9 Taxonomia

• describe as completely as possible the basic taxonomic units, or species

• devise an appropriate way of arranging and cataloguing these units

Carl Linnaeus (1707-1778)

• Swedish botanist, zoologist, and physician who formalized binomial nomenclature

• → modern system of naming organisms

• “Father of modern taxonomy“

• Statement or tabulation of the characteristics of each strain

• List of characteristics considered essential for membership in the taxon

• List of characteristics which qualify the taxon for membership in the next higher taxon

• The reactions of the type strain of a new species

• List of diagnostic characteristics, i.e. characters which distinguish the taxon from closely related taxa

• Designation of the type for that taxon

• Genome sequences of the type strains of prokaryotes

• 16S rRNA gene should also be provided (separately from genome sequence)

• Proof of deposit that any proposed prokaryote type strains have been deposited in two or more public culture collections (with no restrictions)

Species

‘A species consists of strains of common origin which are more similar to each other than they are to any other strain’

Strain

‘… an isolate or group of isolates that can be distinguished from other isolates of the same genus and species by phenotypic characteristics or genotypic characteristics or both’

Clone

‘Genetically related isolates (clones) are isolates that are indistinguishable from each other by a variety of genetic tests, or that are so similar that they are presumed to be derived from a common parent’

• The type strain is essentially the “definition” of a species

• Serves as the comparative reference point for the identification of new strains and the assignment to existing species

between 25% and 75%

• Found in all living organisms

• rRNAs offer a type of sequence information that makes them excellent descriptors of an organism's evolutionary history

• No detectable horizontal gene transfer

  • very important for prokaryotes (bacteria)

• Large and growing databases •

  • SILVA contains ~10 million SSU rRNA

component of the 30S small subunit of a prokaryotic ribosome that binds to the Shine -Dalgarno sequence

due to the slow rates of evolution of this region of the gene

Shotgun metagenomics -> MAGs Metagenome Assembled Genomes

BUT there are issues that limit the value of these genomes

• gaps

• local assembly errors

• chimeras

• contamination by fragments from other genomes