An improved approach to identify bacterial pathogens to human in environmental metagenome

Jihoon Yang, Adina Howe, Jaejin Lee, Keunje Yoo, Joonhong Park

Research output: Contribution to journalArticlepeer-review


The identification of bacterial pathogens to humans is critical for environmental microbial risk assessment. However, current methods for identifying pathogens in environmental samples are limited in their ability to detect highly diverse bacterial communities and accurately differentiate pathogens from commensal bacteria. In the present study, we suggest an improved approach using a combination of identification results obtained from multiple databases, including the multilocus sequence typing (MLST) database, virulence factor database (VFDB), and pathosystems resource integration center (PATRIC) databases to resolve current challenges. By integrating the identification results from multiple databases, potential bacterial pathogens in metagenomes were identified and classified into eight different groups. Based on the distribution of genes in each group, we proposed an equation to calculate the metagenomic pathogen identification index (MPII) of each metagenome based on the weighted abundance of identified sequences in each database. We found that the accuracy of pathogen identification was improved by using combinations of multiple databases compared to that of individual databases. When the approach was applied to environmental metagenomes, metagenomes associated with activated sludge were estimated with higher MPII than other environments (i.e., drinking water, ocean water, ocean sediment, and freshwater sediment). The calculated MPII values were statistically distinguishable among different environments (p < 0.05). These results demonstrate that the suggested approach allows more for more accurate identification of the pathogens associated with metagenomes.

Original languageEnglish
Pages (from-to)1335-1342
Number of pages8
JournalJournal of microbiology and biotechnology
Issue number9
Publication statusPublished - 2020 Sept 28

Bibliographical note

Funding Information:
This research was supported by Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (No. 2018R1A6A1A08025348).

Publisher Copyright:
Copyright © 2020 by The Korean Society for Microbiology and Biotechnology

All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Applied Microbiology and Biotechnology


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