Alterations of the human gut microbiome in liver cirrhosis

doi:10.1038/nature13568

. 2014 Sep 4;513(7516):59-64.

doi: 10.1038/nature13568. Epub 2014 Jul 23.

Alterations of the human gut microbiome in liver cirrhosis

Nan Qin¹, Fengling Yang², Ang Li², Edi Prifti³, Yanfei Chen², Li Shao¹, Jing Guo⁴, Emmanuelle Le Chatelier⁵, Jian Yao⁶, Lingjiao Wu⁴, Jiawei Zhou⁴, Shujun Ni⁴, Lin Liu⁴, Nicolas Pons⁵, Jean Michel Batto⁵, Sean P Kennedy⁵, Pierre Leonard⁵, Chunhui Yuan⁴, Wenchao Ding⁴, Yuanting Chen⁴, Xinjun Hu⁴, Beiwen Zheng⁶, Guirong Qian⁴, Wei Xu⁴, S Dusko Ehrlich⁷, Shusen Zheng⁸, Lanjuan Li⁶

Affiliations

¹ 1] State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China [2] Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, 310003 Hangzhou, China [3].
² 1] State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China [2].
³ 1] Metagenopolis, Institut National de la Recherche Agronomique, 78350 Jouy en Josas, France [2].
⁴ State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China.
⁵ Metagenopolis, Institut National de la Recherche Agronomique, 78350 Jouy en Josas, France.
⁶ 1] State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China [2] Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, 310003 Hangzhou, China.
⁷ 1] Metagenopolis, Institut National de la Recherche Agronomique, 78350 Jouy en Josas, France [2] King's College London, Centre for Host-Microbiome Interactions, Dental Institute Central Office, Guy's Hospital, London Bridge, London SE1 9RT, UK.
⁸ 1] Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, 310003 Hangzhou, China [2] Key Laboratory of Combined Multi-organ Transplantation, Ministry of Public Health, the First Affiliated Hospital, Zhejiang University, 310003 Hangzhou, China.

PMID: 25079328
DOI: 10.1038/nature13568

Alterations of the human gut microbiome in liver cirrhosis

Nan Qin et al. Nature. 2014.

. 2014 Sep 4;513(7516):59-64.

doi: 10.1038/nature13568. Epub 2014 Jul 23.

Authors

Affiliations

¹ 1] State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China [2] Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, 310003 Hangzhou, China [3].
² 1] State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China [2].
³ 1] Metagenopolis, Institut National de la Recherche Agronomique, 78350 Jouy en Josas, France [2].
⁴ State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China.
⁵ Metagenopolis, Institut National de la Recherche Agronomique, 78350 Jouy en Josas, France.
⁶ 1] State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China [2] Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, 310003 Hangzhou, China.
⁷ 1] Metagenopolis, Institut National de la Recherche Agronomique, 78350 Jouy en Josas, France [2] King's College London, Centre for Host-Microbiome Interactions, Dental Institute Central Office, Guy's Hospital, London Bridge, London SE1 9RT, UK.
⁸ 1] Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, 310003 Hangzhou, China [2] Key Laboratory of Combined Multi-organ Transplantation, Ministry of Public Health, the First Affiliated Hospital, Zhejiang University, 310003 Hangzhou, China.

PMID: 25079328
DOI: 10.1038/nature13568

Abstract

Liver cirrhosis occurs as a consequence of many chronic liver diseases that are prevalent worldwide. Here we characterize the gut microbiome in liver cirrhosis by comparing 98 patients and 83 healthy control individuals. We build a reference gene set for the cohort containing 2.69 million genes, 36.1% of which are novel. Quantitative metagenomics reveals 75,245 genes that differ in abundance between the patients and healthy individuals (false discovery rate < 0.0001) and can be grouped into 66 clusters representing cognate bacterial species; 28 are enriched in patients and 38 in control individuals. Most (54%) of the patient-enriched, taxonomically assigned species are of buccal origin, suggesting an invasion of the gut from the mouth in liver cirrhosis. Biomarkers specific to liver cirrhosis at gene and function levels are revealed by a comparison with those for type 2 diabetes and inflammatory bowel disease. On the basis of only 15 biomarkers, a highly accurate patient discrimination index is created and validated on an independent cohort. Thus microbiota-targeted biomarkers may be a powerful tool for diagnosis of different diseases.

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Comment in

Cirrhosis and dysbiosis: New insights from next-generation sequencing.
Gorham J, Gleeson M. Gorham J, et al. Hepatology. 2016 Jan;63(1):336-8. doi: 10.1002/hep.28133. Epub 2015 Oct 10. Hepatology. 2016. PMID: 26313376 No abstract available.
Decompensated cirrhosis and microbiome interpretation.
Bajaj JS, Betrapally NS, Gillevet PM. Bajaj JS, et al. Nature. 2015 Sep 17;525(7569):E1-2. doi: 10.1038/nature14851. Nature. 2015. PMID: 26381988 Free PMC article. No abstract available.
Qin et al. reply.
Qin N, Le Chatelier E, Guo J, Prifti E, Li L, Ehrlich SD. Qin N, et al. Nature. 2015 Sep 17;525(7569):E2-3. doi: 10.1038/nature14852. Nature. 2015. PMID: 26381989 No abstract available.

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References

1. Nature. 2012 Jun 13;486(7402):207-14 - PubMed
1. Nature. 2006 Dec 21;444(7122):1027-31 - PubMed
1. Lancet. 1995 Jul 29;346(8970):270-4 - PubMed
1. Genome Res. 2010 Feb;20(2):265-72 - PubMed
1. Proc Natl Acad Sci U S A. 2010 Aug 17;107(33):14691-6 - PubMed

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[1] Nature. 2012 Jun 13;486(7402):207-14 - PubMed

[2] Nature. 2012 Jun 13;486(7402):207-14 - PubMed

[3] Nature. 2006 Dec 21;444(7122):1027-31 - PubMed

[4] Nature. 2006 Dec 21;444(7122):1027-31 - PubMed

[5] Lancet. 1995 Jul 29;346(8970):270-4 - PubMed

[6] Lancet. 1995 Jul 29;346(8970):270-4 - PubMed

[7] Genome Res. 2010 Feb;20(2):265-72 - PubMed

[8] Genome Res. 2010 Feb;20(2):265-72 - PubMed

[9] Proc Natl Acad Sci U S A. 2010 Aug 17;107(33):14691-6 - PubMed

[10] Proc Natl Acad Sci U S A. 2010 Aug 17;107(33):14691-6 - PubMed

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Alterations of the human gut microbiome in liver cirrhosis

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Alterations of the human gut microbiome in liver cirrhosis

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