Humans have just three types of gut bacteria populations

4 May 2011

Every person’s intestinal system falls into one of three clearly distinguishable types of gut microbiota, comparable to blood types. These types are not related to race, native country or diet, according to a new study on human microbe genetics published in Nature [1].

The study was conducted by the European Metagenomics of the Human Intestinal Tract (MetaHIT) Consortium. The consortium consists of 13 partners from academia and industry, from eight countries. It is funded by the European Commission under the 7th FP programme. A similar project in the US, the Human Microbiome Project, is cataloguing the bacteria found in the nose, mouth, skin, gut, and urinary and genital tracts.

The MetaHIT consortium published in March 2010 the first comprehensive catalog of human intestinal bacterial genes, dubbed our second genome. It was found that the gut bacteria encode 150 times as many genes as our own genome and that each individual harbours some 170 bacterial species out of a total of about 1000 that are predominant in the gut. Most of these species are common to many individuals, showing that we are all rather similar.

The current study has refined this view. A bioinformatic analysis at the European Microbiology Lab (EMBL) showed that human populations are split into three groups by the particular combinations of bacterial species they harbor, independently of the geographic origin, health status (obesity or inflammatory bowel disease) or age.

The types of gut microbiota (called enterotypes) can be classified into three large, clearly distinguishable groups: Bacteroides, Prevotella and Ruminococcus. They are named for the bacteria that dominate the intestines of the respective groups. It is still unclear whether people can change from one group to another during their lives.

“The three gut types can explain why the uptake of medicines and nutrients varies from person to person,” says bioinformatician Jeroen Raes of the VIB Department of Molecular and Cellular Interactions and Vrije Universiteit Brussel, one of the two lead researchers in the study. “This knowledge could form the basis of personalized therapies. Treatments and doses could be determined on the basis of the gut type of the patient.”

The research used three different study populations. One included 39 individuals from three continents (Danish, French, Italians and Spaniards from Europe; Japanese and Americans), another comprised 85 Danes and the last 154 Americans. The same three enterotypes were observed with all.

In parallel, bacterial genes that can be used as biomarkers for disease and age have also been found. This indicates that the bacterial communities from our gut not only divide human populations in large groups but can also signal the health status of an individual.

Enterotypes will impact human biology, which will have to explain their existence and the effects they have on humans. Enterotypes will impact medicine and nutrition, by allowing the grouping of individuals and determining their particular needs more efficiently.

Furthermore, gut microbial populations appear to contain novel and promising biomarkers, which will impact detection and possibly treatment of chronic diseases such as obesity and its complications (metabolic syndrome, diabetes and cardiovascular pathologies).

The researchers foresee development of personalized and preventative medicine and nutrition based on gut microbial populations, leading to the overall improvement of human health and wellbeing.


1. Arumugam A, et al. Enterotypes of the human gut microbiome. Nature (2011) doi:10.1038/nature09944.

Further information

2. Gut study divides people into three types. Nature. News. doi:10.1038/news.2011.249

3. The MetaHIT website:


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