Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison

Abstract

The pragmatic species concept for Bacteria and Archaea is ultimately based on DNA-DNA hybridization (DDH). While enabling the taxonomist, in principle, to obtain an estimate of the overall similarity between the genomes of two strains, this technique is tedious and error-prone and cannot be used to incrementally build up a comparative database. Recent technological progress in the area of genome sequencing calls for bioinformatics methods to replace the wet-lab DDH by in-silico genome-to-genome comparison. Here we investigate state-of-the-art methods for inferring whole-genome distances in their ability to mimic DDH. Algorithms to efficiently determine high-scoring segment pairs or maximally unique matches perform well as a basis of inferring intergenomic distances. The examined distance functions, which are able to cope with heavily reduced genomes and repetitive sequence regions, outperform previously described ones regarding the correlation with and error ratios in emulating DDH. Simulation of incompletely sequenced genomes indicates that some distance formulas are very robust against missing fractions of genomic information. Digitally derived genome-to-genome distances show a better correlation with 16S rRNA gene sequence distances than DDH values. The future perspectives of genome-informed taxonomy are discussed, and the investigated methods are made available as a web service for genome-based species delineation.

Bacillus velezensis is not a later heterotypic synonym of Bacillus amyloliquefaciens; Bacillus methylotrophicus, Bacillus amyloliquefaciens subsp. plantarum and ‘Bacillus oryzicola’ are later heterotypic synonyms of Bacillus velezensis based on phylogenomics

“…The digital DNA-DNA hybridizations (DDH) were determined online at http://ggdc.dsmz.de/distcalc2.php using the Genome-to-Genome Distance Calculation (GGDC) version 2.0 as described in Meier- Kolthoff et al (2013). The estimated DDH values were calculated using formula two at the GGDC website, originally described in Auch et al (2010) and updated in Meier- Kolthoff et al (2013). Average Nucleotide Identity (ANI) was performed as previously described (Goris et al, 2007), with the following options; minimum length 700 bp, minimum identity 70 %, minimum alignment 50 %, BLAST window size 1000 bp and step size of 200 bp.…”

Pseudorhodobacter psychrotolerans sp. nov., a psychrotolerant bacterium isolated from terrestrial soil, and emended description of the genus Pseudorhodobacter

“…Celera Assembler (version 7.0) was used for assembly (Myers et al, 2000). The degree of pairwise genome-based relatedness was estimated by both the average nucleotide identity (ANI) value following the BLAST-based ANI calculation method described by Goris et al (2007) and the genome-to-genome distance calculation method described by Auch et al (2010). The genomic DNA G+C content was calculated directly from the genome sequence.…”

Bacillus nakamurai sp. nov., a black-pigment-producing strain

“…The estimated DDH values were calculated using formula two at the GGDC website, originally described by Auch et al (2010) and updated by Meier-Kolthoff et al (2013). Formula two of the GGDC is the only function appropriate to analyse draft genomes, which is the case for most of the genomes in this study (Meier-Kolthoff et al, 2013).…”