BackgroundBiofilters have been broadly applied to degrade the odorous gases from industrial emissions. To explore biofilter potentials, the microbial community structure and function must be well defined. Using of improved biofilter, changes in microbial community structures and functions were investigated by metagenomic analysis. ResultsOdorous gases have the potential to alter the microbial community structure in the sludge of biofilter. A total of 90,016 unigenes assigned into various functional metabolic pathways were identified. In the improved biofilter, the dominant phyla were Proteobacteria, Planctomycetes, and Chloroflexi, and the dominant were Thioalkalivibrio, Thauera, and Pseudomonas. Several xenobiotic biodegradation-related pathways showed significant changes during the treatment process. Compared with the original biofilter, Thermotogae and Crenarchaeota phyla were significantly up-regulated in the improved biofilter, suggesting its important role in nitrogen-fixing. Furthermore, nitrogen metabolic pathway-related genes, such as nirA and nifA, and sulfur metabolic pathway-related genes, such as fccB and phsA, were considered to be efficient genes involved in removing odorous gases. ConclusionsOur findings can be used for improving the efficiency of biofilter and helping the industrial enterprises to reduce the emission of waste gas.