title: A reference gene catalogue of the pig gut microbiome.
abstract: 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.
authors.affiliation: BGI-Shenzhen, 518083 Shenzhen, China.
authors.forename: Liang
authors.initials: L
authors.lastname: Xiao
authors.affiliation: GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
authors.forename: Jordi
authors.initials: J
authors.lastname: Estellé
authors.affiliation: Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark.
authors.forename: Pia
authors.initials: P
authors.lastname: Kiilerich
authors.affiliation: GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
authors.forename: Yuliaxis
authors.initials: Y
authors.lastname: Ramayo-Caldas
authors.affiliation: BGI-Shenzhen, 518083 Shenzhen, China.
authors.forename: Zhongkui
authors.initials: Z
authors.lastname: Xia
authors.affiliation: BGI-Shenzhen, 518083 Shenzhen, China.
authors.forename: Qiang
authors.initials: Q
authors.lastname: Feng
authors.affiliation: BGI-Shenzhen, 518083 Shenzhen, China.
authors.forename: Suisha
authors.initials: S
authors.lastname: Liang
authors.affiliation: SEGES Pig Research Centre, DK-1609 Copenhagen V, Denmark.
authors.forename: Anni Øyan
authors.initials: AØ
authors.lastname: Pedersen
authors.affiliation: SEGES Pig Research Centre, DK-1609 Copenhagen V, Denmark.
authors.forename: Niels Jørgen
authors.initials: NJ
authors.lastname: Kjeldsen
authors.affiliation: BGI-Shenzhen, 518083 Shenzhen, China.|Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome.
authors.forename: Chuan
authors.initials: C
authors.lastname: Liu
authors.affiliation: MICALIS Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
authors.forename: Emmanuelle
authors.initials: E
authors.lastname: Maguin
authors.affiliation: MICALIS Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.|MetaGénoPolis, INRA, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
authors.forename: Joël
authors.initials: J
authors.lastname: Doré
authors.affiliation: MetaGénoPolis, INRA, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Pons
authors.affiliation: MetaGénoPolis, INRA, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
authors.forename: Emmanuelle
authors.initials: E
authors.lastname: Le Chatelier
authors.affiliation: MetaGénoPolis, INRA, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
authors.forename: Edi
authors.initials: E
authors.lastname: Prifti
authors.affiliation: BGI-Shenzhen, 518083 Shenzhen, China.|Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research.
authors.forename: Junhua
authors.initials: J
authors.lastname: Li
authors.affiliation: BGI-Shenzhen, 518083 Shenzhen, China.
authors.forename: Huijue
authors.identifier: http://orcid.org/0000-0002-3592-126X
authors.initials: H
authors.lastname: Jia
authors.affiliation: BGI-Shenzhen, 518083 Shenzhen, China.
authors.forename: Xin
authors.initials: X
authors.lastname: Liu
authors.affiliation: BGI-Shenzhen, 518083 Shenzhen, China.
authors.forename: Xun
authors.initials: X
authors.lastname: Xu
authors.affiliation: MetaGénoPolis, INRA, Université Paris-Saclay, 78350 Jouy-en-Josas, France.|King's College London, Centre for Host-Microbiome Interactions, Dental Institute Central Office, Guy's Hospital, London SE1 9RT, UK.
authors.forename: Stanislav D
authors.initials: SD
authors.lastname: Ehrlich
authors.affiliation: BGI-Shenzhen, 518083 Shenzhen, China.|Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark.|National Institute of Nutrition and Seafood Research (NIFES), Postboks 2029, Nordnes, N-5817 Bergen, Norway.
authors.forename: Lise
authors.identifier: http://orcid.org/0000-0001-6108-1236
authors.initials: L
authors.lastname: Madsen
authors.affiliation: BGI-Shenzhen, 518083 Shenzhen, China.|Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark.
authors.forename: Karsten
authors.initials: K
authors.lastname: Kristiansen
authors.affiliation: GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
authors.forename: Claire
authors.initials: C
authors.lastname: Rogel-Gaillard
authors.affiliation: BGI-Shenzhen, 518083 Shenzhen, China.|Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark.
authors.forename: Jun
authors.initials: J
authors.lastname: Wang