scholarly journals Application of high throughput sequencing in veterinary science

2022 ◽  
Vol 78 (02) ◽  
pp. 6622-2022
Author(s):  
ALEKSANDRA GIZA ◽  
EWELINA IWAN ◽  
DARIUSZ WASYL
Keyword(s):  
High Throughput ◽  
Environmental Samples ◽  
Pathogenic Bacteria ◽  
High Throughput Sequencing ◽  
Veterinary Science ◽  
Expression Of Genes ◽  
Outbreak Investigations ◽  
Genomic Studies ◽  
Identification Of Bacteria ◽  
The One

High throughput sequencing (HTS) creates an opportunity for comprehensive genomic studies. It can be applied in veterinary science, bacteriology and virology, diagnostics of animal diseases, food safety, examinations of the composition of environmental samples, and even in veterinary vaccinology. Thus HTS a wide-ranging method that can be applied in different areas of the One Health approach. In particular, the whole genome sequencing (WGS) of bacteria is routinely used in food hygiene and outbreak investigations for phylogenetic analysis of pathogenic bacteria isolated from various sources across timeline, molecular characterisation of bacteria, plasmids, antibiotic resistance and identification of virulence factors. Metagenomics can be used to characterize the composition of microbiota in environmental samples. It makes it possible to obtain a taxonomic identification of bacteria, fungi or plants present in a metasample. It can also be used for the monitoring and epidemiological tracing of viruses, such as SARS-CoV-2. The transcriptomic approach makes it possible to study the expression of genes associated with various infections and diseases. HTS is a highly versatile method, but the selection of the proper application is crucial to obtain expected outcomes. The paper presents some HTS approaches and examples of research in veterinary science.

scholarly journals DETECTION OF POTENTIALLY PATHOGENIC BACTERIA IN THE BRACKISH RIVERS FLOWING INTO THE ELTON LAKE BY HIGH-THROUGHPUT SEQUENCING

2018 ◽  
pp. 87-95 ◽  
Author(s):  
E. A. Selivanova ◽  
Yu. A. Khlopko ◽  
N. E. Gogoleva ◽  
A. O. Plotnikov
Keyword(s):  
High Throughput ◽  
Pathogenic Bacteria ◽  
Bacterial Contamination ◽  
High Throughput Sequencing ◽  
Pore Diameter ◽  
Pathogenic Microorganisms ◽  
Membrane Filters ◽  
Marine Habitats ◽  
Dna Libraries ◽  
Enzymatic Lysis

Aim. To indicate potentially pathogenic bacteria in plankton of the brackish rivers flowing into the Elton Lake by high-throughput sequencing of 16S ssuRNA gene. Materials and methods. The water samples from brackish rivers Lantsug and Chernavka, flowing into the Elton Lake, were taken up in a volume of 50 ml, filtered through membrane filters (pore diameter - 0.22 pm). Total DNAwas obtained by phenol-chloroform extraction with preliminary homogenization and enzymatic lysis. DNA libraries for sequencing were created by protocol Illumina with primers to a variable V3-V4 region of 16S ssuRNA gene. Sequencing was performed on a platform MiSeq («Illumina», США). Results.There were found the phylotypes of potentially pathogenic bacteria of Proteobacteria phylum from the families Enterobacteriaceae, Pseudomonadaceae, Campylobacteraceae, Vibrionaceae, Aeromonadaceae, Moraxellaceae, Legionellaceae, Alcaligenaceae, Campylobacteraceae, and also of Firmicutes, Bacteroidetes, Actinobacteria phyla in the plankton samples of the brackish rivers. Probable source of bacterial contamination is large and small cattle. Conclusion. These data demonstrate that the continental brackish waters, along with freshwater and marine habitats perform a reservoir function to potentially pathogenic microorganisms. High-throughput sequencing can be used to screen the presence of pathogens in water.

