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From Germ Theory to the Microbiome: Why Microbes Still Rule Our Lives

We now have an opportunity to shift the focus from simply diagnosing and treating ill health to understanding, curing and preventing it. Caring for our microbes gives us a chance to conquer this new wave of illness, and live healthier, happier lives.
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I have an autoimmune disease. My husband is allergic to cats. My mum has hypothyroidism. My brother has a serious nut allergy. Two of my cousins have IBS. My best friend has Type 1 diabetes. My sister-in-law has celiac disease. My boss has rheumatoid arthritis. My friend from university has ulcerative colitis. My neighbor is obese. My friend's 5-year-old daughter has autism. My nephew has allergic asthma. And my aunt has depression.

Okay, those statements were lies. But the truth is, someone close to me does suffer from each of these conditions -- I've just changed the relationships to protect their privacy. In fact, I barely know anyone who doesn't have allergies, an autoimmune disease, a mental health condition, a digestive disorder, or a weight problem.

It might seem like these illnesses are just part of being human, but that's not the case. One hundred years ago, each of these conditions was rare in the developed world. They remain relatively uncommon in developing countries, though rates of each of them are on the rise as the industrialized, Western way of life pushes out the past. It's easy to assume that increased awareness has simply revealed more sufferers, but although better diagnosis has surely made its contribution to the case load, the experts agree that the upsurge in illness is a genuine one.

As it stands, two-thirds of adults are overweight or obese, 1 in 68 children has autism, around 15-20 percent of people have IBS, and something like one in 10 people have an autoimmune condition. If these disorders are not part of the human condition, then what's causing them?

It has been fashionable to blame genetics, as more and more genes linked to ill health are uncovered. But the pace of change is quicker than evolution would allow, and anyway, variants of genes that result in disease rarely gain the favor of natural selection and become more common. Genetics may predispose particular people to illness, but it's not the sole cause of these conditions.

If it's not altered genetics behind the rise in these modern chronic health problems, it has to be a change in the environment. Our modern, medicated, antiseptic lives, though nearly free of deadly infections, come with a downside. We are neglecting 90 percent of our cells. They are not human cells, but microbes -- and we are only just beginning to realize how much they matter to us.

Humans and microbes have evolved together from the start -- they coat our surfaces, both inside and out. The vast majority of them live within our guts, alongside masses of immune tissue. Together, our immune systems and our microbes collaborate to protect us from harmful invaders, such as viruses, and to learn to tolerate harmless bystanders, including pollen and food molecules.

But if we disrupt our community of beneficial microbes, the immune system goes into overdrive, attacking harmless particles and causing inflammation in our human cells. It's this inflammation that's at the root of our modern, Western illnesses. It's easy, then, to see how it can result in allergies and autoimmune diseases, which are the result of a dysfunctional immune system, but how can obesity be linked to microbes?

Take this example: Transferring the gut microbes from twin sisters -- one obese and the other lean -- into "germ-free" mice that were raised in an isolation bubble makes those mice given the obese twin's microbes rapidly gain weight, while those which receive the lean twin's microbes remain a healthy weight. The mice are genetically identical and eat the same amount and type of food. The only difference is their microbes, which change the way the mice regulate energy storage.

So what's causing our conflict with our bodies' microbes? Compared with people living in parts of the world unaffected by modern lifestyles and modern disease, we in the West have a much lower diversity of bacterial species living in our guts. Four main aspects of our lives are harming our microbial communities:

(1) Our use of antibiotics. While these are important, life-saving drugs, we need to balance their benefits with the emerging risks of using them, and compensate for the collateral damage they cause using probiotics.

(2) Our low-fiber, animal-based diets. Our ancestors ate far more plant-based foods -- grains, vegetables, nuts and seeds, for example -- than we do now, which contain higher levels of fibre and encourage beneficial microbes in our guts.

(3) Our shift away from long-duration, exclusive breastfeeding. Breast milk nurtures a different set of microbes in babies than formula milks, as well as protecting against harmful infections. For some women, breastfeeding isn't an option, but many others are not getting the support they need.

(4) Our high rate of Caesarean sections. C-sections are a crucial alternative to natural birth for some women and babies, but birth by C-section seeds babies' guts with skin and hospital bacteria, rather than the milk-loving, protective bacteria they would encounter on their way through the birth canal.

Some 160 years ago, we had no idea what caused the diseases that ravaged our society. Infectious diseases -- smallpox, cholera, tuberculosis, and so on -- killed the majority of people back then. But along came germ theory -- Pasteur, Koch and others showed that harmful microbes were causing these fatal diseases -- and everything changed. Now, we live twice as long, thanks to medications that sprang from this revolution in our understanding of health and disease.

Today, we are in the midst of a new era in human disease, and, fortunately, a second revolution in our understanding of its cause. It's one that will probably change our lives just as profoundly as the acceptance of germ theory. Decoding the human genome was supposed to be our second revolution and it didn't quite deliver, but a "microbiome revolution" is far more promising anyway. For one, we can't change our genes, but we can change our microbes.

Recognizing that we are just 10 percent human, and that the 100 trillion microbes that live in and on us -- making up the other 90 percent of "our" cells -- will make all the difference to how we live, the medicines we take, and the diseases of civilization we currently suffer. Allergies, obesity, autoimmune diseases, and mental ill health don't have to be part of the human condition. We now have an opportunity to shift the focus from simply diagnosing and treating ill health to understanding, curing and preventing it. Caring for our microbes gives us a chance to conquer this new wave of illness, and live healthier, happier lives.