Our bowels are home to trillions of bacteria – but how do we know which are the bad bacteria and how do we get rid of them?

IT’S HARDLY the most appetising thought, but your large bowel contains trillions of bacteria that outnumber all the other cells in your body by more than 10 to one.

They are not just idle hitchikers though – studies suggest that bugs in your gut play roles in nutrition and the immune system and that an imbalance between the “good” and “bad” bacteria may be linked with bowel conditions or even obesity.

But what do we really know about our gut flora, and particularly about potentially health-promoting probiotics that can help establish a healthy balance in there?

Previously, our understanding of what is in the “microbiota” has been hampered by techniques that rely on isolating and growing bacteria in the lab to identify them, explains Dr Paul O’Toole, a lecturer at the department of microbiology at University College Cork. “In practice, 70 per cent or more of the bacteria in the gut cannot be cultured in conventional media. So it’s the tip of the iceberg, where you miss the 70 per cent below the water line,” he says

But in recent years new, molecular methods are now being used to figure out what’s in there. “New advances in DNA sequencing have been at the forefront of that development,” says O’Toole. He describes as a “landmark” a new study published by Nature this month that used molecular techniques on faecal samples from 124 European individuals to build a catalogue of microbial genes in the human gut.

Their findings suggest that the makeup of gut bacteria can vary considerably between people and that each individual in the study harboured more than 160 different species of bugs in their bowels. The balance of those bacterial types and their effects on health are the subject of many investigations – including a stream of studies in recent years looking at the relationship between gut bugs and obesity.

It’s a controversial question, according to O’Toole. “The most neutral interpretation of a complex area, even for us specialists, is that probably several microbial products are recognised by the body, and that disruption of this microbial antagonism-host reaction balance can drive inflammation and obesity,” he says.

Meanwhile, there’s increasing interest in the impact of the microbiota on bowel diseases, according to consultant gastroenterologist Eamonn Quigley, professor of medicine and human physiology at UCC, who notes that gut microbes have been so far relatively ignored from a clinical perspective.

“We have a long way to go, but I think there’s accumulating evidence that changes in the composition in the microbiota can have an impact on disease models,” he says. “In most cases I think it’s fair to say we have strong hints of what is going on but we don’t know precisely what is going on.”

Yet, while we might not understand the exact mechanisms, there are some conditions where harnessing the gut bacteria can make a difference, notes Quigley, who is currently president of the World Gastroenterology Organisation. “There’s no question that certain probiotics are effective in diarrhoeal illness and that has a potentially very significant impact in terms of things like daycare diarrhoea and travellers’ diarrhoea,” he says.

Irritable bowel syndrome (IBS) and inflammatory bowel disease have also been linked with the microbiota, and Quigley has been involved in the development of Align, a probiotic supplement that is available commercially in the US. It targets the symptoms of IBS with a probiotic bacterium called Bifantis, which was developed through the Alimentary Pharmabiotic Centre in Cork and eventually licensed to Procter Gamble.

But it’s not just a case of swallowing any probiotic to get the benefits – it has to be the right one, as Quigley explains.

“You can take two bacteria which are so closely genetically related that there may be a 1 per cent difference, but one may have a potent anti-inflammatory effect, the other may have no effect or even have a pro-inflammatory effect. So that is why knowing exactly what you are dealing with and what it is doing is terribly important,” he says.

“On the positive side, there is a lot of good science going on at the moment and there are a lot of centres throughout the world, including here, where people are looking very critically at everything from genome level all the way through to clinical studies, and trying to do that at the highest standard possible. That’s the good news.”

That might sound surprising in light of the avalanche of probiotic-enriched products that have hit supermarket shelves in recent years, claiming to boost health. “There are a lot of claims out there that have no evidence to support them,” says Quigley. “So for the consumer it’s very difficult to make recommendations at the moment because you don’t have the data in front of you that shows that this contains what it is supposed to contain and that has been identified at genome level.”

The European Food Safety Authority is now coming down hard on food manufacturers, insisting on scientific data to support any health claims they use to market their probiotic-containing products. “If you are going to make health claims you have to back it up with science,” explains O’Toole. “It’s up to the scientist to produce a dossier showing clinical effects, and when we have had discussions with industry we have always firmly held the line that we accept wholeheartedly the requirement of us to produce top-level science to support health claims.”