MetCap: a bioinformatics probe design pipeline for large-scale targeted metagenomics
Kushwaha, Sandeep LU ; Manoharan, Lokeshwaran LU
; Meerupati, Tejashwari
LU
; Hedlund, Katarina
LU
and Ahrén, Dag
LU
(2015)
In BMC Bioinformatics
16.
- Abstract
- 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... (More)
- 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. (Less)
Please use this url to cite or link to this publication:
https://lup.lub.lu.se/record/5300492
- author
- Kushwaha, Sandeep
LU
; Manoharan, Lokeshwaran
LU
; Meerupati, Tejashwari
LU
; Hedlund, Katarina
LU
and Ahrén, Dag
LU
- organization
- publishing date
- 2015
- type
- Contribution to journal
- publication status
- published
- subject
- keywords
- Bioinformatics, Environmental sequencing, Functional genes, Metagenome, Probe design pipeline, Targeted metagenomics, Sequence capture, MetCap
- in
- BMC Bioinformatics
- volume
- 16
- article number
- 65
- publisher
- BioMed Central (BMC)
- external identifiers
-
- wos:000350619700001
- pmid:25880302
- scopus:84924867194
- pmid:25880302
- ISSN
- 1471-2105
- DOI
- 10.1186/s12859-015-0501-8
- language
- English
- LU publication?
- yes
- id
- 08325422-7df4-4b2b-b8d6-d835674ffa6a (old id 5300492)
- date added to LUP
- 2016-04-01 13:32:33
- date last changed
- 2024-01-24 11:54:31
@article{08325422-7df4-4b2b-b8d6-d835674ffa6a,
abstract = {{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.}},
author = {{Kushwaha, Sandeep and Manoharan, Lokeshwaran and Meerupati, Tejashwari and Hedlund, Katarina and Ahrén, Dag}},
issn = {{1471-2105}},
keywords = {{Bioinformatics; Environmental sequencing; Functional genes; Metagenome; Probe design pipeline; Targeted metagenomics; Sequence capture; MetCap}},
language = {{eng}},
publisher = {{BioMed Central (BMC)}},
series = {{BMC Bioinformatics}},
title = {{MetCap: a bioinformatics probe design pipeline for large-scale targeted metagenomics}},
url = {{http://dx.doi.org/10.1186/s12859-015-0501-8}},
doi = {{10.1186/s12859-015-0501-8}},
volume = {{16}},
year = {{2015}},
}