scholarly journals Studying the gut virome in the metagenomic era: challenges and perspectives

BMC Biology ◽  
2019 ◽  
Vol 17 (1) ◽  
Author(s):  
Sanzhima Garmaeva ◽  
Trishla Sinha ◽  
Alexander Kurilshikov ◽  
Jingyuan Fu ◽  
Cisca Wijmenga ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Human Health ◽  
Next Generation ◽  
Human Gut ◽  
Sequencing Technologies ◽  
Quantum Leap ◽  
Complex Ecosystem ◽  
Technical Challenges ◽  
Generation Sequencing

Abstract The human gut harbors a complex ecosystem of microorganisms, including bacteria and viruses. With the rise of next-generation sequencing technologies, we have seen a quantum leap in the study of human-gut-inhabiting bacteria, yet the viruses that infect these bacteria, known as bacteriophages, remain underexplored. In this review, we focus on what is known about the role of bacteriophages in human health and the technical challenges involved in studying the gut virome, of which they are a major component. Lastly, we discuss what can be learned from studies of bacteriophages in other ecosystems.

scholarly journals The journey from next-generation sequencing to personalized medicine?

2021 ◽  
Author(s):  
Marion Vandeputte
Keyword(s):  
Next Generation Sequencing ◽  
Personalized Medicine ◽  
Genome Project ◽  
Next Generation ◽  
Sequencing Technology ◽  
Sequencing Technologies ◽  
Significant Step ◽  
The Human Genome Project ◽  
Generation Sequencing

Following the completion of the Human Genome Project in 2003, sequencing has become one of the most influential tools in biomedical research. Sequencing took off in earnest with the development of next-generation sequencing techniques in the early 2000s, making sequencing high throughput, faster, more affordable and commercially available to individual laboratories. With the improved understanding of the role of genetics in human disease, coupled with rapid advancement in sequencing technology, we are progressively unlocking the secrets of how our genes control the development of diseases. This has the potential to revolutionize medicine and healthcare, providing a significant step towards personalized medicine. How did we arrive here? What are the major achievements of sequencing technologies of the past two decades and how does it help us to piece the clues together towards personalized treatments and diagnosis?

scholarly journals Application of next-generation sequencing technologies in virology

2012 ◽  
Vol 93 (9) ◽  
pp. 1853-1868 ◽  
Author(s):  
Alan D. Radford ◽  
David Chapman ◽  
Linda Dixon ◽  
Julian Chantrey ◽  
Alistair C. Darby ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Next Generation ◽  
Sequencing Technologies ◽  
Diagnostic Work ◽  
Scientific Questions ◽  
Scientific Imagination ◽  
Improved Methods ◽  
Advance Knowledge ◽  
Generation Sequencing

The progress of science is punctuated by the advent of revolutionary technologies that provide new ways and scales to formulate scientific questions and advance knowledge. Following on from electron microscopy, cell culture and PCR, next-generation sequencing is one of these methodologies that is now changing the way that we understand viruses, particularly in the areas of genome sequencing, evolution, ecology, discovery and transcriptomics. Possibilities for these methodologies are only limited by our scientific imagination and, to some extent, by their cost, which has restricted their use to relatively small numbers of samples. Challenges remain, including the storage and analysis of the large amounts of data generated. As the chemistries employed mature, costs will decrease. In addition, improved methods for analysis will become available, opening yet further applications in virology including routine diagnostic work on individuals, and new understanding of the interaction between viral and host transcriptomes. An exciting era of viral exploration has begun, and will set us new challenges to understand the role of newly discovered viral diversity in both disease and health.

Role of Next-Generation Sequencing Technologies

2013 ◽  
pp. 1-16
Author(s):  
Siddhartha Devarakonda ◽  
Daniel Morgensztern ◽  
Ramaswamy Govindan
Keyword(s):  
Next Generation Sequencing ◽  
Next Generation ◽  
Sequencing Technologies ◽  
Generation Sequencing

scholarly journals Role of Next-Generation Sequencing Technologies in Personalized Medicine

2019 ◽  
pp. 125-154 ◽  
Author(s):  
Stefania Morganti ◽  
Paolo Tarantino ◽  
Emanuela Ferraro ◽  
Paolo D’Amico ◽  
Giulia Viale ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Personalized Medicine ◽  
Next Generation ◽  
Sequencing Technologies ◽  
Generation Sequencing

scholarly journals Environmental Surveillance through Next-Generation Sequencing to Unveil the Diversity of Human Enteroviruses beyond the Reported Clinical Cases

Viruses ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 120
Author(s):  
Andrés Lizasoain ◽  
Daiana Mir ◽  
Gisella Masachessi ◽  
Adrián Farías ◽  
Nélida Rodríguez-Osorio ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Next Generation ◽  
Echovirus 30 ◽  
Coxsackievirus B4 ◽  
Important Region ◽  
Enterovirus A71 ◽  
Wastewater Samples ◽  
Valuable Role ◽  
Generation Sequencing

The knowledge about circulation of Human Enteroviruses (EVs) obtained through medical diagnosis in Argentina is scarce. Wastewater samples monthly collected in Córdoba, Argentina during 2011–2012, and then in 2017–2018 were retrospectively studied to assess the diversity of EVs in the community. Partial VP1 gene was amplified by PCR from wastewater concentrates, and amplicons were subject of next-generation sequencing and genetic analyses. There were 41 EVs detected, from which ~50% had not been previously reported in Argentina. Most of the characterized EVs (60%) were detected at both sampling periods, with similar values of intratype nucleotide diversity. Exceptions were enterovirus A71, coxsackievirus B4, echovirus 14, and echovirus 30, which diversified in 2017–2018. There was a predominance of types from EV-C in 2017–2018, evidencing a common circulation of these types throughout the year in the community. Interestingly, high genetic similarity was evidenced among environmental strains of echovirus 30 circulating in 2011–2012 and co-temporal isolates obtained from patients suffering aseptic meningitis in different locations of Argentina. This study provides an updated insight about EVs circulating in an important region of South America, and suggests a valuable role of wastewater-based epidemiology in predicting outbreaks before the onset of cases in the community.

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