scholarly journals The Dark Matter of Human Microbiota: Virobiota and Virome

2021 ◽  
Author(s):  
Gülendam Bozdayı ◽  
Işıl Fidan
Keyword(s):  
High Throughput Sequencing ◽  
Inflammatory Diseases ◽  
Human Microbiome ◽  
Endogenous Retroviruses ◽  
Therapeutic Approaches ◽  
Sequencing Technologies ◽  
Health And Disease ◽  
New Generation Sequencing ◽  
New Generation ◽  
Generation Sequencing

The viral component of the human microbiome is referred as ‘virobiota’. The virobiota is the sum of all viruses found in or on humans. The set of all genes of virobiota is referred as ‘virome’. The human virome consists of virus-derived genetic elements found in human genome constituted of viruses that infect eukaryotic cells, bacteriophages, prokaryotic cells, and, endogenous retroviruses. The development of new sequencing technologies, such as high-throughput sequencing techniques allowed the analysis of the human virome. Many new viruses have been discovered lately, using new generation sequencing technology. In recent years, there has been an increase in the studies of the human virome as changes in virome have been observed in diseases. The alterations in the human virome may be associated with infectious, inflammatory diseases, cancer and autoimmunity. The understanding of how the virome affects human health and disease can provide the development of potential therapeutic approaches that target the members of the virome.

scholarly journals Human Virome and Disease: High-Throughput Sequencing for Virus Discovery, Identification of Phage-Bacteria Dysbiosis and Development of Therapeutic Approaches with Emphasis on the Human Gut

Viruses ◽  
2019 ◽  
Vol 11 (7) ◽  
pp. 656 ◽  
Author(s):  
Tasha M. Santiago-Rodriguez ◽  
Emily B. Hollister
Keyword(s):  
High Throughput Sequencing ◽  
Human Microbiome ◽  
Endogenous Retroviruses ◽  
Present Review ◽  
Therapeutic Approaches ◽  
Human Gut ◽  
Bioinformatic Tools ◽  
Immunodeficiency Virus ◽  
Inflammatory Bowel

The virome is comprised of endogenous retroviruses, eukaryotic viruses, and bacteriophages and is increasingly being recognized as an essential part of the human microbiome. The human virome is associated with Type-1 diabetes (T1D), Type-2 diabetes (T2D), Inflammatory Bowel Disease (IBD), Human Immunodeficiency Virus (HIV) infection, and cancer. Increasing evidence also supports trans-kingdom interactions of viruses with bacteria, small eukaryotes and host in disease progression. The present review focuses on virus ecology and biology and how this translates mostly to human gut virome research. Current challenges in the field and how the development of bioinformatic tools and controls are aiding to overcome some of these challenges are also discussed. Finally, the present review also focuses on how human gut virome research could result in translational and clinical studies that may facilitate the development of therapeutic approaches.

RESEARCH OF THE MICROBIOM OF THE GASTROINTESTINAL TRACT OF THE ABERDIN-ANGUS BREED CATTLE

2021 ◽  
Author(s):  
А.Т. ДАУГАЛИЕВА ◽  
С.Т. ДАУГАЛИЕВА ◽  
Б.С. АРЫНГАЗИЕВ ◽  
Т.А. ЛАВРЕНТЬЕВА
Keyword(s):  
Genetic Identification ◽  
Intestinal Microbiome ◽  
Taxonomic Structure ◽  
Sequencing Technology ◽  
Microbial Composition ◽  
Angus Cattle ◽  
Taxonomic Profile ◽  
New Generation Sequencing ◽  
New Generation ◽  
Generation Sequencing

Целью исследования было определение таксономической структуры микробиома кишечника крупного рогатого скота породы Абердин-Ангус с помощью технологии секвенирования нового поколения. 16S метагеномный анализ, позволил определить микробный состав содержимого кишечника, минуя стадию культивирования на питательных средах. Проведена генетическая идентификация и получен таксономический профиль всех присутствующих бактерий, в том числе и некультивируемых форм. The aim of the study was to determine the taxonomic structure of the intestinal microbiome of Aberdeen Angus cattle using a new generation sequencing technology. 16S metagenomic analysis made it possible to determine the microbial composition of the intestinal contents bypassing the stage of cultivation on nutrient media. Genetic identification was carried out and a taxonomic profile of all bacteria present, including non-cultivated forms, was obtained. Key words: microbiome, cattle, Aberdeen Angus, next generation sequencing.

scholarly journals Profiling DNA Methylation Based on Next-Generation Sequencing Approaches: New Insights and Clinical Applications

Genes ◽  
2018 ◽  
Vol 9 (9) ◽  
pp. 429 ◽  
Author(s):  
Daniela Barros-Silva ◽  
C. Marques ◽  
Rui Henrique ◽  
Carmen Jerónimo
Keyword(s):  
Dna Methylation ◽  
Next Generation Sequencing ◽  
High Throughput Sequencing ◽  
Epigenetic Modification ◽  
Response To Therapy ◽  
Next Generation ◽  
Sequencing Technologies ◽  
Prognosis And Prediction ◽  
Novel Biomarkers ◽  
Generation Sequencing

