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Unlocking the ‘gut microbiome’ – and its massive significance to our health

"Lots of things that people don't think about, like depression or anxiety, are clearly modified by your gut microbes."

If you want to learn more about what’s going on in your gut, the first step is to turn your poo blue. How long it takes for a muffin dyed with blue food colouring to pass through your system is a measure of your gut health: the median is 28.7 hours; longer transit times suggest your gut isn’t as healthy as it could be. We are only now beginning to understand the importance of the gut microbiome: could this be the start of a golden age for gut-health science?

“The gut #microbiome is the most important scientific discovery for human healthcare in recent decades,” says James Kinross, a microbiome scientist and surgeon at Imperial College London. “We discovered it – or rediscovered it – in the age of genetic sequencing less than 15 years ago. The only organ which is bigger is the liver.” And, for all that the internet may be full of #probiotic or wellness companies making big health claims about gut health, “We don’t really know how it works,” he says. At the risk of sounding like the late Donald Rumsfeld, there’s what we know, what we think we know, and an awful lot that we don’t yet have a clue about.

Your gut microbiome weighs about 2kg and is bigger than the average human brain. It’s a bustling community of trillions of bacteria, archaea, fungi and viruses, containing at least 150 times more genes than the human genome. We are filled to the brim with microbes, which form microbiomes on our skin, in our mouths, lungs, eyes, and reproductive systems. These have co-evolved alongside us since the beginning of human history. But the gut’s is the largest and most significant for our short- and long-term health. It is massively complex and its residents vary enormously from person to person. According to a study in 2020 by the European Bioinformatics Institute, which pooled more than 200,000 gut genomes to create a genetic database of human gut microbes, 70% of the microbial populations it listed – 2,000 species – hadn’t yet been cultured in a lab and were previously unknown.

“It’s a vital organ in your body and you need to look after it. If you do that, it will look after you,” says Professor Tim Spector, an epidemiologist at King’s College London, author of two books on dietary and gut health, and co-founder of the ZOE app, initially developed as a gut health programme, but temporarily re-engineered as a Covid symptom tracker early in the pandemic. (Whether the gut microbiome can be considered an organ is still up for discussion – many microbiome scientists call it an organ, given that it is both inherited and essential, while others use superorgan, supporting organ or microbial organ.) “Lots of things that people don’t think about, like depression or anxiety, are very clearly modified by your gut microbes. Appetite and ability to digest food are modified by gut microbes. The key finding recently is the link with the immune system. Basically, the gut microbiome is controlling it, sending signals, because most of your immune system is in your gut, helping you fight infections, such as Covid and early cancers, that the immune system is picking off.”

Studies suggest having a diverse population of gut microbes is associated with better health. But when human populations urbanise, microbial diversity declines. Professor Jack Gilbert is an award-winning microbiome scientist at the University of California San Diego and author of Dirt Is Good. “Over the past 80 years and since the dawn of antibiotics, there has been multi-generational loss of microbes that appear to be important for human health,” he says. “They’re passed from mother to child [during birth, via breastmilk and skin contact] throughout the generations, but at some point in the last three or four generations, we lost some. We’re not entirely sure if the cause was our lifestyle, our diet, cleanliness in our homes or the use of antibiotics. We’re also missing certain immune stimulants that people in the developing world have plenty of.”

What are the implications of this? “Those two things combined may be underlying a large proportion of the chronic diseases our society is suffering from – asthma, food allergies, atopic diseases and auto-immune disorders. It’s difficult to prove epidemiologically – 100 years ago no one gave a crap about allergic diseases because globally 50m people a year were dying of infectious diseases. But over the past 50 years of good scientific record keeping, we’ve seen a significant increase in those disorders [alongside] this loss of microbial diversity in our guts.”

Gut microbes do things the gut can’t do, liberating or synthesising nutrients from food, especially from plants and their polyphenols, living off non-digestible substrates, producing thousands of metabolites – useful chemicals –and making vital short-chain fatty acids that are involved with immunity, with keeping the gut and colon healthy, with moderating the body’s inflammatory responses and with the metabolism of glucose. To do this, microbes need about 30g of fibre a day, but the average intake in the UK is just 10-15g. Is this why modern, low fibre, ultra-processed, high-sugar diets seem so problematic for human gut health?

“It’s very hard to know exactly what it is in junk food that is causing a problem,” says Spector. (When he talks about junk food, Spector means most prepared and packaged foods – including things such as vegetarian lasagne.) “It’s not the fat, carbs and protein, it’s the extra chemicals. The data is probably best for artificial sweeteners that are derived from things like paraffin and the petrol industry, so our bodies and our microbes are not used to breaking them down. But it could be other stuff, like the enzymes you don’t get on the label, or emulsifiers. There are few studies on emulsifiers, and nearly all in animals, but they show that you get reduced diversity and more inflammatory microbes. The idea is that they’re doing the same as they are in cooking: sticking your microbes together, creating an emulsion. Or it could be the lack of fibre and the fact that everything is refined. We haven’t nailed it down, but I think it’s safe to say that ultra-processed foods are bad for your gut microbes and we should avoid eating them regularly.”

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