It doesn't matter how much you wash, you're crawling with microbes – inside and out. Eye of Science / Getty Images

It doesn’t matter how much you wash, you’re crawling with microbes – inside and out.
Credit: Eye of Science / Getty Images

We are not alone. Our bodies are teeming metropolises of microscopic life – and the microbes that call us home influence everything from bowel to brain.

Over the past decade, technological advances in the lab have allowed us to take a census of our microbial entourage – known as the microbiota – like never before. Instead of seeing only the small fraction of microbes from our skin or poo that blossom on a petri dish, we can now blend, extract and read the genetic essence – the DNA – of all microbes, called the microbiome, to get a better idea of who’s there.

The picture that has emerged is one of staggering complexity. From nostrils to armpits, wisdom teeth to bowels, lungs to vaginas, unique communities of bacteria, fungi, viruses and parasites have got us covered.

“Every single surface of our body is colonised with microbes,” says Laura Cox, a biologist at the Brigham & Women’s Hospital and Harvard Medical School in Boston in the US.

Bacteria alone are as numerous as the cells of our own body. The genes they harbour dwarf our own genetic endowment more than a hundred times over. Together, we work in concert in what some consider a ‘super-organism’ – with our existence as reliant on theirs as theirs is on us.

Gut microbes synthesise vitamins, while those on our skin earn their keep by eating dead cells and transforming oils into natural moisturiser. And microbes everywhere play a role in keeping harmful pathogens at bay.

Families of gut microbes diverged from a common ancestor some 15 million years ago.

On the other side of the ledger, a mother’s milk contains some nutrients useless to her baby, but essential for the early microbial colonisers of her baby’s gut.

The assemblages of species inhabiting each bodily niche represent complex ecosystems that have evolved with us over millennia. The microbes lurking on the doorknob of the public toilet might give us the heebie-jeebies. But those that take up residence on or in us aren’t usually picked up from the environment. They are passed down from generation to generation, and have been for millions of years.

Families of gut microbes living in both us and other apes diverged from a common ancestor some 15 million years ago.

And bacterial strains from Africa and America diverged 1.7 million years ago, around the time early humans made their first forays out of Africa. If you wanted to, you could trace the history of human migrations around the globe using our microbiome.

Our microbes continue to evolve with us, and in response to our modern lifestyles. People living in industrialised societies have less diverse microbial communities than people in places such as Malawi.

Microbiome composition ebbs and flows depending on the food we supply and the various chemicals and drugs we send their way. Not surprisingly, the fluctuations in our microbial residents have clear implications for our health – from immune responses to how we think and act.

Tomorrow, we’ll explore how gut microbes tinker with our metabolism.

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