ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2013
Gene capture coupled to high-throughput sequencing as a strategy for targeted metagenome exploration.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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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.
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Who cites it
28 citing papers in PubMed, 51 citations in OpenAlex.
- Probe Capture Enrichment Sequencing of amoA Genes Improves the Detection of Diverse Ammonia-Oxidising Archaeal and Bacterial Populations.Molecular ecology resources · 2025Article
- Targeted metagenomics using probe capture detect a larger diversity of nitrogen and methane cycling genes in complex microbial communities than traditional metagenomics.ISME communications · 2025Article
- Fungal dye-decolorizing peroxidase diversity: roles in either intra- or extracellular processes.Applied microbiology and biotechnology · 2022Article
- Revealing microbial species diversity using sequence capture by hybridization.Microbial genomics · 2021Article
- New Frontiers of Anaerobic Hydrocarbon Biodegradation in the Multi-Omics Era.Frontiers in microbiology · 2020Review
- Hybridization-based capture of pathogen mRNA enables paired host-pathogen transcriptional analysis.Scientific reports · 2019Article
- High-Level Abundances ofApplied and environmental microbiology · 2019Article
- Comparing 16S rDNA amplicon sequencing and hybridization capture for pea aphid microbiota diversity analysis.BMC research notes · 2018Article
- Nutrient and acetate amendment leads to acetoclastic methane production and microbial community change in a non-producing Australian coal well.Microbial biotechnology · 2018Article
- Hybridization capture reveals microbial diversity missed using current profiling methods.Microbiome · 2018Article
- Article
- Revealing large metagenomic regions through long DNA fragment hybridization capture.Microbiome · 2017Article
- Sequence capture by hybridization reveals elusive hydrocarbon degradation potential.Microbial biotechnology · 2017Article
- The sequence capture by hybridization: a new approach for revealing the potential of mono-aromatic hydrocarbons bioattenuation in a deep oligotrophic aquifer.Microbial biotechnology · 2017Article
- OCaPPI-Db: an oligonucleotide probe database for pathogen identification through hybridization capture.Database : the journal of biological databases and curation · 2017Article
- Sequence capture by hybridization to explore modern and ancient genomic diversity in model and nonmodel organisms.Nucleic acids research · 2016Review
- A metabarcoding framework for facilitated survey of endolithic phototrophs with tufA.BMC ecology · 2016Article
- Metagenomics of Thermophiles with a Focus on Discovery of Novel Thermozymes.Frontiers in microbiology · 2016Review
- Article
- Targeted capture in evolutionary and ecological genomics.Molecular ecology · 2016Review
Corrections and comments
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Authors and funding
9 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Next-generation sequencing (NGS) allows faster acquisition of metagenomic data, but complete exploration of complex ecosystems is hindered by the extraordinary diversity of microorganisms. To reduce the environmental complexity, we created an innovative solution hybrid selection (SHS) method that is combined with NGS to characterize large DNA fragments harbouring biomarkers of interest. The quality of enrichment was evaluated after fragments containing the methyl coenzyme M reductase subunit A gene (mcrA), the biomarker of methanogenesis, were captured from a Methanosarcina strain and a metagenomic sample from a meromictic lake. The methanogen diversity was compared with direct metagenome and mcrA-based amplicon pyrosequencing strategies. The SHS approach resulted in the capture of DNA fragments up to 2.5 kb with an enrichment efficiency between 41 and 100%, depending on the sample complexity. Compared with direct metagenome and amplicons sequencing, SHS detected broader mcrA diversity, and it allowed efficient sampling of the rare biosphere and unknown sequences. In contrast to amplicon-based strategies, SHS is less biased and GC independent, and it recovered complete biomarker sequences in addition to conserved regions. Because this method can also isolate the regions flanking the target sequences, it could facilitate operon reconstructions.
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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.