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Gebregziabher SM, Yalew AW, Sime H, Abera A. Molecular detection of waterborne pathogens in infants' drinking water and their relationship with water quality determinants in eastern Ethiopia: loop-mediated isothermal amplification (LAMP)-based study. JOURNAL OF WATER AND HEALTH 2024; 22:1-20. [PMID: 38295069 PMCID: wh_2023_201 DOI: 10.2166/wh.2023.201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2024]
Abstract
Cryptosporidium, Shigella, toxin-producing Escherichia coli, and rotavirus were reported to be the most responsible for severe and fatal diarrhea among infants. This study aimed to investigate the presence of these pathogens in infants' drinking water samples and analyzing using water quality determinants in eastern Ethiopia. A molecular (LAMP)-based cross-sectional study design was employed. A total of 410 and 37 water samples were tested from infant point-of-use at household and corresponding water source, respectively, from June 2020 to May, 2021. Cryptosporidium, Shigella, toxin-producing E. coli, and rotavirus were detected in 28.5, 30.0, 26.3, and 32.2%, of water samples tested from infant point-of-use, respectively. About 13.2% of the water samples were positive for all (four) pathogens together. Cryptosporidium, Shigella, toxin-producing E. coli, and rotavirus were detected in 27.0, 32.4, 29.7, and 37.8%, of water samples tested from water sources, respectively. Positive significant correlation was observed between infant point-of-consumption and water sources from which it is drawn toward the presence of each targeted pathogen. Unimproved water source showed a strong significant association with the presence of Cryptosporidium, Shigella and toxin-producing E. coli. Therefore, efforts should be made in development of improved water sources, source protection safety and health education to caretakers of infants.
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Affiliation(s)
| | - Alemayehu Worku Yalew
- School of Public Health, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Heven Sime
- Bacterial, Parasitic and Zoonotic Diseases Research Directorate, EPHI, Addis Ababa, Ethiopia
| | - Adugna Abera
- Bacterial, Parasitic and Zoonotic Diseases Research Directorate, EPHI, Addis Ababa, Ethiopia
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Yuan D, Wang W, Liu C, Xu L, Fei H, Wang X, Shen M, Wang S, Wang M, Zhu G. Source, contribution and microbial N-cycle of N-compounds in China fresh snow. ENVIRONMENTAL RESEARCH 2020; 183:109146. [PMID: 31991341 DOI: 10.1016/j.envres.2020.109146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 01/14/2020] [Accepted: 01/15/2020] [Indexed: 06/10/2023]
Abstract
The importance and contribution of nitrogen compounds and the related microbial nitrogen cycling processes in fresh snow are not well understood under the current research background. We collected fresh snow samples from 21 cities that 80% are from China during 2016 and 2017. Principal component analysis showed that SO42- were in the first principal component, and N-compounds were the second. Furthermore, the main pollutant ions SO42- and NO3- were from anthropogenic sources, and SO42- contributed (61%) more to the pollution load than NO3- (29%), which were confirmed through a series of precipitation mechanism analysis. We selected five N-cycle processes (consist of oxidation and reduction processes) for molecular biology experiments, including Ammonia-oxidation process, Nitrite-oxidation process, Denitrification process, Anaerobic-ammoxidation process (Anammox) and Dissimilatory nitrate reduction to ammonium process (DNRA). Except ammonia-oxidizing archaeal (AOA) and bacterial (AOB) amoA genes (above 107 copies g-1), molecular assays of key functional genes in various nitrogen conversion processes showed a belowed detection limit number, and AOB abundance was always higher than AOA. The determination of the microbial transformation rate using the 15N-isotope tracer technique showed that the potential rate of five N-conversion processes was very low, which is basically consistent with the results from molecular biology studies. Taken together, our results illustrated that microbial nitrogen cycle processes are not the primary biological processes causing the pollution in China fresh snow.
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Affiliation(s)
- Dongdan Yuan
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; School of Municipal and Environmental Engineering, Jilin Jianzhu University, Changchun, 130118, China
| | - Weidong Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Chunlei Liu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Liya Xu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Hexin Fei
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Xiaoling Wang
- School of Municipal and Environmental Engineering, Jilin Jianzhu University, Changchun, 130118, China
| | - Mengnan Shen
- School of Municipal and Environmental Engineering, Jilin Jianzhu University, Changchun, 130118, China
| | - Shanyun Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Mengzi Wang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Guibing Zhu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; School of Municipal and Environmental Engineering, Jilin Jianzhu University, Changchun, 130118, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
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Liu M, Xue Y, Yang J. Rare Plankton Subcommunities Are Far More Affected by DNA Extraction Kits Than Abundant Plankton. Front Microbiol 2019; 10:454. [PMID: 30930870 PMCID: PMC6423910 DOI: 10.3389/fmicb.2019.00454] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 02/20/2019] [Indexed: 01/14/2023] Open
Abstract
Advances in high-throughput sequencing technologies allow a more complete study of microbial plankton community composition and diversity, especially in the rare microbial biosphere. The DNA extraction of plankton is a key step for such studies; however, little is known about its influences on the abundant or rare microbial biosphere. Our aim was to quantify the influences of different DNA extraction kits on abundant and rare plankton in the surface waters of a reservoir and provide a reference for the comparisons between microbial community studies with different extraction methods. We evaluated the influence of five common commercial kits on DNA quality, microbial community diversity and composition, and the reproducibility of methods using both 16S and 18S rRNA genes amplicon sequencing. Our data showed that results of Fast DNA Spin Kit for Soil (MPF) had higher α diversity for bacteria and high DNA quality, indicating that it is the most suitable approach for bacterioplankton diversity study. However, DNeasy Blood & Tissue Kit (QD) and QIAamp DNA Mini Kit (QQ) methods could produce results that are easier to replicate for bacteria and eukaryotes, respectively, and were more comparable between studies. The use of different DNA extraction kits had larger influence on the rare taxa compared with abundant taxa. Therefore, the comparability between studies that employed different extraction methods can be improved by removing low-abundance or less-representative OTUs. Collectively, this study provides a comprehensive assessment of the biases associated with DNA extraction for plankton communities from a freshwater reservoir. Our results may guide researchers in experimental design choices for DNA-based ecological studies in aquatic ecosystem.
