Microbiome: diversity is eaten, not bought in capsules

This is one of the rare areas of nutrition where the practical answer is simple, cheap and solidly supported: eat more different plants. Everything else — capsules, courses, detox powders — is secondary, and often sold well above what the evidence allows.

What exactly we are talking about

The gut microbiome is the set of micro-organisms living in your digestive tract, mainly in the colon. They are not passengers: they ferment what your enzymes cannot digest, synthesise certain vitamins, take part in educating the immune system and produce metabolites that circulate throughout the body.

The most studied of those metabolites are the short-chain fatty acids — butyrate, propionate, acetate — produced by fermenting fibre. Butyrate in particular is the preferred fuel of the cells lining the colon. No fermentable fibre, no butyrate: it is the most direct mechanical link between your plate and your intestinal wall.

Diversity rather than quantity

The indicator that comes up most often in the literature is not the number of bacteria, but their diversity. An ecosystem rich in different species is more resilient: it copes better with a course of antibiotics, a bout of gastroenteritis or an abrupt dietary change. Low diversity is found repeatedly in studies of obesity, type 2 diabetes and inflammatory bowel disease.

From that observation came a practical rule popularised by the epidemiologist Tim Spector, from the American Gut project data: people who reported eating thirty different plant species a week had a more diverse microbiome than those eating fewer than ten. This is observational data: it does not prove causation. But the target is concrete, free, risk-free, and consistent with the mechanism.

Not all fibres do the same job

The word “fibre” covers very different molecules, with distinct effects. That is why “eat fibre” is too vague a piece of advice to be useful.

If you have to buy just one: blond psyllium. It is the fibre with the best evidence-to-price-to-tolerance ratio. It regulates stool consistency in both directions — constipation and diarrhoea — and lowers LDL reproducibly across trials. Two euros a week.

Probiotics: what the word hides

A probiotic is defined by its strain, not by its genus. Lactobacillus rhamnosus GG is not interchangeable with another Lactobacillus: they are two different organisms with different effects. Extrapolating from one strain to another makes no more sense than extrapolating from a dog to a wolf.

The direct consequence: a label advertising “20 billion CFU, 10 strains” without saying which ones or what for allows no verification. The CFU count is the most visible and least informative marketing argument in the aisle.

There are nevertheless situations where the data is decent: certain strains documented in preventing antibiotic-associated diarrhoea, others in certain functional bowel disorders. In that case the approach is: identify the indication, find the strain studied for that indication, check it is named on the label, and run a four-week trial.

One last point: probiotics rarely colonise the gut durably. Their effect, where it exists, is generally transient and stops when you stop taking them. They do not install a “new flora”.

Fermented foods: the most interesting lead

A randomised trial run at Stanford and published in Cell in 2021 compared, over ten weeks, a fibre-enriched diet with a diet enriched in fermented foods. The “fermented” group showed an increase in microbial diversity and a fall in several inflammatory markers. The numbers were modest and the duration short: the result needs confirming. But it points the same way as the rest of the field.

In practice: plain yoghurt, kefir, raw sauerkraut, kimchi, miso, aged cheeses. Regularity counts more than quantity — a small daily portion beats a jar on Sunday. Beware of products pasteurised after fermentation: the bacteria in them are no longer alive.

What damages a microbiome

• Antibiotics. Necessary when indicated, but diversity takes weeks to months to rebuild. It is the main reason not to take them for a viral infection.
• An ultra-processed diet low in plants. Little fermentable substrate, so little butyrate.
• Excess alcohol and chronically very low fibre intake.
• Chronic stress and lack of sleep, through the gut-brain axis: the human data is still preliminary on this point, but the direction is consistent.

The protocol, in order of impact

1. Count your plant species over a week. Write them down. Most people discover they run between eight and fifteen.
2. Add a pulse twice a week. It is the highest-return lever: fibre, resistant starch, protein.
3. One portion of fermented food a day.
4. Psyllium, 5 g, once or twice a day, if transit stays irregular despite the diet. Build up gradually, with a large glass of water.
5. A targeted probiotic, only if you have a specific indication, with the strain named. Four weeks, then judge.