I Contain Multitudes: The Microbes Within Us and a Grander View of Life

by Ed Yong

Actually, they far exceed astronomical numbers: there are more bacteria in your gut than there are stars in our galaxy.3

This stereotype is grossly unfair. Most microbes are not pathogens. They do not make us sick. There are fewer than 100 species of bacteria that cause infectious diseases in humans;

‘All the people living in our United Netherlands are not as many as the living animals that I carry in my own mouth this very day,’

Microbes are now so commonly associated with dirt and disease that if you show someone the multitudes that live in their mouth, they will probably recoil in disgust. Leeuwenhoek harboured no such revulsion. Thousands of tiny things? In his drinking water? In his mouth? In everyone’s mouth? How exciting!

If I went to a library and lobbed a microbiology textbook out the window, I could easily concuss a passer-by. If I tore out all the pages that dealt with beneficial microbes, I could just about give someone a nasty paper cut. The narrative of disease and death still dominates our view of microbiology.

‘The germ-free animal is, by and large, a miserable creature, seeming at nearly every point to require an artificial substitute for the germs he lacks,’ wrote Theodor Rosebury.

If you list all the species in a particular microbiome, you can tell who’s there. If you list all the genes in those microbes, you can tell what they are capable of.28 But if you list all the chemicals the microbes produce – their metabolites – you can tell what those species are actually doing.

Milk keeps them restrained. And it does much more than that. Milk is one of the most astounding ways in which mammals control their microbes.

Every mammal mother, whether platypus or pangolin, human or hippo, feeds her baby by literally dissolving her own body to make a white fluid that she secretes through her nipples.

‘Something has happened to give more weight to the pro-inflammatory side and less weight to the anti-inflammatory side. Why do Westerners live in such a hyper-inflammatory state?’

‘America is a constipated nation,’ he said, indelicately. ‘If you pass small stools, you have big hospitals.’26

We now know that when bacteria break down fibre, they produce chemicals called short chain fatty acids (SCFAs); these trigger an influx of anti-inflammatory cells that bring a boiling immune system back down to a calm simmer. Without fibre, we dial our immunostats to higher settings, predisposing us to inflammatory disease. To make matters worse, when fibre is absent, our starving bacteria react by devouring whatever else they can find – including the mucus layer that covers the gut.

Once ubiquitous, H. pylori is now found in just 6 per cent of children in Western countries. Over the last half-century, ‘this ancient, persistent, nearly universal and dominant inhabitant of the human stomach has been essentially disappearing,’ writes Blaser. Its loss means that fewer people suffer from ulcers and stomach cancer – clearly, a good thing. But if Blaser is right, the same loss may have precipitated a rise in reflux and oesophageal cancer. Which matters more, the pros or the cons?

consumer’s stomach. ‘But most of them never arose in the human gut, and they don’t have the factors that allow them to dwell for a long time there,’ says Jeff Gordon. His team confirmed this by monitoring the gut microbiomes of volunteers who ate twice-daily servings of Activia yoghurt for seven weeks. The bacteria in the yoghurt neither colonised the volunteers’ guts, nor changed the composition of their microbiomes.

The patients were effectively stewing in their own microbial juices. And the best way of fixing that was remarkably simple: open a window. The legendary life-saver Florence Nightingale advocated as much some 150 years earlier. She had no explicit knowledge of the microbiome but, during the Crimean War, she noticed that patients would recover from infections more readily if she opened a window.