title: Alterations of Bacteroides sp., Neisseria sp., Actinomyces sp., and Streptococcus sp. populations in the oropharyngeal microbiome are associated with liver cirrhosis and pneumonia.
abstract: BACKGROUND
  The microbiomes of humans are associated with liver and lung inflammation. We identified and verified alterations of the oropharyngeal microbiome and assessed their association with cirrhosis and pneumonia.
  
  
  METHODS
  Study components were as follows: (1) determination of the temporal stability of the oropharyngeal microbiome; (2) identification of oropharyngeal microbial variation in 90 subjects; (3) quantitative identification of disease-associated bacteria. DNAs enriched in bacterial sequences were produced from low-biomass oropharyngeal swabs using whole genome amplification and were analyzed using denaturing gradient gel electrophoresis analysis.
  
  
  RESULTS
  Whole genome amplification combined with denaturing gradient gel electrophoresis analysis monitored successfully oropharyngeal microbial variations and showed that the composition of each subject's oropharyngeal microbiome remained relatively stable during the follow-up. The microbial composition of cirrhotic patients with pneumonia differed from those of others and clustered together in subgroup analysis. Further, species richness and the value of Shannon's diversity and evenness index increased significantly in patients with cirrhosis and pneumonia versus others (p < 0.001, versus healthy controls; p < 0.01, versus cirrhotic patients without pneumonia). Moreover, we identified variants of Bacteroides, Eubacterium, Lachnospiraceae, Neisseria, Actinomyces, and Streptococcus through phylogenetic analysis. Quantitative polymerase chain reaction assays revealed that the populations of Bacteroides, Neisseria, and Actinomycetes increased, while that of Streptococcus decreased in cirrhotic patients with pneumonia versus others (p < 0.001, versus Healthy controls; p < 0.01, versus cirrhotic patients without pneumonia).
  
  
  CONCLUSIONS
  Alterations of Bacteroides, Neisseria, Actinomyces, and Streptococcus populations in the oropharyngeal microbiome were associated with liver cirrhosis and pneumonia.
authors.affiliation: State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, 79 Qingchun Road, Hangzhou, 310003, People's Republic of China. seawindlu@126.com.
authors.forename: Haifeng
authors.initials: H
authors.lastname: Lu
authors.affiliation: Tonglu First People's Hospital, 338 Xuesheng Road, Tonglu, Hangzhou, 311500, People's Republic of China. 293439550@qq.com.
authors.forename: Guirong
authors.initials: G
authors.lastname: Qian
authors.affiliation: State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, 79 Qingchun Road, Hangzhou, 310003, People's Republic of China. 289019097@qq.com.
authors.forename: Zhigang
authors.initials: Z
authors.lastname: Ren
authors.affiliation: Department of Geriatrics, The First Affiliated Hospital, School of Medicine, Zhejiang University, 79 Qingchun Road, Hangzhou, 310003, People's Republic of China. 1048583351@qq.com.
authors.forename: Chunxia
authors.initials: C
authors.lastname: Zhang
authors.affiliation: State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, 79 Qingchun Road, Hangzhou, 310003, People's Republic of China. zh42@163.com.
authors.forename: Hua
authors.initials: H
authors.lastname: Zhang
authors.affiliation: State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, 79 Qingchun Road, Hangzhou, 310003, People's Republic of China. zjuxuw@163.com.
authors.forename: Wei
authors.initials: W
authors.lastname: Xu
authors.affiliation: State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, 79 Qingchun Road, Hangzhou, 310003, People's Republic of China. 1754224256@qq.com.
authors.forename: Ping
authors.initials: P
authors.lastname: Ye
authors.affiliation: Department of Geriatrics, The First Affiliated Hospital, School of Medicine, Zhejiang University, 79 Qingchun Road, Hangzhou, 310003, People's Republic of China. ymyang@zju.edu.cn.
authors.forename: Yunmei
authors.initials: Y
authors.lastname: Yang
authors.affiliation: State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, 79 Qingchun Road, Hangzhou, 310003, People's Republic of China. ljli@zju.edu.cn.
authors.forename: Lanjuan
authors.initials: L
authors.lastname: Li
mesh_terms: D000190:Actinomyces / Q000235:genetics / Q000302:isolation & purification; D000368:Aged; D001419:Bacteria / Q000235:genetics*; D001439:Bacteroides / Q000235:genetics / Q000302:isolation & purification; D001483:Base Sequence; D016022:Case-Control Studies; D058645:Denaturing Gradient Gel Electrophoresis; D005260:Female; D006801:Humans; D008103:Liver Cirrhosis / Q000382:microbiology*; D008297:Male; D064307:Microbiota / Q000235:genetics*; D008875:Middle Aged; D009343:Neisseria / Q000235:genetics / Q000302:isolation & purification; D009960:Oropharynx / Q000382:microbiology*; D010802:Phylogeny; D011014:Pneumonia / Q000382:microbiology*; D016133:Polymerase Chain Reaction; D013291:Streptococcus / Q000235:genetics / Q000302:isolation & purification