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Tuesday 21 January 2020

The Gut

Eat your shitamins

By James Kinross

If you want to live a long life, if you want to treat a disease, if you want to be fitter or stronger or to have a healthier mind, then you have to know something about the gut microbiome. And that’s not just because the microbiome is causally associated with chronic disease. It is because the microbiome is modifiable. We can reverse-engineer it to solve some of our biggest global health problems.

How? The number of options is growing constantly. But you don’t need complicated biotechnology. You could start by changing where you live. For example, migrants from areas with a low incidence of bowel cancer or inflammatory bowel disease will adopt the risk of their new country within one generation – or the other way around. This is in part because they change their gut bugs. If moving is not an option, you could always have a faecal microbiome transplant.

But the simplest way may be to just change your diet – or, more specifically, to de-westernise it. Over recent decades, food in the west (and, increasingly, the rest of the world) has become very clean and very fast. It is served in places such as Subway (42,431 global outlets), McDonald’s (37,855) and Starbucks (30,000). It is homogenous, colorless, bland, fatty, salty and infused with fructose. And it’s wreaked havoc on our microbiomes.

Maintaining a healthy gut microbiome involves common sense and relearning some of the habits of the ancients.

Eat food that is grown sustainably. Buy your food from varied sources, and walk to the shops to get it. Prepare your food yourself with your own hands and share it. Eat five portions of vegetables each day (minimum) and aim for as much fibre as you can, with a target of 50g a day. If you can’t eat wheat, gluten-free is fine. If you want to eat meat, eat more sustainable white meat or fish, and ditch the processed stuff. Stop the fizzy drinks and juices, and cut down your alcohol. If you are going to drink, stick to red wine.

Here’s some more information…

Red meat

One week the Daily Mail says it’s bad, the next that it’s good. Like anything, it is about how much you consume, how you cook it, and what else you consume it with. But because there is so much variation in our gut microbiomes, there is a lot of variation in how meat is metabolised. Red meat contains a lot of carnitine, which is broken down in the gut by the microbiome. Choline is also metabolised the same way. The secondary metabolite of this process, called TMA, is passed to the liver, where it is turned into TMAO and this is the metabolite that causes the damage. It is associated with heart disease, cardiovascular disease, liver disease and bowel cancer. This is why red meat can be bad for you, if you eat it frequently, without any vegetables, and to the exclusion of other types of meat. It doesn’t mean that meat in itself is bad for you; your microbiome can definitely stand up to the occasional sausage. If you like to eat it, carry on, but try to eat less or change at least one portion of red meat a week to white meat or fish. Avoid low quality, processed meat. Jamie Oliver was right about turkey twizzlers.


The available literature suggests that a vegetarian or vegan diet is effective in promoting a diverse ecosystem of beneficial bacteria. Adventists, a group of Protestant Christian churches that trace their origin to the United States in the mid-19th Century, often follow vegetarian diets, and numerous studies show they live longer and have lower risks for many cancers than the general population. It’s not God, it’s the bacteria. Balanced vegetarian diets also provide benefits in preventing and reversing atherosclerosis and they are associated with an overall lower incidence of gastrointestinal and colorectal cancers. The microbiome is definitely playing a role here.


The microbiome also metabolises alcoholic drinks – and it differs depending on your choice of tipple. Dr Caroline Le Roy of King’s College discovered that red wine drinkers have a greater diversity of bacteria living in their guts compared to people who drink beer, cider, white wine or spirits. So, it’s official, drinking red wine is okay. And please don’t take that away from me.


In July 2015, the UK Scientific Advisory Committee on Nutrition (SACN) recommended that the average adult’s fibre intake should be increased from about 24g to 30g a day. That is a lot, considering that there is only about 5g in a bowl of Bran Flakes. But the truth is that, for colonic health, it should probably be nearer 50g a day. This is based on observations by the surgeon Dennis Burkitt, who wrote a 1979 book called Don’t Forget Fibre in your Diet. Burkitt is the godfather of fibre and was the first to note that rural Africans who consume around 50g a day don’t get western diseases of the bowel such as diverticulosis or bowel cancer.

Professor Stephen O’Keefe of Pittsburgh University has since built on Burkitt’s work by investigating the effects of fibre on the microbiome. In one of his tests, African-American men, who have some of the highest rates of colorectal cancer in the world (100/100,000), swapped diets with rural Africans, who have much lower rates (5/100,000). The Americans struggled with the high-fibre, low-fat, low-protein diet they were given every day for two weeks, and the Africans struggled with all that meat.

