Prebiotics Resource – Gut Health and Disease

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Prebiotic Resource

Prebiotics are different form of food that escape digestion in the upper digestive tract. They make their way down to the large intestine virtually unchanged and feed certain beneficial bacteria that are part of our gut microbiome.
In this Prebiotic Resource we explore what prebiotics are, how they benefit you and how to use them.

I have had a number of updates in my thinking on prebiotics over the past year of research and experimentation.

In the beginning I took the same opinion of a number of different practitioners and even wrote about prebiotics and their ability to feed pathogenic bacteria in our gut.

Since then I have delved much deeper into the subject and wanted to share my updated thinking on the subject. I will use this Prebiotic Resource to keep my updated thinking and research in one place.

The following Prebiotic Resource will cover what Prebiotics are, their benefits and how to use them.

Defining Prebiotics

‘Prebiotics are nondigestible food ingredients that beneficially affect the host by selectively stimulating the growth and/or activity of one or a limited number of bacterial species already resident in the colon (1)’

While we have come a long way in our understanding their paper is a great place to start.

To act as a prebiotic the substance has to escape digestion in the small intestine, make it to the colon intact and then finally feed specific and beneficial bacteria. Don’t worry we’ll circle back to that shortly.

Types Of Prebiotics

There are a range of different prebiotics that can be used to boost different beneficial bacteria in the gut. Today we will cover the top most popular types of prebiotics.


Here we can find inulin, oligofructose and fructooligosaccharides (also known as FOS). These prebiotics are very similar in structure and range in size.

All are bifidogenic meaning they promote the growth of Bifidobacteria strains of bacteria (2).

Different foods that contain fructans include chicory root (3) as well as wheat, honey, onion, garlic and banana, barley and tomato (4).

Inulin and FOS are the most commonly available prebiotic fructans available on the market.


Lactulose is an underutilised and relatively unknown prebiotic that has shown some impressive results when used in a range of different gut conditions.

It feeds a few beneficial gut microbes including Faecalibacterium prausnitzii and Bifidobacterium spp.

We have explored the use of lactulose to hinder the growth of pathogenic bacteria by feeding beneficial fermenters which produce short chain fatty acids making the colon more acidic.

One fascinating study improved lactose intolerance in a group of people by supplementing galacto-oligosaccharides for 35 days.


GOS are another type oligosaccharide.

They have been added to infant milk formula in an attempt to replace human milk oligosaccharides (HMO) and boost the beneficial bacteria including Bifidobacterium spp. and Lactobacillus spp. (4). In the process these beneficial bacteria multiply.

How Do Prebiotics Work?

A review just recently published on prebiotics summarised their benefits nicely.

Prebiotics can promote health by:

  1. Increasing Bifidobacteria and Lactobacilli
  2. Producing beneficial metabolites
  3. Increasing calcium absorption
  4. Decreasing protein fermentation
  5. Decreasing pathogenic bacteria populations
  6. Decreasing allergy risk
  7. Effects on gut barrier permeability
  8. Improved immune system defence

Those are some pretty impressive claims!

The image below, taken from Dietary modulation of the human colonic microbiota: introducing the concept of prebiotics shows some of the more prevalent harmful and health promoting bacteria found in the human gut

prebiotics and beneficial microbes health and gut health

Prebiotics Decrease Pathogenic Bacteria

This is the key point and something that I think most people are still unclear on.

Looking again at the image above we can see that a shift towards the right hand side, promoted by prebiotics, is beneficial.

I have come across a dozen blog articles and comments from people who are concerned that prebiotics will actually feed their pathogenic bacteria that they may have found on a stool test. While I do think they are right to be concerned I know believe that the answer is more complicated than ‘yes prebiotics feed them’ or ‘no they don’t’

The concept of dysbiosis, or imbalanced gut flora is one worth understanding.

In a previous article we explored the overgrowth of a phylum of bacteria known as Proteobacteria. These pro-inflammatory bugs are normally kept in check by our beneficial bacteria. When they are allowed to overgrow they can cause inflammation and even leaky gut.

Prebiotics can help to decrease overgrowths of opportunistic bacteria in the gut in a number of different ways.

