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A reference gene catalogue of the pig gut microbiome

Nature Microbiology volume 1, Article number: 16161 (2016) Cite this article

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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.

Domesticated pigs are a major food source worldwide and thus important in global food security, but large-scale pig farming faces environmental challenges. Increasing the understanding of the interaction between the gut microbiota and the host has the potential to facilitate knowledge-based development of sustainable pig production by increasing feed efficiency and general health in pig farming. Furthermore, the spread of antibiotic-resistant bacteria and genes is a matter of great global concern, with legislation and research in this area being important issues6–11. Hence, an evaluation of the impact of prohibiting the use of antibiotics as growth promotants is needed.

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Figure 1: Rarefaction curves and shared metagenome among pigs.
Figure 2: Comparison of the gut microbiome gene catalogues of human, mouse and pig.
Figure 3: Influence of breed, age and sex on the pig gut microbiota composition, as represented by NMDS plots at the NR gene count level.
Figure 4: Prevalence of antibiotic resistance genes (ARGs).

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Acknowledgements

This work was supported financially by the INRA metaprogramme Meta-omics of Microbial Ecosystems (MEM), the Animal Genetics Division of INRA, the Biology Department of the University of Copenhagen and BGI-Shenzhen. Y.R.C. was funded by the European Union, in the framework of the Marie-Curie FP7 COFUND People Program, through the award of an AgreenSkills' fellowship (grant agreement no. 267196) linked to the METALIT project funded by the INRA MEM metaprogramme. This study was supported by the Shenzhen Municipal Government of China (grant nos. JCYJ20140418095735538, DRC-SZ[2015]162, CXB201108250098A and CXZZ20150330171521403), the National Transgenic Project of China (2014ZX0801007B), the Science and Technology Plan of Shenzhen City, the Shenzhen–Hong Kong Innovation Circle Research Fund, China (SGLH20120928140607107). The work was also supported by the Danish Innovation Fund (grant nos. 4105-00011A and 0603-00774B) and Metagenopolis grant ANR-11-DPBS-0001. The authors acknowledge technical support for faecal stool sampling provided by the INRA experimental units (Y. Billon, UE GENESI at le Magneraud; C. Jaeger and H. Demay, UMR SENAH at Saint Gilles; N. Müller, UE0787 at le Rheu; E. Venturi and his team, UE PAO at Nouzilly; J.-L. Gourdine and D. Renaudeau, URZ in the Guadeloupe; J.-J. Leplat, UMR GABI at Jouy-en-Josas). The authors thank K. Pedersen at Svindinge farm, T. Povlsen at Blæsenborg farm, V. Jensen and K. Jensen at Stærsminde farm and H. Loft Hansen for technical assistance in relation to collection of faecal samples from the Danish farms. The authors also thank X. Liu and Zhigang at the Institute of Allergy & Immunology, Shenzhen University, and L. Fang Liang, Q. Wei and Y. Li at the technical unit of the Chinese farms for help with faecal sampling and administration. The authors thank C. Denis (INRA, UMR GABI, Jouy-en-Josas) and F. Levenez (INRA, UMR MICALIS and MetaGenoPolis, Jouy-en-Josas) for faecal DNA preparation. The authors acknowledge the @BRIDGe platform (INRA, Jouy-en-Josas) for safe storage of samples. The authors are grateful to J. Nathaniel Paulson for kind assistance with the use of the R package referred to as metagenomeSeq, and J. Lunney (Animal Parasitic Diseases Laboratory, ARS, USDA, MD, Beltsville, USA) for discussions and the contribution to manuscript editing.

Author information

Author notes

  1. Qiang Feng & Edi Prifti

    Present address: ‡ Present addresses: Department of Human Microbiome, School of Stomatology, Shandong University, Shandong Provincial Key Laboratory of Oral Tissue Regeneration, Jinan, China. (Q.F.). Institute of Cardiometabolism and Nutrition, 75013 Paris, France. (E.P.).,

  2. Liang Xiao, Jordi Estellé and Pia Kiilerich: These authors contributed equally to this work

Authors and Affiliations

  1. BGI-Shenzhen, 518083 Shenzhen, China

    Liang Xiao, Zhongkui Xia, Qiang Feng, Suisha Liang, Chuan Liu, Junhua Li, Huijue Jia, Xin Liu, Xun Xu, Lise Madsen, Karsten Kristiansen & Jun Wang

