Next-Generation Sequencing: Advantages, Disadvantages, and Future

Arı, Şule; Arıkan, Muzaffer

doi:10.1007/978-3-319-31703-8_5

Cited by 58 publications

(47 citation statements)

References 76 publications

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“…[ 5 , 10 , 89 , 90 ]). Both methods, NGS and Sanger, have advantages and disadvantages [ 91 ], nonetheless to move forward in disentangling of the hidden diversity of nematode assemblages, matching DNA sequences with morphology and additional metadata (e.g. gender, habitat, environmental variables, etc), is a vital step in enhancing the utility of molecular data [ 41 , 92 ].…”

Section: Discussionmentioning

confidence: 99%

The identification of sympatric cryptic free-living nematode species in the Antarctic intertidal

et al. 2017

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The diversity of free-living nematodes in the beaches of two Antarctic islands, King George and Deception islands was investigated. We used morphological and molecular (LSU, and two fragments of SSU sequences) approaches to evaluate 236 nematodes. Specimens were assigned to at least genera using morphology and were assessed for the presence of cryptic speciation. The following genera were identified: Halomonhystera, Litoditis, Enoploides, Chromadorita, Theristus, Oncholaimus, Viscosia, Gammanema, Bathylaimus, Choanolaimus, and Paracanthonchus; along with specimens from the families Anticomidae and Linhomoeidae. Cryptic speciation was identified within the genera Halomonhystera and Litoditis. All of the cryptic species identified live sympatrically. The two cryptic species of Halomonhystera exhibited no significant morphological differences. However, Litoditis species 2 was significantly larger than Litoditis species 1. The utility of molecular data in confirming the identifications of some of the morphologically more challenging families of nematodes was demonstrated. In terms of which molecular sequences to use for the identification of free-living nematodes, the SSU sequences were more variable than the LSU sequences, and thus provided more resolution in the identification of cryptic speciation. Finally, despite the considerable amount of time and effort required to put together genetic and morphological data, the resulting advance in our understanding of diversity and ecology of free-living marine nematodes, makes that effort worthwhile.

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Section: Discussionmentioning

confidence: 99%

The identification of sympatric cryptic free-living nematode species in the Antarctic intertidal

et al. 2017

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“…The development of next-generation sequencing (NGS) technologies have advanced the metagenomics field by reducing costs and increasing throughput (Ari & Arikan, 2016). To date, several NGS-based microbiome studies investigating the potential effects of different parameters, such as temperature (De Filippis et al, 2018), tea type (Coton et al, 2017), geography (Marsh et al, 2014), and nutritional sources (Reva et al, 2015), on Kombucha have also been published.…”

Section: Introductionmentioning

confidence: 99%

Microbial composition of Kombucha determined using amplicon sequencing and shotgun metagenomics

Arıkan

Mitchell

Finn

et al. 2020

Journal of Food Science

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Kombucha, a fermented tea generated from the co-culture of yeasts and bacteria, has gained worldwide popularity in recent years due to its potential benefits to human health. As a result, many studies have attempted to characterize both its biochemical properties and microbial composition. Here, we have applied a combination of whole metagenome sequencing (WMS) and amplicon (16S rRNA and Internal Transcribed Spacer 1 [ITS1]) sequencing to investigate the microbial communities of homemade Kombucha fermentations from day 3 to day 15. We identified the dominant bacterial genus as Komagataeibacter and dominant fungal genus as Zygosaccharomyces in all samples at all time points. Furthermore, we recovered three near complete Komagataeibacter genomes and one Zygosaccharomyces bailii genome and then predicted their functional properties. Also, we determined the broad taxonomic and functional profile of plasmids found within the Kombucha microbial communities. Overall, this study provides a detailed description of the taxonomic and functional systems of the Kombucha microbial community. Based on this, we conject that the functional complementarity enables metabolic cross talks between Komagataeibacter species and Z. bailii, which helps establish the sustained a relatively low diversity ecosystem in Kombucha.

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“…Despite being one of the most powerful research tools, the NGS sequencing, which is sometimes called second-generation sequencing, is not flawless. Namely, not a single platform can read fragments more than 700 bp [175], thus necessitating DNA fragmentation prior to sequencing. Additionally, second-generation platforms amplify the signal prior to detection.…”

Section: Long Read Sequencingmentioning

confidence: 99%

Current Trends in Diagnostics of Viral Infections of Unknown Etiology

Kiselev

Matsvay

Абрамов

et al. 2020

Viruses

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Viruses are evolving at an alarming rate, spreading and inconspicuously adapting to cutting-edge therapies. Therefore, the search for rapid, informative and reliable diagnostic methods is becoming urgent as ever. Conventional clinical tests (PCR, serology, etc.) are being continually optimized, yet provide very limited data. Could high throughput sequencing (HTS) become the future gold standard in molecular diagnostics of viral infections? Compared to conventional clinical tests, HTS is universal and more precise at profiling pathogens. Nevertheless, it has not yet been widely accepted as a diagnostic tool, owing primarily to its high cost and the complexity of sample preparation and data analysis. Those obstacles must be tackled to integrate HTS into daily clinical practice. For this, three objectives are to be achieved: (1) designing and assessing universal protocols for library preparation, (2) assembling purpose-specific pipelines, and (3) building computational infrastructure to suit the needs and financial abilities of modern healthcare centers. Data harvested with HTS could not only augment diagnostics and help to choose the correct therapy, but also facilitate research in epidemiology, genetics and virology. This information, in turn, could significantly aid clinicians in battling viral infections.

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Next-Generation Sequencing: Advantages, Disadvantages, and Future

Cited by 58 publications

References 76 publications

The identification of sympatric cryptic free-living nematode species in the Antarctic intertidal

The identification of sympatric cryptic free-living nematode species in the Antarctic intertidal

Microbial composition of Kombucha determined using amplicon sequencing and shotgun metagenomics

Current Trends in Diagnostics of Viral Infections of Unknown Etiology

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