scholarly journals EXTRACT: interactive extraction of environment metadata and term suggestion for metagenomic sample annotation

Database ◽  
2016 ◽  
Vol 2016 ◽  
pp. baw005 ◽  
Author(s):  
Evangelos Pafilis ◽  
Pier Luigi Buttigieg ◽  
Barbra Ferrell ◽  
Emiliano Pereira ◽  
Julia Schnetzer ◽  
...  
Keyword(s):  
Metagenomic Sample ◽  
Sample Annotation

scholarly journals SureSelect targeted enrichment, a new cost effective method for the whole genome sequencing of Candidatus Liberibacter asiaticus

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Weili Cai ◽  
Schyler Nunziata ◽  
John Rascoe ◽  
Michael J. Stulberg
Keyword(s):  
Whole Genome Sequencing ◽  
Molecular Characterization ◽  
Genome Sequencing ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Coverage ◽  
Metagenomic Sample ◽  
Liberibacter Asiaticus

AbstractHuanglongbing (HLB) is a worldwide deadly citrus disease caused by the phloem-limited bacteria ‘Candidatus Liberibacter asiaticus’ (CLas) vectored by Asian citrus psyllids. In order to effectively manage this disease, it is crucial to understand the relationship among the bacterial isolates from different geographical locations. Whole genome sequencing approaches will provide more precise molecular characterization of the diversity among populations. Due to the lack of in vitro culture, obtaining the whole genome sequence of CLas is still a challenge, especially for medium to low titer samples. Hundreds of millions of sequencing reads are needed to get good coverage of CLas from an HLB positive citrus sample. In order to overcome this limitation, we present here a new method, Agilent SureSelect XT HS target enrichment, which can specifically enrich CLas from a metagenomic sample while greatly reducing cost and increasing whole genome coverage of the pathogen. In this study, the CLas genome was successfully sequenced with 99.3% genome coverage and over 72X sequencing coverage from low titer tissue samples (equivalent to 28.52 Cq using Li 16 S qPCR). More importantly, this method also effectively captures regions of diversity in the CLas genome, which provides precise molecular characterization of different strains.

scholarly journals TASPERT: Target-Specific Reverse Transcript Pools to Improve HTS Plant Virus Diagnostics

Viruses ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 1223
Author(s):  
Andres S. Espindola ◽  
Daniela Sempertegui-Bayas ◽  
Danny F. Bravo-Padilla ◽  
Viviana Freire-Zapata ◽  
Francisco Ochoa-Corona ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Rna Viruses ◽  
Limit Of Detection ◽  
Cost Effective ◽  
Bioinformatic Analysis ◽  
Metagenomic Sample ◽  
Rrna Depletion ◽  
Virus Diagnostics ◽  
Management Preparation ◽  
Reverse Transcript

High-throughput sequencing (HTS) is becoming the new norm of diagnostics in plant quarantine settings. HTS can be used to detect, in theory, all pathogens present in any given sample. The technique’s success depends on various factors, including methods for sample management/preparation and suitable bioinformatic analysis. The Limit of Detection (LoD) of HTS for plant diagnostic tests can be higher than that of PCR, increasing the risk of false negatives in the case of low titer of the target pathogen. Several solutions have been suggested, particularly for RNA viruses, including rRNA depletion of the host, dsRNA, and siRNA extractions, which increase the relative pathogen titer in a metagenomic sample. However, these solutions are costly and time-consuming. Here we present a faster and cost-effective alternative method with lower HTS-LoD similar to or lower than PCR. The technique is called TArget-SPecific Reverse Transcript (TASPERT) pool. It relies on pathogen-specific reverse primers, targeting all RNA viruses of interest, pooled and used in double-stranded cDNA synthesis. These reverse primers enrich the sample for only pathogens of interest. Evidence on how TASPERT is significantly superior to oligodT, random 6-mer, and 20-mer in generating metagenomic libraries containing the pathogen of interest is presented in this proof of concept.

scholarly journals MetaSee: An Interactive and Extendable Visualization Toolbox for Metagenomic Sample Analysis and Comparison

PLoS ONE ◽  
2012 ◽  
Vol 7 (11) ◽  
pp. e48998 ◽  
Author(s):  
Baoxing Song ◽  
Xiaoquan Su ◽  
Jian Xu ◽  
Kang Ning
Keyword(s):  
Sample Analysis ◽  
Metagenomic Sample

scholarly journals On the complexity of haplotyping a microbial community

2020 ◽  
Author(s):  
Samuel M Nicholls ◽  
Wayne Aubrey ◽  
Kurt De Grave ◽  
Leander Schietgat ◽  
Christopher J Creevey ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Community Sample ◽  
Population Level ◽  
Single Individual ◽  
Metagenomic Sample ◽  
Potential Benefits ◽  
Software Implementations ◽  
Occurrence Matrix ◽  
Number Of Individuals ◽  
Traversal Algorithm

