ArticleJournal of visualized experiments : JoVE2014
Purifying the impure: sequencing metagenomes and metatranscriptomes from complex animal-associated samples.
Article in Journal of visualized experiments : JoVE, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
16 citing papers in PubMed, 30 citations in OpenAlex.
- Intrapulmonary percussive ventilation improves lung function in cystic fibrosis patients chronically colonized with Pseudomonas aeruginosa: a pilot cross-over study.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2018Trial
- DNA sequencing for microbial surveillance in cystic fibrosis airways: advances, challenges, and clinical translation.Clinical microbiology reviews · 2026Review
- Article
- Evaluation of Host Depletion and Extraction Methods for Shotgun Metagenomic Analysis of Bovine Vaginal Samples.Microbiology spectrum · 2022Article
- Discovery and Surveillance of Tick-Borne Pathogens.Journal of medical entomology · 2021Article
- Direct identification and molecular characterization of zoonotic hazards in raw milk by metagenomics usingMicrobial genomics · 2021Article
- The role of fuel type and combustion phase on the toxicity of biomass smoke following inhalation exposure in mice.Archives of toxicology · 2019Article
- Cystic Fibrosis Rapid Response: Translating Multi-omics Data into Clinically Relevant Information.mBio · 2019Article
- Human and Extracellular DNA Depletion for Metagenomic Analysis of Complex Clinical Infection Samples Yields Optimized Viable Microbiome Profiles.Cell reports · 2019Article
- Article
- Getting Our Fingers on the Pulse of Slow-Growing Bacteria in Hard-To-Reach Places.Journal of bacteriology · 2018Article
- Recent insights into the tick microbiome gained through next-generation sequencing.Parasites & vectors · 2018Review
- Shotgun metagenomics, from sampling to analysis.Nature biotechnology · 2017Review
- Sputum DNA sequencing in cystic fibrosis: non-invasive access to the lung microbiome and to pathogen details.Microbiome · 2017Article
- Analysing Microbial Community Composition through Amplicon Sequencing: From Sampling to Hypothesis Testing.Frontiers in microbiology · 2017Review
- Unraveling the unseen players in the ocean - a field guide to water chemistry and marine microbiology.Journal of visualized experiments : JoVE · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 4 institutions in 1 country.
Funding
Abstract
The accessibility of high-throughput sequencing has revolutionized many fields of biology. In order to better understand host-associated viral and microbial communities, a comprehensive workflow for DNA and RNA extraction was developed. The workflow concurrently generates viral and microbial metagenomes, as well as metatranscriptomes, from a single sample for next-generation sequencing. The coupling of these approaches provides an overview of both the taxonomical characteristics and the community encoded functions. The presented methods use Cystic Fibrosis (CF) sputum, a problematic sample type, because it is exceptionally viscous and contains high amount of mucins, free neutrophil DNA, and other unknown contaminants. The protocols described here target these problems and successfully recover viral and microbial DNA with minimal human DNA contamination. To complement the metagenomics studies, a metatranscriptomics protocol was optimized to recover both microbial and host mRNA that contains relatively few ribosomal RNA (rRNA) sequences. An overview of the data characteristics is presented to serve as a reference for assessing the success of the methods. Additional CF sputum samples were also collected to (i) evaluate the consistency of the microbiome profiles across seven consecutive days within a single patient, and (ii) compare the consistency of metagenomic approach to a 16S ribosomal RNA gene-based sequencing. The results showed that daily fluctuation of microbial profiles without antibiotic perturbation was minimal and the taxonomy profiles of the common CF-associated bacteria were highly similar between the 16S rDNA libraries and metagenomes generated from the hypotonic lysis (HL)-derived DNA. However, the differences between 16S rDNA taxonomical profiles generated from total DNA and HL-derived DNA suggest that hypotonic lysis and the washing steps benefit in not only removing the human-derived DNA, but also microbial-derived extracellular DNA that may misrepresent the actual microbial profiles.
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What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.