What’s bugging you now? The amazing potential of our bodies’ own bacteria

Scientists hope our trillions of resident microbes can help us beat disease and improve mental health

News & Analysis

18th February 2016

This is a murky story of vast armies standing guard over myriad territories, of battles fought in deep, dark crevasses, of warriors competing on your behalf — yet without your awareness — for your very existence. It’s the story of the human microbiota; the legions of ‘friendly’ and sometimes not so friendly bacteria and other microbes that we all carry in and on our bodies.

We each play host to 100 trillion microbes, mostly in our gut but also on our skin and elsewhere. That’s around ten times more cells than our own human ones; your body is little more than an empty vessel carrying an alien horde. These microbes carry a vast range of genetic material, known as the microbiome. It is the activity of these genes, more numerous and varied than our own DNA, which scientists are trying to pin down. And it’s becoming clear that they control some of our body’s vital processes, producing chemicals that drive activities ranging from healing wounds to affecting our mood, our immune defences and our entire metabolism. If we can understand what the microbiome is doing, the scope for manipulating health and disease may be huge.

But this is a field of research that is not yet well understood, and about which many doctors remain sceptical. After recently giving a talk in my hospital about the fascinating possibilities currently being explored, a senior colleague introduced me to one of the hospital’s psychiatrists with a playful suggestion that he might help me with my ‘flight of fantasy’. But the teasing backfired when the psychiatrist enthusiastically responded with news of research suggesting that the bacteria in our gut may influence anxiety levels. The idea that our microbes may be controlling our minds is just one of many intriguing theories now under the microscope.

We picture newborns as uncontaminated and germ-free, but it is now known that mothers start seeding their babies with bacteria while they are still in the womb. Then, during birth, the baby picks up a wider variety of microbes, determined in part by the method of delivery. Babies delivered naturally acquire bacterial communities similar to their mother’s vaginal microbiota, while babies born by caesarean section pick up a narrower range of types found mostly on the skin. These microbes may immediately start to confer lifelong advantages or disadvantages linked to health or disease.

Many factors then drive changes in the microbiota, from how the baby is bathed to whether it is breast- or bottle-fed and with whom it comes into contact. Over time, the microbiota settles down as each species finds its own niche, determined by factors such as moisture levels or skin temperature. Eventually, different species predominate in different corners of the body in a remarkably consistent way. Swab the population of any street and you’ll find the bacteria in their armpits, for example, are very similar — more similar than the bacteria found in different places on one individual.

As we walk through life we collect microbes from everything and everyone we come close to. Some are harmful ‘pathogenic’ bacteria that can invade the body and cause infection. But others just merge with our established horde. For example, a recent study found that during an intimate kiss with full tongue contact and saliva exchange (a courtship behaviour unique to humans and found in more than 90 per cent of cultures, according to lead researcher Remco Kort from the VU University, Amsterdam), 80 million bacteria are exchanged within ten seconds and some settle down into the surface of the tongue to establish colonies.

In these ways we develop our own unique bacterial signal or ‘footprint’ and we leave a trail of it everywhere we go. Bacterial signals persist for weeks, and forensic pathologists are now developing techniques to identify those present at the scene of a crime by the bacteria they leave behind.

So from our very first breath, our microbiota is busy shaping our story. Science is racing to discover this hidden world, but at this point a large red flag must be waved. Most studies so far have used animal subjects and need to be thoroughly repeated on humans. Even so, the excitement in the research world is palpable.

Most people are already familiar with the idea that ‘friendly bacteria’ are important in keeping the gut healthy and harmful microorganisms at bay. Antibiotics can wipe out the gut bacteria, damaging the cells lining the gut and causing diarrhoea. Research is accumulating to show that supplements of bacteria (probiotics) and the nutrients which ‘feed’ our own bacteria (prebiotics) can re-establish the microbiota and may prevent this antibiotic-associated diarrhoea. Probiotics may also shorten the course of diarrhoea in acute gastroenteritis. And with necrotising enterocolitis — a serious condition with a 30 per cent mortality rate in pre-term infants — evidence of the benefits of probiotics is so clear, with a more than 50 per cent reduction in risk, that a recent review from the Cochrane Collaboration has strongly recommended a change of practice to allow their routine use. This is one of the first formal calls for their regular use but, reflecting ongoing medical scepticism, professional societies have been slow to adapt treatment guidelines.

