The microbiota in human health
and well being.

Quantitative Metagenomics

Gut microbiota constitutes an ecosystem of major interest for the biomedical field. Quantitative metagenomics focuses on the collective genome of the species composing this particular ecosystem. Using this approach, we can analyse bacterial DNA diversity and establish its components relative abundance. The approach has been extensively used over the past 5 years, notably in MetaHIT and Micro-Obes projects coordinated at INRA respectively by S. Dusko Ehrlich and Joel Doré, both PI in Metagenopolis.


These projects led to major scientific discoveries and demonstrate MGP’s leadership in this field of research:

2010 - Establishment of the gut microbial gene catalogue (Qin et al., Nature 2010)

2011 - Discovery of enterotypes (Arumugam et al., Nature 2011)

2012 - Characterization of the gut microbiota of patients with type 2 Diabete (Junjie et al.,  Nature 2012)

2013 - Discovery of bacterial species associated to low diversity and establishment of highly accurate stratification models which may have predictive value for identification at risk for obesity-related complications Lechatelier et al., Nature 2013

Dietary intervention impact on gut microbiome gene richness (Cotillard et al., Nature 2013)

2014 - Discovery of a method, based on the analysis of the gut microbiota, to diagnose people affected with liver cirrhosis (Nan Qin et al., Nature 2014)

2014 - Extension of the gut microbial gene catalogue to 9.8 Million genes (Junhua Li et al. Nature Biotechnology 2014)

2014 - Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes (Nielsen et al. Nature Biotechnology 2014)


The discoveries described in these publication are based on our capacity to detect the presence and calculate the abundance of each gene from the catalogue, as well as the variants of the strains and genes in each individual.

Brought together, these technologies set the stage for the exploration of microbiota in many pathologies, and the development of applications of interest for the academic, medical and industrial communities:


Apply new diagnostic/prognostic, biomarkers of disease

Modulate the microbiome in patients

Rationalize interventions aiming to modulate the intestinal microbiota


Provide evidence for health effects of certain foods

Extensive characterization of natural starter cultures (in collaboration with the INRA-MICALIS research Unit)

Anticipate the impact of production processes on the microbiota of fermented products (in collaboration with the INRA-MICALIS research Unit)

Personnalised medicine and care

Develop personalized treatments based on the stratification of patients and differentiation of good or poor responders

Identify biomarkers links to diet

Base nutrition recommandation on microbiota status

Quantitative metagenomics projects combine the expertise of SAMBO, METAQUANT and IBS


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