We have been developing a portable system for rapid bacterial composition determination for the diagnosis of infectious diseases using a nanopore technology-based sequencer, MinION, combined with laptop computers. We improved this system using new sequence search programs as well as new sequencing kits, and applied it to detect the causative bacteria of 11 meningitis patients (6 culture-positive and 5 culture-negative) in Zambia. DNA was extracted from each patient and almost full-length region of their 16S rRNA genes are amplified. Then, sequencing library was prepared and sequenced. Simultaneously, sequenced reads were processed without internet connection. As a result, we found that 4 among 6 culture-positive samples sequencing results were consistent with those of conventional culture-based methods. In these samples, major bacteria species for each sample appeared only in the 3-minitue sequencing data. For the other 2 culture-positive samples and 5 culture-negative samples, the major bacteria species were detected but these cannot be determined whether they exist or not. On the other hand, as a whole, although the number of sequencing reads are small in a short time sequencing, major bacteria species has not changed during time. We also found that the calculation time is strongly correlated with the number of sequencing reads used for the analysis.