Research is increasingly showing that the myriad of microorganisms that live inside our bodies could quite literally hold the answers to many of our health ailments. Just a decade ago, this was little was known about our gut but now researchers believe they could change the future of human health.

Inspired by her own gastrointestinal problems, Amanda Kabage, a paediatrics researcher at the University of Minnesota underwent a procedure known as faecal microbiota transplantation or FMT to deal with a bacterial infection known as Clostridium difficile. Although this bacterium can be found in the guts of most people, if it grows out of control it can release toxins that damage the intestines and kill other bacteria that keep the organ functioning.

FMT is a process where donor stool with a healthy concoction of microbes is transplanted into your gut to replace your damaged microbiota.

Clostridium difficile has caused millions of infections and thousands of deaths around the world every year. One recent review estimated around 323 cases for every 100,000 people, or about 25 million cases globally.

Kabage says that the effect of FMT was rapid and astounding. After 14 months of suffering, two weeks after her treatment Kabage was back to her normal self. The gastrointestinal issues had fully disappeared.

The treatment she received is the culmination of a growing realisation that microorganisms that make their homes inside our bodies play an important if somewhat underappreciated role in our health. Scientific research has helped to uncover the complex interactions between our general wellbeing and the flora flourishing on and in our mouths, noses, airways, lungs, stomachs, colons, sexual organs and skin.

As our understanding of this complex and life-long relationship grows, we are beginning to understand how to harness this knowledge to optimise our health.

The microbiome functions like a city of communities. It is made up of trillions of bacteria, fungi, and virus neighbours, all jostling for space inside and on the surface of our bodies. As they live out their existence in their own neighbourhoods, they also perform roles that benefit the wider body. A healthy microbiota is an abundantly diverse one, and everything from our diet to our environment can potentially influence how well it functions.

Studies have shown that the overuse of antibiotics and the overconsumption of processed foods are destroying our gut microbiota which leads to increased susceptibility to infections such as Clostridium difficile and other forms of disease.

Now that we know just how crucial our microbiota is, we need to firstly, take better care of it, and secondly, find ways to effectively use our microbiota to help us treat or even prevent disease.

With some bacteria becoming antibiotic-resistant, treatments such as FMT has offered an alternative in the battle against infections such as C. difficile. By effectively restocking a healthy balance of microbes in the gut, it allows those bacteria to bring numbers of C. difficile back under control.

This could well be the new era of health where we decrease our reliance on antibiotics, and instead, seek to work with what is already naturally present in our bodies.

While this can be viewed as a breakthrough in modern medicine, it is important to note that the concept of using faecal matter in medical treatments can be traced back to ancient Egypt. The Egyptians had used human and animal stools as active ingredients against a variety of ailments. But as modern medicine led doctors to appreciate the need for hygiene to maintain aseptic environments, the use of faeces fell out of use.

Patients can now receive FMT in the form of a colonoscopy, an enema, or oral ingestion through small capsules of frozen-faecal material.

This new era of innovation in microbiome therapeutics could at least help patients depart from the ick factor tied to FMT, says Christian Lodberg Hvas, a clinical associate professor at Aarhus University in Denmark. “Swallowing faeces is quite controversial for most people,” he says.

In the future, he thinks we might even reach a point where it will be possible to pick and choose microbes from a library of helpful bacteria to treat different diseases. “Targeted microbiota therapy – basically live biotherapeutics – is going to be rising. And then FMT will be placed somewhere in a corner,” he says. “But we don’t even know if we’re focusing on the right things. We have high hopes in microbiota and some of the hopes are realistic and may be achieved, and a lot of the hopes are illusions.”

Scientists are also looking into using microbiota transplants for a wide range of disorders, such as insomnia, Parkinson’s disease, HIV, chronic fatigue, multiple sclerosis, obesity, insulin resistance, metabolic syndrome, and autism.

This could well be the dawn of a new age for modern medicine.