title: Alterations of the human gut microbiome in liver cirrhosis.
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.
authors: 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].
authors: Nan
authors: N
authors: Qin
authors: 1] State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China [2].
authors: Fengling
authors: F
authors: Yang
authors: 1] State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China [2].
authors: Ang
authors: A
authors: Li
authors: 1] Metagenopolis, Institut National de la Recherche Agronomique, 78350 Jouy en Josas, France [2].
authors: Edi
authors: E
authors: Prifti
authors: 1] State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China [2].
authors: Yanfei
authors: Y
authors: Chen
authors: 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].
authors: Li
authors: L
authors: Shao
authors: State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China.
authors: Jing
authors: J
authors: Guo
authors: Metagenopolis, Institut National de la Recherche Agronomique, 78350 Jouy en Josas, France.
authors: Emmanuelle
authors: E
authors: Le Chatelier
authors: 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.
authors: Jian
authors: J
authors: Yao
authors: State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China.
authors: Lingjiao
authors: L
authors: Wu
authors: State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China.
authors: Jiawei
authors: J
authors: Zhou
authors: State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China.
authors: Shujun
authors: S
authors: Ni
authors: State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China.
authors: Lin
authors: L
authors: Liu
authors: Metagenopolis, Institut National de la Recherche Agronomique, 78350 Jouy en Josas, France.
authors: Nicolas
authors: N
authors: Pons
authors: Metagenopolis, Institut National de la Recherche Agronomique, 78350 Jouy en Josas, France.
authors: Jean Michel
authors: JM
authors: Batto
authors: Metagenopolis, Institut National de la Recherche Agronomique, 78350 Jouy en Josas, France.
authors: Sean P
authors: SP
authors: Kennedy
authors: Metagenopolis, Institut National de la Recherche Agronomique, 78350 Jouy en Josas, France.
authors: Pierre
authors: P
authors: Leonard
authors: State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China.
authors: Chunhui
authors: C
authors: Yuan
authors: State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China.
authors: Wenchao
authors: W
authors: Ding
authors: State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China.
authors: Yuanting
authors: Y
authors: Chen
authors: State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China.
authors: Xinjun
authors: X
authors: Hu
authors: 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.
authors: Beiwen
authors: B
authors: Zheng
authors: State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China.
authors: Guirong
authors: G
authors: Qian
authors: State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China.
authors: Wei
authors: W
authors: Xu
authors: 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.
authors: S Dusko
authors: SD
authors: Ehrlich
authors: 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.
authors: Shusen
authors: S
authors: Zheng
authors: 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.
authors: Lanjuan
authors: L
authors: Li
mesh_terms: D016022:Case-Control Studies; D002908:Chronic Disease; D003924:Diabetes Mellitus, Type 2 / Q000382:microbiology; D005243:Feces / Q000382:microbiology; D041981:Gastrointestinal Tract / Q000382:microbiology*; D005819:Genetic Markers / Q000235:genetics; D006262:Health; D006801:Humans; D015212:Inflammatory Bowel Diseases / Q000382:microbiology; D008103:Liver Cirrhosis / Q000175:diagnosis* / Q000382:microbiology*; D056186:Metagenomics; D064307:Microbiota / Q000235:genetics* / Q000502:physiology*; D009055:Mouth / Q000382:microbiology; D010802:Phylogeny; D015203:Reproducibility of Results
chemical_list: D005819:Genetic Markers