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Synthetic Sequencing Standards: A Guide to Database Choice for Rumen Microbiota Amplicon Sequencing Analysis [PDF]
Frontiers in Microbiology, 2020 Our understanding of complex microbial communities, such as those residing in the rumen, has drastically advanced through the use of high throughput sequencing (HTS) technologies.
Paul E Smith +2 more
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Amplicon sequence data of locust
2022Changes of microbial community in migratory locusts after Beauveria bassiana infection.
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Amplicon Sequencing using the Long-Read Sequencing Technologies
Journal of Visualized ExperimentsThe World Health Organization (WHO) continues to emphasize the urgent need for a rapid, cost-effective, and user-friendly diagnostic method for tuberculosis (TB) and drug-resistant TB (DR-TB). Next-generation sequencing (NGS) technologies, endorsed by the WHO, have significantly improved the detection of DR-TB.
Morwasehla, Modjadji +7 more
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Pitfalls in the statistical analysis of microbiome amplicon sequencing data
Molecular Ecology Resources, 2022Microbiome data are characterized by several aspects that make them challenging to analyse statistically: they are compositional, high dimensional and rich in zeros. A large array of statistical methods exist to analyse these data. Some are borrowed from other fields, such as ecology or RNA‐sequencing, while others are custom‐made for microbiome data ...
Hendriek C Boshuizen, Dennis E te Beest
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Targeted Amplicon Genotyping by Sanger Sequencing
This chapter presents a protocol for Sanger sequencing, a conventional yet rapid, cost-effective, and highly accurate method for targeted sequencing. It involves designing specific primers for forward and reverse template extension reactions, during which fluorophore labeled, chain terminating dideoxynucleotides are incorporated into newly replicated ...Anthony Torres, Reginald Gaudino
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Effect of Amplicon Sequencing Depth in Environmental Microbiome Research
Current Microbiology, 2021Amplicon sequencing approach is commonly employed in microbiome studies and sequencing depth is considered as a major factor influencing the outcome of data analyses. As of now, the effect of amplicon sequencing depth in environmental microbiome analyses is not explicitly illustrated.
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A quantitative SMRT cell sequencing method for ribosomal amplicons
Journal of Microbiological Methods, 2017Advances in sequencing technologies continue to provide unprecedented opportunities to characterize microbial communities. For example, the Pacific Biosciences Single Molecule Real-Time (SMRT) platform has emerged as a unique approach harnessing DNA polymerase activity to sequence template molecules, enabling long reads at low costs.
Bethan M, Jones, Adam B, Kustka
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16S rRNA Amplicon Sequencing for Metagenomics
2018The 16S rRNA amplicon sequencing technique is a microbiome analysis where different samples are analyzed at the same time using multiplexing. The results can be used to evaluate microbial diversity at genus, family, order, class, and phylum levels. The resolution is normally insufficient to evaluate the species level.
Henrik Christensen +3 more
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Inconsistent Denoising and Clustering Algorithms for Amplicon Sequence Data
Journal of Computational Biology, 2014Abstract Natural microbial communities have been studied for decades using the 16S rRNA gene as a marker. In recent years, the application of second-generation sequencing technologies has revolutionized our understanding of the structure and function of microbial communities
Kaisa Koskinen +3 more
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Characterization of Eukaryotic Microbiome Using 18S Amplicon Sequencing
2018With the advent of low-cost, high-throughput sequencing, taxonomic profiling of complex microbial communities through 16S rRNA marker gene surveys has received widespread interest, uncovering a wealth of information concerning the bacterial composition of microbial communities, as well as their association with health and disease.
Ana, Popovic, John, Parkinson
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