DNA methylation is an epigenetic modification that plays a pivotal role in regulating gene expression and, consequently, influences a wide variety of biological processes and diseases. The advances in next-generation sequencing technologies allow for genome-wide profiling of methyl marks both at a single-nucleotide and at a single-cell resolution. These profiling approaches vary in many aspects, such as DNA input, resolution, coverage, and bioinformatics analysis. Thus, the selection of the most feasible method according with the project’s purpose requires in-depth knowledge of those techniques. Currently, high-throughput sequencing techniques are intensively used in epigenomics profiling, which ultimately aims to find novel biomarkers for detection, diagnosis prognosis, and prediction of response to therapy, as well as to discover new targets for personalized treatments. Here, we present, in brief, a portrayal of next-generation sequencing methodologies’ evolution for profiling DNA methylation, highlighting its potential for translational medicine and presenting significant findings in several diseases.

scholarly journals The Important Role of Breast Microbiota in Breast Cancer

2020 ◽  
Author(s):  
Kar-Yan Su ◽  
Wai-Leng Lee ◽  
Vinod Balasubramaniam
Keyword(s):  
Breast Cancer ◽  
Next Generation Sequencing ◽  
Racial Differences ◽  
Breast Tissue ◽  
Bacterial Species ◽  
Cancer Therapies ◽  
Next Generation ◽  
Sequencing Technologies ◽  
Health And Disease ◽  
Generation Sequencing

One in eight women will be diagnosed with breast cancer (BC) in their lifetime, resulting in over 2 million cases annually. BC is the most common cancer among women. Unfortunately, the etiology of majority of cases remains unknown. Recently, evidence has shown that the human microbiota plays an important role in health and disease. Intriguingly, studies have revealed the presence of microorganisms in human breast tissue, which was previously presumed to be sterile. Next-generation sequencing technologies have paved way for the investigation of breast microbiota, uncovering bacterial signatures that are associated with BC. Some of the bacterial species were found to possess pro-carcinogenic and/or anti-carcinogenic properties, suggesting that the breast microbiota has potentially crucial roles in maintenance of breast health. In this review, we summarize the recent findings on breast tissue microbiota and its interplay with BC. Bacterial signatures identified via next-generation sequencing as well as their impact on breast carcinogenesis and cancer therapies are reviewed. Correlation of breast tissue microbiota and other factors, such as geographical and racial differences, in BC is discussed. Additionally, we discuss the future directions of research on breast microbiota as well as its potential role in prevention, diagnosis and treatment of BC.

Understanding and exploiting the genetics of plant root traits

2021 ◽  
pp. 395-466
Author(s):  
Roberto Tuberosa ◽  
◽  
Elisabetta Frascaroli ◽  
Marco Maccaferri ◽  
Silvio Salvi ◽  
...  
Keyword(s):  
Environmental Impact ◽  
Plant Root ◽  
Root Traits ◽  
The Past ◽  
Vast Literature ◽  
New Generation Sequencing ◽  
New Generation ◽  
Constrained Conditions ◽  
Major Emphasis ◽  
Generation Sequencing

This chapter illustrates how genomics and other -omics approaches coupled with new-generation sequencing (NGS) platforms have been deployed to dissect the genetic make-up of RSA traits and better understand their functions, particularly under environmentally constrained conditions that commonly occur in most farmed soils. The major emphasis is devoted to studies during the past two decades in crops and only occasional reference is provided to the vast literature from RSA studies conducted in Arabidopsis and other model plants. The chapter also provides examples on how, in some cases, this knowledge is already benefiting farmers and how it can help in reducing the environmental impact of agriculture worldwide.

The Importance of New Generation Sequencing (NGS) HLA Typing in Renal Transplantation—Preliminary Report

2018 ◽  
Vol 50 (6) ◽  
pp. 1605-1615 ◽  
Author(s):  
M. Kotowski ◽  
A. Bogacz ◽  
J. Bartkowiak-Wieczorek ◽  
A. Bukowska ◽  
N. Surowiec ◽  
...  
Keyword(s):  
Renal Transplantation ◽  
Preliminary Report ◽  
Hla Typing ◽  
New Generation Sequencing ◽  
New Generation ◽  
Generation Sequencing

scholarly journals ‘There and back again’: revisiting the pathophysiological roles of human endogenous retroviruses in the post-genomic era

2013 ◽  
Vol 368 (1626) ◽  
pp. 20120504 ◽  
Author(s):  
Gkikas Magiorkinis ◽  
Robert Belshaw ◽  
Aris Katzourakis
Keyword(s):  
Human Genome ◽  
High Throughput Sequencing ◽  
Immune Escape ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Endogenous Retroviruses ◽  
Human Endogenous Retroviruses ◽  
The Past ◽  
Sequencing Technologies ◽  
Research Questions

Almost 8% of the human genome comprises endogenous retroviruses (ERVs). While they have been shown to cause specific pathologies in animals, such as cancer, their association with disease in humans remains controversial. The limited evidence is partly due to the physical and bioethical restrictions surrounding the study of transposons in humans, coupled with the major experimental and bioinformatics challenges surrounding the association of ERVs with disease in general. Two biotechnological landmarks of the past decade provide us with unprecedented research artillery: (i) the ultra-fine sequencing of the human genome and (ii) the emergence of high-throughput sequencing technologies. Here, we critically assemble research about potential pathologies of ERVs in humans. We argue that the time is right to revisit the long-standing questions of human ERV pathogenesis within a robust and carefully structured framework that makes full use of genomic sequence data. We also pose two thought-provoking research questions on potential pathophysiological roles of ERVs with respect to immune escape and regulation.

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