Your skin is teeming with bacteria. There are billions of them, living on the dry parched landscapes of your forearms, and the wet, humid forests of your nose. On your feet alone, every square centimetre has around half a million bacteria. These microbes are more than just passengers, hitching a ride on your bodies. They also affect how you smell.
Skin bacteria are our own natural perfumers. They convert chemicals on our skin into those that can easily rise into the air, and different species produce different scents. Without these microbes, we wouldn’t be able to smell each other’s sweat at all. But we’re not the only ones who can sniff these bacterial chemicals. Mosquitoes can too. Niels Verhulst from Wageningen University and Research Centre has just found that the bacteria on our skin can affect our odds of being bitten by a malarial mosquito.
Imagine taking a course of antibiotics and suddenly finding that your sexual preferences have changed. Individuals who you once found attractive no longer have that special allure. That may sound far-fetched, but some fruit flies at Tel Aviv University have just gone through that very experience. They’re part of some fascinating experiments by Gil Sharon, who has shown that the bacteria inside the flies’ guts can actually shape their sexual choices.
The guts of all kinds of animals, from flies to humans, are laden with bacteria and other microscopic passengers. This ‘microbiome’ acts as a hidden organ. It includes trillions of genes that outnumber those of their hosts by hundreds of times. They affect our health, influencing the risk of obesity and chronic diseases. They affect our digestion, by breaking down chemicals in our food that we wouldn’t normally be able to process. And, at least in flies, they can alter sexual preferences, perhaps even contributing to the rise of new species.
You are outnumbered by a factor of 10 to one, by forces you cannot see. Your body has around ten trillion cells, but it’s also home to a hundred trillion bacteria. For every gene in your genome, there are 100 bacterial ones. Most of these are found the dark, dank environment of your bowel but their incredible diversity is being brought to the surface. Say hello to the gut metagenome.
Together with a team of international scientists, Junjie Qin and Ruiqiang Li from BGI-Shenzen had the unenviable task of studying the bacteria from the faeces of 124 Europeans. They used a formidable and audacious technique called metagenomics, which analyses all the genetic material in a sample, without bothering to culture the individual species first. It’s a shoot-first-ask-questions-later method that captures all the data and lets other programmes sort out the mess.
Stool samples from 33 people have already been analysed in this way, but Qin and Li managed to sequence almost 200 times as much DNA. Brace yourself for some big numbers. Their project uncovered just under 3.3 million bacterial genes, more than 150 times as many as reside in the entire human genome. By their estimate, your bowel and mine harbour at least 160 bacterial species each and we share many of our tenants (I say bacteria, but around 1% of the genes came from archaea, a superficially similar group but one that’s actually as different from bacteria as bacteria are from us).
The quest to understand gut microbes may seem like an arcane niche of science, but it’s actually very important for public health. We rely on these microscopic passengers more than we realise. They harvest energy from our food, provide us with nutrients that would otherwise be denied to us, prevent the growth of harmful bacteria, and more. In many ways, they’re like a forgotten organ. They can also go rogue, changing their community in ways that are linked to obesity or bowel diseases. Indeed, Qin and Li showed that the gut microbiome of a health person looks very different to that of someone with a bowel condition like Crohn’s disease or ulcerative colitis.
All in all, over 1,000 species make their living in the human bowel but a common cadre of 57 are shared by the vast majority of us. Even for this common set, each individual species could be thousands of times more common in your gut compared to mine. With such variation, it’s no wonder that earlier smaller studies concluded that people have very different gut lodgers.
It’s a diverse melting-pot of different groups, with hundreds of different cultures living together in harmony, many sticking to their own preferred areas. No, not London, New York or any other cosmopolitan city; I’m talking about your skin. It may all look the same to you, but to the bacteria living on it, it’s an entire realm of diverse habitats.
From a microscopic perspective, the hairy, moist surface of your armpits is worlds apart from the smooth, dry skin of your forearms. Even though they are separated by mere inches, these patches of skin are as different to their microscopic residents as rainforests and deserts are to us.
The true diversity of the bacteria on our bodies has just been revealed by Elizabeth Grice from the National Human Genome Research Institute, who has done a thorough survey of our “skin microbiome”. She recruited 10 healthy volunteers and took swabs from 20 distinct patches of their skin, all areas that are often afflicted by skin disorders. These areas represent a broad range of habitats from the oily lakes of the eyebrows, nose, inner ear and upper chest, to the moist jungles of the groin, nose, armpit and navel, to dry deserts of the forearms and palm.
By sequencing the distinctive 16S rRNA gene of over 112,000 bacterial samples, Grice catalogued a much broader menagerie of microbes than expected, with representatives from 19 different phyla and 205 different genera. Previous attempts at doing this have been biased towards species that grow easily in laboratory conditions such as Staphylococcus, but Grice’s more thorough approach revealed a surprising degree of diversity. It also showed that bacteria from a specific body part have more in common than those from a specific person. Your butt microbes have more in common with mine than they do with your elbow microbes.
You are not alone. Even if you’re currently reading this in complete isolation, you are still far from a singular individual. You’re more of a colony – one human, together with microbes in their trillions. For every one of your own genes, your body is also host to thousands of bacterial ones. Some of the most important of these tenants – the microbiota – live in our gut. Their genes, collectively known as our microbiome, provide us with the ability to break down sources of food, like complex carbohydrates, that we would otherwise find completely indigestible.
Peter Turnbaugh from the Washington University School of Medicine has spent his career studying the microbiome. His latest work reveals both tremendous differences and similarities between the bacterial tenants of our digestive systems. Your bowels may be home to very different species of bacteria to mine, but both our sets share a core group of genes.
Turnbaugh likens the situation within our guts to that of islands. Real islands may be home to very different species of animals but all have representatives that perform certain roles; there will always be grazers, predators, insect-eating specialists, fishermen and so on. Across islands, animals approach a set of core lifestyles in different ways, and so it is with the microbiota – every man is an island, home to unique collections of bacteria that nonetheless carry out some core functions. And the further an person’s microbiota strays from this standard template, the more likely they are to be obese.