On the skin and other surfaces, the microbiome may play an essential role in wound healing. According to researcher Michieli Kleerebezem of the Host-Microbe Interactomics Group in the Netherlands, certain lactobacillus species have been shown to switch on the genes that help to heal wounds, increasing the rate of repair. Intriguingly, this might explain the capacity of honey to help in wound treatment because it contains large amounts of lacto-bacilli and associated chemicals. Another area causing researchers to chew hard on their chicory (one of the richest natural sources of prebiotics) is the idea that our gut microbes may determine whether we are lean or fat. If the microbiota from obese mice are transplanted into lean mice, they also become obese. This has triggered a vogue among overweight people to try home-made faecal transplants from thin friends.

But we may not need to go to such extremes. Professor Tim Spector of King’s College London is lead investigator for ‘The British Gut Project’, which is studying the microbiota. He partly blames a fall in the variety of our gut bacteria over the past 50 years for the current levels of obesity, and this is a consequence of eating more processed foods.

‘Microbes are not only essential to how we digest food, they control the calories we absorb,’ he says. His new book, The Diet Myth, emphasises the need to consume a wide range of different foods. ‘It is clear that the more diverse your diet, the more diverse your microbes and the better your health at any age,’ he says.

There is even some far-fetched research in progress to find out if we could harness our gut bacteria to power our mobile phones. Which takes me back to my conversation with the psychiatrist. The link between gut and brain has been known for more than 200 years. Think anger and indigestion, anxiety and a rush to the toilet.

Now, work coming out of academic initiatives such as the Alimentary Pharmabiotic Centre at University College Cork suggests that the microbiota may be the conductor in this gut-brain axis. The idea even has a name — psychobiosis. Research in Cork by Professor John Cryan shows that the gut microbiota is essential to maintain normal stress, antidepressant and anxiety responses, as well as social cognition and visceral pain. For example, germ-free mice, which lack a microbiota, are more antisocial and tolerate stress very poorly.

Cryan warns that there are critical time-windows when the effects of the microbiota on brain and behaviour appear to be more potent. Could this mean that anything that alters an infant’s microbes may leave them vulnerable to depression or anxiety later in life? A study under way around the world is looking at the effect of gathering a mother’s birth-canal bacteria and wiping them on to babies born by Caesarean section. Initial results show that this doubles the diversity of the infant’s microbiota, but will this in turn lead to more robust mental health? Alternatively, could feeding a baby prebiotics provide protection against mental illness?

The diversity of the microbiota decreases as we age, so would manipulating it reduce the inflammation associated with age or perk up the natural decline in immunity? And while reports are flooding in about changes in the microbiota associated with asthma, heart disease, liver disease, infantile colic, irritable bowel syndrome, inflammatory bowel disease and even diabetes, do these changes indicate cause or effect?

These questions demonstrate our current dilemma. Despite huge eagerness to hook in to the microbiome, so much remains unknown. We have yet to nail down all the different bacterial species and what their genes do. Until this is clearer, it is difficult to know which bacteria we need to encourage, and which are irrelevant or even dangerous. The probiotic cookbook is still very experimental.

Fortunately, most people are unlikely to come to any harm by nurturing their microbiota — although those with lowered immune defences, such as people undergoing chemotherapy, should first take advice from their medical team. So eat a diverse diet made up from as many natural ingredients as possible, with lots of fresh fruit and vegetables rather than junk or processed foods. Try probiotics if you like, and avoid unnecessary antibiotics or skin disinfectants.

Meanwhile, never has the cry of ‘more research is needed’ seemed so burning.


  • Gustavo Woltmann

    Its amazing to know that our body has its own good bacteria that fights off bad bacteria. Been looking for some food that has good bacteria and is easy to prepare for the kids. I will share this article to our publishers office.

  • Thea Rodriguez

    Omg was idol of mine he’s using copywriting & quotes
    from online and missing some key primary factors here!