Pre- and pro-biotics

Photo by Tim-Oliver Metz on Unsplash

There is an abundance of evidence that our gut microbiota influence many aspects of our biology, including brain function, and this evidence is only likely to get stronger with time. We also know that the gut microbiota are dysbiotic (imbalanced) in many clinical conditions. But, the question that is less clear is this — can we manipulate our gut microbiota to improve our health, reverse or cure certain clinical conditions or protect ourselves from developing those conditions? Unfortunately, while there is much promise, there is little evidence — there are few definitive studies in humans.


This is probably the most straightforward approach — usually by consuming dietary fibre or resistant starches that our resident gut microbiota metabolise. This is a routine part of the diets of people eating whole (real) foods rather than processed ‘food-like substances’ (to quote M. Pollan). While I recommend ketogenic diets, there would be some benefit expected for anyone who moved away from processed food (even fibre-enriched processed food) on any diet. I am not sure there have been definitive studies of this though, as there are many confounds (is it the nutrients in the whole food, and not the fibre, that confers a benefit?).

There is also more to it than fibre. Our gut microbiota can readily metabolise amino acids from dietary protein.


These usually come in capsule (or pill) form, and contain a curated selection of bacteria thought to be beneficial to, or typical of, our resident microbiota. They contain billions of bacteria, mostly lactic acid bacteria (Lactobacillus acidophilus, L. brevis, L. bulgaricus, L. plantarum, and/or L. rhamnosus). Other common probiotics are the Bifidobacteria (B. Bifidum), Streptococcus thermophilus and Enterococcus faecium. Bear in mind, though, that our resident microbiota is measured in trillions, and a probiotic containing billions of microbes will be just adding about 0.1% to that.

Two issues to consider are whether these are delivered in sufficient numbers to make a difference, and whether they form colonies with our resident microbiota or whether they are transient.

It looks like species diversity may be important for a well-functioning gut microbiota, although this is not settled. With many microbial species resident, a certain functional outcome can be achieved in more than one way, giving us resilience. There were thought to be about 1,000 bacterial species in the human gut, however recently it has been suggested that it might be ~30,000. So, is it likely that adding a small number of bacteria from a few species to our resident microbiota will translate into a health benefit? Further, there will be significant probiotic death during transit of the stomach, reducing numbers and further reducing diversity as only the most acid-resistant microbes will survive.

Are probiotics resident or transient? They can be measured in stools, and the general consensus is that they are transient. A healthy gut microbiota would naturally resist foreign microbes or a pill of microbes in an unnatural combination. However, it normally takes 1–2 days for faeces to travel the length of the large intestine, and that gives probiotics the opportunity to interact (for good or bad) with resident microbes. It is the transience of probiotics that makes it necessary to take them daily.

The next consideration is whether probiotics confer a benefit on otherwise healthy individuals. This has not been answered, however there have been studies investigating whether probiotics can alter faecal microbe composition, a first step to potentially modifying health.

A recent review of available randomised control trials (the gold-standard) that addressed this question, concluded that there was insufficient evidence to draw a conclusion one way or the other. The problem was the lack of standardisation across studies. They highlighted these issues: small sample sizes (that’s number of participants by the way, in case you were thinking something else); low resolution-methods for assessing faecal microbiota composition; inter-individual differences in susceptibility to the probiotic; the use of different probiotic strains; variations in dosage; the administration mode; duration of intervention and; variation in the habitual diet of participants.

Likewise for psychological outcomes. A randomised control trial review concluded “Overall, there is very limited evidence for the efficacy of probiotic interventions in psychological outcomes. The evidence base is incomplete and lacks applicability.

What these studies show is that if there is an effect-size of probiotics, it is small and gets lost in the background ’noise’ (e.g. from inter-subject variability). This will mean that there is no detectable average effect across a group, which is what science looks for. It does not mean that there will not be an effect for some individuals. So, science doesn’t rule out trying probiotics for yourself, but it does lower expectations substantially. However, if manufacturers are making health claims for their probiotic, be aware that they are not science-based claims of a high order.

Naturally-fermented foods

There are even more confounds in determining health effects of fermented foods, which include at least as many versions as there are human societies. Ferments may be thought of as another class of probiotics (although probiotic manufacturers might dispute that). Some ferments, such as sauerkraut, are both prebiotic and probiotic (referred to as synbiotic). My comments in the previous paragraph apply to ferments too — are there sufficient numbers of microbes, how well do they survive stomach acids (and small intestine bile), what is their interaction with our resident microbiota and so forth.

It may be thought that because ferments have been nurtured and maintained in so many societies for so long, they must be healthy. Perhaps they are, but it doesn’t follow that it’s because of their microbial inhabitants. This food survived for so many generations and in so many places because it was a way to store food for leaner times. Our forebears were not thinking how good eating this stuff is for their gut microbiota, they were thinking how good it was to have any food at all to eat in winter.

Our skin microbiota

This post has been about gut microbiota, because this is the largest single repository of microbes on our body. But, I don’t want to leave this post without commenting on a curious thing — many of us deliberately nurture our gut microbes (or try to), but we don’t have the same regard for our skin microbiota, even though they perform many of the same roles as those of the gut. Our resident skin microbiota have a key role in keeping our skin intact and healthy, they: communicate with our immune system and are a large reservoir for holding immune memory cells (T-cells); interact with other microbes and with human cells; are involved in wound healing and tissue repair; control inflammation, and; produce defensive anti-microbial molecules. The physical barrier of the skin is actually classified as part of our immune system, and the microbes on it are just as important.

Nevertheless, many of us scrub and shower with soaps and antibiotic washes on a daily basis. We use antiperspirants and deodorants, and rub on skin ’care’ products that may be detrimental to our helpful bacteria. In short, we disrupt our skin microbial colonies regularly, and without care. The irony is that we wash our bodies more than ever, even though our environment is more sanitised than ever.



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