Microbiome & gut flora

The gut microbiome consists of some 38 trillion bacteria and interacts with the immune system and metabolism; links with mood, weight and energy are being researched. Imbalances of the gut flora (dysbiosis) are looked at in bloating, constipation, diarrhoea and exhaustion; studies have also linked them with a more permeable gut lining and inflammatory reactions.

What the gut flora does in the gut

Most gut bacteria live in the large intestine, where there is hardly any oxygen. There they ferment dietary fibre, which humans cannot break down with their own enzymes, into short-chain fatty acids: butyrate is the main energy source of the cells lining the colon, propionate travels to the liver and feeds into sugar and fat metabolism, and acetate is used throughout the body. The bacteria also produce vitamin K2 and some B vitamins, convert bile acids and occupy nutrients and attachment sites, so that incoming microbes find it hard to settle. Through the mucosa they are in constant exchange with the gut-associated immune system, which learns there to tell harmless microbes from harmful ones.

Few protective bacteria – what happens in the gut?

When fibre-fermenting bacteria are missing, fewer short-chain fatty acids are formed. The colon cells then have less butyrate as fuel, consume less oxygen, and more oxygen remains at the mucosa – which favours microbes that cope with oxygen, such as enterobacteria. The mucus layer is renewed less, the connections between mucosal cells are less supported, and regulatory immune cells that dampen inflammation are formed less often. Typical triggers are antibiotics, gastrointestinal infections and a low-fibre diet; after antibiotic treatment, microbes such as Clostridioides difficile can also spread more easily.

Many unwanted microbes – what happens in the gut?

When protein-fermenting or pro-inflammatory microbes take over, metabolism in the large intestine shifts: instead of short-chain fatty acids, more ammonia, hydrogen sulphide, phenols and indoles are produced, which can irritate the mucosa. Gram-negative bacteria carry lipopolysaccharides (LPS) in their outer membrane, which activate immune cells in the gut wall via the receptor TLR4. Additional gas formation stretches the gut, and altered fermentation products affect how much water stays in the stool and how fast the gut transports its contents.

The interpretation is given in your report.