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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.    Electronic supplementary material  The online version of this article (doi:10.1186/s12879-015-0977-x) contains supplementary material, which is available to authorized users.

bmc infectious diseases

Alterations of Bacteroides sp., Neisseria sp., Actinomyces sp., and Streptococcus sp. populations in the oropharyngeal microbiome are associated with liver cirrhosis and pneumonia