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24, chemin de Borde Rouge –Auzeville – CS52627
31326 Castanet Tolosan CEDEX - France

Dernière mise à jour : Mai 2018

Menu Logo Principal AgroParisTech Université Paris-Saclay


GABI : Génétique Animale et Biologie IntégrativeUnité Mixte de Recherche INRA - AgroParisTech

The pig gut microbiome: the first catalogue with 7.7 million of genes is now available

The pig gut microbiome
We produced and characterized a catalogue of 7.7 million bacterial genes in the pig gut microbiome. This is a first for a livestock species, following the catalogues characterized for the human gut microbiome in 2010 and that of mice in 2015. These studies open important perspectives for the understanding of the interactions between the host, the gut microbiome and the environment. They provide major resources for biomedical and agricultural research.

Context and Stakes

The gut microbiome, through its different functions, is a biological compartment containing a lot of information, little known in livestock and potentially associated with the observed phenotypic variations. Microbiome DNA sequencing will provide access to the cultivated and non-cultivated bacteria. Initially based on the characterization of RNAr 16S coding gene, the analysis of the microbiome has been enlarged to all the genes if a reference gene catalogue exists, as in man. Since the pig is a major species for world food production and an animal model often used in biomedicine, scientists have made the establishment of its gene catalogue for the gut microbiome a priority.
A consortium led by the Inra in partnership with the BGI-Shenzhen and the University of Copenhagen has been formed to perform this work, supported by the MEM metaprogram (an international action and the METALIT 2012-2014 project). This work is important for the fine functional analyses of pig gut microbiome and its interactions with the host.


The gene catalogue of the pig gut microbiome was established using pig DNA sequencing of fecal samples from 287 pigs from France, Denmark and China. These animals from 17 breeds or lineages are from 11 different farms in these three countries. The collected data have allowed identifying 7.7 million of genes. A small sub-group of genes was found in all pigs, confirming the existence of shared bacterial genes but also an important individual variability. Ninety-six percent of the biological functions identified in the gut microbiome of man are present in pigs, confirming the potential interest of using pigs for biomedical research. Inversely, only 78% of the functions identified in the pig gene catalogue are present in men, suggesting additional functions in the pig digestive system. These results suggest that sex, age and host genetics have an influence on the composition of the pig gut microbiome. We showed the presence of genes for antibiotic resistance in all pigs, independently of country of origin or antibiotic supplementation. We showed, however, that there are higher numbers of antibiotic resistance genes in Chinese pigs, which receive antibiotics continuously. These results confirm the efficacy of eliminating the use of antibiotics in animal food to reduce the risk, associated with farming practices, of the dissemination of antibiotic resistance genes to the environment.


The gene catalogue of the pig gut microbiome is a major reference resource, in the continuity of the information provided by the sequencing of the pig genome. It will enable approaching in detail the functionalities of the pig gut microbiome in relation with the physiological variations of the host (animal efficiency, immune defenses, etc). These results open the way to new research in predictive and integrative biology in pigs, with a strong potential for the development of innovative strategies and the identification of policy levers for breeding and sustainable food systems for tomorrow.


Scientific Publication

Xiao L, et al. 2016. A reference gene catalogue of the pig gut microbiome. , Nature Microbiology 1, Article number: 16161: 10.1038/nmicrobiol.2016.161

INRA press release

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