EU-funded researchers sequence human gut microbe genome

EU-funded researchers have sequenced the genome of the community of microbes that lives in our guts. The study sheds new light on the influence of these microbes on our health and could lead to the development of new treatments and diagnostic tests for a variety of diseases.

Published in the journal Nature, the work represents the first major outcome of the EU-funded METAHIT (Metagenomics of the human intestinal tract) project, which is funded to the tune of EUR 11.4 million under the Health theme of the Seventh Framework Programme (FP7).

Our bodies are home to some 100 trillion microbes, most of which live in our intestines where they make a vital contribution to our health by breaking down toxins, making vitamins and amino acids and boosting our immune system.

Despite their importance to our wellbeing, little is known about this community of 'friendly bacteria' in our guts. In this study, METAHIT researchers analysed the microbial DNA found in faecal samples taken from 124 adult Europeans. The study participants came from Denmark and Spain and included people of healthy weight as well as overweight and obese individuals. Some also suffered from inflammatory bowel disease (IBD).

In the course of their research, the team sequenced 576.7 gigabases of genetic material, more than any other similar study to date. This microbial gene set comprises 3.3 million genes, making it 150 times bigger than the human genome.

Over 99% of the microbial species in the samples turned out to be bacteria; 1,150 species were identified, many of them new to science. Each individual harboured at least 160 microbe species in their guts, and the researchers were surprised to find that the gut microbe communities found in the samples were fairly similar to one another.

Jeroen Raes of the Free University of Brussels (VUB) in Belgium explained that human gut flora has two components: a 'core' group that is common to everyone and another group that varies from individual to individual. "It is from this variable part that we hope to find explanations for why some people get intestinal diseases or are prone to obesity," he said.

"We already see that there is a relationship between an irregular gut flora and certain intestinal diseases, such as Crohn's disease or ulcerative colitis. We hope that this research could lead to a greater insight into intestinal diseases, or to the development of new treatments."

The core group of genes common to all samples includes the genes that our bacteria need to break down complex sugars, synthesise vitamins and amino acids, and survive in the challenging environment of the human gut where the pH is low and there is little oxygen.

Looking to the future, the scientists would like to find out whether these essential genes are found in the same species of bacteria in different humans. They also plan to carry out detailed comparisons of the bacterial genes of the individuals who provided the samples.

"Knowing which combination of genes is necessary for the right balance of microbes to thrive within our gut may allow us to use stool samples, which are non-invasive, as a measure of health," commented Peer Bork of the European Molecular Biology Laboratory (EMBL) in Germany. "One day, we may even be able to treat certain health problems simply by eating a yoghurt with the right bacteria in it."

"Beyond providing the global view of the human gut microbiome, the extensive gene catalogue we have established enables future studies of association of the microbial genes with human phenotypes and, even more broadly, human living habits, taking into account the environment, including diet, from birth to old age," the researchers conclude. "We anticipate that these studies will lead to a much more complete understanding of human biology than the one we presently have."

The aim of the METAHIT project is to characterise the genes and the functions of the microbes that live in our gut and investigate how they affect human health. The 4-year project began in 2008 and brings together 14 partners from China, Denmark, France, Germany, Italy, the Netherlands, Spain, and the UK.

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