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Captured metagenomics: large-scale targeting of genes based on 'sequence capture' reveals functional diversity in soils.

Manoharan, Lokeshwaran LU ; Kushwaha, Sandeep LU ; Hedlund, Katarina LU and Ahrén, Dag LU (2015) In DNA Research 22(6). p.451-460
Abstract
Microbial enzyme diversity is a key to understand many ecosystem processes. Whole metagenome sequencing (WMG) obtains information on functional genes, but it is costly and inefficient due to large amount of sequencing that is required. In this study, we have applied a captured metagenomics technique for functional genes in soil microorganisms, as an alternative to WMG. Large-scale targeting of functional genes, coding for enzymes related to organic matter degradation, was applied to two agricultural soil communities through captured metagenomics. Captured metagenomics uses custom-designed, hybridization-based oligonucleotide probes that enrich functional genes of interest in metagenomic libraries where only probe-bound DNA fragments are... (More)
Microbial enzyme diversity is a key to understand many ecosystem processes. Whole metagenome sequencing (WMG) obtains information on functional genes, but it is costly and inefficient due to large amount of sequencing that is required. In this study, we have applied a captured metagenomics technique for functional genes in soil microorganisms, as an alternative to WMG. Large-scale targeting of functional genes, coding for enzymes related to organic matter degradation, was applied to two agricultural soil communities through captured metagenomics. Captured metagenomics uses custom-designed, hybridization-based oligonucleotide probes that enrich functional genes of interest in metagenomic libraries where only probe-bound DNA fragments are sequenced. The captured metagenomes were highly enriched with targeted genes while maintaining their target diversity and their taxonomic distribution correlated well with the traditional ribosomal sequencing. The captured metagenomes were highly enriched with genes related to organic matter degradation; at least five times more than similar, publicly available soil WMG projects. This target enrichment technique also preserves the functional representation of the soils, thereby facilitating comparative metagenomics projects. Here, we present the first study that applies the captured metagenomics approach in large scale, and this novel method allows deep investigations of central ecosystem processes by studying functional gene abundances. (Less)
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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
in
DNA Research
volume
22
issue
6
pages
451 - 460
publisher
Oxford University Press
external identifiers
  • pmid:26490729
  • wos:000366631700006
  • scopus:84950248831
ISSN
1756-1663
DOI
10.1093/dnares/dsv026
language
English
LU publication?
yes
id
341c9ec8-5940-4ecd-8ca7-a1a11f53afe1 (old id 8148683)
date added to LUP
2015-11-17 11:04:32
date last changed
2017-10-01 03:25:35
@article{341c9ec8-5940-4ecd-8ca7-a1a11f53afe1,
  abstract     = {Microbial enzyme diversity is a key to understand many ecosystem processes. Whole metagenome sequencing (WMG) obtains information on functional genes, but it is costly and inefficient due to large amount of sequencing that is required. In this study, we have applied a captured metagenomics technique for functional genes in soil microorganisms, as an alternative to WMG. Large-scale targeting of functional genes, coding for enzymes related to organic matter degradation, was applied to two agricultural soil communities through captured metagenomics. Captured metagenomics uses custom-designed, hybridization-based oligonucleotide probes that enrich functional genes of interest in metagenomic libraries where only probe-bound DNA fragments are sequenced. The captured metagenomes were highly enriched with targeted genes while maintaining their target diversity and their taxonomic distribution correlated well with the traditional ribosomal sequencing. The captured metagenomes were highly enriched with genes related to organic matter degradation; at least five times more than similar, publicly available soil WMG projects. This target enrichment technique also preserves the functional representation of the soils, thereby facilitating comparative metagenomics projects. Here, we present the first study that applies the captured metagenomics approach in large scale, and this novel method allows deep investigations of central ecosystem processes by studying functional gene abundances.},
  author       = {Manoharan, Lokeshwaran and Kushwaha, Sandeep and Hedlund, Katarina and Ahrén, Dag},
  issn         = {1756-1663},
  language     = {eng},
  number       = {6},
  pages        = {451--460},
  publisher    = {Oxford University Press},
  series       = {DNA Research},
  title        = {Captured metagenomics: large-scale targeting of genes based on 'sequence capture' reveals functional diversity in soils.},
  url          = {http://dx.doi.org/10.1093/dnares/dsv026},
  volume       = {22},
  year         = {2015},
}