Sep 1, 2018

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

BMC Bioinformatics
Adeola M RotimiOleg N Reva

Abstract

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. 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 ...Continue Reading

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Mentioned in this Paper

Microorganism
Metabolic Process, Cellular
Study
Ribosomal Proteins
Genome
Genes
Metagenome
Environment
Genetic Markers
Physiologic Resolution

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