, lactulose, that is not quite as popular in the research but may be worth exploring for its benefits.

Today we will cover fructooligosaccharides and save both galactooligosaccharides and lactulose for their separate articles.

FOS – Fructooligosaccharides

Fructooligosaccharides have been well researched with a range of different human studies looking into the benefits of use.

One review found in a range of different foods including barley, tomatoes, onion, bananas, brown sugar, rye, garlic and honey fructooligosaccharides promote the growth of Bifidobacterium and actually have an inhibitory effect on Clostridium perfringens, listed as being one of the top causes of food poisoning in the United States (4).

The first review referenced proposed the concept of a lowered pH in the colon, caused by the the growth of Bifidobacteria which then produced an abundance of acetate and lactate, as being one mechanism for the inhibitory effects on genera including Bacteroides and Clostridia.

They continued to speculate on other mechanisms of inhibition of pathogens caused by a boost in the beneficial Bifidobacteria in the colon. Particularly the possibilities that Bifidobacteria might secrete an antimicrobial bacteriocin-like substance.  With this in mind it is interesting to note the decrease in Bacteroides, Clostridia and Fusobacteria that went along with a marked increase in Bifidobacteria seen in a human trial cited by the same review.

While it is true that there are members of Bacteroides, Clostridia and Fusobacteria that are non-pathogenic, and even beneficial, it is worth noting that all three genera contain some seriously problematic and pathogenic species.  

The other two prebiotics that I will be covering in future articles show similar effects in selectively boosting very specific beneficial bacteria in the colon but are different in their own way.

References and Resources

  1. Prebiotics – Gut Boosting Review
  2. Dietary Modulation of the Human Colonic Microbiota Introducing the Concept of Prebiotics
  3. Oligosaccharides: a boon from nature’s desk

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  1. Hey Todd, what about Klebsiella? I did a comprehensive stool test through doctor’s data, and in the results section they say that Klebsiella really likes FOS. What do you do in that situation?

    1. Hi Nick. I’m still not 100% sure where all this klebsiella and FOS came from and I have been searching the literature for it for awhile.

      That said, FOS is not my favourite prebiotic for dysbiosis (I may need to circle back and update this article to include others such as partially hydrolysed guar gum and even galactooligosaccharides, particularly the Bimuno GOS).

      As with most prebiotics the effects of FOS on the human gut (very important here, we can’t be extrapolating in-vitro studies here) is a decrease in the pH of the ecosystem (more here – This is encourages the growth of beneficial bacteria and discourages many of the pathobionts including Klebsiella.

      Often times it takes a number of different bacteria working in synergy to lower the pH of the gut. We are still teasing out the details but certain prebiotics and probiotics can work together to effectively reduce Klebsiella overgrowths. Herbal medicine can be the third arm of the treatment if there is considerable overgrowth!


      1. Hi

        Any update on what prebiotics/ probiotics are best to reduce Klebsiella? And does FOS help or hinder ?


        1. Hi Chris,

          Thanks for the update. I use a lactobacillus reuteri probiotic frequently for klebsiella combined with the prebiotic PHGG. I don’t have any issues with FOS but generally avoid it as it can flare SIBO symptoms which may be co-present. There is an order of therapeutics that we can tweak to each patient. Generally FOS is down the line when the small bowel has been balanced.

          Hope this helps. Apologies on the delay!

  2. Hi Todd

    I have high Klebsiella (GI Ecologix comprehensive stool test) along with other undesirables such as methenobrevibactor.

    I don’t have any obvious symptoms other than constipation and gas.

    I have been taking GOS, Liver support, digestive enzymes and a probiotic supplement. My question is should I be taking an anti microbial, and also what sort of diet should I be following

    Many thanks

  3. Hi Todd,

    I have high Klebsiella although SIBO test was negative and low Bifidobacteria. Symptoms mainly dry skin/some food intolerances (cruciferous and nuts). Im trying to build Bifido whilst reducing Klebsiealla at the same time, and trying to do by taking anti-microbials (cinnamon,andrographis, neem) with probiotics (2hours apart – Lacto/Bifido + PHGG). Is it possible to rebuild the positive bacteria at the same time as trimming the bad?


    1. 100%! This is a great approach and where I see improvements in most patients. I am hoping to put together an article on this trifecta approach (herbs, probiotics and prebiotics).

  4. Hi Todd,

    You mentioned L reuteri as a probiotic you use to treat klebsiella. I used it and it helped my constipation a lot but it also effected histamine issues. Should I continue with it despite histamine issues along with GOS and PHGG?

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