Gut Microbiota in Nutrition And Health

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Sneaky Peek

I shouldn’t be writing this. I have an exam in two weeks. There are 4 children unpacking the food shopping in the kitchen. Whilst playing darts. And arguing. And the Sauerkrautathon octopus continues to engulf me with its tentacles. And yet, here I am. Writing this.

Because this morning, I read a really good review on the role of gut microbes in nutrition and health. I have set out the fundamentals here. 

Nature or Nurture?

Whilst our human genes have some influence over the gut microbes that inhabit us and in what proportions, environmental factors such as diet, drugs, stress and sleep have more influence. How we live affects which microbes are in us and what they are producing (metabolites and by-products). I think about this when I decide what to eat, what to drink, what medication to take, how much sleep I am getting and how much stress I am under (they are playing DARTS). Because these choices influence our microbes and our microbes influence our health.



Gut microbes (bacteria, fungi and viruses) are key to human health – to the functioning of our immune system, to energy metabolism; they affect appetite, they influence neural activity. They influence physical, emotional and mental health. What we can’t yet measure though, is the extent to which these relationships are causal. Are changes in microbial populations and the substances they produce a cause of health issues or a consequence? Scientists are working on this one. The answer is unlikely to be black and white.


Short Chain Fatty Acids (SCFAs)

Gut microbes ferment non-digestible substrates such as dietary fibre and intestinal mucus. In doing so, they release nutrients for us and produce (amongst other things) SCFAs – mainly Acetate, Butyrate and Proprionate. Fibre consumption is beneficial for them and for us.

Acetate is essential for the growth of other bacteria. It is used in cholesterol metabolism and fat production and may be involved in regulating our appetite. 

Butyrate is an energy source for the cells lining our large intestine. It can help kill colon cancer cells and is involved in energy production.

Proprionate is transferred to the liver where it, too, helps to regulate energy production and feelings of fullness.

Higher levels of SCFAs have been correlated with lower levels of obesity and lower levels of insulin resistance (diabetes).



Sugar substitutes such as aspartame and sucralose may be worse for microbes than sugar.

Emulsifiers – found in almost all processed foods – appear to have an adverse effect on microbes.

Restrictive diets such as vegan, raw food, “clean eating”, gluten-free (where not allergic) and low FODMAP (a pet concern of mine) affect our gut microbiome and maybe not in a good way.

Small studies into vegan versus omnivore diet showed that, whilst there may not always be large differences in gut bacterial communities between the groups, there can be striking changes in the microbial by-products produced depending on the diet consumed. But there is vegan (eating pasta and tomato sauce endlessly) and vegan (eating a wide range of plant-based products) and omnivore (Western diet – low fibre, highly processed foods) and omnivore (high proportions of whole grain and plant-based foods with moderate levels of grass fed meat and dairy products). Future research needs to drill down into these distinctions.

Gluten free diets may increase the risk of heart disease – possibly due to reduced consumption of whole grains or due to the increased consumption of other, less healthy foods. Or a combination of both factors maybe?

Low FODMAP diets can lead to profound changes in our gut microbial community and the by-products they produce. We don’t yet know what the consequences of this will be. Low FODMAP diets were never intended to be continued long term.

Our food influences our gut microbial composition and what substances they produce. And our microbial composition influences our response to foods. It is possible our microbes are influencing food choices and appetite. However, a “healthy microbiome”, it appears, may be resilient to extensive change via dietary intervention. So, one hedonistic weekend of microbial abuse should not ruin things if the baseline is healthy.

Useful Infographic from the the Review Paper

Useful Infographic from the the Review Paper

Fibre, in Particular

Fermentable dietary fibre – the stuff our microbes like to digest (also known as microbiota accessible carbohydrate (MACs)) is not broken down by our digestive enzymes. It is not absorbed in our small intestine, it makes its way to our large intestine (where most of our gut microbes live). Which microbes benefit from which MACs depends on the enzymes they can produce to access the food source and how well they can tolerate the conditions generated by the fermentation process (e.g fermentation often creates a more acidic environment). It is a competitive environment.

MACs can influence the make-up of our microbial community, which means that they might, in the future, be a good way of systematically and positively influencing microbial make-up. We have a way to go in terms of research before that is a reality though.

Low fibre intake reduces the production of SCFAs and shifts microbial metabolism to use less favourable nutrients, thereby producing potentially problematic metabolites, which may cause inflammation. The low fibre Western diet is connected to inflammation, which is connected to a wide range of chronic diseases.


Microbial Make-Up

Gut microbes produce other substances that have been connected to our health or lack of it – Indoleproprionic acid helps soak up free radicals, so helps to protect our system from damage. Trimethylamine N-oxide (made by gut microbiota from meat and dairy via the liver) is associated with increased risk of blocked arteries and heart issues. What they are producing impacts our health.

Gut microbes play a role in the development and progression of obesity. Microbes such as Christensenella and Akkermansia are somehow connected to leanness. The amounts of these I have are TINY.

Low microbial diversity may be correlated with long term weight gain – so weight gain may not only be affected by microbial diversity but also the presence or absence of key players such as Christensenella and Akkermansia.  AND dietary fibre intake is a crucial factor in this dynamic. More is better (within reason).



Probiotics (live micro-organisms that, when administered in adequate amounts confer a health benefit on the host) can help to support health. Whilst they may not always establish themselves in our gut permanently, they can influence us directly through our immune system and through the metabolites they produce. Research has shown them to be of benefit in diarrhoea, necrotising enterocolitis, acute respiratory infections, complications with cystic fibrosis and eczema. I think our understanding of the complex ways that probiotics benefit us will grow over time, as will the list of what is defined as probiotic.



Laxatives, Progesterone, TNF- inhibitors (anti-inflammatory drugs) and Rupatadine (antihistamine) in a large study were all shown to impact our gut microbial community. Not in a good way. We also know antibiotics do this, as do proton pump inhibitors for acid reflux. Some medication has a strong influence on gut microbiota composition in some people. Bear this in mind if you have a choice over whether to take medication. And do what you can to support your microbes if you don’t have a choice.

Wondergut Wisdom

The state of our gut microbiome matters. Gut microbial communities vary between people, which means our response to diet, drugs, stress, food additives and other environmental factors will differ. The optimal diet for individuals will, in future, probably be tailored to their gut microbes. But that is going to take scientists time to work out.

In the meantime, fibre consistently appears to benefit the vast majority of us. Fibre is a key nutrient for a healthy microbiome and, for some reason, we have allowed ourselves to be distracted from this knowledge by intense arguments about sugar and fat. Whilst we wait for science to complete the mind-bogglingly intricate jigsaw that is the gut microbiome, we can start eating more whole grains and vegetables and less processed food, safe in the knowledge that this is very likely to be a positive thing to do to support our health.

And we can contemplate the fact that other environmental factors over which we have at least some control - such as drugs/medication, sleep (lack of it) and stress are all in the mix there too. I am off to confiscate the darts.


Spreading straightforward information about the fundamental importance of a healthy gut microbiome.