AbstractBACKGROUNDUp to now, there has been no report on the taxonomic and functional analysis of the microbial community in fermenting puer tea by pyrosequencing. In this study, metagenomic pyrosequencing was first used in fermenting puer tea to delineate a relatively comprehensive overview of the microbial taxonomy while also preliminarily characterising the functional ontologies of microbial genes present in puer tea pile fermentation.RESULTSA total of 251 738 pyrosequencing reads (9197 contigs and 145 402 singletons) were generated by pyrosequencing. Taxonomic analysis revealed three dominant bacterial phyla, Proteobacteria (23.56%), Actinobacteria (23.35%) and Firmicutes (11.37%), and one dominant eukaryotic phylum, Ascomycota (30.47%). A total of 58 664 hits were categorised into 28 functional subsystems based on the SEED database. Moreover, two categories, ‘metabolism of terpenoids and polyketides’ and ‘biosynthesis of other secondary metabolites’, were selectively analysed and 69 enzyme genes were presented in 16 pathways.CONCLUSIONThe dominant microbes of puer tea fermentation were bacteria in the present study, and yeasts rather than moulds accounted for the overwhelming majority of Eukaryota. The analysis of functional genes and metabolic pathways will be helpful for further study of the mechanism of puer tea fermentation at molecular level. © 2013 Society of Chemical Industry