Defining bacterial species in the genomic era: insights from the genus Acinetobacter

Abstract

Background: Microbial taxonomy remains a conservative discipline, relying on phenotypic information derived from growth in pure culture and techniques that are time-consuming and difficult to standardize, particularly when compared to the ease of modern high-throughput genome sequencing. Here, drawing on the genus Acinetobacter as a test case, we examine whether bacterial taxonomy could abandon phenotypic approaches and DNA-DNA hybridization and, instead, rely exclusively on analyses of genome sequence data.

Results: In pursuit of this goal, we generated a set of thirteen new draft genome sequences, representing ten species, combined them with other publically available genome sequences and analyzed these 38 strains belonging to the genus. We found that analyses based on 16S rRNA gene sequences were not capable of delineating accepted species. However, a core genome phylogenetic tree proved consistent with the currently accepted taxonomy of the genus, while also identifying three misclassifications of strains in collections or databases. Among rapid distance-based methods, we found average-nucleotide identity (ANI) analyses delivered results consistent with traditional and phylogenetic classifications, whereas gene content based approaches appear to be too strongly influenced by the effects of horizontal gene transfer to agree with previously accepted species.

Conclusion: We believe a combination of core genome phylogenetic analysis and ANI provides an appropriate method for bacterial species delineation, whereby bacterial species are defined as monophyletic groups of isolates with genomes that exhibit at least 95% pair-wise ANI. The proposed method is backwards compatible; it provides a scalable and uniform approach that works for both culturable and non-culturable species; is faster and cheaper than traditional taxonomic methods; is easily replicable and transferable among research institutions; and lastly, falls in line with Darwin's vision of classification becoming, as far as is possible, genealogical.

Figure 1

Phylogenetic tree based on the 16S rRNA gene sequences. The tree was built for 37 Acinetobacter isolates (A. baumannii 6014059 was excluded as only partial 16S sequence was identified) and rooted at midpoint. Outgoing branches of a node are depicted in black if bootstrap support (100 replicates) at the node is ≥ 70%; in grey otherwise. The tree is significantly divergent from previous published results, e.g. the monophyly of the ACB complex is not preserved.

Figure 2

Phylogenetic tree based on 127 CDSs present in all 38 strains. The 127 CDSs used for this tree are present in all strains, have no paralogs and show no signs of recombination. The tree is rooted at midpoint. Outgoing branches of a node are depicted in black if bootstrap support (100 replicates) at the node is ≥ 70%; in grey otherwise.

Figure 3

The Average Nucleotide Identity (ANI) dendogram for the 38 strains. The vertical dashed line represents the 95% species cutoff value proposed by Goris et al. (10).