Probiotics Learning Lab Impartially created by the experts at OptiBac
In February earlier this year a very interesting research paper was published which summarised an expert panel discussion held at the International Scientific Association for Probiotics and Prebiotics (ISAPP) Annual Meeting in Washington DC in May 20151. We've summarised their conclusions, as well as framed the larger debate which you all, as CAM practitioners, will no doubt be familiar with.

The ISAPP discussion centred on the definition of a prebiotic. As is common in any field of work, as time progresses bringing with it new knowledge, definitions evolve. The publication is a nice example of this. It describes how the term ‘prebiotic’ in relation to the gut microbiome was coined twenty years ago and since then various organisations have put forward their stance on what a prebiotic actually is. These definitions have included referring to prebiotics as non-digestible carbohydrates, which initiate changes in the composition of the gut microflora, and selectively feed friendly bacteria, and in most cases prebiotics are thought to have a positive overall impact on gut health. Fructooligosaccharides (FOS) is a type of prebiotic, and generally the most commonly found type of prebiotic in supplements in the UK and Ireland.

Artichokes, particularly Jerusalem artichokes, are a naturally high source of prebiotics
Artichokes, particularly Jerusalem artichokes, are naturally rich in prebiotics

What was the aim of the discussion?

The paper does not aim to correct any of these definitions with a final and conclusive new definition of a prebiotic; instead it points out that with recent advances in research bringing better techniques for scientists to identify and measure microorganisms, we can now see more comprehensively the changes that take place in the gut microflora, when prebiotics are eaten, and this means that we should be more open to the possibilities of what a prebiotic is.

It’s suggested that by looking at the research we widen our scope in terms of what a prebiotic is as an ingredient (many more complex carbohydrates used in the food industry are now being shown to have possible prebiotic effects). The effects prebiotics have on the gut microbiome, and the way in which prebiotics actually work, are becoming much wider topics of discussion and debate.

Over the years, we have encountered the question of "Do Fructooligosaccharides (FOS) feed pathogens?". When we use the well accepted and most widely used definition of a prebiotic, (that a probiotic selectively supports the growth of friendly bacteria), by definition, the answer is that no, prebiotics will not feed bad bacteria. In light of this publication however, we are taking a fresh look at that definition, and how this might change the way we respond to the question.

Balance is key

First of all let’s recap that a ‘healthy gut microbiome’ is generally considered to be one which consists of a highly diverse array of bacterial species and strains, with a high ratio of friendly bacteria over pathogenic bacteria. So in a healthy gut there will be some pathogens (bad bacteria), but providing the levels of friendly bacteria outweigh them, this should not compromise good health - in fact this is considered optimal. Balance is the key.

Let’s now look at the negative stories which have circulated in the industry surrounding prebiotics. Generally these reports tend to be along the lines of ‘FOS feeds pathogens’ with not much further explanation of how this statement is backed up by research, or what it could mean in the context of health. It is tempting to assume this must be a 'bad' thing, and unfortunately this haste has led some to turn against FOS.

The origin and interpretation of these statements is unclear, but from what we understand, there are some blog posts online which caution against prebiotics for the reason that they feed the growth of pathogens. One such website – Breaking the Vicious Cycle - claims:

This sentence is not referenced in the text but there is a list of references at the end of the article. Interestingly, most of the references link through to publications describing the positive effects of prebiotics on the gut microflora and health. There is one reference however for a publication published in 2000 in Russian, and at present we only have access to the abstract2. The abstract describes an in-vitro study looking at how inulin influenced the activities of various bacteria including Salmonella, E. coli and Klebsiella. Whereas the activity of Salmonella and E. coli was restricted by the inulin, it appeared to increase for the Klebsiella. A search for other studies investigating the effect of inulin and other prebiotics on pathogens including those in the Enterobacteriaceae family such as Klebsiella, shows that some Enterobacteriaceae including Klebsiella do indeed appear to use prebiotics as a food source to grow3 (NB: This reference is also noted on Wikipedia ‘Fructooligosaccharide’).

However, we must be careful not to jump to conclusions that this is a ‘bad’ thing, or at least not for most individuals in a normal state of health. We started off by recapping the mantra by which many things in life, including the gut microflora, have in common: balance is the key.

