A Genomic Distance Based on MUM Indicates Discontinuity between Most Bacterial Species and Genera

Abstract

The fundamental unit of biological diversity is the species. However, a remarkable extent of intraspecies diversity in bacteria was discovered by genome sequencing, and it reveals the need to develop clear criteria to group strains within a species. Two main types of analyses used to quantify intraspecies variation at the genome level are the average nucleotide identity (ANI), which detects the DNA conservation of the core genome, and the DNA content, which calculates the proportion of DNA shared by two genomes. Both estimates are based on BLAST alignments for the definition of DNA sequences common to the genome pair. Interestingly, however, results using these methods on intraspecies pairs are not well correlated. This prompted us to develop a genomic-distance index taking into account both criteria of diversity, which are based on DNA maximal unique matches (MUM) shared by two genomes. The values, called MUMi, for MUM index, correlate better with the ANI than with the DNA content. Moreover, the MUMi groups strains in a way that is congruent with routinely used multilocus sequence-typing trees, as well as with ANI-based trees. We used the MUMi to determine the relatedness of all available genome pairs at the species and genus levels. Our analysis reveals a certain consistency in the current notion of bacterial species, in that the bulk of intraspecies and intragenus values are clearly separable. It also confirms that some species are much more diverse than most. As the MUMi is fast to calculate, it offers the possibility of measuring genome distances on the whole database of available genomes.

Separating Significant Matches from Spurious Matches in DNA Sequences

“…First, measuring the distances between complete genomes is not as simple as for short DNA sequences. Most of the existing approaches deal with the evaluation of the cumulative length of common words between sequences such as the D 2 statistic or the MUMi index (Deloger et al, 2009) or, with a more flexible definition, the determination of the conserved subsequences between genomes, called the ''backbone'' (Chiapello et al, 2005). This means that distant genomes are not sequences that share homologous regions with a low percentage of identity, but rather they are sequences that share few highly conserved subsequences.…”

“…To evaluate the distance between each pair, we used the MUMi index that was especially designed to measure distances between closely related complete genome sequences (Deloger et al, 2009). Briefly, MUMi evaluates the ratio of cumulative length of maximal unique matches (MUMs) to the total genome length.…”

“…The second approach consists in retrieving the maximal exact matches (MEMs), which are WMs that cannot be extended either from their left nor from their right. MEMs are widely used as anchor points in complete genome alignment (Höhl et al, 2002) as well as in alignment-free methods (Deloger et al, 2009). It is noteworthy that, in comparative genomics, most of the studies that use WMs are based on the detection of MEMs rather than k-words.…”

Ilumatobacter nonamiense sp. nov. and Ilumatobacter coccineum sp. nov., isolated from seashore sand

“…MUMi also indicated that the two strains represent different species, since the value between strains YM16-303 T and YM16-304 T was 0.91. The MUMi distance value is expressed over the range of 0 (nearest) to 1 (furthest) and correlates very well with DNA-DNA hybridization (Deloger et al, 2009). Furthermore, the two novel isolates and Ilumatobacter fluminis YM22-133 T differed from each other in some points: cell shape, major fatty acids and physiological properties (Table 1).…”

“…An ANI value of 95 % corresponds to 70 % DNA-DNA hybridization, and strains are regarded as belonging to different species if the ANI is lower than 95 %. MUMi, which represents genomic distance based on DNA maximal unique matches shared by two genomes, was calculated using the Mummer (version 3.0) program (Deloger et al, 2009). MUMi is used to estimate rapidly the distance between closely related bacterial genomes, and detects the level of DNA conservation of the core genome.…”