We developed a portable system for metagenomic analyses consisting of nanopore technology-based sequencer, MinION, and laptop computers, and assessed its potential ability to determine bacterial compositions rapidly. We tested our protocols using mock bacterial community that contained equimolar 16S rDNA and a pleural effusion from a patient with empyema for time effectiveness and accuracy. MinION sequencing targeting 16S rDNA detected all of 20 bacteria present in the mock bacterial community. Time course analysis indicated that sequence data obtained during the first 5-minute sequencing were enough to detect all 20 bacteria species in the mock sample and determine their compositions with sufficient accuracy. Additionally, using a clinical sample extracted from the pleural effusion of a patient with empyema, we could identify major bacteria in a pleural effusion by rapid sequencing and analysis. All of these results are comparable to or even better than the conventional 16S rDNA sequencing results using IonPGM sequencer. Our results suggest that rapid sequencing and bacterial composition determination is possible within 2 hours. Our integrative system is applicable to rapid diagnostic tests for infectious diseases in near future.