A comparative assessment of conventional and molecular methods, including MinION nanopore sequencing, for surveying water quality.

ABSTRACT: Nucleic acid based techniques, such as quantitative PCR (qPCR) and next generation sequencing (NGS), provide new insights into microbial water quality, but considerable uncertainty remains around their correct interpretation. We demonstrate, for different water sources in informal settlements in the Kathmandu Valley, Nepal, significant Spearman rank correlations between conventional and molecular microbiology methods that indicate faecal contamination. At family and genera level, 16S rRNA amplicon sequencing results obtained with the low-cost, portable next generation sequencer MinION from Oxford Nanopore Technologies had significant Spearman rank correlations with Illumina MiSeq sequencing results. However, method validation by amplicon sequencing of a MOCK microbial community revealed th

SUBMITTER: Acharya K 

PROVIDER: S-EPMC6823499 | biostudies-literature | 2019 Oct

REPOSITORIES: biostudies-literature