Next-generation sequencing for investigating the diversity of microorganisms and pathogenic bacteria in a water source

Yingliang, Ge; Shuili, Yu

doi:10.4314/tjpr.v16i7.7

Cited by 9 publications

(8 citation statements)

References 21 publications

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“…However, the massively parallel sequencing techniques of hypervariable regions of 16S rRNA genes are associated with several biases that are partially overcome by optimized extraction methods, increased sequencing depth, improved bioinformatic tools, choice of primers as well as the use of replicates ( Robasky et al, 2014 ; Hugerth and Andersson, 2017 ). So far, replicates have been used for DNA extraction and PCR amplification, respectively ( Vivien et al, 2016 ; Ge and Yu, 2017 ), but samples were almost exclusively pooled prior to sequencing, thus making comprehensive evaluations of replicates impossible ( Staley et al, 2015 ).…”

Section: Introductionmentioning

confidence: 99%

Assessment of Microbial Community Dynamics in River Bank Filtrate Using High-Throughput Sequencing and Flow Cytometry

et al. 2018

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Surface-groundwater interactions play an important role in microbial community compositions of river bank filtrates. Surface water contaminations deriving from environmental influences are attenuated by biogeochemical processes in the hyporheic zone, which are essential for providing clean and high-quality drinking water in abstraction wells. Characterizing the flow regime of surface water into the groundwater body can provide substantial information on water quality, but complex hydraulic dynamics make predictions difficult. Thus, a bottom up approach using microbial community shifting patterns as an overall outcome of dynamic water characteristics could provide more detailed information on the influences that affect groundwater quality. The combination of high-throughput sequencing data together with flow cytometric measurements of total cell counts reveals absolute abundances among taxa, thus enhancing interpretation of bacterial dynamics. 16S rRNA high-throughput sequencing of 55 samples among six wells in a well field in Austria that is influenced by river bank filtrate within a time period of 3 months has revealed both, clear differences as well as strong similarity in microbiome compositions between wells and dates. A significant community shift from April to May occurred in four of six wells, suggesting that surface water flow regimes do affect these wells stronger than others. Triplicate sampling and subsequent sequencing of wells at different dates proved the method to be reproducible. Flow cytometric measurements of total cells indicate microbial shifts due to increased cell counts and emphasize the rise of allochthonous microorganisms. Typical freshwater bacterial lineages (Verrucomicrobia, Bacteroidetes, Actinobacteria, Cyanobacteria, Armatimonadetes) were identified as most increasing phyla during community shifts. The changes are most likely a result of increased water abstraction in the wells together with constant river water levels rather than rain events. The results provide important knowledge for future implementations of well utilization in dependency of the nearby Danube River water levels and can help drawing conclusions about the influence of surface water in the groundwater such that hygienically save and clean drinking water with a stable microbial community can be provided.

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Section: Introductionmentioning

confidence: 99%

Assessment of Microbial Community Dynamics in River Bank Filtrate Using High-Throughput Sequencing and Flow Cytometry

et al. 2018

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“…Next-generation sequencing platforms are useful for comprehensive assessment of drinking water microbiota and has begun to be employed in both resource-rich and constrained settings [18]. By employing next generation sequencing techniques, it is possible to detect and identify the presence and diversity of pathogenic microorganisms that cannot be achieved with classical methods [19].…”

Section: Introductionmentioning

confidence: 99%

Microbial Community Structure and Diversity in Drinking Water Supply, Distribution Systems as Well as Household Point of Use Site in Addis Ababa City, Ethiopia

