Bats, bacteria and their role in health and disease

2017 ◽  
Vol 38 (1) ◽  
pp. 28 ◽  
Author(s):  
Kristin Mühldorfer
Keyword(s):  
High Throughput Sequencing ◽  
Habitat Preferences ◽  
Data Sets ◽  
Infectious Agents ◽  
Emerging Pathogens ◽  
Microbial Detection ◽  
White Nose Syndrome ◽  
Sequencing Technologies ◽  
Health And Disease ◽  
Reservoir Hosts

Bats are ancient and among the most diverse mammals in terms of species richness, diet and habitat preferences, characteristics that may contribute to a high diversity of infectious agents. During the past two decades, the interest in bats and their microorganisms largely increased because of their role as reservoir hosts or carriers of important pathogens. Rapid advances in microbial detection and characterisation by high-throughput sequencing technologies have led to large genetic data sets but also improved our possibilities and speed of identifying unknown infectious agents. Assessing the risk of infectious diseases in bats and their pathological manifestation, however, is still challenging because of limited access to appropriate material and field data, and continuing limitations in wildlife diagnostics and the interpretation of genetic results. As a consequence, emerging pathogens can suddenly appear with devastating effects as happened for the white nose syndrome. To date, much research on bats and infectious agents still focusses on viruses, whilst the knowledge on bacteria and their role in disease is comparatively low.

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.

Read mapping

2016 ◽  
Vol 58 (3) ◽  
Author(s):  
Steve Hoffmann ◽  
Peter F. Stadler
Keyword(s):  
High Throughput Sequencing ◽  
Reference Genome ◽  
Data Sets ◽  
Biological Processes ◽  
Sequencing Technology ◽  
Matching Problem ◽  
Read Mapping ◽  
Mapping Problem ◽  
Sequencing Technologies ◽  
Exact Origin

AbstractThe Read Mapping problem asks for the exact origin of a nucleotide sequence in a reference genome. It translates to a conceptually simple approximate string matching problem. The practical difficulty, however, arises from the typical size of the data sets produced by modern high throughput sequencing technologies, from the biological processes involved in derivation of the query molecule from its genomic source, and from the technical processes of the sequencing technology itself.

scholarly journals EMBED: a low dimensional reconstruction of gut microbiome dynamics based on ecological normal modes

2021 ◽  
Author(s):  
Mayar Shahin ◽  
Brian W Ji ◽  
Purushottam D Dixit
Keyword(s):  
Dimensionality Reduction ◽  
Gut Microbiome ◽  
High Throughput Sequencing ◽  
Complex Dynamics ◽  
Normal Modes ◽  
Ecological Factors ◽  
Data Sets ◽  
Sequencing Technologies ◽  
Dimensional Reconstruction ◽  
Low Dimensional

The gut microbiome is well-established to be a significant driver of host health and disease. Longitudinal studies involving high-throughput sequencing technologies have begun to unravel the complex dynamics of these ecosystems, and quantitative frameworks are now being developed to better understand their organizing principles. Dimensionality reduction can offer unique insights into gut bacterial dynamics by leveraging collective abundance fluctuations of multiple bacteria driven by similar underlying ecological factors. However, methods providing lower-dimensional representations of gut microbial dynamics both at the community and individual taxa level are currently missing. To that end, we develop EMBED: Essential Microbiome Dynamics. Similar to normal modes in structural biology, EMBED infers ecological normal modes (ECNs), which represent the unique set of orthogonal dynamical trajectories capturing the collective behavior of a community. We show that a small number of ECNs accurately describe gut microbiome dynamics across data sets that encompass dietary changes and antibiotic-related perturbations. Importantly, we find that ECNs often reflect specific ecological behaviors, providing natural templates along which the dynamics of individual bacteria may be partitioned. Collectively, our results highlight the utility of dimensionality reduction approaches to understanding the dynamics of the gut microbiome and provide a framework to study the dynamics of other high-dimensional systems as well.

