You Are Not a Zoo

Ever since they began to realize how important the vast colonies of bacteria living inside us might be to our health, scientists have been speculating that one day, people will receive medical treatments specifically tailored to their own "gut flora." That day is getting closer. An international group of researchers has found that humans fall into a few neat categories based on their gut bacteria. These categories might define us as clearly as blood types, with broad implications for our health and for medicine in general.

The easiest way for scientists to study the bacteria in people's guts is to study the bacteria that are, ah, evacuated from the gut. So the researchers obtained fecal samples from 22 people in four European countries. By sequencing the DNA in each sample and weeding out all the human bits, they were left with a set of bacterial DNA for each person. They pooled this information with previously existing data from two Americans and nine Japanese subjects to create an intercontinental set of gut microbe DNA.

By combing through these DNA sequences for matches to previously published bacterial genomes, the scientists assembled a list of bacterial types in each subject. Then they looked for relationships among these diverse casts of gut bacteria. They found a startlingly clear pattern: There were three distinct bacterial ecosystems, and each person fell into just one of these three categories.

Each category--the researchers dubbed them enterotypes--was characterized by one dominant bacterial type, coexisting with up to a dozen other main bacterial players. This led the authors to believe that the bacteria inside you aren't a random grouping. Instead, they make up a stable and discrete ecosystem. Your gut might be a desert or a tundra or a wetland, but it's not a zoo.

How do we come to house one of these bacterial ecosystems? The researchers found that people's enterotypes didn't correspond to their age, gender, body mass index (BMI), or nationality. Perhaps whatever types of bacteria are the first to colonize us when we're sterile newborns--some random accident of the hospital or house where we're delivered--determine our microbial fate.

And to what degree is our microbiome our fate? It's not clear yet. We rely on our gut bacteria to help us digest our foods and to produce certain vitamins. The researchers found that each enterotype was especially good at producing a certain necessary vitamin--but no enterotype was lacking in any vitamin production.

While there was no pattern to who fell into what enterotype (except that one type was somewhat more frequent in Japan), there were correlations between human features and the genes of their gut bacteria. Some types of bacterial genes corresponded to nationality, gender, age, or BMI. This might reflect the demands that we make on our gut bacteria. We don't determine which ecosystem populates us, but our diet and lifestyle could affect the balance of species in their population.

The researchers also looked at a larger set of data from American and Danish subjects, and found that their gut microbe DNA seemed to fit into the same three clusters. But further research might reveal more enterotypes, or subcategories among them. Individuals from less westernized societies, or from remote rural areas, might reveal new patterns. Additionally, fecal bacteria don't represent all the bacteria living in our guts. But these three enterotypes represent an exciting step toward defining our individual microbiomes.

Scientists are only beginning to understand how our gut bacteria affect our overall health, tendency toward diseases or obesity, and even mental health. As more of their functions become clear, doctors may be able to offer diagnoses--or treatments--specific to our enterotypes. Medicine based on the the non-human organisms living inside us, strange as it seems, might be more personalized than ever before.