Genomic variation landscape of the human gut microbiome

A joint effort between EMBL and WashU scientist have permitted to make genomic analysis on metagenomic data using some ecological metadata (geography, time sampling) ...

Gut microbiota for Health expert exchange

gut microbiota for health GMFHx

A new web platform related to gut microbiota field was recently launched. This web platform aims to enhance debate between scientists and clinicians using selection of article related to specific subject like “gut brain axis” or “metabolic conditions”. Nine categories are reported including a media room which help visitors to be aware about last symposium related gut microbiota.

The web platform is supported by ESNM and could be found with the link below :

International Human Microbiome Congress Paris 2012

The next International Human Microbiome Congress (IHMC) organized by MetaHIT be held in Paris, 19-21 March 2012, at the Palais Brongniart. This conference is under the patronage of UNESCO and supported by the European Commission. This is the largest conference on the Human microbiome, the latest taking place in Shenzhen in 2010 and Vancouver in 2011.

Scientific exchanges will be around the analysis of the human microbiome, data organization and interpretation. Then, researchers will present their recent work about associations between the microbiome to human health and the potential to modulate it. Finally, the conference will end around a debate about the challenges of the future.

Personally, I invited you to pay attention on Iradj Sobhani’s talk who will present our latest study about colon cancer microbiome and we could have a chat around the poster of Ling Chun Kong who will present our latest result about the gastric bypass effect on gut microbiota.

Join the conversation on twitter using the hashtag #IHMC2012.

auditorium brongniart paris ihmc2012

To be read :

[FR] La métagénomique et les défis pour la bioinformatique au goût #IHMC2012

To be view :

IHMC Principal investigator interview in video

my.microbes, an open large-scale human microbiome study

The discoverers of enterotypes launched a large scale project called my.microbes. Since Sept. 8, the project is open to anyone who wants to contribute. The study aims to analyze, through high throughput technologies and innovative bioinformatics tools, the microbiome of any person in the world. People can help by giving a sample and a donation.

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Commensal gut bacteria and immune modulation

NF-kb pathway After the development of a cell reporter system for NF-kB pathway and identification of new potential therapeutic molecule by metagenomic screening, INRA scientists have focused directly on intestinal bacteria isolated in the laboratory. The ability to modulate the NF-kB pathway, central for immune response, was studied for 49 commensal strains.

Interestingly, according to the cell lines, enterocytes or colonocytes, the modulatory capacity of commensal bacteria was different and was correlated for some of them with the presence of butyrate or propionate, which are known to be energetic for intestinal cells.

“The cell-based screening method employed in the present study provides a rapid identification of potentially interesting commensal species, however their effects require further confirmation and characterization using other techniques of NF-κB detection. Moreover, the potential implication of these commensal bacteria and their host cells regulating properties in human health and disease may need to be evaluated.” Lakhdari et al

Human gut microbiome and enterotypes


A joint effort between scientists from EMBL (Heidelberg, Germany) and the others partners from the European MetaHIT project have permit to describe that Humans can be split in different group based on their gut microbiota composition. Those groups, named enterotypes, are found across nations and continent. Their discovery, published in Nature Journal1, indicates the existence of a limited number of well-balanced host-microbial symbiotic states that might respond differently to diet and drug intake. Combining three different human gut microbiota datasets generated with different methodologies, the enterotypes are mostly driven by microbial composition and in particularly by Bacteroides, Prevotella and Clostridiales species.

  1. Enterotypes of the human gut microbiome. Manimozhiyan Arumugam, Jeroen Raes, Eric Pelletier, Denis Le Paslier, Takuji Yamada, Gabriel R. Fernandes, Julien Tap, Thomas Bruls, Jean-Michel Batto, Marcelo Bertalan, Natalia Borruel, Francesc Casellas, Leyden Fernandez, Laurent Gautier, Torben Hansen, Masahira Hattori, Tetsuya Hayashi, Michiel Kleerebezem, Ken Kurokawa, Marion Leclerc, Florence Levenez, Chaysavanh Manichanh, H. Bjorn Nielsen, Trine Nielsen, Nicolas Pons, Julie Poulain, Junjie Qin, Thomas Sicheritz-Ponten, Sebastian Tims, David Torrents, Edgardo Ugarte, Erwin G. Zoetendal, Jun Wang, Francisco Guarner, Oluf Pedersen Willem M. de Vos, Soren Brunak, Joel Doré, MetaHIT Consortium, Jean Weissenbach, S. Dusko Ehrlich, Peer Bork. Nature 2011. 

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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>