After just two weeks of dietary change, the results were spectacular. The researchers didn’t observe a wholesale change in the gut microbiome, but what they did see was very dramatic changes in how the different elements of the microbiome work together to metabolise food. The Americans shifted from a gut engine designed to metabolise meat to one that metabolises fibre very quickly. With that came dramatic increases in the sorts of metabolites that these bacteria produce. For example, they observed an increase in the concentrations of faecal short-chain fatty acids (these metabolites are anti-carcinogenic) and reductions in bile salt excretion (which are carcinogenic). This drove down levels of inflammation in the gut, as well as cancer risk as measured in biopsies from the gut. As for the Africans, their bile acid excretion rose by 400 per cent. This is bad.


In 2015, a group from Tufts University estimated that, among all worldwide annual deaths from diabetes and cardiovascular diseases, about 178, 000 were attributable to sugary drink consumption. The fructose syrup in those drinks is also associated with the development of numerous cancers.

Again, the microbiome’s role has not been considered until very recently. Studies involving humanised mice have shown that switching from a low-fat, plant polysaccharide-rich diet to a high-fat, high-sugar diet with lots of fructose – as typically found in a western diet – causes an even more dramatic shift in the structure and function of the gut microbiome. Within a single day, the bacteria within the guts of these animals switch on genes that produce metabolites associated with poor gut health. Fructose also prevents colonisation of beneficial microbes in the gut that may promote gut health.

Weight-loss diets

Losing weight is generally a really healthy and positive thing to do, if you achieve this through sensible dietary change and exercise. But losing weight does not necessarily equate to being healthy if you choose to do it through an extreme intervention. For example, the Atkin’s diet is great for shedding pounds, but it is absolutely terrible for your gut. It is essentially the most pro-inflammatory meal you could have.

Just about every extreme diet is bad for your microbiome in some way and most likely has some deleterious and unintended health consequences that are not detected because these diets are not subjected to detailed analysis or trial. Remember, your gut bacteria work together, and so they need a varied diet to sustain themselves and prevent colonisation by less friendly species. If you are buying powdered shakes off the internet to keep healthy, you should seriously think about what they are doing to your gut. The chances are they are not doing anything good.

Having said this, dietary regimes such as calorie restriction and intermittent fasting also have some science to support them. The mechanisms are complex, but they also enrich bacteria in the gut that are generally important for health, such as Lactobacillus and Bifidobacterium, and reduce phylotypes associated with poor health, such as Helicobacter. Calorie restriction may have an important role to play in longevity and it is probable that part of this effect is mediated by the gut microbiome.

Probiotics and prebiotics

A probiotic is a live bacteria that has a health benefit. It is classified as a food.

Prebiotics are complex sugars that help to fuel microorganisms, and they too must confer a health benefit. If used carefully, they can also deliver results. Tests have shown that prebiotics can increase the relative abundance of lactose-fermenting Bifidobacterium, Faecalibacterium and Lactobacillus – which is a particular boon for those who are deficient in intestinal lactase, the enzyme required for the digestion of lactose, which is about 70 per cent of adults globally.

Taking a probiotic may not make you live longer, but that does not mean that probiotics are worthless. There is good evidence to support their prescription in various cases, including mild to moderate ulcerative colitis, acute diarrhoea and IBS. I use them in a targeted way in my clinical practice.

What should you take? Most probiotics in current use are from the genera Lactobacillus and Bifidobacterium. But Saccharomyces, Bacillus, E. coli, Enterococci and Weissella sub-species are also available. My advice is to buy something with as many strains as you can get and then use it for one month. After this time, it will have colonised your gut and you should notice a benefit. If it doesn’t work, stop and save your money.

Or make your own kefir; it works extremely well. This may not be due to the bacteria themselves, but the sugars and short-chain fatty acids in the fermented milk, or the molecules produced by these bacteria. The problem with many of the artisan fermented products is the type, number and functions of the bacteria within them are so variable because the ingredients and manufacturing practices are also so variable. Basically there is no quality control. So you never really know what you are getting.

This may all sound like common sense. That’s because it is. The gut is very variable between people and the truth is we have no way of knowing at present which important bugs are missing or which ones need to be replaced. So a diet or probiotic that works for one person may not work for another. What is more important is actually what functions are missing or broken.

We are fast approaching an era of personalised nutrition based on computational analysis of your gut. You now know that if anyone promises that they can tailor your diet very accurately based on an exclusive and expensive sequencing analysis of your genome alone, they are lying.

A much more sensible strategy is to target the gut microbiome and link this to wearable sensors or mobile-based AI tools that provide physiological information or data on the content of your food, which can then be integrated into a decision-making tool. This approach is already being trialled in the management of diabetes.

In that future, food will be a medicine prescribed like a drug. And Delia Smith MD will win a Nobel Prize.

Bonus audio: Head over to the Playlist tab in your Tortoise app to listen to a conversation about Food 4.0, the next stage of our dietary evolution, between James Harding and Chris Damman, a Senior Program Officer at the Bill & Melinda Gates Foundation.

All photographs Getty Images

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