A reference gene catalogue of the pig gut microbiome
2016
Xiao, Liang | Estellé, Jordi | Kiilerich, Pia | Ramayo Caldas, Yuliaxis | Xia, Zhongkui | Feng, Qiang | Liang, Suisha | Kjeldsen, Niels Jørgen | Liu, Chuan | Maguin, Emmanuelle | Dore, Joel | Pons, Nicolas | Le Chatelier, Emmanuelle | Prifti, Edi | Li, Junhua | Jia, Huijue | Liu, Xin | Xu, Xun | Ehrlich, Dusko | Madsen, Lise | Kristiansen, Karsten | Rogel Gaillard, Claire | Wang, Jun | Beijing Genomics Institute [Shenzhen] (BGI) | Génétique Animale et Biologie Intégrative (GABI) ; Institut National de la Recherche Agronomique (INRA)-AgroParisTech | Laboratory of Genomics and Molecular Biomedicine, Department of Biology ; Department of Biology [Copenhagen] ; Faculty of Science [Copenhagen] ; University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Science [Copenhagen] ; University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH) | Pig Research Centre ; Danish Agriculture and Food Council (DAFC) | Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome | Département Microbiologie et Chaîne Alimentaire (MICA) ; Institut National de la Recherche Agronomique (INRA) | MICrobiologie de l'ALImentation au Service de la Santé (MICALIS) ; Institut National de la Recherche Agronomique (INRA)-AgroParisTech | MetaGenoPolis ; Institut National de la Recherche Agronomique (INRA) | Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research | Centre for Host-Microbiome Interactions, Dental Institute Central Office, Guy's Hospital ; King‘s College London | National Institute of Nutrition and Seafood Research (NIFES) | INRA metaprogramme Meta-omics of Microbial Ecosystems (MEM) | Animal Genetics Division of INRA | Biology Department of the University of Copenhagen | ANR-11-DPBS-0001,MGP,MetaGenoPolis(2011) | European Project: 267196,EC:FP7:PEOPLE,FP7-PEOPLE-2010-COFUND,AGREENSKILLS(2012)
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 diseases(1). The importance of the gut microbiota in complementing the physiology and genome of the host is now well recognized(2). Knowledge of the functional interplay between the gut microbiota and host physiology in humans has been advanced by the human gut reference catalogue(3,4). Thus, establishment of a comprehensive pig gut microbiome gene reference catalogue constitutes a logical continuation of the recently published pig genome(5). 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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