A thousand bacteria can fit into a single human cell, but what bacteria lack in size, they make up for in numbers. In fact, you are outnumbered by the microbes living inside you, where only approximately 43% of the cells in your body are human cells. Similarly, just 1% of the genetic material in your body is human, due to the diversity of microbes in your gut.

The population of bacteria, archaea, viruses and eukaryotic microbes that reside in our intestines is known as the gut microbiome. These microbes are in competition with each other for resources such as space on the lining of your gut and food, which they need to proliferate. All microbes do not rely on the same foods for energy, though. Some may thrive on simple sugars whereas others might prefer to digest fibrous foods. In this way, what you eat determines the microbial make-up in your gut and, given the vast array of possibilities, it is quite likely that specific set up in your gut is unique to you.

Whether a species of bacteria thrives in your gut depends on what you eat, so it may come as no surprise that they have evolved ways to communicate their desires to us. These bacteria can send crude messages to the brain along what is called the “gut-brain” axis, commandeering your mind and controlling your tastes. For example, a craving for something fibrous might originate from the bifidobacteria species in our gut that require it to grow. In return for feeding these bacteria, they produce a fatty acid called butyrate which heals the lining of the gut, improves your mood, and dampens inflammation. In this way, bacteria can condition you to keep them fed.

“only approximately 43% of the cells in your body are human cells”

This intricate relationship with the bacteria living in our gut is a remarkable example of symbiotic evolution. We inherit the bacterial make-up of our microbiome from our mother, and several species have evolved to live a life solely confined to the human intestines. Without us, they’re toast. On the other hand, these bacteria protect our gut lining, a vulnerable part of the human body often targeted by pathogens. It is essential we care for the beneficial bacteria because, although we have struck a deal with many strands, they don’t all have our interests in mind. The challenge for the immune system is then to know the naughty bacteria from the nice. If our immune system loses track of which bacteria are dangerous and can be eradicated, numerous health issues can result. With possibly a thousand different species of bacteria living on or in you at any instant, this is quite the task. Harmful strands can begin to flourish in our gut if the immune system is poorly trained, leading to problems such as irritable bowel syndrome (IBS). Alternatively, our immune system can begin to attack itself, resulting in inflammatory bowel diseases (IBD) like Crohn’s disease.

The health issues can be more even more widespread. Certain pathogens can leave microscopic holes in the gut, through which food can leak into the bloodstream. The immune system kicks into overdrive attacking these food particles, leading to food allergies. Curiously, curing underlying gastrointestinal issues such as IBS and IBD often resolves mental disorders too, and microbial imbalance in the gut has links to anxiety and depression. In May 2000, the water supply of a town in Ontario became  contaminated with E. coli. Over two thousand people were taken ill and, after recovering from the initial infection, hundreds of these people developed IBS and depression. The microbiome has also been linked to conditions such Parkinson’s disease, autism, and even obesity. In one study, researchers took feces from lean and obese humans and transplanted the bacteria into mice. The mice then became thinner or fatter, depending on which microbiome they received.

Researchers have hypothesized that the overuse of antibiotics and the shift to a diet higher in artificial sweeteners in Western societies may be contributing to the dramatic rise in allergy conditions, autoimmune diseases, anxiety, and depression. Antibiotics are excellent for treating infectious diseases such as smallpox, tuberculosis and MRSA, but they destroy the healthy bacteria in the colon too. Such research has a profound impact on how we treat disease and stay healthy in the first place. Many experiments have shown how gut function, and hence the food we eat, has a measurable impact on our mental health. Conversely, studies have shown that cognitive behaviour therapy can help people suffering from IBS.

“These bacteria can send crude messages to the brain along what is called the ‘gut-brain’ axis, commandeering your mind and controlling your tastes.”

Such is the sway that the gut has over our decisions, the gut microbiome is known by some as the “second brain”. While it may seem like we are giving these microbes a lot of credit, the gut has its own nervous system independent of the central nervous system, and this “second brain” relies on the same neurochemistry to process information (90% of the body’s serotonin is found in the gut). When researchers at McMaster University transplanted feces between mice with an exploratory nature and timid mice, the exploratory trait transferred too, demonstrating that the gut can affect personality characteristics, in rodents at least. Professors Ted Dinan and John Cryan at University College Cork found that mice raised in a germ-free environment tend to be more anxious. Dinan and Cryan also found that rats became depressed when they transferred fecal matter from humans with depression into the rats, thereby transferring mood between species to some extent.

Psychobiotics, a term coined by Dinan and Cryan, are microbes that, when ingested, can affect your mood by acting on the gut. Dinan and Cryan are two of the leading researchers in the field of psychobiotics and, although the science is still in its infancy, their work is upending long-held beliefs about gut function. Dinan and Cryan hope someday to treat patients suffering from psychiatric illnesses with psychobiotics and early results are promising. Experiments with rats have shown certain psychobiotics to have antidepressant or anxiety-reducing properties. When humans were given psychobiotics, they became less anxious and showed improvements in cognitive functions such as memory.

Cryan opens his recent book with Dinan, The Psychobiotic Revolution, by saying “if microbes are controlling the brain, then microbes are controlling everything” so maybe we’ve no choice but to trust our gut instincts.