A wider look at the research

Actually, a comprehensive look at the research available, and the willingness to understand this phenomenon in its rightful context shows that although prebiotics may feed some ‘pathogens’ this is greatly outweighed by the rate at which they feed friendly bacteria. For example, a study conducted last year took faecal samples from healthy human volunteers, extracted the microbial content, and then analysed how these samples reacted when inulin was added (a negative control and a positive control (cellulose) were also added to separate samples)4. The results demonstrate that inulin caused the Lactobacilli and Bifidobacterium to flourish, and also caused a slight increase in Enterobacteriaceae, the family to which Klebsiella belongs.

However, in the same way that when we look at cholesterol and heart health, we do not fixate on the Total Cholesterol (TC) reading only, but rather view it in the context of the LDL (‘bad’ cholesterol) and HDL (‘good’ cholesterol) - because it gives us a much more accurate picture of what is going on physiologically in the body and the symptoms the individual may experience, as well as predicting the risks they are at* – it is good practise to apply this logic in this situation also.

That is why the authors of this paper analysed the ratio of the Lactobacilli and Bifidobacteria to the Enterobacteria, to give us a better idea of the balance between them. What their results show confirms that we need not be worried about a slight increase in Enterobacteria. This is because their results showed that for every 10 Enterobacteria in a negative control group (no prebiotic) there were 18 Lactobacilli (to 1 decimal place). But when inulin prebiotic was added this jumped to 30 Lactobacilli per 10 Enterobacteria, a 3 to 1 ratio, which is a much healthier balance than without the prebiotic. Similarly, for the Bifidobacteria: Enterobacteria ratio, in the negative control group (no prebiotic); for every 10 Enterobacteria there were 17 Bifidobacteria but when the inulin is added this jumped to 45 Bifidobacteria per 10 Enterobacteria, a 4.5 to 1 ratio, which is again a much healthier ratio. It should be said that this study was carried out in-vitro, and, as always, it’s best to have results confirmed in human clinical trials, but it is extremely illustrative of the argument of balance.

Bifidobacterium is a genus of probiotics thought to most benefit from prebiotics

Over the years numerous studies have confirmed that prebiotics seem to have the predominant effect of increasing levels of friendly bacteria in the gut, particularly Bifidobacteria5,6,7. Given the wide range of individual variability, studies have not confirmed an exact rate of change of different genus and species in the gut when different types and amounts of prebiotics are taken. However the overall consistent outcome from the clinical trials is that prebiotics have a positive impact on the gut microflora. We definitely do not see from the clinical research that levels of pathogens flourish to an unhealthy level, actually in most cases the overall pathogen load decreases.

Why does bad bacteria decrease as a result of prebiotics?

There are a number of theories as to why the pathogen load in the gut decreases as a result of prebiotic supplementation. The main theories are that as friendly bacteria such as Bifidobacteria feed on the prebiotic, acids are produced which lowers the pH in the gut, making it less favourable for the growth of pathogens. Secondly, we know from the in-vitro studies on our products that friendly bacteria produce antibacterial substances to 'ward off' the growth of pathogens in their vicinity. Thirdly is the simple theory that friendly bacteria 'out-compete' pathogens in the gut; attaching to the intestinal wall & pushing them out / leaving them less space physically to multiply. A proliferation in friendly bacteria as a result of prebiotic supplementation will increase these three effects further.

Finally, a theorised reason for the temporary symptoms (bloating & gas) experienced by some individuals, when they first take prebiotics, could be that in these cases there may be a lag time for the friendly bacteria levels to out-grow pathogen levels. Until a few days have passed and the friendly bacteria levels are well established, potentially some pathogens are also able to ferment on the FOS, giving the temporary side effects. Pathogenic bacteria produce more smelly gases (such as sulphur gases) which distend the abdomen much more than the gases produced by friendly bacteria (such as carbon dioxide). Without doubt once this short period of time has passed the FOS supplementation is very likely to give benefits for the individual e.g. better bowel movements, less bloating etc. Studies have not proven this is the case, it is simply a theory at this stage.

For the very small number of individuals who seem to be sensitive to FOS even in the long run, this could be a sign that there is a more complex dysbiosis in the gut and it may be advisable to avoid prebiotics (e.g. take a live cultures supplement without FOS or inulin) and consult with a practitioner such as a nutritionist to do some core work on improving the digestive system holistically. Another explanation is that, as with any supplement or medication, not everything suits everybody, so there may be an odd case where the individual has otherwise healthy gut microbiome, but they are just not suited to prebiotic supplementation.

