It's one of medicine's hot topics – that the microbes in our gut may contribute to hard-to-treat problems such as allergies, autoimmune disease, irritable bowel syndrome, inflammatory bowel disease and even obesity and diabetes.

Ideally, these different bugs – and there are about 100 trillion of them in there – should keep us healthy by helping to regulate our immune systems and metabolism. Emerging evidence suggests our health can suffer when the balance of these microbes goes awry.

It's complex science and we're a long way from  knowing the answers, but an intriguing example of how gut microbes might influence our health came from Dutch scientists this year after they took microbes from the guts of lean people and put them into the guts of people with metabolic syndrome – the cluster of symptoms that include  excess weight, high blood pressure and high blood sugar and which can lead to diabetes. Six weeks later the recipients' insulin sensitivity had improved, meaning their bodies  controlled blood sugar better.

The factors that might be disrupting gut microbes are on the list of topics at the Lifestyle Medicine Conference in Sydney next weekend. Our sanitised environment and changing diet are among the suspects, but one of the conference speakers, Sydney gastroenterologist Professor Tom Borody, says it's six decades of using antibiotics that has most upset the balance of gut microbes.

''Gut microbiota perform so many essential roles in the body that they work like an organ in their own right,'' he says. ''Yet we're damaging this important organ by knocking out valuable bacteria with recurrent use of antibiotics. We should only use antibiotics when we really need them, not when we have a cold, for instance.''

But if, as some research suggests, problems such as irritable bowel syndrome or inflammatory bowel disease are related to disrupted gut microbes, it could take more than a tub of yoghurt to fix the problem.

''Probiotics are promising – there's evidence they can help in part to restore the balance after antibiotics, for instance – but we don't  yet have a probiotic that can undo all the damage,''  Borody says.

He has another idea – recolonising the gut with microbes from a healthy gut. Called faecal microbiota transplantation (FMT) and still considered a fringe therapy here, it involves harvesting microbes from donor poo and transferring it to recipients in a procedure similar to a colonoscopy. It's more widely accepted in the US, where it's often used to treat a potentially serious bacterial gut infection, Clostridium difficile, which kills about 100,000 Americans a year.

''But there's also some evidence that other conditions, including ulcerative colitis, chronic severe diarrhoea and IBS can be improved with FMT,'' says Borody, who uses the technique in his  practice and believes we need more research to explore its potential.

As for what we can do ourselves to keep our gut microbiota in good shape, he suggests avoiding antibiotics where possible, but if you do need them, take probiotics as well.

Fibre in the diet may help, too, by providing food that helps good microbes flourish, he says. And if you're travelling to exotic locations, a glass of wine or two won't hurt. ''It's quite common for IBS to begin after an overseas trip, but a small amount ofalcohol can work together with stomach acid to prevent new bacteria colonising the bowel.''

Listen to the experts

A free pre-Lifestyle Medicine Conference forum is on from 5.30pm next Friday at Freshwater. The Science Show's Robyn Williams will speak about ''Science and Wellbeing: Facing the Doubters''. The Australian Conservation Foundation's Professor Ian Lowe will talk about the influence of the environment and unlimited economic growth on public health. See lifestylemedicine.com.au.

Paula Goodyer blogs at smh.com.au/chewonthis.