An optimized, amplicon-based approach for sequencing of SARS-CoV-2 from patient samples using COVIDSeq assay on Illumina MiSeq sequencing platforms

An amplicon-based approach for sequencing of SARS-CoV-2 using COVIDSeq assay on Illumina MiSeq sequencing platforms

10.31219/osf.io/6e5cw ◽

2021 ◽

Author(s):

Rahul C. Bhoyar ◽

Vigneshwar Senthivel ◽

Bani Jolly ◽

Mohamed Imran ◽

Abhinav Jain ◽

...

Keyword(s):

Genetic Epidemiology ◽

Rapid Development ◽

Illumina Miseq ◽

Diagnostic Tools ◽

Illumina Miseq Sequencing ◽

Miseq Sequencing ◽

Sequencing Platforms

Sequencing genomes of SARS-CoV-2 is crucial for understanding the genetic epidemiology of COVID-19pandemic. It is also critical for understanding the evolution of the virus and also for the rapid development of the diagnostic tools. The present protocol is the modification of the Illumina COVIDSeq amplicon-based sequencing approach adapted for benchtop sequencers like MiSeq, iSeq and MiniSeq.

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Pollutant-Removing Biofilter Strains Associated with High Ammonia and Hydrogen Sulfide Removal Rate in a Livestock Wastewater Treatment Facility

Sustainability ◽

10.3390/su13137358 ◽

2021 ◽

Vol 13 (13) ◽

pp. 7358

Author(s):

Dong-Hyun Kim ◽

Hyun-Sik Yun ◽

Young-Saeng Kim ◽

Jong-Guk Kim

Keyword(s):

Wastewater Treatment ◽

Hydrogen Sulfide ◽

Microbial Community ◽

Microbial Communities ◽

Illumina Miseq ◽

Illumina Miseq Sequencing ◽

Miseq Sequencing ◽

Treatment Facility ◽

Livestock Wastewater ◽

Wastewater Treatment Facility

This study analyzed the microbial community metagenomically to determine the cause of the functionality of a livestock wastewater treatment facility that can effectively remove pollutants, such as ammonia and hydrogen sulfide. Illumina MiSeq sequencing was used in analyzing the composition and structure of the microbial community, and the 16S rRNA gene was used. Through Illumina MiSeq sequencing, information such as diversity indicators as well as the composition and structure of microbial communities present in the livestock wastewater treatment facility were obtained, and differences between microbial communities present in the investigated samples were compared. The number of reads, operational taxonomic units, and species richness were lower in influent sample (NLF), where the wastewater enters, than in effluent sample (NL), in which treated wastewater is found. This difference was greater in June 2019 than in January 2020, and the removal rates of ammonia (86.93%) and hydrogen sulfide (99.72%) were also higher in June 2019. In both areas, the community composition was similar in January 2020, whereas the influent sample (NLF) and effluent sample (NL) areas in June 2019 were dominated by Proteobacteria (76.23%) and Firmicutes (67.13%), respectively. Oleiphilaceae (40.89%) and Thioalkalibacteraceae (12.91%), which are related to ammonia and hydrogen sulfide removal, respectively, were identified in influent sample (NLF) in June 2019. They were more abundant in June 2019 than in January 2020. Therefore, the functionality of the livestock wastewater treatment facility was affected by characteristics, including the composition of the microbial community. Compared to Illumina MiSeq sequencing, fewer species were isolated and identified in both areas using culture-based methods, suggesting Illumina MiSeq sequencing as a powerful tool to determine the relevance of microbial communities for pollutant removal.

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Analysis of bacterial diversity of Chinese Luzhou-flavor liquor brewed in different seasons by Illumina Miseq sequencing

Annals of Microbiology ◽

10.1007/s13213-016-1223-5 ◽

2016 ◽

Vol 66 (3) ◽

pp. 1293-1301 ◽

Cited By ~ 25

Author(s):

Weining Sun ◽

Huazhi Xiao ◽

Qian Peng ◽

Qiaoge Zhang ◽

Xingxing Li ◽

...

Keyword(s):

Bacterial Diversity ◽

Illumina Miseq ◽

Illumina Miseq Sequencing ◽

Miseq Sequencing ◽

Different Seasons

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Comparing dental plaque microbiome diversity of extrinsic black stain in the primary dentition using Illumina MiSeq sequencing technique

BMC Oral Health ◽

10.1186/s12903-019-0960-9 ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 1

Author(s):

Lulu Chen ◽

Qiong Zhang ◽

Yan Wang ◽

Keke Zhang ◽

Jing Zou

Keyword(s):

