A decades of metagenomics approach based studies, a text mining overview

The microbiota is the sum of microbial element of a given ecosystem which can be ocean, soils or human body site like oral and gut. In the 90’s, scientist studied microbiota using classical microbiology culture-dependent approach. However, the majority of microbes aren’t cultivable yet and trying to understand interaction in a microbial ecosystem is clearly biased without independent culture approach.

Rondon et al published in 2000 for the first time a soil study using the metagenomic approach. Basically, it consist to study all the DNA extracted from an environmental sample. As a result, whereas the number of microbiota study continued to increase, the number of paper using metagenomic took off. The metagenomic approach is the “association” of environmental ecology and genomic.

I always got the feeling from my lecture than this full association was not done between ecologist and genomic people. To test this association, I extracted the 10/04/2011 from the pubmed database all articles with this query : give me article where you find in title or in the abstract the keyword “metagenomic” or “microbiota” since 1991. With this query, I obtained 5193 articles.

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Functional metagenomics

PHENOS platform plateforme INRA functional metagenomic

Functional metagenomic appears to be totally complementary to the conventional Shotgun metagenomics approach that uses only metagenomics high throughput sequencing to access the biodiversity of an ecosystem. Two studies (see Publications) have used this means to explore functionalities of the human intestinal microbiota. The first driven by INSA (Toulouse) has led to identification of new catalytic modules present in abundance in the intestinal microbiota. These modules permit to degrade  complex substrate including dietary fiber.

"Here, it was applied to identify highly prevalent genes encoding enzymes that are involved in the catabolism of the dietary fibers by the human gut microbiome, and provided new insights into the gastro-intestinal tract functional trophic chain." Tasse et al.


The second study conducted at INRA (Jouy en Josas) has allowed to identify new functions involved in crosstalk between the  human intestinal cells and the intestinal microbiota. Understanding this crosstalk is the key to better understanding inflammatory bowel disease for example.

"We suggest that they are likely to help identify genes that human-associated microbes may use to affect expression of genes and  pathways of their host and thus open avenues towards   , the development of potentially new probiotics or therapeutic molecules." Lakhdari et al.


  1. Functional metagenomics to mine the human gut microbiome for dietary fiber catabolic enzymes. Lena Tasse, Juliette Bercovici, Sandra Pizzut-Serin, Patrick Robe, Julien Tap, Christophe Klopp, Brandi L. Cantarel, Pedro M. Coutinho, Bernard Henrissat, Marion Leclerc, Joël Doré, Pierre Monsan, Magali Remaud-Simeon and Gabrielle Potocki-Veronese. Genome Research. 2010. (In Press)
  2. Functional metagenomics : a high throughput screening method to decipher microbiota-driven NF-kB modulation in the human gut. Lakhdari O, Cultrone A, Tap J, Gloux K, Bernard F, Ehrlich SD, Lefevre F, Dore J, Blottière HM. PLoS ONE. 2010. </li> </ol>