10% Human: How Your Body’s Microbes Hold the Key to Health and Happiness. Alanna Collen

down the throat towards the stomach sees the enormous diversity of species found in the mouth drop dramatically. The highly acidic stomach kills many of the microbes that enter with food, and just one species is known for certain to reside there permanently in some people – Helicobacter pylori, whose presence may be both a blessing and a curse. From this point on, the journey through the digestive tract reveals an ever-greater density – and diversity – of microbes. The stomach opens into the small intestine, where food is rapidly digested by our very own enzymes and absorbed into the bloodstream. There are still microbes here though; around ten thousand individuals in every millilitre of gut contents at the start of this 7-m-long tube, rising to an incredible ten million per millilitre at the end, where the small intestine meets the large intestine’s starting point.

      Just outside the safe-house created by the appendix is a teeming metropolis of microbes, in the heart of the microbial landscape of the human body – the tennis-ball-like caecum, to which the appendix is attached. This is the epicentre of microbial life, where trillions of individual microbes of at least 4,000 species make the most of the partially digested food that has passed through round one of the nutrient-extraction process in the small intestine. The tough bits – plant fibres – are left over for the microbes to tackle in round two.

      The colon, which forms most of the length of the large intestine, running up the right-hand side of your torso, across your body under your rib cage, and back down the left-hand side, provides homes for microbes, numbering one trillion (1,000,000,000,000) individuals per millilitre by now, in the folds and pits of its walls. Here, they pick up the scraps of our food and convert them into energy, leaving their waste products to be absorbed into the cells of the colon’s walls. Without the gut’s microbes, these colonic cells would wither and die – whilst most of the body’s cells are fed by sugar transported in the blood, the colonic cells’ main energy source is the waste products of the microbiota. The colon’s moist, warm, swamp-like environment, in parts completely devoid of oxygen, provides not only a source of incoming food for its inhabitants, but a nutrient-rich mucus layer, which can sustain the microbes in times of famine.

       The human gut.

      Because HMP researchers would have to cut open their volunteers to sample the different habitats of the gut, a far more practical way of collecting information about the gut’s inhabitants was to sequence the DNA of microbes found in the stool. On its passage through the gut, the food we eat is mostly digested and absorbed, both by us and our microbes, leaving only a small amount to come out the other end. Stool, far from being the remains of our food, is mostly bacteria, some dead, some alive. Around 75 per cent of the wet weight of faeces is bacteria; plant fibre makes up about 17 per cent.

      At any one time, your gut contains about 1.5 kg of bacteria – that’s about the same weight as the liver – and the lifespans of individuals are a matter of just days or weeks. The 4,000 species of bacteria found in the stool tell us more about the human body than all the other sites put together. These bacteria become a signature of our health and dietary status, not only as a species, but as a society, and personally. By far the most common group of bacteria in the stool are the Bacteroides, but because our gut bacteria eat what we eat, bacterial communities in the gut vary from person to person.

      The gut microbes aren’t just scavengers, though, taking advantage of our leftovers. We have exploited them too, especially when it comes to outsourcing functions that would take us time to evolve for ourselves. After all, why bother having a gene for a protein that makes Vitamin B12, which is essential for our brain function, when Klebsiella will do it for you? And who needs genes to shape the intestine’s walls, when Bacteroides have them? It’s much cheaper and easier than evolving them afresh. But, as we will discover, the role of the microbes living in the gut goes far beyond synthesising a few vitamins.

      The Human Microbiome Project began by looking only at the microbiotas of healthy people. With this benchmark set down, the HMP went on to ask how they differ in poor health, whether our modern illnesses could be a consequence of those differences, and if so, what was causing the damage? Could skin conditions like acne, psoriasis and dermatitis signal disruption to the skin’s normal balance of microbes? Might inflammatory bowel disease, cancers of the digestive tract and even obesity be due to shifts in the communities of microbes living in the gut? And, most extraordinarily, could conditions that were apparently far removed from microbial epicentres, such as allergies, autoimmune diseases and even mental health conditions, be brought on by a damaged microbiota?

      Lee Rowen’s educated guess in the sweepstake at Cold Spring Harbor hinted at a much deeper discovery. We are not alone, and our microbial passengers have played a far greater role in our humanity than we ever expected. As Professor Jeffrey Gordon puts it:

      This perception of the microbial side of ourselves is giving us a new view of our individuality. A new sense of our connection to the microbial world. A sense of the legacy of our personal interactions with our family and environment early in life. It’s causing us to pause and consider that there might be another dimension to our human evolution.

      We have come to depend on our microbes, and without them, we would be a mere fraction of our true selves. So what does it mean to be just 10 per cent human?

       ONE

       Twenty-First-Century Sickness

      In September 1978, Janet Parker became the last person on Earth to die of smallpox. Just 70 miles from the place where Edward Jenner had first vaccinated a young boy against the disease with cowpox pus from a milkmaid, 180 years earlier, Parker’s body played host to the virus in its final outing in human flesh. Her job as a medical photographer at the University of Birmingham in the UK would not have put her in direct jeopardy were it not for the proximity of her dark room to the laboratory beneath. As she sat ordering photographic equipment over the telephone one afternoon that August, smallpox viruses travelled up the air ducts from the Medical School’s ‘pox’ room on the floor below, and brought on her fatal infection.

      The World Health Organisation (WHO) had spent a decade vaccinating against smallpox around the world, and that summer they were on the brink of announcing its complete eradication. It had been nearly a year since the final naturally occurring case of the disease had been recorded. A young hospital cook had recovered from a mild form of the virus in its final stronghold of Somalia. Such a victory over disease was unprecedented. Vaccination had backed smallpox into a corner, ultimately leaving it with no vulnerable humans to infect, and nowhere to go.

      But the virus did have one tiny pocket to retreat to – the Petri dishes filled with human cells that researchers used to grow and study the disease. The Medical School of Birmingham University was one such viral sanctuary, where one Professor Henry Bedson and his team were hoping to develop the means to quickly identify any pox viruses that might emerge from animal populations now that smallpox was gone from humans. It was a noble aim, and they had the blessing of the WHO, despite inspectors’ concerns about the pox room’s safety protocols. With just a few months left before Birmingham’s lab was due to close anyway, the inspectors’ worries did not justify an early closure, or an expensive refit of the facilities.

      Janet Parker’s illness, at first dismissed as a mild bug, caught the attention of infectious disease doctors a fortnight after it had begun. By now she was covered in pustules, and the possible diagnosis turned to smallpox. Parker was moved into isolation, and samples of fluid were extracted for analysis. In an irony not lost on Professor Bedson, his team’s expertise in identifying pox viruses was called upon for verification of the diagnosis. Bedson’s fears were confirmed, and Parker was moved to a specialist isolation hospital nearby. Two weeks later on 6 September, with Parker still critically ill in hospital, Professor Bedson was found dead at his home by his wife, having slit his own throat. On 11 September 1978, Janet Parker died of her disease.

      Janet