Building microbial diversity

Healthy state

A healthy gut hosts hundreds of bacterial species. Many perform similar tasks. If one drops out, another takes over, much like in a species-rich forest. This redundancy makes the ecosystem resilient to disturbances such as infections, travel or a change in diet. Experts speak of resilience: after a disturbance, the system returns to its starting state. The more species with overlapping abilities there are, the more likely that is.

When people talk about “diversity”, two things are meant. Species count (richness) tells you how many different species occur. Evenness tells you whether the shares are spread similarly or one species dominates everything. Studies often combine both into a single number, which is only a rough guide to health. What matters is usually less the number itself than whether the important jobs are covered: breaking down fibre, making butyrate Butyrate A short-chain fatty acid and the main energy source for the cells of the colon wall. It strengthens the barrier and dampens inflammation. More in the chapter “Butyrate and other short-chain fatty acids”, converting bile acids Bile acids Substances made by the liver that make fat digestible. About 95 percent are reabsorbed in the last part of the small intestine; gut bacteria transform the rest. More in the chapter “Bile acids: when bile causes diarrhoea”, using mucus in moderation.

The species are closely interwoven. Bifidobacteria, for example, break down fibres such as inulin and release acetate and lactate in the process. Butyrate producers such as Faecalibacterium prausnitzii use these intermediate products to make butyrate, which feeds the gut cells. Experts call this cross-feeding. If one link in the chain drops out, the whole chain suffers.

Diversity is not only about bacteria. The gut also hosts archaea (such as the methane producers), viruses, above all bacteriophages Bacteriophages Viruses that only infect bacteria. In the gut there are probably about as many phages as bacteria, perhaps more, and they help determine which bacteria prevail. More in the chapter “Bacteriophages: the hunters in the gut” that infect bacteria and help regulate their numbers, and fungi. The fungal community in healthy people is low in diversity and dominated by yeasts such as Saccharomyces, Malassezia and Candida; it varies strongly from person to person. Whether these groups matter for overall diversity is still being researched; what is certain is that they interact with the bacteria.

Diversity does not arise equally everywhere. In the stomach and small intestine there are few germs per millilitre, because stomach acid, bile, digestive enzymes and the cleaning wave between meals (the migrating motor complex Migrating motor complex A wave of muscle contractions that sweeps the stomach and small intestine empty about every one and a half to two hours when fasting. Eating interrupts it. More in the chapter “Intermittent fasting and meal timing: 16:8, 5:2 and Ramadan”) keep them small. The great diversity belongs in the large intestine, where contents move slowly and fibre arrives as food. The mucus layer Mucus layer A gel layer of mucins on the gut wall that keeps bacteria at a distance. In the colon, the inner layer is almost free of microbes. More in the chapter “The mucus layer and additives” and the immune system shape it too: secretory IgA IgA (secretory IgA) The antibody of the mucous membranes. It is released into the gut in large amounts, where it holds germs in the mucus without causing inflammation. More in the chapter “IgA: the antibody that keeps the gut clean, and what vitamin A, D and omega-3 have to do with it” and the gut lining help decide who may settle permanently. The diversity in stool is thus the result of an entire digestive route, not just of the bacteria.

Disrupted state: causes and effects

In industrialised countries, the diversity of the gut microbiota Microbiome, gut microbiota The community of all microbes in the gut, mainly bacteria, plus viruses, fungi and archaea. Most live in the colon. is lower than in people living traditional lifestyles. Low-fibre diets, frequent antibiotics and highly processed foods are considered the reasons. That fibre deficiency alone can do a lot is shown by a mouse experiment: on low-fibre food, mice carrying a human gut microbiota lost more and more species over several generations, and these did not return through fibre alone. They were simply missing from the population and had to be reintroduced as well. This cannot be transferred one to one to humans, but it explains why diversity is hard to “feed back”.

After antibiotic treatment, some species do not come back. In three people who took ciprofloxacin twice, diversity dropped markedly within a few days, and in the weeks afterwards it mostly recovered only partly; each person reacted differently. Low diversity goes along with overweight, inflammatory bowel disease Inflammatory bowel disease Umbrella term for Crohn’s disease and ulcerative colitis: long-term, relapsing inflammation of the gut that needs medical treatment. More in the chapter “Immune system and inflammation” and susceptibility to infections, although cause and effect often cannot be clearly separated.

Medicines other than antibiotics matter too: about one in four of the non-antibiotic drugs tested inhibited the growth of at least one gut bacterial species in the lab. Acid blockers let more mouth bacteria reach deeper sections and lowered diversity after only four weeks in one study. Sweeteners, emulsifiers Emulsifiers Additives that mix fat and water, such as carboxymethylcellulose or polysorbate 80. Some damage the mucus layer in studies. More in the chapter “The mucus layer and additives” and mould toxins have their own chapters.

Some tasks are mastered by only a few specialists, such as the conversion of bile acids by certain clostridia. If they are lost, the function is missing, even if the total number of bacteria is back to normal. Diversity is therefore also insurance for rare abilities.

One caveat matters: more diversity is not always better. With slow gut transit, that is firm, infrequent stool, a higher species count is often measured, but fermentation shifts from carbohydrates towards protein, and more protein breakdown products appear in the urine. High diversity with constipation is therefore not a sign of health. A stool test that only reports a diversity number also tells you little. Symptoms, stool rhythm and what you eat are more informative.

Differences between people are large. Children build up their microbiota in the first years of life; older people often lose species, partly because they eat less variety. A year on a Mediterranean diet shifted the microbiota in people aged 65 to 79 towards species linked to less frailty.