scholarly journals Investigation of the Plasma Virome from Cases of Unexplained Febrile Illness in Tanzania from 2013 to 2014: a Comparative Analysis between Unbiased and VirCapSeq-VERT High-Throughput Sequencing Approaches

mSphere ◽  
2018 ◽  
Vol 3 (4) ◽  
Author(s):  
Simon H. Williams ◽  
Samuel Cordey ◽  
Nishit Bhuva ◽  
Florian Laubscher ◽  
Mary-Anne Hartley ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Positive Selection ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Viral Infections ◽  
Febrile Illness ◽  
Clinical Samples ◽  
Barr Virus ◽  
Outbreak Investigations ◽  
Epstein Barr

ABSTRACT High-throughput sequencing can provide insights into epidemiology and medicine through comprehensive surveys of viral genetic sequences in environmental and clinical samples. Here, we characterize the plasma virome of Tanzanian patients with unexplained febrile illness by using two high-throughput sequencing methods: unbiased sequencing and VirCapSeq-VERT (a positive selection system). Sequences from dengue virus 2, West Nile virus, human immunodeficiency virus type 1, human pegivirus, and Epstein-Barr virus were identified in plasma. Both sequencing strategies recovered nearly complete genomes in samples containing multiple viruses. Whereas VirCapSeq-VERT had better sensitivity, unbiased sequencing provided better coverage of genome termini. Together, these data demonstrate the utility of high-throughput sequencing strategies in outbreak investigations. IMPORTANCE Characterization of the viruses found in the blood of febrile patients provides information pertinent to public health and diagnostic medicine. PCR and culture have historically played an important role in clinical microbiology; however, these methods require a targeted approach and may lack the capacity to identify novel or mixed viral infections. High-throughput sequencing can overcome these constraints. As the cost of running multiple samples continues to decrease, the implementation of high-throughput sequencing for diagnostic purposes is becoming more feasible. Here we present a comparative analysis of findings from an investigation of unexplained febrile illness using two strategies: unbiased high-throughput sequencing and VirCapSeq-VERT, a positive selection high-throughput sequencing system.

scholarly journals NPARS—A Novel Approach to Address Accuracy and Reproducibility in Genomic Data Science

2021 ◽  
Vol 4 ◽  
Author(s):  
Li Ma ◽  
Erich A. Peterson ◽  
Ik Jae Shin ◽  
Jason Muesse ◽  
Katy Marino ◽  
...  
Keyword(s):  
High Throughput ◽  
Quantitative Methods ◽  
Data Science ◽  
High Throughput Sequencing ◽  
Genomic Data ◽  
Scientific Data ◽  
Genomic Research ◽  
Data Sets ◽  
Novel Approach ◽  
Genomic Studies

Background: Accuracy and reproducibility are vital in science and presents a significant challenge in the emerging discipline of data science, especially when the data are scientifically complex and massive in size. Further complicating matters, in the field of genomic-based science high-throughput sequencing technologies generate considerable amounts of data that needs to be stored, manipulated, and analyzed using a plethora of software tools. Researchers are rarely able to reproduce published genomic studies.Results: Presented is a novel approach which facilitates accuracy and reproducibility for large genomic research data sets. All data needed is loaded into a portable local database, which serves as an interface for well-known software frameworks. These include python-based Jupyter Notebooks and the use of RStudio projects and R markdown. All software is encapsulated using Docker containers and managed by Git, simplifying software configuration management.Conclusion: Accuracy and reproducibility in science is of a paramount importance. For the biomedical sciences, advances in high throughput technologies, molecular biology and quantitative methods are providing unprecedented insights into disease mechanisms. With these insights come the associated challenge of scientific data that is complex and massive in size. This makes collaboration, verification, validation, and reproducibility of findings difficult. To address these challenges the NGS post-pipeline accuracy and reproducibility system (NPARS) was developed. NPARS is a robust software infrastructure and methodology that can encapsulate data, code, and reporting for large genomic studies. This paper demonstrates the successful use of NPARS on large and complex genomic data sets across different computational platforms.

