Next Generation High Throughput Sequencing to Assess Microbial Communities: An Application Based on Water Quality

Wani, Gowher A.; Khan, Mohd Asgar; Dar, Mudasir A.; Shah, Manzoor Ahmad; Reshi, Zafar A.

doi:10.1007/s00128-021-03195-7

Cited by 22 publications

(11 citation statements)

References 49 publications

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“…Limitations of this approach have been addressed by the development of metagenomic analysis that uses sequencing, and now high-throughput sequencing and microarray technologies-"open-format" and "closed-format" detection technologies, respectively-combined with high-performance computational tools, to provide information on the species composition of a microbiome [15]. In recent years, next generation sequencing technology has been used to rapidly and efficiently profile whole microbial communities in various samples, revolutionizing genome research because of its capability to produce a large quantity of sequence data in a relatively short period of time [93]. Shotgun metagenomic sequencing, a relatively new and powerful sequencing approach that uses the random sequencing of all genomic content of a microbiome, allows researchers to measure all genes in all organisms present in the community of the study sample, overcoming many of the limitations of amplicon sequencing.…”

Section: Metagenomics Approaches To Study Microbial Communitiesmentioning

confidence: 99%

The Interaction among Microbiota, Epigenetic Regulation, and Air Pollutants in Disease Prevention

Pulliero

Traversi²,

Franchitti³

et al. 2021

JPM

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Environmental pollutants can influence microbiota variety, with important implications for the general wellbeing of organisms. In subjects at high-risk of cancer, gut, and lung microbiota are distinct from those of low-risk subjects, and disease progression is associated with microbiota alterations. As with many inflammatory diseases, it is the combination of specific host and environmental factors in certain individuals that provokes disease outcomes. The microbiota metabolites influence activity of epigenetic enzymes. The knowledge of the mechanisms of action of environmental pollution now includes not only the alteration of the gut microbiota but also the interaction between different human microbiota niches such as the lung–gut axis. The epigenetic regulations can reprogram differentiated cells in response to environmental changes. The microbiota can play a major role in the progression and suppression of several epigenetic diseases. Accordingly, the maintenance of a balanced microbiota by monitoring the environmental stimuli provides a novel preventive approach for disease prevention. Metagenomics technologies can be utilized to establish new mitigation approaches for diseases induced by polluted environments. The purpose of this review is to examine the effects of particulate matter exposure on the progression of disease outcomes as related to the alterations of gut and lung microbial communities and consequent epigenetic modifications.

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Section: Metagenomics Approaches To Study Microbial Communitiesmentioning

confidence: 99%

The Interaction among Microbiota, Epigenetic Regulation, and Air Pollutants in Disease Prevention

Pulliero

Traversi²,

Franchitti³

et al. 2021

JPM

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“…And there are still problems of uneven distribution and water pollution, which lead to water quality and biosecurity of drinking water have been widely addressed (Gunnarsdottir et al, 2020 ). The water quality is closely affected by the composition of the microbial community in the water (Wani et al, 2021 ). The composition of microbial communities will rapidly vary, once their habitats have changed slightly.…”

Section: Introductionmentioning

confidence: 99%

The spatiotemporal variations of microbial community in relation to water quality in a tropical drinking water reservoir, Southmost China

Wu,

Zou,

Xiao

et al. 2024

Front. Microbiol.

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It is well-known that water quality has great significance on microbial community composition in aquatic environments. In this study, we detected water column indicates the microbial community composition of nine sampling sites over two seasons using Illumina TruSeq sequencing in Songtao Reservoir, Hainan Province, Southmost China. The study indicated that the dominant phylum was Actinobacteria, Proteobacteria, Bacteroidetes, and Cyanobacteria. The diversity parameters showed that the microbial community composition had significant spatiotemporal variations, including the significantly higher Shannon index and Simpson index upstream than those midstream and downstream. Besides, there were significantly higher Chao1 index, Shannon index, and Simpson index in winter than in summer. Principal coordinates analysis (PCoA) showed the microbial structural composition had significant seasonal differences. The results of microbial community composition further revealed that the eutrophication level upstream was higher than that of midstream and downstream. The redundancy analysis (RDA) diagram indicated that the abundance of microbiology species significantly correlated with temperature, total phosphorus, Se, and Ni. Furthermore, the mantel's test showed that the temperature and total phosphorus significantly affected the community composition of archaea and bacteria. Overall, our finding here partially validated our hypothesis that the spatiotemporal variations of microbial community composition are significantly related to nutrients, physicochemical factors and metals, which has been unknown previously in tropical drinking waterbodies. This study substantially contributed to understanding of the composition of microbial community in tropical drinking water reservoirs and the main environmental driving factors in tropical zones. It also provided a reference for the management of reservoir operation to ensure drinking water safe.

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“…New metagenomic software that uses machine learning, such as SourceTracker and FEAST, is being trialed as a useful approach for fecal source assignments using the microbial community identified in water samples (the sink) and comparing it with the microbial community profiles identified in animal fecal sources (the sources) [ 10 , 11 , 12 , 13 ]. A recent study using SourceTracker noted that while this program has value in community profiling microbial source tracking studies, there is still a lot of research required to understand its limitations, and they advised using local community fecal libraries relevant to the known fecal sources [ 14 ].…”

Section: Introductionmentioning

confidence: 99%

Exploring the Bacterial Community in Aged Fecal Sources from Dairy Cows: Impacts on Fecal Source Tracking

et al. 2023

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(1) Background: This paper discusses the impact of agricultural activities on stream health, particularly in relation to dairy cow fecal pollution. The study explores the fecal microbiome of cattle and the potential ecological implications of aging fecal pollution on waterways. (2) Methods: The study examines changes in the bacterial community available for mobilization from in-situ decomposing cowpats and the effects of simulated rainfall. The microbiome of individual cowpats was monitored over 5.5 months. We used 16S rRNA metagenomics and machine learning software, FEAST (Fast Expectation-mAximization for microbial Source Tracking), for bacterial and fecal source assignments. (3) Results: The phyla Bacillota and Bacteroidota are dominant in the fecal microbiota of fresh cow feces but shift to Pseudomonodota, Actinomycetota, and environmental Bacteroidota in aged cowpats. Potential impacts of these bacterial community shifts on inputs to local agricultural streams are discussed in relation to water quality monitoring and aging sources of fecal contamination. We identified taxon orders that are potential indicators of fresh cattle sources (Oscillospirales and Bacteroidales) and aged sources (Peptostreptococcales-Tissierellales) in water bodies. (4) The paper highlights that bacterial metagenomic profiling can inform our understanding of the ecology of microbial communities in aquatic environments and the potential impacts of agricultural activities on ecosystem health.

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Next Generation High Throughput Sequencing to Assess Microbial Communities: An Application Based on Water Quality

Cited by 22 publications

References 49 publications

The Interaction among Microbiota, Epigenetic Regulation, and Air Pollutants in Disease Prevention

The Interaction among Microbiota, Epigenetic Regulation, and Air Pollutants in Disease Prevention

The spatiotemporal variations of microbial community in relation to water quality in a tropical drinking water reservoir, Southmost China

Exploring the Bacterial Community in Aged Fecal Sources from Dairy Cows: Impacts on Fecal Source Tracking

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