Exploring Human Genetic Variation – Scientific and Ethical Challenges

2018 ◽  
Author(s):  
Paula Dobosz ◽  
Jakub Zawiła-Niedźwiecki
Keyword(s):  
Genetic Variation ◽  
High Throughput Sequencing ◽  
Current Knowledge ◽  
Human Genetic Variation ◽  
Ethical Challenges ◽  
New Techniques ◽  
Public And Private ◽  
Sequencing Technologies ◽  
Health And Disease ◽  
And Storage

Since the genomic era is a reality nowadays, we need deeper understanding and consideration upon the benefits and challenges it brings. Apart from all the enthusiasm, there are also concerns related to genomics, specifically to the use and storage of personal genetic information as well as concerns regarding, for instance, so-called incidental findings, and right not to know. It started with Mendel’s simple experiments, but led to high-throughput sequencing technologies, resulting complex genomic data is constantly poured into public and private databases, inevitably changing our current knowledge. With the advent of new techniques and methods, like CRISPR/Cas9 engineering, researchers are provided with improved and expanded repertoire of research tools to analyse an organism in health and disease. This paper is aimed at providing examples of the applications and challenges, both practical and theoretical, in exploring human genetic variation.

DETECTION OF ALFACORONAVIRUSES, BETACORONAVIRUSES AND ASTROVIRUSES IN BAT FECAL SAMPLES FROM MOSCOW REGION

2020 ◽  
Author(s):  
E.V. Korneenko ◽  
◽  
А.E. Samoilov ◽  
I.V. Artyushin ◽  
M.V. Safonova ◽  
...  
Keyword(s):  
High Throughput ◽  
Viral Genome ◽  
High Throughput Sequencing ◽  
Pcr Amplification ◽  
Moscow Region ◽  
Fecal Samples ◽  
Genus Level ◽  
Zoonotic Viruses ◽  
Reservoir Hosts ◽  
Blastn Search

In our study we analyzed viral RNA in bat fecal samples from Moscow region (Zvenigorod district) collected in 2015. To detect various virus families and genera in bat fecal samples we used PCR amplification of viral genome fragments, followed by high-throughput sequencing. Blastn search of unassembled reads revealed the presence of viruses from families Astroviridae, Coronaviridae and Herpesviridae. Assembly using SPAdes 3.14 yields contigs of length 460–530 b.p. which correspond to genome fragments of Coronaviridae and Astroviridae. The taxonomy of coronaviruses has been determined to the genus level. We also showed that one bat can be a reservoir of several virus genuses. Thus, the bats in the Moscow region were confirmed as reservoir hosts for potentially zoonotic viruses.

scholarly journals Reassortment of Genome Segments Creates Stable Lineages Among Strains of Orchid Fleck Virus Infecting Citrus in Mexico

2020 ◽  
Vol 110 (1) ◽  
pp. 106-120 ◽  
Author(s):  
Avijit Roy ◽  
Andrew L. Stone ◽  
Gabriel Otero-Colina ◽  
Gang Wei ◽  
Ronald H. Brlansky ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Sensu Stricto ◽  
Genome Segment ◽  
Rt Pcr ◽  
Sequence Comparisons ◽  
Orchid Fleck Virus ◽  
Reverse Transcription Pcr ◽  
Sequencing Technologies ◽  
Negative Sense

The genus Dichorhavirus contains viruses with bipartite, negative-sense, single-stranded RNA genomes that are transmitted by flat mites to hosts that include orchids, coffee, the genus Clerodendrum, and citrus. A dichorhavirus infecting citrus in Mexico is classified as a citrus strain of orchid fleck virus (OFV-Cit). We previously used RNA sequencing technologies on OFV-Cit samples from Mexico to develop an OFV-Cit–specific reverse transcription PCR (RT-PCR) assay. During assay validation, OFV-Cit–specific RT-PCR failed to produce an amplicon from some samples with clear symptoms of OFV-Cit. Characterization of this virus revealed that dichorhavirus-like particles were found in the nucleus. High-throughput sequencing of small RNAs from these citrus plants revealed a novel citrus strain of OFV, OFV-Cit2. Sequence comparisons with known orchid and citrus strains of OFV showed variation in the protein products encoded by genome segment 1 (RNA1). Strains of OFV clustered together based on host of origin, whether orchid or citrus, and were clearly separated from other dichorhaviruses described from infected citrus in Brazil. The variation in RNA1 between the original (now OFV-Cit1) and the new (OFV-Cit2) strain was not observed with genome segment 2 (RNA2), but instead, a common RNA2 molecule was shared among strains of OFV-Cit1 and -Cit2, a situation strikingly similar to OFV infecting orchids. We also collected mites at the affected groves, identified them as Brevipalpus californicus sensu stricto, and confirmed that they were infected by OFV-Cit1 or with both OFV-Cit1 and -Cit2. OFV-Cit1 and -Cit2 have coexisted at the same site in Toliman, Queretaro, Mexico since 2012. OFV strain-specific diagnostic tests were developed.

