The human microbiome – Of people and microbes

Many years ago, I learned in my undergraduate immunology class to think about bacteria as potentially dangerous microbes that could cause disease and had to be fought off by the immune system. In 2010, I attended an international immunology conference where one of the sessions was about gut immunity. I left the lecture hall positively excited about all the research that was emerging about the interactions between the body’s commensal bacteria and the immune system.

It’s been clear for a long time that bacteria are not just a group of bad guys. In fact, there is a whole lot of them that have evolved to live in and on people, providing their host with beneficial functions (for example, helping in the digestion of complex carbohydrates) in exchange for shelter and food. In the past few years, biologists have become more and more interested in the “microbiome”, the collection of the body’s commensal bacteria and their genes, and how it affects human health and disease.

In 2011, a European consortium analyzed the different bacterial species present in the gut of 22 Europeans and compared these microbiomes with about 12 others already characterized in Japan and the US. As the bacteria found in the intestine have evolved to grow in an oxygen-free environment, growing them in Petri dishes in the lab to study them is difficult. However, researchers can catalog the bacterial species making up the microbiome by collecting microbial samples from the body, extracting the genetic material and identifying the various species present based on differences in a certain bacterial gene.

Although the gut microflora varies from individual to individual, most of the bacterial species identified in the European consortium study fell roughly into three groups (called enterotypes), which the researchers dubbed Bacteroides, Prevotella, and Ruminococcus after the dominant microbe in each. The presence of these three enterotypes was confirmed in two other larger cohorts (154 Americans and 85 Danes). These data suggest that there is a limited number of microbial communities in the human gut.

Research on the microbiome (characterization of the species making up the human microbiome, but also studies investigating its role in disease, development and immune function) was one of the runners-up for the 2011 “breakthrough of the year” of the major scientific journal Science. The year 2012 has also been rich in advances in the understanding of the microbiome’s interactions with its host. Let’s see if it will make it again to the list of the top breakthroughs of the year. I’m looking forward to the list anyway!


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