Human Resistome Study with Metagenomic Sequencing Data

Jae Hong Shin; Mina Rho

doi:10.7599/hmr.2018.38.2.73

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Shin and Rho: Human Resistome Study with Metagenomic Sequencing Data

Review

Hanyang Medical Reviews 2018; 38(2): 73-79.

Published online: 30 June 2018

DOI: https://doi.org/10.7599/hmr.2018.38.2.73

Human Resistome Study with Metagenomic Sequencing Data

Jae Hong Shin¹, Mina Rho^1,²

¹Department of Computer Science and Engineering, College of Engineering, Hanyang University, Seoul, Korea.

²Department of Biomedical Informatics, Hanyang University, Seoul, Korea.

Corresponding Author: Mina Rho. Department of Computer Science and Engineering, College of Engineering, Hanyang University, Department of Biomedical Informatics, Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul 04763, Korea. Tel: +82-2-2220-2379 Fax: +82-2-2220-1886 minarho@hanyang.ac.kr

Received 3 April 2018 Revised 5 May 2018 Accepted 12 June 2018

Hanyang University College of Medicine · Institute of Medical Science

(open-access):

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

With the introduction of synthetic antibiotics, many lives including humans and animals have been saved against bacterial infection. An increasing level of antibiotics use, however, raises serious problems of multi-drug resistance and transferring of resistance genes across different environments and countries. Advances in high-throughput sequencing technology and efficient bioinformatics methods allow us to perform a large-scale screening and analysis of resistomes in the human and environmental microbiomes. Recent studies on human microbiomes have revealed a diverse distribution of resistance genes and their transferring activities in the communities. This review discusses recent progresses in metagenomic approaches to identify resistance genes in the human microbiome, including genomic sequence search and functional metagenomics methods. Using Rifampicin ADP-ribosyltransferase as an example, an integrative approach that analyzes the sequences and three-dimensional structures of the proteins derived from resistance genes is also introduced.

Keywords: Human microbiome, Metagenome, Antibiotics resistance

Figures and Tables

Fig. 1

Chemical structure of rifamycin families.

Fig. 2

Mutiple sequence alignment of rifampicin ADP-ribosyltransferase se quencs and three-dimentional X-ray structure of Arr-ms and rifampicin (PDBID: 2HW2).

Table 1

Summary of microbiome studies characterizing human and environmental resistomes

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