In summary

It’s important to consider the full context of a particular health situation; we have particularly demonstrated this in the interpretation of cholesterol readings and in the interpretation of the prebiotic – pathogen relationship. Although some studies, mainly in-vitro experiments, have demonstrated that some prebiotics may feed certain pathogens such as Enterobacteriaceae (e.g. Klebsiella), if we attempt to scale up these test tube experiments to relate the real life scenario in an individual’s gut, the clinical trials do not support this as being an issue for human health. Instead the overwhelming evidence from clinical trials is that prebiotics mainly feed the growth of friendly bacteria, which with continued supplementation tend to far outweigh any additional growth of ‘unfriendly microorganisms’. As friendly bacteria flourish with prebiotic supplementation the pH of the gut decreases, which acts as a natural deterrent to the growth of pathogens, and this coupled with the antibacterial effects of the friendly bacteria themselves, helps to keep a healthy balance of friendly to unfriendly microorganisms in the gut.

Enjoy this post? Read more here:
Do probiotics survive to reach the gut alive?
Prebiotics: A closer look at FOS and Inulin

Notes & References:

* Blood test reports for cholesterol markers generally include a TC:HDL ratio, and the lower this ratio (i.e. the higher the HDL) the better. For example if the TC = 5 and the HDL = 1.5 this will give a TC:HDL ratio of 3.3. However if the TC = 6 and the HDL = 1.8 this also gives a ratio of 3.3. Many leading consultants would consider both readings to have similar significance in determining the risk of that individual having a cardiac event. However if we fixate on the TC figure only, many individuals would be unnecessarily worried if they had a TC = 6 compared to a TC = 5.

1. Hutkins (2016) Prebiotics: Why definitions matter. Curr. Opin. Biotechnol; 37: 1-7.
2. Valyshev (2000) The effect of inulin on the biological properties of enterobacteria. Zh Mikrobiol Epidemiol Immunobiol; 1:79-80. (Article in Russian)
3. Hartemink (1997) Growth of Enterobacteria on Fructooligosaccharides. J, Appl. Microbiol; 83, 3: 367-74.
4. Jung (2015) In Vitro Effects of Dietary Inulin on Human Fecal Microbiota and Butyrate Production. J. Microbiol. Biotechnol; 25, 9: 1555-1558.
5.Gibson (1999) Dietary modulation of the human gut microflora using the prebiotics oligofructose and inulin. J. Nutr; 129, (7 Suppl): 1438S-41S.
6. Kolida (2002) Prebiotic effects on inulin and oligofructose. Br J Nutr; 87, Suppl 2: S193-7.
7. Langlands (2004) Prebiotic carbohydrates modify the mucosa associated microflora of the human large bowel. Gut; 53, 11: 1610-6.


  • Keep up the good influence. We need more information about our gut to make decisions. Thanks

  • Probiotics Learning Lab

    Hi Cliff,

    Thank you for your lovely feedback.

    We really appreciate the encouragement and we'll certainly endeavour to keep providing more interesting information about the gut flora, so watch this space!

    Have lovely week.

    With warm wishes,

    Nutritional Advisor


  • Hello,
    I agree with the information given in the article, but one thing isn't completely clear to me.
    Consider this citation: " ...although prebiotics may feed some ‘pathogens’ this is greatly outweighed by the rate at which they feed friendly bacteria. For example, a study conducted last year took faecal samples from HEALTHY human volunteers......"
    There definitely shouldn't be any problems with consuming prebiotics in healthy people, it's quite logical: such people have more or less healthy intestinal flora. But what about people with compromised intestinal flora??? If a person has IBS, for example, or some other serious health issues, will the effect of consuming prebiotics be the same or perhaps bad bacteria will actually proliferate?
    I'll be grateful to you if you can comment on this. Thank you.

  • Probiotics Learning Lab

    Hello Evgeny,

    Thank you for your very good question.

    Before I specifically address your question, I think it’s important to put this whole issue into further context.

