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Trading chemistry for ecology with poo transplants

Antibiotics joined our growing arsenal of weapons in the fight against disease over seventy years ago. Their target – the bacterial infections that putrefied our wounds, filled our lungs with pneumonia…

As simple as the procedure sounds, we don’t yet fully understand how faecal transplants work. Image from shutterstock.com

Antibiotics joined our growing arsenal of weapons in the fight against disease over seventy years ago. Their target – the bacterial infections that putrefied our wounds, filled our lungs with pneumonia, and made our genitals less than appealing to our lovers. Bacteria were worthy opponents, and with antibiotics, the war against infection seemed ours to win.

But gradually, two facts have become abundantly evident. The first is that not all bacteria are foe. There are billions of bacteria – many of them essential to our health – that call us home. We’re each colonised by trillions of microbes forming communities that occupy every imaginable niche in our body.

These microbial commensals – known collectively as our microbiome – have evolved with us over millennia, and a co-dependent relationship has resulted.

While we provide a cosy niche and abundant supply of food to the microbes living in our intestine or on our skin, they in turn help to release nutrients from otherwise indigestible dietary fibre, synthesise essential vitamins, or produce a moisturising film to keep our skin soft and supple.

The second fact is that antibiotics may be thwarting our best efforts to stave off infection by messing with the delicate ecosystems that our microbial companions form. By indiscriminately annihilating microbes with antibiotics, we are taking a carpet-bombing approach where an assassination is more what we’re after. Innocent bystanders, as well as some of our closest allies, inevitably end up as casualties.

Unsurprisingly, some wily species of bacteria have evolved to take advantage of an ecosystem that has been thrown out of balance. The diarrhoea-causing bacterium, Clostridium difficile, is one such organism that flourishes in the power vacuum that results after antibiotic treatment.

Clostridium difficile. AJC1

A small number of people naturally harbour C. difficile in their large intestine, but most become infected in hospitals or nursing homes, the typical breeding grounds for superbugs.

In recent years, a highly toxic strain of C. difficile has emerged in hospitals in North America. In 2010, it was estimated that half a million people in the US were infected with C. difficile, and up to 20,000 of those died from the infection. The C. difficile superbug is also on the move, with cases in Europe and Australia rising.

For an increasing number of people, even the strongest antibiotics are powerless against C. difficile. In these cases, exasperation has turned to ingenuity, with an increasing number of doctors abandoning chemical warfare in favour of an ecological approach to fighting C. difficile infection.

Introducing the poo transplant

The unsavoury, yet highly effective treatment that has been adopted as an alternative to antibiotics is the faecal microbiota transplant, aka the poo transplant. A poo transplant is exactly as it sounds – taking faeces from a healthy donor, and transferring it, usually via enema, to a willing recipient.

It’s a simple idea, really. By replacing a depleted, out-of-balance gut ecosystem with a robust and healthy one, balance is restored. C. difficile becomes out-competed by friendly bacteria and the diarrhoea ceases. Unlike blood infusions and tissue transplants, faecal transplants require no immunological typing (tests to determine donor-recipient compatibility) to prevent rejection.

Poo transplants are the ultimate in probiotics. Although consuming a tub of lactobacillus-laden yoghurt is easier to swallow than the idea of a faecal enema, the principals are essentially the same.

There has been a resurgence of the technique, faecal transplants are not new. A Denver surgeon, Dr Ben Eiseman, and his colleagues published the first report of the procedure in 1958. And once again, doctors are discovering what Eiseman did 50 years ago – that poo transplants work.

A recent review of all reported studies of faecal transplants to treat C. difficile infection found poo transplants to be effective in over 90% of cases. Recurrence of infection is rare and there has not been a single report of adverse side effects.

Antibiotics may be thwarting our best efforts to stave off infection by messing with the delicate ecosystem of the gut. sparktography

As simple as the procedure sounds, we don’t yet fully understand how faecal transplants work. This may be set to change, however, as global efforts to make sense of the staggering complexity of our microbiome ramp up. The Human Microbiome Project funded by the National Institutes of Health in the United States, and the European Commission-funded Metagenomics of the Human Intestinal Tract project, are beginning to define our most intimate microbial co-habitants.

As we grapple with the complexity of our microbial ecology, perhaps we will discover which specific microbes are responsible for reigning in C. difficile during a faecal transplant. It might be a single species, or perhaps it’s a combination of several.

By identifying the microbes responsible, the poo transplant could eventually be replaced with a probiotic pill containing only the necessary species required to right the system. The “yuck” factor would be removed.

Or perhaps there are particular foods and supplements that we could consume as prebiotics to favour the growth of healthy bacteria when superbugs take hold.

In the meantime, the simplest, and perhaps most obvious way of modifying our gut ecology when superbugs take hold may well be to transfer an ecosystem en masse, through the under-appreciated technique of the poo transplant.


This is the eighth article in Superbugs vs Antibiotics, a series examining the rise of antibiotic-resistant superbugs. Click on the links below to read the other instalments.

Part one: Washing our hands of responsibility for hospital infections

Part two: Superbugs, human ecology and the threat from within

Part three: We can beat superbugs with better stewardship of antibiotics

Part four: The hunt is on for superbugs in Australian animals

Part five: The last stand: the strongest of the superbugs and their antibiotic nemesis

Part six: Unblocking the pipeline for new antibiotics against superbugs

Part seven: A peek at a world with useless antibiotics and superbugs

Part nine: New antibiotics: what’s in the pipeline?