Tropical Journal of Pharmaceutical Research

Original Research Article | OPEN ACCESS

Next-generation sequencing for investigating the diversity of microorganisms and pathogenic bacteria in a water source

Yingliang Ge^1,2, Shuili Yu¹

¹School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin, Heilongjiang Province 150090; ²School of Food Science and Technology, Harbin University, Harbin, Heilongjiang Province 150080, China.

For correspondence:- Shuili Yu Email: shuiliyuhu@163.com

Received: 13 April 2017 Accepted: 24 June 2017 Published: 31 July 2017

Citation: Ge Y, Yu S. Next-generation sequencing for investigating the diversity of microorganisms and pathogenic bacteria in a water source. Trop J Pharm Res 2017; 16(7):1503-1512 doi: 10.4314/tjpr.v16i7.7

© 2017 The authors.
This is an Open Access article that uses a funding model which does not charge readers or their institutions for access and distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0) and the Budapest Open Access Initiative (http://www.budapestopenaccessinitiative.org/read), which permit unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited..

Abstract

Purpose: To employ next-generation sequencing (NGS) to investigate the diversity of microorganisms and pathogenic bacteria from a water source in Tai Lake, China, in winter.

Methods: Water samples from the same source were collected over a period of 3 months (December 2013 to February 2014), and their physicochemical characteristics were determined. The DNA of the samples were extracted and amplified by polymerase chain reaction (PCR). The PCR products were sequenced by Miseq PE300 pyro sequencing platform. The results for 16S rDNA were analysed using visualization software Gephi, and the 16S rDNA gene pool of known pathogenic bacteria was established.

Results: A total of 144,292 16S rDNA gene sequences were obtained and ranked by RDP classifier. The average length of the sequences was 395.66 bp. They revealed 580 operational taxonomic units (OTUs) classified into 16 phyla. A full length of 16S rDNA gene database of common pathogenic bacteria was established. After blasting, 17 species of pathogenic bacteria were found. The most abundant potential human pathogenic bacteria were affiliated to B. tribocorum. Most environmental factors had significant impact on pathogenic bacteria.

Conclusion: These results indicate that NGS can be used for the simultaneous detection of most recognized water-borne pathogenic bacteria. Variations in microorganisms in water source at different periods in winter can provide insight into the diversity of microorganisms in the water.

Keywords: Next-generation sequencing, Pathogenic bacteria, Diversity, 16S rDNA gene