Five potential mechanisms are proposed including

  • The production of short chain fatty acids by the beneficial bacteria that consume prebiotics lowers the colonic pH. Many pathogenic bacteria aren’t tolerant of the more acidic environment and thus can’t thrive
  • Due to the selective feeding there are less sites for pathogens to take hold
  • Many lactic acid bacteria (beneficial bugs) produce inhibitory peptides
  • Competition for nutrients which may be limiting
  • Enhancement of the immune system.

When To Use Prebiotics

I have been contacted by a number of people that have been concerned by the lower than optimal counts of their beneficial bacteria from their stool test.

There are a few important points to mention here.

To really get a reliable snapshot of your gut microbiome you need to be using DNA based technology. Ubiome is a good example of this type of testing. While the CDSA technology is helpful for detecting different bacterial infections their readouts on the beneficial number counts have been shown to be unreliable.

Here is a deep dive article on a recently released gut test here in Australia that can help to provide this much needed information called the Complete Microbiome Map or the GI-Map from Nutripath.

Apart from a faecal microbiota transplant it is very difficult to re-populate a beneficial species of bacteria once they have been killed off.

While probiotics are extremely helpful in a range of different ways they cannot ‘reseed’ your gut. In fact most, if not all, probiotic species are transient. This means that they pass through your gut quite quickly.

If you want your beneficial microbes to thrive you need to feed them.

That is the real beauty of prebiotics. They keep our beneficial microbes happy and well fed so that they can contribute the beneficial effects listed above and keep our health primed.

Prebiotics can be used in a range of different gut conditions

Best Practices For Using Prebiotics

Start low and slow.

This is probably the best advice around for prebiotic use.

In most people the beneficial bacteria will adapt to the new food source and multiply. If you start with a high dose of prebiotic material then you will almost definitely experience flatulence and possibly even stomach pains.

If you do experience bloating or distention then scale back on the prebiotic or cut it out completely. Bloating within the first hour could indicate SIBO (small intestinal bacterial overgrowth), or after the first hour could indicate bacterial overgrowths in the large intestine. Something to consider if you are experiencing significant bloating after meals.

For many different prebiotics the beneficial alterations to the gut microflora happen over the course of 2-3 weeks. As a therapeutic intervention you will need to be on a consistent dose for this period of time.

I think here is also a good place to mention that not all prebiotics suit all people. For me this is the prebiotic FOS. Some people have speculated that this is because it is a quick burning prebiotic that is used up quite quickly when it hits the large intestine. I’m not 100% why but for me FOS and even inulin don’t sit well in my tummy.

On the other had the prebiotic lactulose does wonders for my digestion and really helped to improve my symptoms when I was struggling with Blastocystis hominis and Dientamoeba fragilis infections

Stay Current

As you may have noticed I have quite the interest in prebiotics and gut health. Each month I publish articles based on scientific research and traditional knowledge of herbalism, gut health, prebiotics, probiotics, parasite infections and bacterial imbalances in the gut.

Here you can find the most recent articles discussing the use of prebiotics in a range of gut and non-gut related illnesses.

This is an ongoing exploration into prebiotics. If you have experimented with prebiotics then leave a comment below so others can learn from your experience


  1. Unless I do myself more scientifically non quationable research I think this is a informative article.I love to read.
    Thanks a lot And I appreciate.

  2. Nice post, Good to be here, thanks for sharing this kind of useful stuff. The information was great. I was suffering from gut health issues when I heard about colon hydrotherapy and gathered information from different resources . I would love to read an article on gut health by you. Keep sharing.

  3. Great post, Good to be here. The information was really good, some time ago I was also suffering from gut health issues that I have to go through a colon cleanse. This article is really useful for me. Keep sharing.

  4. Had the same thinking as yourself that prebiotics would feed the bad bugs. Another great article. thank you

  5. Fantastic blog post about gut health! 👏👏 Your article offers a comprehensive and easily understandable overview of the topic. As someone who has personally faced gut problems, I found your tips and insights to be incredibly valuable. Your expertise is evident in every paragraph, and I truly appreciate the consistently professional tone maintained throughout the article. I highly recommend checking out colon hydrotherapyfor anyone seeking solutions to gut issues.

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