2 Citations (Scopus)

Abstract

Bacterial populations are routinely characterized based on microscopic examination, colony formation, and biochemical tests. However, in the recent past, bacterial identification, classification, and nomenclature have been strongly influenced by genome sequence information. Advances in bioinformatics and growth in genome databases has placed genome-based metadata analysis in the hands of researchers who will require taxonomic experience to resolve intricacies. To achieve this, different tools are now available to quantitatively measure genome relatedness within members of the same species, and genome-wide average nucleotide identity (gANI) is one such reliable tool to measure genome similarity. A genome assembly with a gANI score of <95% at the intraspecies level is generally considered indicative of a separate species. In this study, we have analysed 300 whole-genome sequences belonging to 26 different bacterial species available in the NCBI Genome database and calculated their similarity at the intraspecies level based on gANI score. At the intraspecies level, nine bacterial species showed less than 90% gANI and more than 10% of unaligned regions. We suggest the appropriate use of available bioinformatics resources after genome assembly to arrive at the proper bacterial identification, classification, and nomenclature to avoid erroneous species assignments and disparity due to diversity at the intraspecies level.

Original languageEnglish
Pages (from-to)45-52
Number of pages8
JournalGenome
Volume62
Issue number2
DOIs
Publication statusPublished - 01-01-2019

Fingerprint

Genome
Nucleotides
Computational Biology
Terminology
Databases
Research Personnel
Growth

All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Molecular Biology
  • Genetics

Cite this

Paul, Bobby ; Dixit, Gunjan ; Murali, Thokur Sreepathy ; Satyamoorthy, Kapaettu ; Hao, W. / Genome-based taxonomic classification. In: Genome. 2019 ; Vol. 62, No. 2. pp. 45-52.
@article{566216594c014740a516f41fe4a806e1,
title = "Genome-based taxonomic classification",
abstract = "Bacterial populations are routinely characterized based on microscopic examination, colony formation, and biochemical tests. However, in the recent past, bacterial identification, classification, and nomenclature have been strongly influenced by genome sequence information. Advances in bioinformatics and growth in genome databases has placed genome-based metadata analysis in the hands of researchers who will require taxonomic experience to resolve intricacies. To achieve this, different tools are now available to quantitatively measure genome relatedness within members of the same species, and genome-wide average nucleotide identity (gANI) is one such reliable tool to measure genome similarity. A genome assembly with a gANI score of <95{\%} at the intraspecies level is generally considered indicative of a separate species. In this study, we have analysed 300 whole-genome sequences belonging to 26 different bacterial species available in the NCBI Genome database and calculated their similarity at the intraspecies level based on gANI score. At the intraspecies level, nine bacterial species showed less than 90{\%} gANI and more than 10{\%} of unaligned regions. We suggest the appropriate use of available bioinformatics resources after genome assembly to arrive at the proper bacterial identification, classification, and nomenclature to avoid erroneous species assignments and disparity due to diversity at the intraspecies level.",
author = "Bobby Paul and Gunjan Dixit and Murali, {Thokur Sreepathy} and Kapaettu Satyamoorthy and W. Hao",
year = "2019",
month = "1",
day = "1",
doi = "10.1139/gen-2018-0072",
language = "English",
volume = "62",
pages = "45--52",
journal = "Genome",
issn = "0831-2796",
publisher = "National Research Council of Canada",
number = "2",

}

Genome-based taxonomic classification. / Paul, Bobby; Dixit, Gunjan; Murali, Thokur Sreepathy; Satyamoorthy, Kapaettu; Hao, W.

In: Genome, Vol. 62, No. 2, 01.01.2019, p. 45-52.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Genome-based taxonomic classification

AU - Paul, Bobby

AU - Dixit, Gunjan

AU - Murali, Thokur Sreepathy

AU - Satyamoorthy, Kapaettu

AU - Hao, W.

PY - 2019/1/1

Y1 - 2019/1/1

N2 - Bacterial populations are routinely characterized based on microscopic examination, colony formation, and biochemical tests. However, in the recent past, bacterial identification, classification, and nomenclature have been strongly influenced by genome sequence information. Advances in bioinformatics and growth in genome databases has placed genome-based metadata analysis in the hands of researchers who will require taxonomic experience to resolve intricacies. To achieve this, different tools are now available to quantitatively measure genome relatedness within members of the same species, and genome-wide average nucleotide identity (gANI) is one such reliable tool to measure genome similarity. A genome assembly with a gANI score of <95% at the intraspecies level is generally considered indicative of a separate species. In this study, we have analysed 300 whole-genome sequences belonging to 26 different bacterial species available in the NCBI Genome database and calculated their similarity at the intraspecies level based on gANI score. At the intraspecies level, nine bacterial species showed less than 90% gANI and more than 10% of unaligned regions. We suggest the appropriate use of available bioinformatics resources after genome assembly to arrive at the proper bacterial identification, classification, and nomenclature to avoid erroneous species assignments and disparity due to diversity at the intraspecies level.

AB - Bacterial populations are routinely characterized based on microscopic examination, colony formation, and biochemical tests. However, in the recent past, bacterial identification, classification, and nomenclature have been strongly influenced by genome sequence information. Advances in bioinformatics and growth in genome databases has placed genome-based metadata analysis in the hands of researchers who will require taxonomic experience to resolve intricacies. To achieve this, different tools are now available to quantitatively measure genome relatedness within members of the same species, and genome-wide average nucleotide identity (gANI) is one such reliable tool to measure genome similarity. A genome assembly with a gANI score of <95% at the intraspecies level is generally considered indicative of a separate species. In this study, we have analysed 300 whole-genome sequences belonging to 26 different bacterial species available in the NCBI Genome database and calculated their similarity at the intraspecies level based on gANI score. At the intraspecies level, nine bacterial species showed less than 90% gANI and more than 10% of unaligned regions. We suggest the appropriate use of available bioinformatics resources after genome assembly to arrive at the proper bacterial identification, classification, and nomenclature to avoid erroneous species assignments and disparity due to diversity at the intraspecies level.

UR - http://www.scopus.com/inward/record.url?scp=85062710926&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85062710926&partnerID=8YFLogxK

U2 - 10.1139/gen-2018-0072

DO - 10.1139/gen-2018-0072

M3 - Article

AN - SCOPUS:85062710926

VL - 62

SP - 45

EP - 52

JO - Genome

JF - Genome

SN - 0831-2796

IS - 2

ER -