Inmagic DB/Text WebPublisher PRO: 2 records

Your search found 2 records

1 Acharya, K.; Blackburn, A.; Mohammed, Jemila; Haile, Alemseged Tamiru; Hiruy, A. M.; Werner, D. 2020. Metagenomic water quality monitoring with a portable laboratory. Water Research, 184:116112. [doi: https://doi.org/10.1016/j.watres.2020.116112]

Water quality ; Water analysis ; Monitoring ; Wastewater treatment plants ; Microbiological analysis ; Waterborne diseases ; Faecal coliforms ; Chemicophysical properties ; Portable equipment ; Costs ; Case studies / Ethiopia / United Kingdom / Addis Ababa / Birtley / Akaki River

(Location: IWMI HQ Call no: e-copy only Record No: H049934)

https://www.sciencedirect.com/science/article/pii/S0043135420306497/pdfft?md5=3d548784ecadc5dc3734e797551d099c&pid=1-s2.0-S0043135420306497-main.pdf
https://vlibrary.iwmi.org/pdf/H049934.pdf

(1.54 MB) (1.54 MB)

We describe the technical feasibility of metagenomic water quality analysis using only portable equipment, for example mini-vacuum pumps and filtration units, mini-centrifuges, mini-PCR machines and the memory-stick sized MinION of Oxford Nanopore Technologies, for the library preparation and sequencing of 16S rRNA gene amplicons. Using this portable toolbox on site, we successfully characterized the microbiome of water samples collected from Birtley Sewage Treatment Plant, UK, and its environs. We also demonstrated the applicability of the portable metagenomics toolbox in a low-income country by surveying water samples from the Akaki River around Addis Ababa, Ethiopia. The 16S rRNA gene sequencing workflow, including DNA extraction, PCR amplification, sequencing library preparation, and sequencing was accomplished within one working day. The metagenomic data became available within 24e72 h, depending on internet speed. Metagenomic analysis clearly distinguished the microbiome of pristine samples from sewage influenced water samples. Metagenomic analysis identified the potential role of two bacterial genera not conventionally monitored, Arcobacter and Aeromonas, as predominant faecal pollution indicators/waterborne hazards. Subsequent quantitative PCR analysis validated the high Arcobacter butzleri abundances observed in the urban influenced Akaki River water samples by portable next generation sequencing with the MinION device. Overall, our field deployable metagenomics toolbox advances the capability of scientists to comprehensively monitor microbiomes anywhere in the world, including in the water, food and drinks industries, the health services, agriculture and beyond.

2 Werner, D.; Acharya, K.; Blackburn, A.; Zan, R.; Plaimart, J.; Allen, B.; Mgana, S. M.; Sabai, S. M.; Halla, F. F.; Massawa, S. M.; Haile, Alemseged Tamiru; Hiruy, A. M.; Mohammed, J.; Vinitnantharat, S.; Thongsamer, T.; Pantha, K.; Filho, C. R. M.; Lopes, B. C. 2022. MinION nanopore sequencing accelerates progress towards ubiquitous genetics in water research. Water, 14(16):2491. (Special issue: Field Methods for Water Quality Surveying) [doi: https://doi.org/10.3390/w14162491]

Water ; Research ; Biomass ; Bioinformatics ; Sustainable Development Goals ; Goal 6 Clean water and sanitation

(Location: IWMI HQ Call no: e-copy only Record No: H051555)

https://www.mdpi.com/2073-4441/14/16/2491/pdf?version=1660812648
https://vlibrary.iwmi.org/pdf/H051555.pdf

(1.66 MB) (1.66 MB)

In 2014, Oxford Nanopore Technologies (ONT) introduced an affordable and portable sequencer called MinION. We reviewed emerging applications in water research and assessed progress made with this platform towards ubiquitous genetics. With >99% savings in upfront costs as compared to conventional platforms, the MinION put sequencing capacity into the hands of many researchers and enabled novel applications with diverse remits, including in countries without universal access to safe water and sanitation. However, to realize the MinION’s fabled portability, all the auxiliary equipment items for biomass concentration, genetic material extraction, cleanup, quantification, and sequencing library preparation also need to be lightweight and affordable. Only a few studies demonstrated fully portable workflows by using the MinION onboard a diving vessel, an oceanographic research ship, and at sewage treatment works. Lower nanopore sequencing read accuracy as compared to alternative platforms currently hinders MinION applications beyond research, and inclusion of positive and negative controls should become standard practice. ONT’s EPI2ME platform is a major step towards user-friendly bioinformatics. However, no consensus has yet emerged regarding the most appropriate bioinformatic pipeline, which hinders intercomparison of study results. Processing, storing, and interpreting large data sets remains a major challenge for ubiquitous genetics and democratizing sequencing applications.