Alterations of the human gut microbiome in liver cirrhosis

Nan Qin (1) , Fengling Yang (1) , Ang Li (1) , Edi Prifti (2) , Yanfei Chen (1) , Li Shao (1) , Jing Guo (1) , Emmanuelle E. Le Chatelier (2) , Jian Yao (1) , Lingjiao Wu (1) , Jiawei Zhou (1) , Shujun Ni (1) , Lin Liu (1) , Nicolas N. Pons (2) , Jean-Michel J.-M. Batto (2) , Sean S. Kennedy (2) , Pierre Léonard (2) , Chunhui Yuan (1) , Wenchao Ding (1) , Yuanting Chen (1) , Xinjun Hu (1) , Beiwen Zheng (1) , Guirong Qian (1) , Wei Xu (1) , S. Dusko Ehrlich (2, 3) , Shusen Zheng (1) , Lanjuan Li (1)

1 Zhejiang University
2 MetaGenoPolis
3 King‘s College London

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.

Domaines: Sciences du Vivant [q-bio]

Nan Qin, Fengling Yang, Ang Li, Edi Prifti, Yanfei Chen, et al.. Alterations of the human gut microbiome in liver cirrhosis. Nature, 2014, 513 (7516), pp.59-64. ⟨10.1038/nature13568⟩. ⟨hal-02639870⟩