Halfway through reading Ed Yong’s first book, I found myself in A&E with a son in anaphylactic shock after he unwittingly ate some nuts. According to the book I’m reading, I told the medics gathered round his bed, the surge in allergies over the past fifty years could be due to our obsession with eradicating bacteria. Nobody was listening. They were too busy jabbing him full of adrenaline to calm his overwrought immune system. But they should have been listening. We should all be listening.

Microbes, most of them bacteria, have populated this planet since long before animal life developed and they will be here long after we have gone. Invisible to the naked eye, they are ubiquitous. They inhabit the soil, air, rocks and water and are present within every form of life, from seaweed and coral to dogs and humans. And, as Yong explains in his utterly absorbing and hugely important book, we mess with them at our peril.

Every species has its own colony of microbes, called a microbiome, yet these microbes vary not only between species but also between individuals and within different parts of each individual. The average human, Yong tells us, contains about 30 trillion human cells and 39 trillion microbial ones. We are at best only 50 per cent human. Indeed, some scientists even suggest we should think of each species and its microbes as a single unit, dubbed a ‘holobiont’.

Each part of the human body has its own distinct microbes ideally adapted to that environment. Those in the gut differ from those on the skin and teeth, in the armpits and on the genitals. These communities are constantly changing too. The right hand shares just one sixth of its microbes with the left hand. And, of course, we are surrounded by microbes. Every time we eat, we swallow a million microbes in each gram of food; we are continually swapping microbes with other humans, pets and the world at large.

It’s a fascinating topic and Yong, a young British science journalist, is an extraordinarily adept guide. Writing with lightness and panache, he has a knack of explaining complex science in terms that are both easy to understand and totally enthralling. Yong is on a mission. Leading us gently by the hand, he takes us into the world of microbes – a bizarre, alien planet – in a bid to persuade us to love them as much as he does. By the end, we do.

For most of human history we had no idea that microbes existed. They were first spotted when a Dutch lens maker, Antonie van Leeuwenhoek, noticed ‘animalcules’ in rainwater in 1675. It was nearly two hundred more years until Louis Pasteur discovered that some of these microbes caused disease. His ‘germ theory’ gave bacteria the poor PR image that endures today.

We all remember television advertisements promising cleaning agents that would kill ‘all known germs. Dead’. The idea of a battlefield in which bacteria are the common enemy still pervades our lives. At the same time we are sold ‘probiotic’ yoghurts and drinks that supposedly nurture ‘friendly’ bacteria. In reality, says Yong, bacteria should not be viewed as either friends or foes, villains or heroes. Instead we are locked in a partnership, a symbiosis, that can be mutually beneficial or mutually destructive.

In fact, fewer than one hundred species of bacteria cause illness in humans, while many thousands more play a vital role in maintaining our health. New research is now unravelling the ways in which bacteria help us digest food, regulate our immune systems, break down toxins, produce vitamins, affect our behaviour and even combat obesity. ‘They actually help us become who we are,’ says Yong. Yet our obsession with hygiene, overuse of antibiotics and fibre-poor diets are disrupting that bacterial balance and may be responsible for soaring rates of allergies and immune problems, such as inflammatory bowel disease (IBD).

The most recent research turns accepted norms upside down. Scrubbing the toilet kills the microbes that normally keep faecal bacteria at bay, meaning that a ‘clean’ toilet actually has more dangerous germs. Keeping a dog gives children early exposure to a diverse range of bacteria, which may guard against allergies later. And now scientists are looking at ways to manipulate our partnership with bacteria in order to tackle some of our most intractable health problems, from dengue fever to IBD. One trial among patients with persistent diarrhoea due to the bacterium Clostridium difficile found that 94 per cent were cured by a faecal microbiota transplant – yes, that’s transplanting excrement from donor to patient – to restore the microbial balance.

In describing this quest, Yong meets scientists with some of the weirdest jobs in the world – including the devotee who collects scents from the anal glands of hyenas – and some of the strangest creatures. The beewolf wasp daubs its burrow with an antibacterial paste to protect its larvae, while the desert woodrat has gut bacteria that kill toxins in the creosote bush leaves it eats.

I Contain Multitudes is popular science writing at its best. Reading this book will make you view the world differently. You won’t be able to see the microbes we share the planet with any better, but you will know a damn sight more about them. And when you next reach for the antibacterial spray you might just think twice before you kill those microbes. Dead.