Atanfu

Desta

Assefa

2021

Preprint

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BackgroundUnderstanding ecology of microbiomes in drinking water distribution systems is the most important notion in delivering safe drinking water. Despite cultivation-based methods routinelyemployed in monitoring drinking water quality, cultivation of specific indicator organisms alone is not always guarantee for assuring safe drinking water delivery. The presence of complex microbiomes in drinking water distribution systems affects treatment effectiveness leading to poor quality water which as a result affects health of human and animals. Drinking water treatment and distribution systems harbor various microbiota despite efforts made in improving water infrastructures and several waterborne diseases become serious problems in the water industry, specially, in developing Countries. Intermittent water supply, long-time of water storage, low water pressure in distribution systems, storage tankers and pipes as well as contaminated source water are among many of the factors responsible for low drinking water quality which in turn affecting health of people. The aim of this study was to explore microbial diversity and structure in water samples collected from source water, treated water, reservoirs, and several household points of use locations (taps). High throughput Illumina sequencing technology was employed by targeting V4 region of 16S rRNA following Illumina protocol to analyze the community structure of bacteria. ResultsThe core dominating taxa were Proteobacteria followed by Firmicutes, Bacteroidetes and Actinobacteria. Gamma proteobacteria were dominant among other Proteobacterial classes across all sampling points. Opportunistic bacterial genera such as Pseudomonas, Legionella, Klebsiella, Escherichia, Actinobacteria, as well as eukaryotic microbes like Cryptosporidium, Hartmanella, Acanthamoeba, Aspergillus, and Candida were also the abundant taxa found alongthe distribution systems. The shift in microbial community structure from source to point of uselocations were influenced by factors such as residual free chlorine, intermittent water supply andlong-time storage at the household. The shift in microbial community structure from source to point of use locations were influenced by factors such as residual free chlorine, intermittent water supply and long-time storage at the household.ConclusionsThe complex microbiota which was present in different sample sites receiving treated water from the two treatment plants (Legedadi and Gefersa) starting from source water to household point of consumption across the distribution systems in Addis Ababa brings drinking water quality problem which further causes significant health problems to both human and animal health. Treatment ineffectiveness, disinfection inefficiency, poor maintenance actions, leakage of sewage and other domestic wastes are few among many other factors responsible for degraded drinking water quality in this study putting health at high risk which, this, leads to morbidity and mortality. Findings of this research provide important and bassline information to understand the microbial profiles of drinking water along source water and distribution systems.

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“…Another advanced molecular technique, next-generation sequencing (NGS) has been widely applied in the studies of whole genome sequencing of animals and plants, transcriptome sequencing, and metagenomic investigations such as microorganism diversity [16]. One of the NGS technology amplicon sequencing combining with a gene marker shows promise in food authentication practices as it can meet the need for detecting target organism ingredients or revealing unknown ingredients.…”

Section: Introductionmentioning

confidence: 99%

Combining a COI Mini-Barcode with Next-Generation Sequencing for Animal Origin Ingredients Identification in Processed Meat Product

Pan¹,

Deyi²,

Chen³

et al. 2020

Journal of Food Quality

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For revealing animal species in complex or adulterated processed meat product, we presented a method combining a novel cytochrome oxidase I (COI) mini-barcode with next-generation sequencing (NGS), which identifies various animal species (swine, bovine, Caprinae, and some of fish, shrimp, and poultry) accurately and efficiently in processed meat products. We designed a universal primer based on 140 sequences from 51 edible animal species. A mixture of 12 species raw meat samples were identified with the clone sequencing and also with a mini-barcode- (136 bp) combined NGS method, respectively. The mini-barcode of these 12 species was 100% identical to the target species sequence by Sanger sequencing. Compared to the clone sequencing method, the NGS method is superior in accuracy, sensitivity, and detection efficiency. Various edible animal species were identified in the species level both in the mixed samples and the 7 heavily processed food products. Moreover, some unlabeled species and dubious contamination were detected as well.

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Next-generation sequencing for investigating the diversity of microorganisms and pathogenic bacteria in a water source

Abstract: Purpose: To employ next-generation sequencing (NGS) to investigate the diversity of microorganisms and pathogenic bacteria from a water source in Tai Lake

Cited by 9 publications

References 21 publications

Assessment of Microbial Community Dynamics in River Bank Filtrate Using High-Throughput Sequencing and Flow Cytometry

Assessment of Microbial Community Dynamics in River Bank Filtrate Using High-Throughput Sequencing and Flow Cytometry

Microbial Community Structure and Diversity in Drinking Water Supply, Distribution Systems as Well as Household Point of Use Site in Addis Ababa City, Ethiopia

Combining a COI Mini-Barcode with Next-Generation Sequencing for Animal Origin Ingredients Identification in Processed Meat Product

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