    Much of this debate over whether FOS feeds pathogens has been sparked by a very interesting research paper, which summarised an expert panel discussion held at the International Scientific Association for Probiotics and Prebiotics Annual Meeting in Washington DC in May 2015.

    Our own resident microbiologist was actually present at the meeting in Washington and reports that the discussion centred on refining the definition of a prebiotic (because as new evidence emerges, definitions may evolve and change). Over the past 20 years the term ‘prebiotic’ has encompassed a number of interpretations and recognised properties: they are non-digestible carbohydrates, they initiate changes in the composition of the gut microflora, selectively feed friendly bacteria in particular Bifidobacteria, and in many cases that they have an overall positive impact on general health particularly gut health.

    However, in light of new research into FOS and other prebiotics, it does seem to be accepted by scientists that FOS can feed a variety of bacteria which includes both desirable bacteria such as Lactobacillus and Bifidobacterium, and undesirable (pathogens) such as Enterobacteria. Pathogens tend to be opportunistic and adaptable so this is probably no surprise, though it is important to note that selectivity (e.g. which micro-organisms are choosing to metabolise prebiotics) is difficult to define. Scientists still do not know whether there is a limit for the number of species or genus a prebiotic can increase, and it’s difficult to truly measure selectivity due to cross feeding in the gut. So the definition may evolve further as technology evolves and we can truly measure how prebiotics are being fermented in live time both in vitro and in vivo and what health benefits this is having.

    As Jacob explains in the blog, there will always be a diversity of good, bad, and benign bacteria in the typical gut microbiome at any one time, but we cannot deny that there is enough research to date to suggest that FOS and other prebiotics ultimately more specifically stimulate the growth of desirable species. If you take another look at the blog, this effect is illustrated nicely in the last study which looked at the ratio when a prebiotic was administered against a control group. Initially the control group the ratio of Lactobacilli to Enterobacteria was 10:18 but when prebiotic was added the ratio changed to 30:10 which is much more positive. The same happened between the control group and Bifidobacterium where the ratio changed from 10:17 and then when prebiotic was added it improved to 45:10. This study was carried out in vitro (in the laboratory) but there is extensive research suggesting positive effects from prebiotics, including numerous human clinical trials.

    There are a number of theories as to why the number of pathogens decrease proportionally as a result of prebiotic supplementation. Firstly the good bacteria produce acids which lower the pH of the gut and make it harder for pathogens to survive. The friendly bacteria also secrete anti-bacterial substances as part of their own defence system to compete for space in the gut. But primarily the reason that FOS encourages good rather than bad micro-organisms is because good bacteria such as Lactobacilli & Bifidobacteria contain enzymes that are very specific and are able to metabolise different structures of prebiotics; not all FOS’, inulins, GOS’ are the same; their physical structure will vary on how they were made.

    A lot of pathogens simply do not contain these enzymes, so they cannot break down some of these prebiotic structures and this is why they tend to like simple sugars such as glucose, one of the reasons why practitioners will restrict these in the diet when addressing an overgrowth. In fact most micro-organisms will opt for simple sugar as a food source (including the good guys!), but the enzymic potential of beneficial bacteria such as Lactobacilli and Bifidobacteria allows them to more easily utilise other foods sources.
    This raises the question over whether the pathogens are actually utilising the prebiotics or are their numbers slightly increasing due to end products from the good bacteria? In truth, it's extremely difficult to ascertain this in vivo, we just have to measure the results of supplementing with prebiotics which tend to be positive.

    But to more specifically answer your question, we would agree that there may be instances when the active use of prebiotics is not appropriate, for example when following a low-FODMAP diet: in some complex digestive disorders such as SIBO, practitioners may choose to address known overgrowths of pathogens with antibiotics/antimicrobials, use a low-FODMAP diet and address underlying causes before using either probiotics or prebiotics to rebalance the microbiome. So for this reason, we would always advise anyone with chronic and complex digestive issues to seek professional advice to determine what the best approach is for them.

    However, don't forget that we naturally consume prebiotics as part of a healthy diet, in fruits, vegetables, pulses, and whole-grains, and we know that our beneficial bacteria can happily ferment these natural fibres.

    I hope that this information is useful.

    Best wishes,

    Kerry Beeson BSc (Nut. Med) Nutritional Therapist

  • This is an excellent answer, thank you very much!

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