Genome sequence-based species delimitation with confidence intervals and improved distance functions

By Jan P. Meier-Kolthoff, Alexander F. Auch, Hans-Peter Klenk, Markus Göker. BMC Bioinformatics, 2013

6,216 citations recorded by the source corpus.

For the last 25 years species delimitation in prokaryotes (Archaea and Bacteria) was to a large extent based on DNA-DNA hybridization (DDH), a tedious lab procedure designed in the early 1970s that served its purpose astonishingly well in the absence of deciphered genome sequences. With the rapid progress in genome sequencing time has come to directly use the now available and easy to generate genome sequences for delimitation of species. GBDP (Genome Blast Distance Phylogeny) infers genome-to-genome distances between pairs of entirely or partially sequenced genomes, a digital, highly reliable estimator for the relatedness of genomes. Its application as an in-silico replacement for DDH was recently introduced. The main challenge in the implementation of such an application is to produce digital DDH values that must mimic the wet-lab DDH values as close as possible to ensure consistency in the Prokaryotic species concept. Correlation and regression analyses were used to determine the best-performing methods and the most influential parameters. GBDP was further enriched with a set of new features such as confidence intervals for intergenomic distances obtained via resampling or via the statistical models for DDH prediction and an additional family of distance functions. As in previous analyses, GBDP obtained the highest agreement with wet-lab DDH among all tested methods, but improved models led to a further increase in the accuracy of DDH prediction. Confidence intervals yielded stable results when inferred from the statistical models, whereas those obtained via resampling showed marked differences between the underlying distance functions. Despite the high accuracy of GBDP-based DDH prediction, inferences from limited empirical data are always associated with a certain degree of uncertainty. It is thus crucial to enrich in-silico DDH replacements with confidence-interval estimation, enabling the user to statistically evaluate the outcomes. Such methodological advancements, easily accessible through the web service at http://ggdc.dsmz.de, are crucial steps towards a consistent and truly genome sequence-based classification of microorganisms.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/c3e04fde210ac458c533a161c46ac9f3c443f396

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Citations in the corpus

Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. (2014, methodology): “The originally proposed threshold value of 97 % (Stackebrandt & Goebel, 1994) has been challenged by higher thresholds (Meier-Kolthoff et al., 2013; Stackebrandt & Ebers, 2006).”
TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes (2021, positive): “Accurate intergenomic GBDP (Genome BLAST Distance Phylogeny) (18) distances and digital DNA:DNA hybridization (dDDH) values are calculated and stored in the TYGS database.”
Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. (2018, methodology): “The proposed and generally accepted species boundary for ANI and dDDH values are 95~96 and 70%, respectively [4, 5, 7].”
TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy (2019, methodology): “GBDP, the Genome BLAST Distance Phylogeny approach 7,11,13,53 , was chosen because it can be used to rapidly infer trees with branch support values from pairwise whole-genome or single-gene distances, which at the same time serve for calculating dDDH values.”
VIRIDIC—A Novel Tool to Calculate the Intergenomic Similarities of Prokaryote-Infecting Viruses (2020, methodology): “The intergenomic similarity or distance is calculated as described below, as previously proposed [17].”
AutoMLST: an automated web server for generating multi-locus species trees highlighting natural product potential (2019, methodology): “Genome based methods have historically served as a powerful tool to discriminate species with the use of DNA-DNA hybridization methods (DDH).”
VICTOR: genome-based phylogeny and classification of prokaryotic viruses (2017, methodology): “Pairwise intergenomic distances were calculated between amino acid and nucleotide sequences with the current version of the Genome BLAST Distance Phylogeny (GBDP) approach (Meier-Kolthoff et al. 2013), including 100 pseudobootstrap replicates (Meier-Kolthoff et al.”