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We know the average human being has about 20,000 genes sitting on 23 pairs of chromosomes. They make us into the unique individuals that we are. Surprisingly, however, we also have many freeloaders – various bacteria, fungi and viruses – within our body that contain about 100 times more genes – at least 2,000,000 and counting.

Each of us therefore has a unique set of ‘bugs’ or microbial fingerprint. Even identical twins show differences, implying that outside forces and environmental factors, are driving the differences. Yet very few bugs can colonise a human gut and those we have, take up residence soon after birth. By the age of 1 year, we have 500-1000 species and by the age of 3, key species are firmly established. They become our lifelong travelling companions – stable and unique to each person.

Nonetheless, changes in diet can profoundly alter the proportions in the mix (or ‘relative abundance’ to use the scientific term) of bacteria in the gut. This leads to the assumption that some changes encourage or discourage disease. Interestingly, some studies suggest that the microbiome can influence appetite levels and dietary preferences and therefore our body weight. We can even classify individuals as being lean or obese simply on their gut microbes. The abundance of one particular bacteria Christensenella in the gut is associated with being lean – the more there are, the lower the Body Mass Index (BMI). What’s more, giving this bug to mice can induce weight loss.

Antibiotics can also be expected to alter the mix of bugs and those taken early in life appear to have a profound effect that can result in later development of obesity, asthma and inflammatory bowel diseases. Couples living together with a dog have more bugs in common than a mum and dad living with a child. Living with pets has been shown to have a positive effect on the microbiome composition and lower risk of asthma.

In a recent issue of the American Journal of Clinical Nutrition, Victoria Gershuni and her colleagues, found that a diet high in saturated fat was associated a higher risk of preterm birth and lower microbial diversity. Higher intakes of animal foods, processed foods, alcohol and sugars have also been implicated.

At the moment, it is not possible to say that these differences are due to the microbiome or simply correlated with it (i.e., a coincidence). Other lifestyle factors such as stress, little exercise and poor sleep correlate with inflammation and differences in relative abundance of some species in the gut microbiome.

In some diseases such as infection with Clostridium difficile, the stools and the microbiome look nothing like healthy stools. Fecal transplants have been found to cure the infection rapidly and re-instate the healthy gut and healthy stools.

In a recent issue of the journal Gut, Laura Bolte and colleagues from the Netherlands review the data suggesting that a Western diet increases the risk of developing inflammatory diseases such as arthritis, ulcerative colitis, Crohn’s disease and irritable bowel syndrome (IBS). On the other hand, plant foods that contain more fibre are linked to better diets because they increase fermentation in the large bowel, producing short-chain fatty acids and lower levels of endotoxins.

Inflammatory bowel disease and type 1 diabetes have been on the increase globally, but we don’t know why. More and more evidence links them to disturbances in the microbiome in early life. Early life corresponds to the development of immunity, physiology and metabolism. Antibiotics at this time could increase the abundance of some bugs at the expense of others.

Finally, gut to brain communication is now recognised. Over the last 10 years, the gut microbiota has emerged as a key regulator of brain processes, behaviour and even mental health.

There’s a lot we still don’t understand. Microbiome stability (resistance to change) and resilience (return to the initial state) are poorly understood. Currently, microbiome research is a process of discovery rather than translation (putting it into practice). What’s certain is that we are entering a decade where microbiome science will inform clinical practice and personalised medicine. Hopefully, one day we will be able to diagnose, treat and prevent human disease and improve well-being by encouraging a healthy microbiome.

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Professor Jennie Brand-Miller holds a Personal Chair in Human Nutrition in the Charles Perkins Centre and the School of Life and Environmental Sciences, at the University of Sydney. She is recognised around the world for her work on carbohydrates and the glycemic index (or GI) of foods, with over 300 scientific publications. Her books about the glycemic index have been bestsellers and made the GI a household word.