An investigation of the microbial population in aquarium water, using next generation sequencing

With many of antibiotics used in the clinic, antibiotic resistant genes (ARG) are widely transferred among bacterial communities. As a result, superbugs possessing several antibiotic resistant genes are a significant threat to public health. Antibiotic resistant pathogens in drinking water or wastewater could therefore influence public health. The aim of this project is to develop and compare protocols for molecular analysis of microbial communities in aquatic samples. In this project, both 16S rRNA genes and whole metagenome of a bacterial community in a freshwater aquarium were analysed using next-generation sequencing (Ion PGM). Sequencing reads were trimmed using CLC genomics workbench. De novo assembly was performed using MetaVelvet and CLC genomics workbench. SILVA NGS, Ion Reporter, and MG RAST were used to determine the bacterial population structure. MG RAST and ardbAnno were used to detect ARG. Analysis including abundance of different pathogens and antibiotic resistance, and comparison of taxonomic analyses among SILVA NGS, Ion Reporter, and MG RAST. This project sets up a pipeline for aquatic pathogenic and antibiotic resistance gene detection using 16S rDNA and whole genome sequencing. In conclusion, MG RAST provides a more comprehensive database than the other two databases, and is more suitable for metagenomics research. ARG were detected in the aquarium but it was not possible to associate these genes with individual species or strains.

Name dc:type.qualificationname

mres

Level dc:type.qualificationlevel

masters-pg

Grantor dc:publisher.institution

University of Strathclyde

Year dc:date.issued

2015

Author dc:creator

• Ding, Qiutao

DOI

10.48730/wgf3-4015

Identifier

T14192

Author Identifier

201452857

OAI identifier oai:identifier

oai:strathclyde:dn39x158j