Be nice to your germs, they keep you alive

The other 90 per cent belong to the trillions of micro-organisms, mainly bacteria, living on or inside you.

Yes, that’s right, you are more microbe than man (or woman).

It’s an unsettling thought considering the reputation germs have as foreign invaders that make us sick. Eliminating harmful germs from our bodies has been one of the major achievements of modern medicine – think antibiotics.

But before reaching for a bottle of hand sanitiser know that the internal ecosystem that inhabits your body, primarily focused in the gut, is essential for wellbeing in ways scientists are just beginning to understand.

Andrew Holmes, a microbial ecologist from the University of Sydney, says only recently has an overwhelming body of evidence demonstrated what a profound effect microbes have on human health.

Over the past five years research has linked the colonies that inhabit the gut to almost every major lifestyle disease including obesity, diabetes, cardio-vascular disease, allergies and asthma.

Just this week Canadian scientists announced that some gut bacteria that break down carbohydrates produce chemicals that lead to tumours forming in mice with genetic mutations that predisposed them to colourectal cancer.

While the research was conducted in mice, the study’s leader Alberto Martin says the findings provide useful insights into a possible mechanism in which gut microbes may be involved in the second most common cancer in humans.

Without a well-balanced community of these microscopic critters we would not survive, says Holmes.

‘‘We shouldn’t view them as a separate thing, we should view them as a part of us,’’ he says.

In a society that has become increasingly germ phobic – a fear marketers capitalise on by adding antibacterial agents to endless consumer products from socks to toys – this is an idea that takes some getting used to.

Rapid advances in technology to sequence our genes have been deployed to characterise and map the microbe communities associated with humans, collectively known as our microbiome.

This new scientific frontier, to probe and catalogue this vast array of organisms, enables researchers to investigate the specific ways in which they interact with their host (us), and each other, to influence health and wellbeing.

While science untangles the complex relationship between disease and gut microbes, the dynamic nature of these colonies suggests it may be simple to treat some microbe-related diseases by cultivating a new community of gut flora for their owners.

Just like a fingerprint, the number and variety of microbes inside the body is unique to individuals.

While humans start life microbe free, once born a baby receives its first coating of micro-sized organisms from their mother’s birth canal or her skin.

Exposure to microbes in the environment – from pets, other people, the air, surfaces we touch – adds to our personal ecosystem over time.

While these tiny tenants are mainly bacteria, there are also species of fungi and bacterial viruses, which combined weigh about 200 grams..

Microbes line the mouth and throat, nestle between teeth, cover the skin and coat the reproductive tracts and entire digestive system.

The largest community rents space in the gut, which is why diet is the other major influence on the type and number of microbes that inhabit the body.

Professor Steve Simpson, also from the University of Sydney, says the average large intestine contains between 500 and 1000 species of bacteria, each competing for space and resources.

‘‘They're engaged in a competition with one another as in any other ecosystem’’ says Simpson, the director the University’s new Charles Perkins Centre. Part of the centre's work on solutions for obesity, diabetes and cardiovascular disease will focus on gut microbes under Holmes' direction.

‘‘Some of those species are protective, some are not so helpful,’’ says Simpson.

In a healthy gut, beneficial and protective species dominate over varieties that are not so helpful.

Far from being ‘‘freeloaders’’, microbes perform essential jobs such as digesting food, manufacturing vitamins and priming the immune system during development to recognise itself from disease-causing pathogens, says Simpson.

But if conditions inside the intestinal neighbourhood change, it can advantage species that don’t offer useful services in exchange for a place to live.

It is this disharmony within the gut community that recent studies have linked to countless aspects of human health, from brain function, autism, Alzheimer’s disease, auto-immune diseases, food allergies, asthma and diabetes.

‘‘It’s turning out to be a far more complex and important interaction between the host and this vast community of things living in the gut than had ever been appreciated,’’ says Simpson.

Numerous internal and external forces can destabilise the harmonious balance of the gut’s microbiota. These include medication, especially antibiotics, and infectious pathogens.

A session of colonic irrigation – a health fad that gained popularity a few years ago – may flush out dried, undigested food but it will also wash away all the beneficial bacteria with it.

But it appears poor diet is one of the major factors that can destabilise gut flora. We really are what we eat.

Studies have shown obese people have different varieties and numbers of microbes than their leaner peers.

‘‘The composition of your food and its overall energy density will have a direct impact on the community structure of the microbes that live in the gut,’’ says Simpson.

To understand these dynamics in more detail, scientists have turned to animal models.

Earlier this year Simpson and Holmes published results from a large study that examined the health of mice on 50 different diets.

As part of the research, the team analysed microbiota in mice guts – scraping them off their teeth and collecting faecal samples – and found dramatic changes in the microbe community structure between rodents on different diets.

Specifically they found a rise or fall in the amount of calories the mice consumed shifted the ratio of the two main phyla of bacteria that lived in their guts – the bacteroides and the firmicutes, which are also found in humans.

The results support similar findings by other researchers, and align with early studies that show a low ratio of B communities to F was associated with obesity in humans. The precise nature of the association has not yet been determined. Holmes says most of the bacteria beneficial for health co-evolved with humans, earning their keep by providing an essential service.

"They're the ones that depend on something our body provides. We feed them some secretion in our gut and they give something back to us in exchange."  But when people eat more than they need, the additional nutrients encourage the wrong species to grow.

‘‘Overeating dilutes the chances of the good bugs to survive,’’ says Holmes.

In the mice study, upsetting the internal ecosystem affected the performance of their immune system and their overall metabolic health.

While it is clear different diets create different gut flora, they don’t vary with every meal, says Holmes. Even so, a study published in the journal Nature in December found when there was a big shift in what a person eats, changes could happen incredibly fast, within three or four days.

Numerous studies in both animals and humans also suggest changes to the microbiota early in life may affect the development of important immune cells that influence a person’s predisposition to allergies later in life.

‘‘Disturbances to initial [microbe] colonisation from inappropriate weaning, use of antibiotics, exposure to the wrong microbes can change your risk of allergies to different compounds,’’ says Holmes.

The higher rates of obesity and allergies reported in children born via caesarean section has some scientists convinced that exposure to the right microbes early in life is key to the development of a balanced gut ecosystem.

This idea is supported by research on mice delivered by caesarean section and raised in a germ-free environment. They are difficult to make obese through diet alone, says Holmes.

But when researchers re-introduced microbes into these previously germ-free mice the mice that were colonised with microbes from fat mice put on a lot more weight than those that were colonised by microbes from lean mice, wrote Holmes, in an article for The Conversation.

"This indicates that the microbes in our gut influence how much of the food we eat actually gets turned into fat," he says.

The dynamic nature of the body's internal ecosystem suggests potential treatments for people with microbe-related diseases could be as simple as re-engineering their microbiota, possibly through medication or a change in diet.

A small number of scientists in Australia and overseas have experimented with faecal microbiota transplants, where a donor human stool, usually from a relative, is injected into a person's intestines or colon. Although there is limited published evidence to support it as a treatment for most conditions, some doctors have reported success treating Crohn's disease and other bowel disorders.

This year St Vincent's hospitals in Sydney and Melbourne began a trial for faecal transplants as a treatment for certain forms of inflammatory bowel disease.