Abstract Motivation Population-level genetic variation enables competitiveness and niche specialization in microbial communities. Despite the difficulty in culturing many microbes from an environment, we can still study these communities by isolating and sequencing DNA directly from an environment (metagenomics). Recovering the genomic sequences of all isoforms of a given gene across all organisms in a metagenomic sample would aid evolutionary and ecological insights into microbial ecosystems with potential benefits for medicine and biotechnology. A significant obstacle to this goal arises from the lack of a computationally tractable solution that can recover these sequences from sequenced read fragments. This poses a problem analogous to reconstructing the two sequences that make up the genome of a diploid organism (i.e. haplotypes), but for an unknown number of individuals and haplotypes. Results The problem of single individual haplotyping (SIH) was first formalised by Lancia et al. in 2001. Now, nearly two decades later, we discuss the complexity of “haplotyping” metagenomic samples, with a new formalisation of Lancia et al’s data structure that allows us to effectively extend the single individual haplotype problem to microbial communities. This work describes and formalizes the problem of recovering genes (and other genomic subsequences) from all individuals within a complex community sample, which we term the metagenomic individual haplotyping (MIH) problem. We also provide software implementations for a pairwise single nucleotide variant (SNV) co-occurrence matrix and greedy graph traversal algorithm. Availability and implementation Our reference implementation of the described pairwise SNV matrix (Hansel) and greedy haplotype path traversal algorithm (Gretel) are open source, MIT licensed and freely available online at github.com/samstudio8/hansel and github.com/samstudio8/gretel, respectively.

scholarly journals Rapid DNA Library Construction for Functional Genomic and Metagenomic Screening

2007 ◽  
Vol 74 (5) ◽  
pp. 1649-1652 ◽  
Author(s):  
Jonathan E. Schmitz ◽  
Anu Daniel ◽  
Mattias Collin ◽  
Raymond Schuch ◽  
Vincent A. Fischetti
Keyword(s):  
Escherichia Coli ◽  
Functional Genomic ◽  
Metagenomic Dna ◽  
Library Construction ◽  
Dna Library ◽  
Metagenomic Sample ◽  
Proof Of Principle

ABSTRACT A rapid protocol was developed for constructing plasmid libraries from small quantities of genomic/metagenomic DNA. The technique utilizes linker amplification with topoisomerase cloning and allows for inducible transcription in Escherichia coli. As proof of principle, several anti-Bacillus lysins were cloned from bacteriophage genomes and an aerolysin was cloned from a metagenomic sample.

Detecting bacterial genomes in a metagenomic sample using NGS reads

2015 ◽  
Vol 8 (4) ◽  
pp. 477-494 ◽  
Author(s):  
Camilo Valdes ◽  
Meghan Brennan ◽  
Bertrand Clarke ◽  
Jennifer Clarke
Keyword(s):  
Bacterial Genomes ◽  
Metagenomic Sample

scholarly journals Towards large-scale sample annotation in gene expression repositories

2009 ◽  
Vol 10 (S9) ◽  
Author(s):  
Erik Pitzer ◽  
Ronilda Lacson ◽  
Christian Hinske ◽  
Jihoon Kim ◽  
Pedro AF Galante ◽  
...  
Keyword(s):  
Gene Expression ◽  
Large Scale ◽  
Sample Annotation

scholarly journals The use of haplotype-specific transcripts improves sample annotation consistency

2014 ◽  
Vol 2 (1) ◽  
Author(s):  
Nicole Hartmann ◽  
Evert Luesink ◽  
Edward Khokhlovich ◽  
Joseph D Szustakowski ◽  
Lukas Baeriswyl ◽  
...  
Keyword(s):  
Sample Annotation

scholarly journals NastyBugs: A simple method for extracting antimicrobial resistance information from metagenomes

F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 1971
Author(s):  
Hsinyi Tsang ◽  
Matthew Moss ◽  
Greg Fedewa ◽  
Sharif Farag ◽  
Daniel Quang ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Multidrug Resistant ◽  
Resistant Bacteria ◽  
Drug Selection ◽  
Global Public Health ◽  
Simple Method ◽  
Metagenomic Sample ◽  
Clinical Tools ◽  
Efficient Selection ◽  
Selection Of

Multidrug resistant bacteria are becoming a major threat to global public health. While there are many possible causes for this, there have so far been few adequate solutions to this problem. One of the major causes is a lack of clinical tools for efficient selection of an antibiotic in a reliable way. NastyBugs is a new program that can identify what type of antimicrobial resistance is most likely present in a metagenomic sample, which will allow for both smarter drug selection by clinicians and faster research in an academic environment.

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