Relative Abundance ◽

Dental Plaque ◽

Illumina Miseq ◽

Primary Dentition ◽

Tooth Surface ◽

Oral Microbiota ◽

Illumina Miseq Sequencing ◽

Miseq Sequencing ◽

Cross Sectional ◽

Sequencing Technique

Abstract Background Extrinsic black stain (EBS) is characterized by discrete dark dots or lines on the tooth surface. The relationship between EBS and oral microbiota in children remains elusive. The aim of this study was to compare dental plaque microbiome in EBS children with that in EBS-free children in the primary dentition. Methods The Illumina MiSeq sequencing technique was utilized in the cross-sectional pilot study to investigate the diversity and composition of the supragingival plaque microbiota from 10 EBS-positive and 10 EBS-free children. The results were analysed with nonparametric Mann-Whitney U test, Pearson Chi-Square test, Fisher’s Exact test and one-way ANOVA tests. Results We identified 13 different phyla, 22 classes, 33 orders, 54 families, 105 genera, and 227 species from a total of 52,646 high-quality sequences. Between two groups, no statistical differences were observed in the estimators of community richness and diversity at 97% similarity, as well as in the Unweighted Unifrac principal co-ordinates analysis (PCoA). At the species level, higher level of relative abundance of Actinomyces naeslundii and lower level of relative abundance of a species belonging to Candidate_division_TM7 was observed in dental plaque of EBS-positive subjects, compared to dental plaque of EBS-free subjects (P < 0.05). This indicated that some species might be involved in the EBS process. Conclusion Changes in dental plaque microbiota is possibly relevant to the process of EBS in the primary dentition.

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Developmental validation of a Nextera XT mitogenome Illumina MiSeq sequencing method for high-quality samples

Forensic Science International Genetics ◽

10.1016/j.fsigen.2018.01.004 ◽

2018 ◽

Vol 34 ◽

pp. 25-36 ◽

Cited By ~ 15

Author(s):

Michelle A. Peck ◽

Kimberly Sturk-Andreaggi ◽

Jacqueline T. Thomas ◽

Robert S. Oliver ◽

Suzanne Barritt-Ross ◽

...

Keyword(s):

Illumina Miseq ◽

Illumina Miseq Sequencing ◽

Miseq Sequencing ◽

High Quality ◽

Sequencing Method ◽

Developmental Validation

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Changes in the Soil Microbiome in Eggplant Monoculture Revealed by High-Throughput Illumina MiSeq Sequencing as Influenced by Raw Garlic Stalk Amendment

International Journal of Molecular Sciences ◽

10.3390/ijms20092125 ◽

2019 ◽

Vol 20 (9) ◽

pp. 2125 ◽

Cited By ~ 3

Author(s):

Muhammad Imran Ghani ◽

Ahmad Ali ◽

Muhammad Jawaad Atif ◽

Muhammad Ali ◽

Bakht Amin ◽

...

Keyword(s):

Microbial Community ◽

High Throughput ◽

Soil Microbial Communities ◽

Illumina Miseq ◽

Soil Microbiome ◽

Plant Residues ◽

Illumina Miseq Sequencing ◽

Miseq Sequencing ◽

Community Structures ◽

Microbial Community Structures

The incorporation of plant residues into soil can be considered a keystone sustainability factor in improving soil structure function. However, the effects of plant residue addition on the soil microbial communities involved in biochemical cycles and abiotic stress phenomena are poorly understood. In this study, experiments were conducted to evaluate the role of raw garlic stalk (RGS) amendment in avoiding monoculture-related production constraints by studying the changes in soil chemical properties and microbial community structures. RGS was applied in four different doses, namely the control (RGS0), 1% (RGS1), 3% (RGS2), and 5% (RGS3) per 100 g of soil. The RGS amendment significantly increased soil electrical conductivity (EC), N, P, K, and enzyme activity. The soil pH significantly decreased with RGS application. High-throughput Illumina MiSeq sequencing revealed significant alterations in bacterial community structures in response to RGS application. Among the 23 major taxa detected, Anaerolineaceae, Acidobacteria, and Cyanobacteria exhibited an increased abundance level. RGS2 increased some bacteria reported to be beneficial including Acidobacteria, Bacillus, and Planctomyces (by 42%, 64%, and 1% respectively). Furthermore, internal transcribed spacer (ITS) fungal regions revealed significant diversity among the different treatments, with taxa such as Chaetomium (56.2%), Acremonium (4.3%), Fusarium (4%), Aspergillus (3.4%), Sordariomycetes (3%), and Plectosphaerellaceae (2%) showing much abundance. Interestingly, Coprinellus (14%) was observed only in RGS-amended soil. RGS treatments effectively altered soil fungal community structures and reduced certain known pathogenic fungal genera, i.e., Fusarium and Acremonium. The results of the present study suggest that RGS amendment potentially affects the microbial community structures that probably affect the physiological and morphological attributes of eggplant under a plastic greenhouse vegetable cultivation system (PGVC) in monoculture.

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