Systems biology, microbiome

Vital new understanding of the microbiome

Thursday 01 Sep 16
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Søren Brunak
Professor
DTU Bioinformatics
+45 45 25 26 40

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Henrik Bjørn Nielsen
Associate Professor
DTU Bioinformatics
+45 40 57 48 64

The common perception among researchers is that our intestinal bacteria compete and cooperate in a complex network of interactions. But no-one has as yet fully understood exactly how this takes place.


By Mette Haagen Marcussen

The common perception among researchers is that our intestinal bacteria compete and cooperate in a complex network of interactions. But no-one has as yet fully understood exactly how this takes place.

New ground-breaking research from the MetaHIT international research team—with researchers from DTU leading the way—has analysed the interactions between intestinal bacteria in 233 Europeans, and the results offer hope for better treatment of disease.

"We have shown that the activity level of many bacteria species depends on which other bacteria they coexist with. By studying the bacterial gene expression in 233 Europeans, we have been able to construct an entire network showing which of the many hundreds of bacteria species influence each other's activities," says senior researcher Henrik Bjørn Nielsen, former Associate Professor at DTU.

The study is the largest gene expression study of the intestinal microbiota to date, and the researchers had to build specially designed measuring equipment for the purpose. This enabled them to measure the activity of over 700,000 genes from several hundred bacteria species at the same time. Only by summarising such large volumes of data was it possible for the researchers to create an overview of the patterns in the bacteria's gene expression, i.e. how active their genes are.

"If you want to introduce probiotics, i.e. bacteria to benefit health, it is important to understand how the bacteria you are introducing interact with the other bacteria in the intestines. "
Postdoc Damian Plichta, DTU Bioinformatics

Damian Plichta from DTU Bioinformatics is the lead author of the study:

"The majority of the interactions resulted in one bacteria species reducing its gene expression when it coexisted with a particular other bacteria species. When we investigated the other bacteria, we often found they expressed genes matching those that were reduced in the first species. The bacteria thus avoid competing with each other. This makes sense, because the theory books say that two species cannot coexist if they do the same things, as one of them will be outcompeted and die out."

Analysis of the intestinal bacteria's interactions is important for our understanding of correlations between intestinal bacteria and various diseases. Damian Plichta continues:

"A bacteria species can behave very differently depending on which other bacteria are also present in our intestines. If you want to introduce probiotics, i.e. bacteria to benefit health, it is important to understand how the bacteria you are introducing interact with the other bacteria in the intestines. Our study therefore provides essential basic knowledge on how we can test probiotics in the future for the treatment of disease."

Professor Søren Brunak, who has headed DTU's work in the MetaHIT consortium, adds:

"When we were planning the work on understanding the bacteria's use of their genes in the intestines, many researchers believed it would not provide much new information compared to simply counting the prevalence of the bacteria. This work shows the opposite, and we are naturally very pleased about this."

The results have just been published in an article entitled Transcriptional interactions suggest niche segregation among microbes in the human gut, in the prestigious Nature Microbiology scientific journal.

MetaHIT

MetaHIT is an abbreviation for Metagenomics of the Human Intestinal Tract, and is a major European consortium drawing together 13 partners from universities and the business community in 8 different countries. The project cost around EUR 21.2 million, more than half of which was funded by the European Union.

The project's primary goal was to map the connections between the genes in the human intestinal microbiota and our health and diseases.

Read more about the results in the MetaHIT Report Summary on the European Union's website.

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