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If you’re suffering from a digestive disease like Crohn’s, there is one treatment of last resort: eating poop. It’s an unappetising prospect, which is why scientists are hard at work to try and turn poop into a pill.

Right now, if a doctor wants to replace the bacteria in our guts, there isn’t an injection you can have or a pill you can take. Instead, there is a procedure known as a Fecal Microbiota Transplantation (FMT). This is literally transferring a stool sample from a healthy person to a patient – often via the mouth – so that ‘good’ bacteria may transfer to the patient.


And in the race to find alternatives, one group of scientists has created a vast database cataloguing the bacteria in our guts. But before you can go from poop to pill, you’ve got to understand what’s going on inside each and every one of us.

Scientists estimate that there are around 400 unique species of bacteria lurking inside our bodies. Rob Finn from the European Bioinformatics Institute and his collaborators led by Trevor Lawley at the Wellcome Sanger Institute have successfully isolated 273 separate species of bacteria, including 173 which have never been sequenced before. These make up the initial dataset, a work-in-progress periodic table of all the creatures lurking inside our guts.

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The research, published in the journal Nature Biotechnology, is based on 20 faecal samples from the UK and Canada, and could lead to genuine medical breakthroughs. Among the new species are several branches types of Clostridium difficile, or C-Diff, and further research into it could one day help people suffering from irritable bowel disease and a range of other conditions.

“We know everyone – or we're beginning to understand everyone,” says Finn, who refers to bacteria as though they are people. “We’re building up that database and once we have that fingerprint we can use much faster techniques to understand who is present in the next person.”


Think of it like the music app Shazam. It listens to just a few seconds of the music, and compares it to a database of millions of tracks, quickly figuring out what you’re listening to. For songs, read bacteria.

“With the [new catalogue] you probably only need a tenth of the amount of sequencing,” says Finn. Once the fingerprints match the record in the database, scientists can be confident on what species they are looking at. What used to be a laborious task could soon be done far quicker, helping to identify bacteria (or lack of bacteria) in samples more efficiently.

Eventually, the hope is to make the database cover every bacteria found in the gut – but this poses some significant challenges. “We reckon [the database] probably represents 20 per cent of all the gut bacteria, but we say that with a lot of caveats,” explains Finn.

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The database, as it currently stands, is 50 per cent larger than previous projects, and contains most of the more common bacteria, but it is still thought there is a lot missing. “Our dataset is really biased as it tends to come from North America and Europe”, explains Finn – and he notes that the sample size is quite small, with just 20 faecal samples tested.


Figuring out exactly what to include is tricky too. “There are lots of bacteria that are always in your gut and some that are just passing through. Maybe they’re on the food you eat”, he says. “So we need more samples to build up a complete picture. There's quite a lot more out there.”

The hope is that one day individual species of bacteria could be packaged up into pills, which is both a safer and quicker way of treating patients in need of a bacterial boost. “There’s lots in the press about the importance of your gut, your microbiome, in maintaining health and there’s a number of different diseases that are caused by bacteria in your gut. This work is forming the platform for getting the bacteria that we can use to start addressing the questions in detail about what they're doing.”

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