In the bioreactor of the wastewater treatment plant, pollutants such as nitrogen and sulfur are removed using microorganisms. Microorganisms in wastewater treatment plants are difficult to analyze due to a large number of inhibitors, particularly, in the case of a transcript, degradation starts immediately from the moment of departure from the environment, so an optimal method is required from the collecting step. This paper introduces a method for successfully collecting the genome and transcripts from microorganisms in wastewater and a method for analyzing them using various bioinformatics programs. By analyzing the results, the community of microorganisms in the wastewater was analyzed, and 13 metagenome-assembled genomes (MAGs) were identified to analyze their phylogenetic characteristics. Through these gene analyses, it was possible to know the biological reactions occurring in the wastewater, and to analyze the specific genes related to nitrogen cycle in more detail. And through transcriptome analysis, it is possible to know the activity of microorganisms at the time of sampling, not the general genetic characteristics, and compare the degree of expression for each gene. It can be applied to various studies using microorganisms in wastewater through the introduced method.