Candidatus

The initial International Code of Nomenclature of Prokaryotes as well as early revisions did not account for the possibility of identifying prokaryotes which were not yet cultivable. Therefore, the term Candidatus was proposed in the context of a conference of the International Committee on Systematics of Prokaryotes, (ICSP, formerly International Committee on Systematic Bacteriology) in 1994 to initiate code revision.[2] Owing to rising numbers of Candidatus taxa associated with ongoing advances of sequencing technologies, the ICSP adopted the International Code of Nomenclature of Prokaryotes in 1996 by adding an appendix for Candidatus taxa[3] (Appendix 11 in the most recent version[4]). However, the nomenclature of Candidatus taxa is still not covered by the general rules of the Prokaryotic Code leading to ongoing discussions and proposals for changing the current code in order to grant priority to Candidatus taxa.[5][6]

Currently, the provisional status “Candidatus” may be used if the following information is provided:

1. Genomic information [...] to determine the phylogenetic position of the organism.
2. All information so far available on:
   1. structure and morphology
   2. physiology and metabolism
   3. reproductive features
   4. the natural environment in which the organism can be identified and
   5. any other available and suitable information.[4]^{: Appendix 11}

The species name of an organism in the status of Candidatus consists of the word Candidatus, followed by an either a genus name with a specific epithet, or only a genus name, or only a specific epithet. Examples include Candidatus Liberobacter asiaticum; Candidatus magnetobacterium; Candidatus intracellularis. A list of all Candidatus taxa is kept by the Judicial Commission of the ICSP in cooperation with the editorial board of the IJSEM and is updated in appropriate intervals.[4] Once a Candidatus taxa has been cultivated successfully, the name has to be removed from this list and a new name has to be proposed in accordance with the International Code of Nomenclature of Prokaryotes.

There are several reasons for why many prokaryotic species do not grow in the lab many of which remain poorly understood. One of these reasons is the environment the species are recovered from which can be difficult to simulate in laboratory conditions. Many prokaryotes have highly specific growth requirements including the need for a specific nutrient composition, specific pH conditions, temperatures, atmospheric pressure or levels of oxygen.[7] Most commercially available growth media and incubation protocols poorly met these requirements making a comprehensive habitat assessment necessary in order to successfully isolate the bacteria of interest from environmental samples.

Most prokaryotic species do not live alone but rather in complex communities with other species from all kingdoms of life. As a consequence, many species depend on metabolites or signaling compounds of their neighboring species for their own cell growth. The identification of the required substances can be challenging but once identified a co-cultivation or addition of the specific compound can be used to potentially cultivate the species of interest.

Many instances of species interaction are of symbiotic nature which is defined as an intimate, long-term relationship between two or more species which can be either mutualistic, neutral or harmful.[8] Depending on the location of the symbiont, the symbionts can be either ectosymbionts or endosymbionts. Drastic genome reduction through gene deletions has been observed in endosymbiotic bacteria which is thought to be owing to the fact that many genes become unnecessary in the sheltered host environment. This frequently affects genes for DNA repair and transcriptional regulation which makes it difficult to cultivate these organisms outside their host.[8]

• Labeda, D. P. (1997). "Judicial Commission of the International Committee on Systematic Bacteriology VIIIth International Congress of Microbiology and Applied Bacteriology: Minutes of the Meetings, 17 and 22 August 1996, Jerusalem, Israel". International Journal of Systematic Bacteriology. 47: 240. doi:10.1099/00207713-47-1-240.
• "International Committee on Systematic Bacteriology VIIth International Congress of Microbiology and Applied Bacteriology: Minutes of the Meetings, 17, 18, and 22 August 1996, Jerusalem, Israel". International Journal of Systematic Bacteriology. 47 (2): 597–600. 1997. doi:10.1099/00207713-47-2-597.
• De Vos, P.; Trüper, H. G.; Tindall, B. J. (2005). "Judicial Commission of the International Committee on Systematics of Prokaryotes; Xth International (IUMS) Congress of Bacteriology and Applied Microbiology; Minutes of the meetings, 28, 29 and 31 July and 1 August 2002, Paris, France". International Journal of Systematic and Evolutionary Microbiology. 55: 525–532. doi:10.1099/ijs.0.63585-0.
• Stackebrandt, E.; Frederiksen, W.; Garrity, G. M.; Grimont, P. A.; Kämpfer, P.; Maiden, M. C.; Nesme, X.; Rosselló-Mora, R.; Swings, J.; Trüper, H. G.; Vauterin, L.; Ward, A. C.; Whitman, W. B. (2002). "Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology". International Journal of Systematic and Evolutionary Microbiology. 52 (Pt 3): 1043–1047. doi:10.1099/ijs.0.02360-0. PMID 12054223.