What is MetaGenoPolis ?

I’m working since 1 year at Metagenopolis unit at INRA institute. Here is below the presentation video.


MetaGenoPolis (MGP) has as strategic goal to demonstrate the impact of the human gut microbiota on health and disease, by making available quantitative and functional Metagenomics technology to the medical, academic and industrial communities.

More about MGP (tools and numbers), download pdf slides

A new metagenomic marker genes method to study microbiota

Numerical ecology analysis of microbiota by metagenomic sequencing, currently depend on the availability of DNA sequences of microbial genomes in the public databases. Often this approach leads to biased interpretation because the majority of the microbial community has no reference genome. To overcome this methodological obstacle, the [MetaHIT](http://www.metahit.eu) consortium presented a new method...

Gastric bypass help the crosstalk between microbiota and host adipocytes


Following their story about gastric bypass and its impact gut microbiota and metabolic parameters, AP-HP, ICAN and INRA scientists continued to bring new discovers about the crosstalk between the gut microbiota and the host adipocytes. Variations of gut microbiota after gastric bypass were associated with changes in white adipose tissue gene expression. Those results may stimulate deeper investigation about relation between gut microbiota and adipocytes during weight loss.

Mycobacterium tuberculosis origins

mycobacterium tuberculosis

In 2006, I worked at Pasteur Institute (Sylvain Brisse groups) on characterization of special smooth strains isolated in Africa1 which seems to be related to M.tuberculosis (known to have a rough phenotype). Using 16 housekeeping genes, we showed that those strains belong to the same species of M. tuberculosis showing an higher diversity than previously observed.

Following this work, in 2013, the Pasteur institute finally published2 a set of genome of those smooth strains concluding that M. tuberculosis emerged from an ancestral pool of mycobacteria by gain of persistence and virulence mechanisms.

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.

Read more

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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