What exactly is your microbiome? We take an in-depth look

Antibiotics continue to be embraced on a global scale by doctors who persistently overuse them without due concern for the consequences, patients who steadfastly demand them for coughs and colds and an agricultural and livestock industry driven by the bottom line.

When the world’s premier scientists assembled in Sydney towards the end of 2018 to discuss their findings and set an agenda for the future of microbiome research, this is a conference I would not have missed for all the vitamin C in a Kakadu plum — which, if you can find one, is richly graced with this nutritive substance.

The microbiome refers to all the bugs in your gastrointestinal system, most of them doing their daily works in your colon, the large chunk of bowel near the place where you do our eliminating. There are a lot of them — 30 trillion organisms, to be exact — and their genes outnumber us by 100:1.  As much as we keep telling ourselves on Facebook that we’re G-d’s gift to the universe, essentially we are the guests at a giant germ party and like cordial hosts we need to start liking them much more than we keep liking us.

What most of us don’t realise is that, despite the multitasking digestive brilliance of the many cells that line our digestive tract, we have a limited capacity to break down foods, especially fibre. Bugs do it for us and, by executing this essential function, vital substances called short-chain fatty acids are manufactured that are our life support in a multitude of ways. They provide the fuel that energises the cells of our gut, they shore up our immune systems, make us feel full after eating and protect us against cancer.

This symbiotic relationship between the fibre we consume (found in corn bran, rice bran, the skins of fruits and vegetables, nuts, seeds, dried beans and wholegrain foods and the life-preserving short-chain fatty acids generated by the benevolent activities of a horde of bacteria that have thrived since the beginning of time) has become violently corrupted with the advent of civilisation.

You can tell a lot about the state of your wellbeing by looking at the microbial composition of your teeth. According to research presented at the conference, Neanderthal man had strong and robust dentition, free of defects. Then came the agricultural age, new farming practices and the onset of the industrial age, which witnessed profound changes in our consuming habits. Milk, sugar, cooked meat and grains have become our staples and appear to coincide with the emergence of poor dentition and the prevalence of disease-producing germs fomenting gum diseases and other more concerning illnesses like heart disease, linked in some ways to unhealthy gums. So far have we strayed from the eating habits of our hunter-gatherer ancestors it’s hard to find similarities in the microbial composition of our teeth, which forms the bedrock of our lineage.

These dramatic changes in the makeup of our microbiome have led to an explosion of research looking at the connection between the imbalance of germs in our gut and just about every disease known to humanity. If we can only replace the beneficial bacteria, we might have a cure for everything from obesity to dementia.

The notion of a healthy microbiome has spawned a huge industry centring on probiotics or the so-called good bacteria, which can purportedly be used to edge out the bad bugs thereby ameliorating and possibly even reversing a host of ailments. Thinking that we can only be doing ourselves some good by taking a health-promoting formulation that might even prevent cancer, it’s not difficult to appreciate why there has been so much enthusiasm for probiotics.

This is where the scientists are at odds with the vitamin companies and commercial interests. For a long while we’ve known that antibiotics do not only eradicate offending bacteria but also cause widespread disruption to healthy gut ecosystems, eliminating a whole lot of germs we need. Reconstituting a resurgent internal environment can take some time, which is why taking probiotics with antibiotics was thought to be an obvious way to offset these developments.

Pioneering research reported in 2018 that examined the effects of probiotics on the detrimental effects of antibiotics has disturbingly demonstrated the exact opposite. By inspecting the internal environment of the gut, unchartered waters when it comes to assessing the benefits or not of probiotics, scientists have discovered that rather than preserve a healthy gut ecology, probiotics actually got in the way, causing disruptions to the normal distribution of germs which took an extended period to reverse. For those of us committed to what we thought was the essentially wholesome nature of probiotics — labelled the so-called “good” bacteria — this is a profoundly unsettling revelation.

It echoes the sentiments of the scientists at the microbiome conference who caution that, when it comes to neutralising the escalating threat of antibiotic resistant bacteria, simply ingesting any of the offerings from the current batch of commercially available probiotics might be a naïve and fraught strategy.