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Scientific progress

13 - 03 - 2017

3D technology to analyse microbiota interactions tested in mice

For the first time, researchers were capable of analysing the interactions between the intestinal microbiota in mice, using a new 3D technology. This device will soon be tested in humans and in the agri-food industry. 

3D technology to analyse microbiota interactions tested in mice


The intestinal microbiota encompasses all the microorganisms (bacteria and viruses) that are present in the digestive tract. More and more studies are showing links and interactions between the microbiota and other organs in the body, with potential effects on the metabolism, mental health, the immune system etc. However, the exact composition of the intestinal microbiota remains complicated to establish, as are the interactions taking place in this ecosystem. Therefore, it is difficult to implement adapted and tailored therapeutic treatments. 

A new technique could, however, change this situation Researchers from the “Spatial regulation of genomes” team at the Pasteur Institute have indeed succeeded in quantifying and exploiting the interactions between bacteria and phages (viruses that infect only bacteria) among the intestinal microbiota of mice.

A detailed map of the phage-bacteria interactions


To do this, they used a new approach: 3D metagenomics. It is a discipline that studies the metagenome, the set of DNA fragments from a microbial community, in this case the intestinal microbiota. The 3D metagenomics used here exploit the physical contacts between the DNA fragments of the sample, and then deduce their proximity. A map of the different interactions can then be established, and an algorithm developed by the team helps reconstruct the genomes (genetic heritage) of the bacteria and phages present. The team can then accurately deduce which phage infects which bacteria.

Initially carried out on samples that were previously identified and quantified, the technology was then successfully tested on a sample of the natural microbiota of mice, via stool samples of the animal. 375,000 microbial DNA fragments were collected and about a hundred bacterial and viral genomes reconstituted. A map of the physical interactions between the bacteria and the phages of this microbiota was then established by the team, an experiment that had never been done before on a complex natural microbiota.

In addition to opening a window to our microbiota ecosystem, this method could help us better understand the mechanisms that lead to antibiotic resistance. For the team, the next step will be to test 3D metagenomics on human samples and samples from the agri-food industry. This approach is still in early research stages, nevertheless, it could one day give rise to improvements in pre-medical diagnostics.  



Hélène Bour


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