scholarly journals Application of Oxford Nanopore Technology to Plant Virus Detection

Viruses ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 1424
Author(s):  
Lia W. Liefting ◽  
David W. Waite ◽  
Jeremy R. Thompson
Keyword(s):  
Plant Virus ◽  
High Throughput Sequencing ◽  
Virus Detection ◽  
Diagnostic Methods ◽  
Plant Virus Detection ◽  
Sequencing Technologies ◽  
Oxford Nanopore ◽  
Virus Diagnostics ◽  
Post Entry ◽  
Read Accuracy

The adoption of Oxford Nanopore Technologies (ONT) sequencing as a tool in plant virology has been relatively slow despite its promise in more recent years to yield large quantities of long nucleotide sequences in real time without the need for prior amplification. The portability of the MinION and Flongle platforms combined with lowering costs and continued improvements in read accuracy make ONT an attractive method for both low- and high-scale virus diagnostics. Here, we provide a detailed step-by-step protocol using the ONT Flongle platform that we have developed for the routine application on a range of symptomatic post-entry quarantine and domestic surveillance plant samples. The aim of this methods paper is to highlight ONT’s feasibility as a valuable component to the diagnostician’s toolkit and to hopefully stimulate other laboratories towards the eventual goal of integrating high-throughput sequencing technologies as validated plant virus diagnostic methods in their own right.

scholarly journals Assessing genotyping errors in mammalian museum study skins using high-throughput genotyping-by-sequencing

2021 ◽  
Author(s):  
Stella C. Yuan ◽  
Eric Malekos ◽  
Melissa T. R. Hawkins
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Massively Parallel Sequencing ◽  
Massively Parallel ◽  
Museum Specimens ◽  
Museum Specimen ◽  
Genotyping Errors ◽  
Allelic Dropout ◽  
Parallel Sequencing ◽  
Sequencing Technologies

AbstractThe use of museum specimens held in natural history repositories for population and conservation genetic research is increasing in tandem with the use of massively parallel sequencing technologies. Short Tandem Repeats (STRs), or microsatellite loci, are commonly used genetic markers in wildlife and population genetic studies. However, they traditionally suffered from a host of issues including length homoplasy, high costs, low throughput, and difficulties in reproducibility across laboratories. Massively parallel sequencing technologies can address these problems, but the incorporation of museum specimen derived DNA suffers from significant fragmentation and exogenous DNA contamination. Combatting these issues requires extra measures of stringency in the lab and during data analysis, yet there have not been any high-throughput sequencing studies evaluating microsatellite allelic dropout from museum specimen extracted DNA. In this study, we evaluate genotyping errors derived from mammalian museum skin DNA extracts for previously characterized microsatellites across PCR replicates utilizing high-throughput sequencing. We found it useful to classify samples based on DNA concentration, which determined the rate by which genotypes were accurately recovered. Longer microsatellites performed worse in all museum specimens. Allelic dropout rates across loci were dependent on sample quantity, with high concentration museum specimens performing as well and recovering quality metrics nearly as high as the frozen tissue sample. Based on our results, we provide a set of best practices for quality assurance and incorporation of reliable genotypes from museum specimens.

scholarly journals Sequencing and Computational Approaches to Identification and Characterization of Microbial Organisms

2013 ◽  
Vol 5 ◽  
pp. BECB.S10886 ◽  
Author(s):  
Brijesh Singh Yadav ◽  
Venkateswarlu Ronda ◽  
Dinesh P. Vashista ◽  
Bhaskar Sharma
Keyword(s):  
Sequence Data ◽  
Microbial Interactions ◽  
Microbial Pathogens ◽  
Nucleotide Sequence Data ◽  
Computational Approaches ◽  
Microbial Detection ◽  
Sequencing Technologies ◽  
Sequencing Platforms ◽  
Identification And Characterization

The recent advances in sequencing technologies and computational approaches are propelling scientists ever closer towards complete understanding of human-microbial interactions. The powerful sequencing platforms are rapidly producing huge amounts of nucleotide sequence data which are compiled into huge databases. This sequence data can be retrieved, assembled, and analyzed for identification of microbial pathogens and diagnosis of diseases. In this article, we present a commentary on how the metagenomics incorporated with microarray and new sequencing techniques are helping microbial detection and characterization.

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