scholarly journals PgRC: Pseudogenome based Read Compressor

2019 ◽  
Author(s):  
Tomasz Kowalski ◽  
Szymon Grabowski
Keyword(s):  
High Throughput ◽  
Compression Ratio ◽  
High Throughput Sequencing ◽  
Sequencing Data ◽  
High Quality ◽  
Link Type ◽  
Sequencing Technologies ◽  
Significant Interest ◽  
The One ◽  
Shortest Common Superstring

AbstractMotivationThe amount of sequencing data from High-Throughput Sequencing technologies grows at a pace exceeding the one predicted by Moore’s law. One of the basic requirements is to efficiently store and transmit such huge collections of data. Despite significant interest in designing FASTQ compressors, they are still imperfect in terms of compression ratio or decompression resources.ResultsWe present Pseudogenome-based Read Compressor (PgRC), an in-memory algorithm for compressing the DNA stream, based on the idea of building an approximation of the shortest common superstring over high-quality reads. Experiments show that PgRC wins in compression ratio over its main competitors, SPRING and Minicom, by up to 18 and 21 percent on average, respectively, while being at least comparably fast in decompression.AvailabilityPgRC can be downloaded from https://github.com/kowallus/[email protected]

Efficacy of a 3rd generation high-throughput sequencing platform for analyses of 16S rRNA genes from environmental samples

2013 ◽  
Vol 95 (2) ◽  
pp. 175-181 ◽  
Author(s):  
Jennifer J. Mosher ◽  
Erin L. Bernberg ◽  
Olga Shevchenko ◽  
Jinjun Kan ◽  
Louis A. Kaplan
Keyword(s):  
16S Rrna ◽  
High Throughput ◽  
Environmental Samples ◽  
High Throughput Sequencing ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Sequencing Platform

scholarly journals Rapid identification of unknown pathogens in environmental samples using a high-throughput sequencing-based approach

Heliyon ◽  
2019 ◽  
Vol 5 (5) ◽  
pp. e01793 ◽  
Author(s):  
Ofir Israeli ◽  
Inbar Cohen-Gihon ◽  
Anat Zvi ◽  
Shirley Lazar ◽  
Ohad Shifman ◽  
...  
Keyword(s):  
High Throughput ◽  
Environmental Samples ◽  
High Throughput Sequencing ◽  
Rapid Identification

scholarly journals Bacterial community profile after the lethal infection of Steinernema–Xenorhabdus pairs into soil-reared Tenebrio molitor larvae

2020 ◽  
Vol 96 (2) ◽  
Author(s):  
Marine C Cambon ◽  
Pierre Lafont ◽  
Marie Frayssinet ◽  
Anne Lanois ◽  
Jean-Claude Ogier ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Gut Microbiota ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Tenebrio Molitor ◽  
Lethal Infection ◽  
Natural Infestation ◽  
The One ◽  
Insect Cadaver ◽  
Tenebrio Molitor Larvae

ABSTRACT The host microbiota may have an impact on pathogens. This is often studied in laboratory-reared hosts but rarely in individuals whose microbiota looks like that of wild animals. In this study, we modified the gut microbiota of the insect Tenebrio molitor by rearing larvae in soil sampled from the field. We showed by high throughput sequencing methods that this treatment modifies the gut microbiota so that it is more diversified than that of laboratory-reared insects, and closely resembled the one of soil-dwelling insects. To describe what the entomopathogenic bacterial symbiont Xenorhabdus (Enterobacteriaceae), vectored by the soil-dwelling nematode Steinernema, might experience in natural conditions, we studied the infestation of the soil-reared T. molitor larvae with three Steinernema–Xenorhabdus pairs. We performed the infestation at 18°C, which delays the emergence of new infective juveniles (IJs), the soil-dwelling nematode forms, but which is a temperature compatible with natural infestation. We analyzed by high throughput sequencing methods the composition of the bacterial community within the insect cadavers before the first emergences of IJs. These bacterial communities were generally characterized by one or two non-symbiont taxa. Even for highly lethal Steinernema–Xenorhabdus pairs, the symbiont does not dominate the bacterial community within the insect cadaver.

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