Not a waste of time: how faecal transplants and microbiome editing signal a new frontier for personalised health
After understanding how to improve human health by altering our DNA, scientists are now targeting the DNA of the trillions of bacteria living inside our guts as well.

How do you feel about the idea of giving or receiving a faecal transplant? If you’ve wrinkled your nose, then you’re unlikely to be alone.

Humans rank among the species that avoid consuming their own excrement. We instinctively recoil from ingesting substances we believe may contain disease causing micro-organisms.

But some species such as rabbits eat their own faeces to extract further nutrients. And the practise isn’t completely unknown among humans.

Back in the fourth century, the Taoist herbalist and alchemist Ge Hong prescribed healthy faeces to cure food poisoning in his famous medical text Zhou Hou Fang (Handbook of Prescriptions for Emergencies).

What Ge Hong didn’t understand is why is faeces can be beneficial in certain circumstances. The answer lies in our microbiota, the 100 trillion bacteria, fungi and viruses living in our guts and contained in our faeces.

Our colonies of gut bacteria are as unique as a fingerprint and change over time depending on what we eat and how we live. Antibiotics, for example, are an especially blunt tool, killing bad bacteria but also plenty of good.

This is problematic given greater diversity of beneficial bacteria is associated with better health. Our microbiome not only exerts control over our immune system, but also our emotions, our weight and whether we will contract certain diseases like Alzheimer’s or Parkinson’s.

Editing bacteria’s DNA

Research into which bacterial strains influence which health conditions and how they interact with each other is still in its infancy but growing fast. Leading scientists in the field include Professor Tim Spector, epidemiologist at Kings College London, whose study of twins demonstrated the importance of the environment and nutrition to microbiome composition.

In the US, the Berkeley Initiative for Optimised Microbiome Editing (BIOME) team includes Jennifer Doudna, who won the Noble Prize for developing the precision gene editing technology CRISPR. As we previously wrote, this tool acts like a pair of scissors, enabling scientists to cut, add or delete genes within our DNA to cure genetic diseases.

Doudna now hopes to use the same technology to alter the DNA of our gut bacteria too. But first, BIOME needs to map the bacteria, no easy task when there’s 100 trillion of them.

It then needs to be able to edit enough bacteria within select colonies to make a positive difference to the overall composition.

Indeed, one of the limitations with consuming probiotics is that even capsules containing up to 50 billion cfu (colony forming units) represent just a drop in the gut bacteria’s vast ocean. Many are based on just one strain – lactobacilli – because it’s the one that survives in oxygen and can be cultured outside of the human body in a lab.

Approving FMT products

In the meantime, faecal microbiota transplants (FMT) – receiving someone else’s faeces – are increasingly aiding or abetting certain diseases, including cancer. So far, they’ve shown the most success (90% rate) killing the superbug behind Clostridioides difficile (C.diff).

Last November, Australia also became the world’s first regulator to approve a donor-derived microbiota product, BIOMICTRA, to treat recurrent C.diff. A frozen syringe formulation is administered rectally, although the biotech is also working on an oral product (popularly known as crapsules or poop pills).

Later the same month, the US Food & Drug Administration (FDA) approved its own first product (REBYOTA), also for C.diff patients. In Germany, FMT is subject to the German Medicines Act, meaning it can be performed as an individualised clinical trial.

In the UK, it’s regulated as a medicinal product. Specialist centres operate licensed stool banks, providing FMT samples for clinical trials and treatment of C.diff infections.

One major hurdle is finding healthy stool donors: people whose microbiomes haven’t been compromised by antibiotics or weakened by sugar-laden and fibre-free diets. Stool also needs to be screened for infectious diseases, autoimmune conditions, and chronic gastrointestinal disorders.

Expanding FMT clinical trials

The research field is growing quickly. As of June 2023, 465 trials were registered on They cover a whole gamut of conditions including: ADHD, autism, Alzheimer’s, depression, IBS, chronic liver disease, Parkinson’s, Type 1 Diabetes and many others:

Deep meditation may also positively regulate gut bacteria thanks to the ongoing dialogue between the gut and the brain through the vagus nerve. A Chinese study examining the faecal microbiota of Tibetan monks found higher levels of bacterial strains associated with a reduced risk of anxiety, depression and cardiovascular disease.

One promising research area concerns cancer: manipulating the microbiome of patients who don’t respond to immunotherapy drugs. Two recent studies, one in Israeli and one in US, demonstrated positive results with melanoma (skin cancer).

In Israel, the faeces of a man who’d successfully responded to the immunotherapy drug nivolumab were given 26 people who had not. FMT benefited one third.

Other trials are examining how re-populating our guts with beneficial bacteria may slow down the ageing process or aid weight loss.

As we previously wrote, many centenarians share large colonies of the bacteria Akkermansia muciniphila. Likewise, obesity is associated with higher levels of Fimicutes bacteria relative to Bacteroidetes.

Many of us have already made the link between what we eat and its impact on our gut bacteria. In the not- too-distant future, we may also start donating what comes out the other end to someone in need or, freezing it when we are younger to top up our bacterial colonies when we are older.


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