Metagenomic Assessment of Microbial Diversity at Five Sewage Treatment Plants (STP) Across Sabah, Malaysia and Impact on Water Quality Parameters

Bacterial metagenomics is an established technology that can be applied to assess the microbial diversity across sewage samples and its contribution to the effective treatment of sewage water in effluent treatment plants. The primary objective of this study was to establish a baseline for the microbial population diversity across five Sewage Treatment Plants (STP) in Sabah, Malaysia. The secondary objective was to elucidate the microbial diversity and correlate this with the quality of the treated effluent. Water samples were collected from the intake, processing and release points within each of the five facilities and 16S rRNA gene amplicon sequencing was performed on Oxford Nanopore MinION using the 16S PCR barcoding kit. Sequences were pre-processed, and data were analysed using EPI2ME platform to classify them based on taxonomy. Water quality parameters of the samples were provided by an accredited laboratory. The microbial profiles from the five treatment plants indicated a diverse range of human gut microflora which included Megamonas funiformis, Anaerobutyricum hallii, Agathobacter rectalis, Ligilactobacillus ruminis, Phascolarctobacterium faecium, Megasphaera elsdenii. Interestingly, no pathogenic bacteria were detected in the influent. Treatment of the effluent using aerobic and anaerobic processes resulted in a significant decrease in the total microbial populations and a shift in the microbial diversity as the nutrient load declined during treatment. The water quality parameters at all five discharge points of all STP were well within the range of the Environmental Quality (Sewage) Regulation 2009 which implies that the current microbial populations have attained an ecological equilibrium and that the STPs are operating at a high efficiency. The metagenomic data will establish a baseline that can be applied to monitor the operation of the STPs and carry out necessary interventions in the event of changes in the quality of effluent.