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MetCap: a bioinformatics probe design pipeline for large-scale targeted metagenomics

Author:
  • Sandeep Kushwaha
  • Lokeshwaran Manoharan
  • Tejashwari Meerupati
  • Katarina Hedlund
  • Dag Ahrén
Publishing year: 2015
Language: English
Publication/Series: BMC Bioinformatics
Volume: 16
Document type: Journal article
Publisher: BioMed Central

Abstract english

Background: Massive sequencing of genes from different environments has evolved metagenomics as central to enhancing the understanding of the wide diversity of micro-organisms and their roles in driving ecological processes. Reduced cost and high throughput sequencing has made large-scale projects achievable to a wider group of researchers, though complete metagenome sequencing is still a daunting task in terms of sequencing as well as the downstream bioinformatics analyses. Alternative approaches such as targeted amplicon sequencing requires custom PCR primer generation, and is not scalable to thousands of genes or gene families. Results: In this study, we are presenting a web-based tool called MetCap that circumvents the limitations of amplicon sequencing of multiple genes by designing probes that are suitable for large-scale targeted metagenomics sequencing studies. MetCap provides a novel approach to target thousands of genes and genomic regions that could be used in targeted metagenomics studies. Automatic analysis of user-defined sequences is performed, and probes specifically designed for metagenome studies are generated. To illustrate the advantage of a targeted metagenome approach, we have generated more than 300,000 probes that match more than 400,000 publicly available sequences related to carbon degradation, and used these probes for target sequencing in a soil metagenome study. The results show high enrichment of target genes and a successful capturing of the majority of gene families. MetCap is freely available to users from: http://soilecology.biol.lu.se/metcap/. Conclusion: MetCap is facilitating probe-based target enrichment as an easy and efficient alternative tool compared to complex primer-based enrichment for large-scale investigations of metagenomes. Our results have shown efficient large-scale target enrichment through MetCap-designed probes for a soil metagenome. The web service is suitable for any targeted metagenomics project that aims to study several genes simultaneously. The novel bioinformatics approach taken by the web service will enable researchers in microbial ecology to tap into the vast diversity of microbial communities using targeted metagenomics as a cost-effective alternative to whole metagenome sequencing.

Keywords

  • Bioinformatics and Systems Biology
  • Bioinformatics
  • Environmental sequencing
  • Functional genes
  • Metagenome
  • Probe design pipeline
  • Targeted metagenomics
  • Sequence capture
  • MetCap

Other

Published
  • ISSN: 1471-2105
Katarina Hedlund
E-mail: katarina [dot] hedlund [at] biol [dot] lu [dot] se

Professor

Biodiversity

+46 46 222 37 98

+46 72 562 10 04

E-A321

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Researcher

Centre for Environmental and Climate Research (CEC)

+46 46 222 37 98

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Centre for Animal Movement Research
Evolutionary Ecology, Department of Biology
Ecology building S-223 62 Lund Sweden