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Developing portable next generation gene sequencing technology

Developing portable next generation gene sequencing technology

Conventional methods for combating microbial diseases include the use of antibiotics and disinfectants. These methods are highly problematic. Other, more innovative methods need advanced tools for monitoring.

Project leader

Dr David Werner

Dates

2019-2020

Project staff

Mr Adrian Blackburn

Dr Soydoa Vinitnantharat, KMUTT

Dr Sawannee Sutheeworapong, KMUTT

Ms Pawinee Patanachan, KMUTT

Dr Pawinee Chaiprasert, KMUTT

Mr Bundit Tirachulee, KMUTT

Ms Rattikan Neamchan, KMUTT

Ms Thunchanok Thongsamer, KMUTT

Mr Thanee Dawrueng, KMUTT

Sponsors

Newton Fund

British Council

Office of the Higher Education Commission

Partners

Small-scale aquaculture farmers in Thailand (six case study sites)

Description

Antibiotics are life-saving medicines in treating human diseases. Their use in agriculture reduces their effectiveness, and leads to antibiotics resistance.

Disinfectants like chlorine form unwanted by-products. They indiscriminately kill good and bad microbes. Eliminating beneficial microorganisms makes aquacultures more vulnerable to invasion by pathogens.

More innovative methods include probiotics and water biofiltration and recirculation schemes. They avoid the excessive use of problematic chemicals. They are thus able to maintain aquacultures as resilient ecosystems in which sudden stock losses are less likely to occur. These new methods need in-depth understanding of aquaculture microbiology. This understanding requires advanced tools for monitoring.

Next generation sequencing (NGS) can provide near real-time monitoring of microbial communities. We are bringing these benefits within reach of aquaculture farmers. Newcastle University is working with King Mongkut's University of Technology Thonburi (KMUTT) in Thailand. We are training KMUTT staff in the use of the NGS tool MinION. Developed by Oxford Nanopore Technologies, MinION is a portable, real-time device for DNA and RNA sequencing. We will then work together to develop the use of NGS for microbial community monitoring and management in aquacultures. We will demonstrate the benefits of the tool at case study aquaculture farms.