Your inner ecosystem (Image: Artpartner-Images/Getty)

You’re probably the member of a club you didn’t even know existed. According to research published this week, we all have one of three ecosystems of bugs in our guts. New Scientist explores what this surprising discovery means, and how our internal fauna might affect our everyday lives.

Why might the types of bugs we carry be important?

We think of our bodies as our own, but actually only a tenth of our cells are human. The rest are all hitch-hikers, mainly harmless bacteria that have evolved with us.

There are 100,000 billion of these bacteria in our guts, where they play a crucial role in our health by helping to break down food and convert it into energy, and by excluding bacteria that are harmful to us. Some are even said to make us happier. In exchange, we provide shelter and a share of our food.


The types of bugs that call us home could explain differences in our ability to digest food and resist disease, and how we react to drugs.

Isn’t it surprising that all humans share only three predominant gut-bug ecosystems, given our diverse diets, lifestyles and gene-profiles?

Yes, and even the researchers who made the discovery are mystified. “At the moment, it’s purely an observation, but the signal is there, and it’s strong and it’s real,” says Jeroen Raes of the Flanders Institute of Biology in Brussels, Belgium, a co-leader of the team in question. “We’re still guessing the implications.”

How did they find out?

Raes and his colleagues analysed DNA in faeces from 33 individuals from Japan, Denmark, the US, France and Spain. By comparing the DNA sequences with publicly available reference sequences for 1500 bacterial and other species, they excluded all human DNA and identified as many bacteria as they could.

What did they find?

To their amazement, they found that broadly, people’s gut bugs segregated into three distinct “enterotypes”, or ecosystems, not unlike the way that all humans share only a handful of blood types.

Isn’t this a big conclusion for such a small sample?

Maybe, but they have gone on to confirm that the pattern is repeated in larger groups of people, including a study of 154 people from the US and 85 from Denmark.

Surely the type of ecosystem you have depends on what you eat?

Wrong, it seems. The other surprise was that the ecosystem you have doesn’t seem to depend on how old you are, where you live in the world or your genetic make-up either. “We found that people from Japan and France, for example, might have ecosystems more similar to one another than to those of their compatriots, even though they have very different diets,” says Raes.

So what are these three ecosystems?

The researchers have named them “bacteriode”, “prevotella” and “ruminococcus”, to reflect the species that dominate in each. People with a bacteriode ecosystem have a bias towards bacteria that get most of their energy from carbohydrates and proteins. Prevotellas specialise in digesting sugar-covered proteins in mucin, the mixture of viscous proteins in the gut – an ability shared by people with a ruminococcus ecosystem.

Does it matter which one you’ve got?

The only difference identified was in the vitamins produced. Bacteriodes had a higher proportion of bacteria that make high amounts of vitamins C, B2, B5 and H, and prevotellan guts had more bacteria that make vitamin B1 and folic acid. The implications for health are not yet clear, however.

Could this explain why some people may be more prone to obesity?

The researchers did find a correlation between obesity and the abundance of bacteria that extract energy rapidly from food for their own use. Raes is currently looking into this in greater detail in a study of 100 people, to see if any strong links emerge.

Why might there be only three ecosystems?

Raes admits he has no answer yet, but says one possibility is that our gut environment is governed by our immune system, by blood type or the “major histocompatibility complex”, which dictates which blood type you are.

A second possibility is the length of time it takes for food to pass through our digestive system. If it goes slowly, it gives opportunities for a more diverse range of species to grow and thrive.

What about links between our health and gut bacteria – might the identification of the three ecosystems shed light on disease?

It has been suggested that eating sushi might help us to get energy from food, and taking probiotics could help babies who suffer from eczema. It has even been suggested that gut bacteria has a role in Crohn’s disease and autism.

Raes says that there are plenty of studies in mice showing that diet can alter gut bacteria. The hope is that future research will reveal more about the possibility of links between our enterotype and conditions such as obesity and diabetes.

Journal reference: Nature, DOI: 10.1038/nature09944