Genomics in Bacterial Taxonomy: Impact on the Genus Pseudomonas.

Jorge Lalucat,Margarita Gomila,Elena García-Valdés,Magdalena Mulet

doi:10.3390/genes11020139

Jorge Lalucat, Margarita Gomila + Show 2 more

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https://doi.org/10.3390/genes11020139

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Abstract

The introduction of genomics is profoundly changing current bacterial taxonomy. Phylogenomics provides accurate methods for delineating species and allows us to infer the phylogeny of higher taxonomic ranks as well as those at the subspecies level. We present as a model the currently accepted taxonomy of the genus Pseudomonas and how it can be modified when new taxonomic methodologies are applied. A phylogeny of the species in the genus deduced from analyses of gene sequences or by whole genome comparison with different algorithms allows three main conclusions: (i) several named species are synonymous and have to be reorganized in a single genomic species; (ii) many strains assigned to known species have to be proposed as new genomic species within the genus; and (iii) the main phylogenetic groups defined by 4-, 100- and 120-gene multilocus sequence analyses are concordant with the groupings in the whole genome analyses. Moreover, the boundaries of the genus Pseudomonas are also discussed based on phylogenomic analyses in relation to other genera in the family Pseudomonadaceae. The new technologies will result in a substantial increase in the number of species and probably split the current genus into several genera or subgenera, although these classifications have to be supported by a polyphasic taxonomic approach.

Highlights

Genomics is profoundly changing the way in which bacterial taxonomy is developing.The knowledge of the whole genome sequence of bacterial strains and analyses of their gene sequences has gained superior value over the phenotypic traits for bacterial classification and identification
The 16S rDNA sequence is mandatory for the description of a new species, and its analyses constitute the backbone of the actual bacterial taxonomy
The genome-to-genome-distance calculations (GGDCs) value was lower than 70%, and the 4-gene multilocus sequence analysis (MLSA) was lower than 95% with any species type strain, confirming the TYGS identification, and all were located in the 3 trees in the same phylogenetic branch

Summary

Introduction

Genomics is profoundly changing the way in which bacterial taxonomy is developing.The knowledge of the whole genome sequence of bacterial strains and analyses of their gene sequences has gained superior value over the phenotypic traits for bacterial classification and identification. Digital whole genome comparisons by using average nucleotide identities (ANIs) or genome-to-genome-distance calculations (GGDCs) are the new gold standards for species circumscription, substituting experimental DNA-DNA hybridization procedures [1,2,3]. The phylogenetic relationships among bacteria can be inferred from the nucleotide sequences of selected genes and allow a natural classification of bacteria based on their evolutionary relationships. The 16S rDNA gene sequence was initially selected in phylogenetic studies, but it is recognized that it lacks sufficient discriminatory power to differentiate species in many genera (e.g., Aeromonas, Bacillus, Pseudomonas, Streptococcus, etc.) [4]. Other housekeeping genes have been proposed as alternative genes for phylogenetic studies [5] These genes have to be universal or at least present in all species in the group to be studied and can be analyzed individually, or their sequences can be concatenated and analyzed from a phylogenetic perspective.

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