ESCMID Online Lecture Library © by Author

Leibniz‐Institut DSMZ‐Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH

A taxonomic life between between Scylla© and by Charybdis author

ESCMIDErko Online Stackebrandt, Lecture DSMZ Library Leibniz‐Institut DSMZ‐Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH

Content • A brief history of taxonomy – Faces and achievements – What is a “species”: Rules and nomenclature – The molecular revolution I: the beginning • The first clash • Reconsolidating polyphasic taxonomy • The molecular revolution II • The second clash © by author ESCMID Online Lecture Library Leibniz‐Institut DSMZ‐Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH

Growth of number of validly published species names since 1980

1792 in 2017

© by author ESCMID Online Lecture Library The situation of taxonomists before the identification of a new bacterial species Leibniz‐Institut DSMZ‐Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH

Louis Pasteur (1822‐1985) Among others (1873‐1891) Mycobacterium© lepraeby author Bacillus anthracis Neisseria gonorrhoeae Robert Koch (1843‐1910) Paul Ehrlich Salmonella typhii (1854ESCMID‐1915) Erysipelothrix Online rusiopathiae Lecture Library Streptococcus pyogenes Christian Vibrio cholerae Gram Clostridium speticum (1853‐1938) Corynebacterium diphtheriae Stain 1884 Julius Petri Malleomyces mallei (1852‐1921) Leibniz‐Institut DSMZ‐Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH The discovery of physiology

Sigurd Orla‐Jensen. 1870‐1949 Sergei Winogradsky 1856‐1953 Martinus Willem © by author Beijerinck, 1851‐1931 Alber Jan ESCMIDKluyver Online Lecture Library 1888‐1956 Roger Stanier, 1916‐1982 Leibniz‐Institut DSMZ‐Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH What is a ‘species’?

In bacteriology, species is a definition, not a concept

Arbitrary, random Artificial, man‐made

Pragmatic, satisfying the needs of the user © by author Buchanan (1955): a species is “ the type culture together with such other cultures or strains of ESCMIDbacteria that are Online accepted Lecture by bacteriologists Library as sufficiently closely related” Leibniz‐Institut DSMZ‐Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH

The community of taxonomists Reviewers Species description (polyphasic) The Code ©The by author author Minimal standards

Approved Lists Always test a range of ESCMIDCharacterization Online LectureIdentification Libraryclosest relatives

A strain Known species Microbiology Leibniz‐Institut DSMZ‐Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH

Delineating species Brian McCarthy and E. T. Bolton, 1961, described a method to compare genetic material from different species using DNA‐DNA hybridization. 70% similarity is the recognized threshold value for species

Different hybridization formats, 1960‐1970:

Josef de Ley © by author John L. Johnson DonESCMID Brenner: reliable Online basis for theLecture classification Library of clinical isolates among members of the Enterobacteriaceae Leibniz‐Institut DSMZ‐Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH

Recognizing the semantides

Emile Zuckerkandl and Linus Pauling

Different types of molecules are discussed in relation to their fitness for providing the basis for a molecular phylogeny. Best fit are the"semantides", i.e. the different types of macromolecules that carry© the by genetic author information or a very extensive translation thereof. ESCMID Online Lecture Library

J. Theoret Biol.( 1965), 357‐366 Linus Pauling Molecules as Documents of Evolutionary History (1901‐1994) Leibniz‐Institut DSMZ‐Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH

Ernst H. Haeckel, 1834‐1919

Carl© Woese, by author 1927‐2012 ESCMID Online Lecture Library Leibniz‐Institut DSMZ‐Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH

1872 ‐ 1980 1978 - 1985

The first clash

Pheno‐species polyphasic geno‐species Leibniz‐Institut DSMZ‐Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH

Wayne et al., 1987 (IJSB 37, 463‐464)

There was general agreement that the complete deoxyri‐ bonucleic acid (DNA) sequence would be the reference standard to determine phylogeny and that phylogeny should determine taxonomy. It is recommended that a distinct genospecies that cannot be differentiated© fromby author another genospecies on theESCMID basis of any Online known phenotypic Lecture property Library not be named until they can be differentiated by some phenotypic property. Microbiology Leibniz‐Institut DSMZ‐Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH Methods generating DNA patterns Chromosomes Gene/protein Genes Genomes patterns RFLP Ribotyping MLST RAPD MALDI‐TOF MLSA ERIC ARDRA, T‐RFLP rrn genes BOX Spacers© by ITS author Pearson correlation (Opt:1.20%) [0.0%-100.0%] REP Cluster Strain 100 70 80 90 DSM 20577T O. turbata I PFGEESCMID Online Lecture LibraryDSM 43878 III DSM 43852T O. enterophila DSM 46000 (F)AFLP II DSM 46001 DSM 46097 DSMZ IV DSM 14281 Deutsche MLVA Sammlung von Mikroorganismen und Zellkulturen GmbH Leibniz‐Institut DSMZ‐Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH

© by author ESCMID Online Lecture Library Pierre-Edouard Fournier, Didier Raoult, Michel Drancourt «New Species Announcement», a new format to prompt the description of new human microbial species Human Microbiome Journal, 2016, Available online 30 May 2016 Leibniz‐Institut DSMZ‐Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH

http://enve-omics.ce.gatech.edu/ani/ Das Bild kann nicht angezeigt werden.

Leibniz‐Institut DSMZ‐Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH

Philos Trans R Soc Lond B Biol Sci. 2006 Nov 29; 361(1475): 1929–1940. The bacterial species definition in the genomic era Konstantinos T Konstantinidis,*Alban Ramette, and James M Tiedje

From 2010 on

The second clash

Planctomycetales –two genera become five genera

Kindly provided by Hans-Peter Klenk Leibniz‐Institut DSMZ‐Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH Conclusions •Taxonomy is a highly conserved discipline and taxonomists do not like to see changes

•Changes are adopted, though with low speed

•The crux in taxonomy is that all species are treated like a closely related taxon

•Within the next few years wet lab DNA-DNA-hybridizations (DDHs) will be fully replaced by digital DDHs (depending on the progress in sequencing type strains) © by author •Soon we will see more and more whole genome sequence-based phylogenies and less 16S rRNA trees

•GenomeESCMID sequences Onlinewill be an integral Lecture part of species Librarydescription