Benchmarking of methods for genomic taxonomy
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Benchmarking of methods for genomic taxonomy. / Larsen, Mette V; Cosentino, Salvatore; Lukjancenko, Oksana; Saputra, Dhany; Rasmussen, Simon; Hasman, Henrik; Sicheritz-Pontén, Thomas; Aarestrup, Frank M; Ussery, David W; Lund, Ole.
In: Journal of Clinical Microbiology, Vol. 52, No. 5, 2014, p. 1529-39.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Benchmarking of methods for genomic taxonomy
AU - Larsen, Mette V
AU - Cosentino, Salvatore
AU - Lukjancenko, Oksana
AU - Saputra, Dhany
AU - Rasmussen, Simon
AU - Hasman, Henrik
AU - Sicheritz-Pontén, Thomas
AU - Aarestrup, Frank M
AU - Ussery, David W
AU - Lund, Ole
PY - 2014
Y1 - 2014
N2 - One of the first issues that emerges when a prokaryotic organism of interest is encountered is the question of what it is--that is, which species it is. The 16S rRNA gene formed the basis of the first method for sequence-based taxonomy and has had a tremendous impact on the field of microbiology. Nevertheless, the method has been found to have a number of shortcomings. In the current study, we trained and benchmarked five methods for whole-genome sequence-based prokaryotic species identification on a common data set of complete genomes: (i) SpeciesFinder, which is based on the complete 16S rRNA gene; (ii) Reads2Type that searches for species-specific 50-mers in either the 16S rRNA gene or the gyrB gene (for the Enterobacteraceae family); (iii) the ribosomal multilocus sequence typing (rMLST) method that samples up to 53 ribosomal genes; (iv) TaxonomyFinder, which is based on species-specific functional protein domain profiles; and finally (v) KmerFinder, which examines the number of cooccurring k-mers (substrings of k nucleotides in DNA sequence data). The performances of the methods were subsequently evaluated on three data sets of short sequence reads or draft genomes from public databases. In total, the evaluation sets constituted sequence data from more than 11,000 isolates covering 159 genera and 243 species. Our results indicate that methods that sample only chromosomal, core genes have difficulties in distinguishing closely related species which only recently diverged. The KmerFinder method had the overall highest accuracy and correctly identified from 93% to 97% of the isolates in the evaluations sets.
AB - One of the first issues that emerges when a prokaryotic organism of interest is encountered is the question of what it is--that is, which species it is. The 16S rRNA gene formed the basis of the first method for sequence-based taxonomy and has had a tremendous impact on the field of microbiology. Nevertheless, the method has been found to have a number of shortcomings. In the current study, we trained and benchmarked five methods for whole-genome sequence-based prokaryotic species identification on a common data set of complete genomes: (i) SpeciesFinder, which is based on the complete 16S rRNA gene; (ii) Reads2Type that searches for species-specific 50-mers in either the 16S rRNA gene or the gyrB gene (for the Enterobacteraceae family); (iii) the ribosomal multilocus sequence typing (rMLST) method that samples up to 53 ribosomal genes; (iv) TaxonomyFinder, which is based on species-specific functional protein domain profiles; and finally (v) KmerFinder, which examines the number of cooccurring k-mers (substrings of k nucleotides in DNA sequence data). The performances of the methods were subsequently evaluated on three data sets of short sequence reads or draft genomes from public databases. In total, the evaluation sets constituted sequence data from more than 11,000 isolates covering 159 genera and 243 species. Our results indicate that methods that sample only chromosomal, core genes have difficulties in distinguishing closely related species which only recently diverged. The KmerFinder method had the overall highest accuracy and correctly identified from 93% to 97% of the isolates in the evaluations sets.
KW - Archaea/genetics
KW - Bacteria/genetics
KW - Bacterial Proteins/genetics
KW - Benchmarking/methods
KW - Classification/methods
KW - DNA, Bacterial/genetics
KW - Genomics/methods
KW - Multilocus Sequence Typing/methods
KW - RNA, Ribosomal, 16S/genetics
U2 - 10.1128/JCM.02981-13
DO - 10.1128/JCM.02981-13
M3 - Journal article
C2 - 24574292
VL - 52
SP - 1529
EP - 1539
JO - Journal of Clinical Microbiology
JF - Journal of Clinical Microbiology
SN - 0095-1137
IS - 5
ER -
ID: 214515824