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Alterations of the human gut microbiome in liver cirrhosis

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  • Nan Qin

    (State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University
    Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University)

  • Fengling Yang

    (State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University)

  • Ang Li

    (State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University)

  • Edi Prifti

    (Metagenopolis, Institut National de la Recherche Agronomique, 78350 Jouy en Josas, France)

  • Yanfei Chen

    (State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University)

  • Li Shao

    (State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University
    Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University)

  • Jing Guo

    (State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University)

  • Emmanuelle Le Chatelier

    (Metagenopolis, Institut National de la Recherche Agronomique, 78350 Jouy en Josas, France)

  • Jian Yao

    (State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University
    Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University)

  • Lingjiao Wu

    (State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University)

  • Jiawei Zhou

    (State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University)

  • Shujun Ni

    (State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University)

  • Lin Liu

    (State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University)

  • Nicolas Pons

    (Metagenopolis, Institut National de la Recherche Agronomique, 78350 Jouy en Josas, France)

  • Jean Michel Batto

    (Metagenopolis, Institut National de la Recherche Agronomique, 78350 Jouy en Josas, France)

  • Sean P. Kennedy

    (Metagenopolis, Institut National de la Recherche Agronomique, 78350 Jouy en Josas, France)

  • Pierre Leonard

    (Metagenopolis, Institut National de la Recherche Agronomique, 78350 Jouy en Josas, France)

  • Chunhui Yuan

    (State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University)

  • Wenchao Ding

    (State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University)

  • Yuanting Chen

    (State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University)

  • Xinjun Hu

    (State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University)

  • Beiwen Zheng

    (State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University
    Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University)

  • Guirong Qian

    (State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University)

  • Wei Xu

    (State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University)

  • S. Dusko Ehrlich

    (Metagenopolis, Institut National de la Recherche Agronomique, 78350 Jouy en Josas, France
    King’s College London, Centre for Host-Microbiome Interactions, Dental Institute Central Office, Guy’s Hospital, London Bridge, London SE1 9RT, UK)

  • Shusen Zheng

    (Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University
    Key Laboratory of Combined Multi-organ Transplantation, Ministry of Public Health, the First Affiliated Hospital, Zhejiang University)

  • Lanjuan Li

    (State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University
    Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University)

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

Suggested Citation

  • Nan Qin & Fengling Yang & Ang Li & Edi Prifti & Yanfei Chen & Li Shao & Jing Guo & Emmanuelle Le Chatelier & Jian Yao & Lingjiao Wu & Jiawei Zhou & Shujun Ni & Lin Liu & Nicolas Pons & Jean Michel Bat, 2014. "Alterations of the human gut microbiome in liver cirrhosis," Nature, Nature, vol. 513(7516), pages 59-64, September.
    • Handle: RePEc:nat:nature:v:513:y:2014:i:7516:d:10.1038_nature13568
    DOI: 10.1038/nature13568
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    Cited by:

    1. Runtan Cheng & Lu Wang & Shenglong Le & Yifan Yang & Can Zhao & Xiangqi Zhang & Xin Yang & Ting Xu & Leiting Xu & Petri Wiklund & Jun Ge & Dajiang Lu & Chenhong Zhang & Luonan Chen & Sulin Cheng, 2022. "A randomized controlled trial for response of microbiome network to exercise and diet intervention in patients with nonalcoholic fatty liver disease," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    2. Yuanyuan Lei & Li Tang & Qiao Chen & Lingyi Wu & Wei He & Dianji Tu & Sumin Wang & Yuyang Chen & Shuang Liu & Zhuo Xie & Hong Wei & Shiming Yang & Bo Tang, 2022. "Disulfiram ameliorates nonalcoholic steatohepatitis by modulating the gut microbiota and bile acid metabolism," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    3. Mohammed Y. Refai & Aala A. Abulfaraj & Israa J. Hakeem & Nehad A. Shaer & Mashael D. Alqahtani & Maryam M. Alomran & Nahaa M. Alotaibi & Hana S. Sonbol & Abdulrahman M. Alhashimi & Nouf S. Al-Abbas &, 2023. "Rhizobiome Signature and Its Alteration Due to Watering in the Wild Plant Moringa oleifera," Sustainability, MDPI, vol. 15(3), pages 1-25, February.
    4. Yu-Feng Wei & Ming-Shyan Huang & Cheng-Hsieh Huang & Yao-Tsung Yeh & Chih-Hsin Hung, 2022. "Impact of Gut Dysbiosis on the Risk of Non-Small-Cell Lung Cancer," IJERPH, MDPI, vol. 19(23), pages 1-17, November.
    5. Qi Su & Qin Liu & Raphaela Iris Lau & Jingwan Zhang & Zhilu Xu & Yun Kit Yeoh & Thomas W. H. Leung & Whitney Tang & Lin Zhang & Jessie Q. Y. Liang & Yuk Kam Yau & Jiaying Zheng & Chengyu Liu & Mengjin, 2022. "Faecal microbiome-based machine learning for multi-class disease diagnosis," Nature Communications, Nature, vol. 13(1), pages 1-8, December.
    6. Wanting Dong & Xinyue Fan & Yaqiong Guo & Siyi Wang & Shulei Jia & Na Lv & Tao Yuan & Yuanlong Pan & Yong Xue & Xi Chen & Qian Xiong & Ruifu Yang & Weigang Zhao & Baoli Zhu, 2024. "An expanded database and analytical toolkit for identifying bacterial virulence factors and their associations with chronic diseases," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    7. Efrat Muller & Itamar Shiryan & Elhanan Borenstein, 2024. "Multi-omic integration of microbiome data for identifying disease-associated modules," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    8. Jennifer T. Wolstenholme & Justin M. Saunders & Maren Smith & Jason D. Kang & Phillip B. Hylemon & Javier González-Maeso & Andrew Fagan & Derrick Zhao & Masoumeh Sikaroodi & Jeremy Herzog & Amirhossei, 2022. "Reduced alcohol preference and intake after fecal transplant in patients with alcohol use disorder is transmissible to germ-free mice," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    9. Ashwag Shami & Rewaa S. Jalal & Ruba A. Ashy & Haneen W. Abuauf & Lina Baz & Mohammed Y. Refai & Aminah A. Barqawi & Hanadi M. Baeissa & Manal A. Tashkandi & Sahar Alshareef & Aala A. Abulfaraj, 2022. "Use of Metagenomic Whole Genome Shotgun Sequencing Data in Taxonomic Assignment of Dipterygium glaucum Rhizosphere and Surrounding Bulk Soil Microbiomes, and Their Response to Watering," Sustainability, MDPI, vol. 14(14), pages 1-21, July.

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