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Poo transplants and probiotics – does anything work to improve the health of our gut?

The ConversationOur gut does more than help us digest food; the bacteria that call our intestines home have been implicated in everything from our mental health and sleep, to weight gain and cravings for certain foods. This series examines how far the science has come.


For more than one hundred years, we believed avoiding bugs or removing them from our system was the simplest way to improve our health.

But while tremendous public health advances have come from controlling dangerous pathogens, we now understand the trillions of other bacteria that live in our body – and in particular, our gut – perform a range of important functions.

So when, and how, should we try to manipulate these microorganisms, collectively referred to as our microbiome?

 What is the human microbiome?

What we eat satisfies the nutrient demands of our microbiome – and subsequently shapes their capacity to further contribute to our health. But the modern lifestyle, particularly diet and hygiene changes, have altered our relationship with our microbes.

To have a healthy microbiome, the best advice is to include natural plant foods, including fibre, in your diet. But although diet has a major role in shaping our microbiome, it’s not a precise way to re-engineer it if things have gone wrong.

There are two broad avenues for microbiome engineering: generic strategies that target large numbers of different microbes (bacteria) simultaneously, such as fecal transplant and antibiotics; or specific strategies that target a small group of microbes, such as probiotics.

Although changes in our microbiome are associated with many chronic diseases, and those changes almost certainly have some contribution to the disease, they are not necessarily the main cause. Microbiome manipulation is most useful when we know exactly how microbes are involved in particular diseases.

But if you don’t have a problem, you don’t need to mess with your microbiome. This is another reason why taking antibiotics when you don’t them is a bad idea.

Poo transplants

Fecal microbial therapy, or fecal transplants, are the transfer of a fecal sample from a healthy donor to a recipient. This can be done via nasogastric tubes (inserted into the nostril, down the throat and into the stomach) or inserted directly into the colon.

Fecal transplants have had spectacular success with treating C. difficile infections. This bacterium causes severe diarrhoea and inflammation. Recurrent infections are extraordinarily debilitating and life-threatening.

Trials of fecal transplants typically show a 90% success rate in treating this condition.

But C. difficile disease is a special case. The disease has one main cause and a consequence of the infection is a greatly reduced microbiota. In the “empty” gut environment of such patients, it’s easy to introduce new organisms. The removal of one problem organism is an easy target.

Most conditions involving gut health – such as obesity, inflammatory bowel disease, and irritable bowel syndrome) – have more complex causes and the gut retains a high-density complex combination of bacteria.

Fecal transplants have raised far more questions than answers. Dundanim/Shutterstock

For complex gut health issues, the effectiveness of fecal transplants is either much lower, or not proven. Of two published studies of fecal transplants for inflammatory bowel disease, for instance, one found a low effect and one no effect.

Although clinical trials of fecal transplants have reported few problems, we should be alert to the risk. There have been reports of patients showing unexpected weight gain after treatment, for instance. This may be attributable to the engineered microbiota, or may simply reflect that they are no longer seriously ill.

For issues of long-term safety and effectiveness, there are still far more questions than there are answers.

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