Selection of marker genes for genetic barcoding of microorganisms and binning of metagenomic reads by Barcoder software tools

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dc.contributor.author Rotimi, A.M. (Adeola)
dc.contributor.author Pierneef, Rian
dc.contributor.author Reva, Oleg N.
dc.date.accessioned 2018-11-29T06:24:46Z
dc.date.available 2018-11-29T06:24:46Z
dc.date.issued 2018-08-30
dc.description.abstract BACKGROUND : Metagenomic approaches have revealed the complexity of environmental microbiomes with the advancement in whole genome sequencing displaying a significant level of genetic heterogeneity on the species level. It has become apparent that patterns of superior bioactivity of bacteria applicable in biotechnology as well as the enhanced virulence of pathogens often requires distinguishing between closely related species or sub-species. Current methods for binning of metagenomic reads usually do not allow for identification below the genus level and generally stops at the family level. RESULTS : In this work, an attempt was made to improve metagenomic binning resolution by creating genome specific barcodes based on the core and accessory genomes. This protocol was implemented in novel software tools available for use and download from http://bargene.bi.up.ac.za/. The most abundant barcode genes from the core genomes were found to encode for ribosomal proteins, certain central metabolic genes and ABC transporters. Performance of metabarcode sequences created by this package was evaluated using artificially generated and publically available metagenomic datasets. Furthermore, a program (Barcoding 2.0) was developed to align reads against barcode sequences and thereafter calculate various parameters to score the alignments and the individual barcodes. Taxonomic units were identified in metagenomic samples by comparison of the calculated barcode scores to set cut-off values. In this study, it was found that varying sample sizes, i.e. number of reads in a metagenome and metabarcode lengths, had no significant effect on the sensitivity and specificity of the algorithm. Receiver operating characteristics (ROC) curves were calculated for different taxonomic groups based on the results of identification of the corresponding genomes in artificial metagenomic datasets. The reliability of distinguishing between species of the same genus or family by the program was nearly perfect. CONCLUSIONS : The results showed that the novel online tool BarcodeGenerator (http://bargene.bi.up.ac.za/) is an efficient approach for generating barcode sequences from a set of complete genomes provided by users. Another program, Barcoder 2.0 is available from the same resource to enable an efficient and practical use of metabarcodes for visualization of the distribution of organisms of interest in environmental and clinical samples. en_ZA
dc.description.department Biochemistry en_ZA
dc.description.librarian am2018 en_ZA
dc.description.sponsorship The South African National Research Foundation (NRF) grant #93664. en_ZA
dc.description.uri https://bmcbioinformatics.biomedcentral.com en_ZA
dc.identifier.citation Rotimi, A.M., Pierneef, R. & Reva, O.N. 2018, 'Selection of marker genes for genetic barcoding of microorganisms and binning of metagenomic reads by Barcoder software tools', BMC Bioinformatics, vol. 19, art. 309, pp. 1-11. en_ZA
dc.identifier.issn 1471-2105 (online)
dc.identifier.other 10.1186/s12859-018-2320-1
dc.identifier.uri http://hdl.handle.net/2263/67400
dc.language.iso en en_ZA
dc.publisher BioMed Central en_ZA
dc.rights © The Author(s). 2018 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License. en_ZA
dc.subject Metabarcoding en_ZA
dc.subject Metagenome en_ZA
dc.subject Bacterial genome en_ZA
dc.subject Software tool en_ZA
dc.subject Receiver operating characteristics (ROC) en_ZA
dc.subject Bacteria en_ZA
dc.subject Barcode en_ZA
dc.subject Next-generation sequencing (NGS) en_ZA
dc.subject Computer aided software engineering en_ZA
dc.subject Computer software en_ZA
dc.subject Bacterial genomes en_ZA
dc.subject Genetic heterogeneitie en_ZA
dc.subject Ribosomal proteins en_ZA
dc.subject Sensitivity en_ZA
dc.subject Specificity en_ZA
dc.subject Genes en_ZA
dc.subject Whole genome sequencing (WGS) en_ZA
dc.title Selection of marker genes for genetic barcoding of microorganisms and binning of metagenomic reads by Barcoder software tools en_ZA
dc.type Article en_ZA


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