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Nat Microbiol. 2016 Sep 19;1:16161. doi: 10.1038/nmicrobiol.2016.161.

A reference gene catalogue of the pig gut microbiome.

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BGI-Shenzhen, 518083 Shenzhen, China.
GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark.
SEGES Pig Research Centre, DK-1609 Copenhagen V, Denmark.
Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome.
MICALIS Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
MetaGénoPolis, INRA, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research.
King's College London, Centre for Host-Microbiome Interactions, Dental Institute Central Office, Guy's Hospital, London SE1 9RT, UK.
National Institute of Nutrition and Seafood Research (NIFES), Postboks 2029, Nordnes, N-5817 Bergen, Norway.


The pig is a major species for livestock production and is also extensively used as the preferred model species for analyses of a wide range of human physiological functions and diseases1. The importance of the gut microbiota in complementing the physiology and genome of the host is now well recognized2. Knowledge of the functional interplay between the gut microbiota and host physiology in humans has been advanced by the human gut reference catalogue3,4. Thus, establishment of a comprehensive pig gut microbiome gene reference catalogue constitutes a logical continuation of the recently published pig genome5. By deep metagenome sequencing of faecal DNA from 287 pigs, we identified 7.7 million non-redundant genes representing 719 metagenomic species. Of the functional pathways found in the human catalogue, 96% are present in the pig catalogue, supporting the potential use of pigs for biomedical research. We show that sex, age and host genetics are likely to influence the pig gut microbiome. Analysis of the prevalence of antibiotic resistance genes demonstrated the effect of eliminating antibiotics from animal diets and thereby reducing the risk of spreading antibiotic resistance associated with farming systems.

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