Abstract
The taxonomic concept of species has received continuous attention. A microbial species as a discrete box contains a limited number of highly similar microorganisms assigned to that taxon, following a polyphasic approach. In the 21st Century, with the advancements of sequencing technologies and genomics, the existence of a huge prokaryotic diversity has become well known. At present, the prokaryotic species might no longer have to be understood as discrete values (such as 1 or 2, by homology to Natural numbers); rather, it is expected that some microorganisms could be potentially distributed (according to their genome features and phenotypes) in between others (such as decimal numbers between 1 and 2; real numbers). We propose a continuous species concept for microorganisms, which adapts to the current knowledge on the huge diversity, variability and heterogeneity existing among bacteria and archaea. Likely, this concept could be extended to eukaryotic microorganisms. The continuous species concept considers a species to be delimited by the distance between a range of variable features following a Gaussian-type distribution around a reference organism (i.e., its type strain). Some potential pros and cons of a continuous concept are commented on, offering novel perspectives on our understanding of the highly diversified prokaryotic world, thus promoting discussion and further investigation in the field.
Highlights
Naming and classifying all living creatures is a requirement for science and humanity
The use of genomic approaches is required to complement phenotypic characteristics, defining what has been established as a polyphasic approach mandatory for the description of novel prokaryotic species [8,10]
The taxonomic analyses and phylogeny of prokaryotic diversity have been based on 16S rRNA gene sequencing technologies, which have boosted our current understanding of the diversity in the microbial world and keep providing us with highly valuable information on prokaryote distribution and ecology [15,18,19]
Summary
Naming and classifying all living creatures is a requirement for science and humanity. On top of that complexity generated by the huge diversity existing among the prokaryotes, the current taxonomical methodologies have incorporated scarce statistical approaches in defining the limits and the variability of a prokaryotic species This should be considered, and it is essential to objectively classify a newly isolated strain, clone or cultivated prokaryotic cell line within a species, or as a newly proposed species or taxon. More recently ANI (average nucleotide identity) analysis [1,31] of complete or draft genome sequences has been marked at 95% similarity to determine the strict classification of a prokaryote within a species Neither of these thresholds consider statistical limits for species limits and variability. The aim of this study is to propose a novel framework, Microorganisms 2020, 8, 1723 and some of its (dis)advantages and consequences, representing a statistically solid perspective to understand the range limits of the prokaryotic species and to adapt to the current knowledge on prokaryote diversity and its increasingly known heterogeneity
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