Novel Primer Sets for Next Generation Sequencing-Based Analyses of Water Quality

Lee, Elvina; Khurana, Maninder S.; Whiteley, Andrew S.; Monis, Paul; Bath, Andrew; Gordon, Cameron; Ryan, Una; Paparini, Andrea

doi:10.1371/journal.pone.0170008

Cited by 14 publications

(24 citation statements)

References 58 publications

(65 reference statements)

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“…By applying this approach, functional and taxonomic microbial diversity can be described and then changes in communities can be monitored over time and space in response to anthropogenic or environmental impacts related to human health (Port et al ., 2012). The growing accessibility of next-generation DNA sequencing (NGS) methods has greatly advanced our understanding of microbial diversity in medical and environmental science (Lee et al ., 2017). The Next-generation sequencing (NGS) methods have prominently increased sequencing throughput by using massively parallel sequencing (Sogin et al ., 2006).…”

Section: Introductionmentioning

confidence: 99%

First report on Bacterial Diversity of Potable Spring water of Indian Himalayan Region

Singh

et al. 2018

Preprint

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16Water quality of a region directly corroborates with the health index of people. People in the 17 Himalayan hills mainly depend upon the spring water for potability. To determine the microbial 18 ecology of the spring waters of Sikkim, the variable region of 16S rRNA has been sequenced 19 using Illumina MiSeq. Phylum wise annotation showed the East and North district are mostly 20 dominated by Proteobacteria (41% and 35.80%), whereas West and South district is dominated 21 by Planctomycetes (38.46%) and Verrucomicrobia (33%). The consistent dominance phyla in 22 the all the four districts were Bacteriodetes (34-24%) which was highest dominancy in North 23 district and lowest in wets district. Genus wise distribution showed the abundance of Brevifolis, 24 2 Flavobacterium, Verrucomicrobia subdivision3, Emticica, Cytophaga, Prosthecobacter, 25 Planctomycetes, Varivorax, Arcicella, Isosphera, Sedimunibacterium etc. The East district 26 showed highest dominancy of genus Emticicia whereas Planctomycetes in the West district. The 27North district was mainly dominated by genus Arcicella and Brevifollis in the South district. 28North on the antonymous showed totally different sets of microbial diversity. North district 29 showed an abundance of Arcicella, Planctomycetes, Schlerensia and Azohydromonas. The heat 30 map produced by Bray Curtis distance method produced three clusters which showed the close 31 relationship between West and East district microbiome that further related to South district. The 32 sample of North district formed out group that showed different community structure from other 33 three districts. The principle component analysis was showed that the east and South district 34 samples are closely related and distantly correlated to the west Sikkim, but the North district 35 showed completely different microbial community. The canonical correspondence analysis 36 showed correlation between bacterial diversity and hydrochemistry and it was found that the 37 bacterial diversity was influenced by the concentration of different metallic ions like sodium, 38 calcium, barium and iron. This is a first report from the Eastern Himalayan region of India and it 39 largely enhances our knowledge about the microbial structure of potable spring water of Eastern 40 Himalayan. This study is useful for Government of India as well as the state government to adopt 41 the different strategic treatment procedures to improve the quality of water that is supplied to the 42 community resides in the Himalayan regions and solely dependent on this untreated spring water. 43 44 45 46 47 48Microbial communities are the key members of many ecosystems on the earth 49 (Lagkouvardos et al., 2016). The word microbial communities can be described in the terms 50 of richness or evenness as well as composition i.e. abundance of taxa and genes in the sample 51 (Rothschild, 1991). They play a significant role in crucial biological functions ranging from 52 nitrogen and carbon cycles in the environment to regulation of metabolic...

