Denmark: Researchers uncover new knowledge about our intestines

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Researchers uncover new knowledge about our intestines

Monday 07 Jul 14

DTU researchers have identified and mapped 500 previously unknown microorganisms and more than 800 bacterial viruses in our intestinal flora. A discovery which—in the long term—can replace antimicrobial agents and perhaps improve treatment and prevention of, e.g., type 2 diabetes, asthma and certain intestinal disorders.

By Signe Gry Braad

DTU researchers have identified and mapped 500 previously unknown microorganisms and more than 800 bacterial viruses in our intestinal flora.

A discovery which—in the long term—can replace antimicrobial agents and perhaps improve treatment and prevention of, e.g., type 2 diabetes, asthma and certain intestinal disorders.

Researchers from DTU Systems Biology have mapped 500 previously unknown microorganisms in human intestinal flora as well as 800 also unknown bacterial viruses (also called bacteriophages) which attack intestinal bacteria.

To map the microorganisms, the researchers have developed a new principle for analysing DNA sequence data, which they have named the co-abundance principle. A principle which basically assumes that different pieces of DNA from the same organism will occur in the same amount in a sample, and that this amount will vary over a series of samples.

“Using our method, researchers are now able to identify and collect genomes from previously unknown microorganisms in even highly complex microbial societies. This provides us with an overview we have not enjoyed previously,” says Professor Søren Brunak who has co-headed the study together with Associate Professor Henrik Bjørn Nielsen.

So far, 200-300 intestinal bacterial species have been mapped. Now, the number will be more than doubled, which could significantly improve our understanding and treatment of a large number of diseases such as type 2 diabetes, asthma and obesity.

Viruses—not antimicrobial agents

The two researchers have also studied the mutual relations between bacteria and viruses.

“Our study tells us which bacterial viruses attack which bacteria, something which has a noticeable effect on whether the attacked bacteria will survive in the intestinal system in the long term,” says Henrik Bjørn Nielsen...

Read more: http://www.dtu.dk/english/News/Nyhed?id=fe4b6c9a-c07a-4e2d-b87d-8a99c188eeca

Journal Reference:

H Bjørn Nielsen, Søren Brunak, S Dusko Ehrlich et al.

Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes.

Nature Biotechnology, 2014; DOI: 10.1038/nbt.2939

Abstract

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Most current approaches for analyzing metagenomic data rely on comparisons to reference genomes, but the microbial diversity of many environments extends far beyond what is covered by reference databases.

De novo segregation of complex metagenomic data into specific biological entities, such as particular bacterial strains or viruses, remains a largely unsolved problem.

Here we present a method, based on binning co-abundant genes across a series of metagenomic samples, that enables comprehensive discovery of new microbial organisms, viruses and co-inherited genetic entities and aids assembly of microbial genomes without the need for reference sequences.

We demonstrate the method on data from 396 human gut microbiome samples and identify 7,381 co-abundance gene groups (CAGs), including 741 metagenomic species (MGS).

We use these to assemble 238 high-quality microbial genomes and identify affiliations between MGS and hundreds of viruses or genetic entities.

Our method provides the means for comprehensive profiling of the diversity within complex metagenomic samples.

http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.2939.html