  2. GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France

    Jordi Estellé, Yuliaxis Ramayo-Caldas & Claire Rogel-Gaillard

  3. Department of Biology, Laboratory of Genomics and Molecular Biomedicine, University of Copenhagen, DK-2100 Copenhagen, Denmark

    Pia Kiilerich, Lise Madsen, Karsten Kristiansen & Jun Wang

  4. SEGES Pig Research Centre, DK-1609 Copenhagen V, Denmark

    Anni Øyan Pedersen & Niels Jørgen Kjeldsen

  5. Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome,

    Chuan Liu

  6. MICALIS Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France

    Emmanuelle Maguin & Joël Doré

  7. MetaGénoPolis, INRA, Université Paris-Saclay, 78350 Jouy-en-Josas, France

    Joël Doré, Nicolas Pons, Emmanuelle Le Chatelier, Edi Prifti & Stanislav D. Ehrlich

  8. Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research,

    Junhua Li

  9. King's College London, Centre for Host–Microbiome Interactions, Dental Institute Central Office, Guy's Hospital, London SE1 9RT, UK

    Stanislav D. Ehrlich

  10. National Institute of Nutrition and Seafood Research (NIFES), Postboks 2029, Nordnes, N-5817 Bergen, Norway

    Lise Madsen

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  1. Liang Xiao
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Contributions

C.R.-G., J.W., L.M., E.M., J.D., S.D.E. and K.K. conceived and designed the project. K.K., C.R.-G., L.M., S.D.E., J.W., L.X., J.E., P.K., Y.R.-C., X.X., X.L., N.J.K. and Z.X. monitored the project. A.Ø.P., C.L. and E.P. collected samples and performed experiments. K.K., C.R.-G., L.M., J.W., J.E., Y.R.-C., P.K., N.P., E.L.C., E.P., S.D.E., Z.X., Q.F., S.L., A.Ø.P. and J.L. analysed and interpreted the data. K.K., C.R.-G., J.E., Y.R.-C., S.D.E., L.M., P.K., H.J. and L.X. wrote the paper. All authors commented on the manuscript.

Corresponding authors

Correspondence to Karsten Kristiansen, Claire Rogel-Gaillard or Jun Wang.

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Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary information

Supplementary Figures 1–8, legends for Supplementary Tables 1–9 (PDF 2038 kb)

Supplementary Table 1

Background information on the 287 pig samples. (XLSX 14 kb)

Supplementary Table 2

Description of the assembly data from the 287 samples. (XLSX 9 kb)

Supplementary Table 3

Assembly results of the pig, human and mouse data. (XLSX 10 kb)

Supplementary Table 4

Significantly differentially abundant genes in the gut microbiota composition between castrated males and females (Svindinge farm) at the genus and species bacteria levels. (XLSX 11 kb)

Supplementary Table 5

Significantly differentially represented KEGG pathways in the gut microbiota between castrated males and females (Svindinge farm). (XLSX 9 kb)

Supplementary Table 6

Significantly differentially abundant genes in the gut microbiota composition between males and females (Stæminde farm, wet feed) at the genus and species bacteria levels. (XLSX 12 kb)

Supplementary Table 7

Significantly differentially abundant MGSs in the gut microbiota composition of males and females (Stæminde farm, wet feed). (XLSX 17 kb)

Supplementary Table 8

Significantly differentially represented KEGG pathways in the gut microbiota between males and females (Stæminde farm, wet feed). (XLSX 54 kb)

Supplementary Table 9

List of the KEGG pathways mapped by iPATH2 that were significantly differentially represented in the gut microbiota between males and females (11 males, 14 females, Stæminde farm, wet feed). The three most represented pathways are highlighted in grey. This list is derived from Supplementary Table 8 and correspond to the differentially abundant functions mapping against the KEGG, according to iPATH2 tools. (XLSX 27 kb)

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Xiao, L., Estellé, J., Kiilerich, P. et al. A reference gene catalogue of the pig gut microbiome. Nat Microbiol 1, 16161 (2016). https://doi.org/10.1038/nmicrobiol.2016.161

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