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Affiliation(s)
- Min Liu
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yuanyuan Xue
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jun Yang
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
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Mateus-Barros E, Meneghine AK, Bagatini IL, Fernandes CC, Kishi LT, Vieira AAH, Sarmento H. Comparison of two DNA extraction methods widely used in aquatic microbial ecology. J Microbiol Methods 2019; 159:12-17. [PMID: 30738110 DOI: 10.1016/j.mimet.2019.02.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 02/05/2019] [Accepted: 02/05/2019] [Indexed: 11/20/2022]
Abstract
In recent years, the rapid advances of culture-independent methods and new molecular tools have revolutionized our understanding of microbial biodiversity and ecological functions. DNA extraction from microbial communities is a critical step in this process and several methods have been proposed and used, but the influence of the extraction method on the outcome and ultimately on ecological inferences from the results is not yet precisely determined. Here, we compared two of the most commonly used extraction methods in aquatic microbial ecology, and investigated whether the two methods yielded comparable results for community ecology analyses. We extracted DNA from 15 different shallow lakes with phenol:chloroform, a classical and widely used extraction method, and with the PowerSoil DNA isolation Kit, often suggested as the standard DNA extraction method, with some adaptations for aquatic environments. We found that although only 5% of all OTUs showed significant differences in pairwise comparisons (using the 15 lakes as replicates), these OTUs accounted for >35% (on average) of the relative abundance. Diversity and richness did not differ significantly between the two extraction methods, but the beta-dispersion of the communities indicated that the organic extraction yielded more homogeneous communities, while the kit extraction generated variability. Consequently, we conclude that despite the small number of OTUs with significant differences, their impact on the community composition obtained was not negligible, and therefore the results from these two extraction methods were not comparable.
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Affiliation(s)
- Erick Mateus-Barros
- Universidade Federal de São Carlos (UFSCar), Department of Hydrobiology, Laboratory of Microbial Processes and Biodiversity, São Carlos, SP 13565-905, Brazil; Post Graduate Program in Ecology and Natural Resources (PPGERN), UFSCar, São Carlos, SP 13565-905, Brazil
| | - Aylan K Meneghine
- Universidade Federal de São Carlos (UFSCar), Department of Hydrobiology, Laboratory of Microbial Processes and Biodiversity, São Carlos, SP 13565-905, Brazil
| | | | - Camila C Fernandes
- Universidade Estadual Paulista (UNESP), Faculdade de Ciências Agrárias e Veterinárias, Departamento de Tecnologia, Laboratório de Bioquímica de Microrganismos e Plantas - LBMP, Jaboticabal, SP 14884-900, Brazil; UNESP, Faculdade de Ciências Agrárias e Veterinárias, Departamento de Tecnologia, Laboratório Multiusuário Centralizado para Sequenciamento de DNA em Larga Escala e Análise de Expressão Gênica - LMSeq, Jaboticabal, SP 14884-900, Brazil
| | - Luciano T Kishi
- Universidade Estadual Paulista (UNESP), Faculdade de Ciências Agrárias e Veterinárias, Departamento de Tecnologia, Laboratório de Bioquímica de Microrganismos e Plantas - LBMP, Jaboticabal, SP 14884-900, Brazil; UNESP, Faculdade de Ciências Agrárias e Veterinárias, Departamento de Tecnologia, Laboratório Multiusuário Centralizado para Sequenciamento de DNA em Larga Escala e Análise de Expressão Gênica - LMSeq, Jaboticabal, SP 14884-900, Brazil
| | - Armando A H Vieira
- UFSCar, Department of Botany, Laboratory of Phycology, São Carlos, SP 13565-905, Brazil
| | - Hugo Sarmento
- Universidade Federal de São Carlos (UFSCar), Department of Hydrobiology, Laboratory of Microbial Processes and Biodiversity, São Carlos, SP 13565-905, Brazil.
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