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Section: Introductionmentioning

confidence: 99%

First report on Bacterial Diversity of Potable Spring water of Indian Himalayan Region

Singh

et al. 2018

Preprint

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“…OTUs that did not cluster with known taxa at 97% identity or higher in the database were clustered de novo and not de novo (UCLUST) (Edgar, 2010). Representative sequences for each OTU were then aligned using PyNast [ 20 ], and taxonomy was assigned using the RDP classifier (Version 2.2) [ 21 ]. A phylogenetic tree was built using FastTree.…”

Section: Methodsmentioning

confidence: 99%

Microbial Diversity of Chronic Wound and Successful Management of Traditional Chinese Medicine

Guo

et al. 2018

Evidence-Based Complementary and Alternative Medicine

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Chronic ulcer, including diabetic ulcer, varicose ulcer, and pressure ulcer, negatively affects patients' quality of life. As microbiology plays an important role in the mechanism of pathology for chronic wound healing, this study concentrates on microecology environment of the wound and how Traditional Chinese Medicine (TCM) regulates wound bacteria. Method. The study took wound samples from 35 patients and analyzed bacteria variation before and after TCM treatment by 16s rRNA sequencing. All samples were evaluated from aspects of α-diversity, β-diversity, and Simpson's Diversity index. Result. After total DNA extraction, PCR, and 16S rRNA sequencing of wound bacteria from 35 individuals, it was discovered that younger patients with shorter course of disease have a higher microbial diversity and were easier to recover from ulcers. Additionally, gender also played a vital role in wound healing, and a significant microbial diversity existed between male and female patients. Conclusion. Patients with chronic ulcers achieved a positive effect after TCM treatment (skin-producing ointment). Mechanistically, TCM helped promote wound healing by regulating the wound microbiota.

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“…Therefore, this tool has been used as an assessment approach to quantify the risk of exposure to cyanobacteria and their toxins that pose threats to human health. Furthermore, the classification of cyanobacteria has been carried out by previous studies using PCR [36][37][38] , with much effort being directed towards the assessment of cyanobacterial diversity. Cyanobacteria have been identified up to the genus level using the 16S rRNA gene sequencing 37 .…”

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confidence: 99%

“…Cyanobacteria have been identified up to the genus level using the 16S rRNA gene sequencing 37 . However, factors such as sequencing method, amplicon targeted (locus and region), bioinformatics pipeline, thermal cycling conditions used, and choice of primers have been identified to affect the success and resultant quality of PCR-based sequencing 38 . Therefore, 16S rRNA coupled with available sequencing information gives higher detectability and allows taxonomic classification of cyanobacteria, potentially to species level [38][39][40] .…”

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Using FlowCam and molecular techniques to assess the diversity of Cyanobacteria species in water used for food production

Mutoti

Jideani

Gumbo

2022

Sci Rep

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Globally, the occurrence of cyanobacteria in water currently remains an important subject as they produce cyanotoxins that pose threat to human health. Studies on the contamination of maize meals during mill grinding processes using cyanobacteria-contaminated water have not been conducted. The present study aimed to assess the diversity of cyanobacteria in the samples (process water, uncooked maize meal, and cooked maize meal (porridge)). Polymerized Chain Reaction (PCR) and Advanced digital flow cytometry (FlowCAM) were used to detect and identify cyanobacterial species available in these samples. 16S Primers (forward and reverse) tailed with Universal Sequences were used for amplification and sequencing of full-length 16S rRNA genes from cyanobacteria found in all samples. Cyanobacterial species from order Nostocales, Pseudanabaenales, Oscillatoriales Chroococcales, Synechococcales, and unclassified cyanobacterial order, some of which have the potential to produce cyanotoxins were amplified and identified in process water, raw maize meal and porridge samples using PCR. Images of the genus Microcystis, Phormidium, and Leptolyngbya were captured in process water samples using FlowCAM. These findings show the presence of cyanobacteria species in process water used for maize meal and the absence in cooked maize meal. The presence of cyanobacteria in process water is likely another route of human exposure to cyanotoxins.

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Novel Primer Sets for Next Generation Sequencing-Based Analyses of Water Quality

Cited by 14 publications

References 58 publications

First report on Bacterial Diversity of Potable Spring water of Indian Himalayan Region

First report on Bacterial Diversity of Potable Spring water of Indian Himalayan Region

Microbial Diversity of Chronic Wound and Successful Management of Traditional Chinese Medicine

Using FlowCam and molecular techniques to assess the diversity of Cyanobacteria species in water used for food production

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