Free access
Editor's Choice

Naming new taxa of prokaryotes in the 21st century

Publication: Canadian Journal of Microbiology
28 February 2023

Abstract

The nomenclature of prokaryotes is regulated by the rules of the International Code of Nomenclature of Prokaryotes (ICNP) and is based on the Linnaean binomial system. The current rules of the Code only cover the nomenclature of the cultivated minority. Proposals to incorporate the uncultivated majority of bacteria and archaea under the rules of the Code were recently rejected by the International Committee on Systematics of Prokaryotes. The provisional rank of Candidatus can be used to name uncultivated prokaryotes whose names cannot be validly published under the rules of the ICNP, but their names can now be validated under the Code of Nomenclature of Prokaryotes Described from Sequence Data (the SeqCode), which was recently established to cover the nomenclature of the uncultivated majority. Metagenomics, single-cell genomics, and high-throughput cultivation techniques have led to a flood of new organisms currently waiting to be named. Automated programs such as GAN and Protologger can assist researchers in naming and describing newly discovered prokaryotes, cultivated as well as uncultivated. However, Latin and Greek skills remain indispensable for proper quality control of names that must meet the standards set by the codes of nomenclature.
“And Adam gave names to all cattle, and to the fowl of the air, and to every beast of the field” (Genesis 2: 20)
“The beginning of wisdom is to call things by their proper name” (Confucius)

Background

At the time this paper was written (December 2022), names of 22 919 species of prokaryotes have been validly published under the rules of the International Code of Nomenclature of Prokaryotes (ICNP, referred to below as the Code) (Parker et al. 2019). Nomenclature of bacteria and archaea follows the binomial system proposed by Linnaeus in his Philosophia Botanica of 1751. Many of the rules and recommendations of the ICNP and of the other codes of biological nomenclature were derived directly from this classic book. Names of prokaryotes are Latin or latinized words treated as Latin, and they are usually taken from Latin and classical Greek. These names often contain information about the properties of the organisms and(or) the source of their isolation. Thus, Eilatimonas milleporae is a monad isolated from the Gulf of Eilat from the coral genus Millepora. Salibaculum (“the salt rod”) halophilum loves salt, and Salibaculum griseiflavum is colored grey and yellow. Many scientific names honor famous microbiologists from the past and the present. For example, Rhodobacter veldkampii(Hansen and Imhoff 1985), Syntrophomonas wolfei (McInerney et al. 1981), and Vibrio shilonii (Kushmaro et al. 2011) were named, respectively, after Hans Veldkamp, Ralph Wolfe, and Moshe Shilo, who were my teachers at different stages of my career. Similarly, Bob Murray has been honored by the naming of the genus Robertmurraya (Gupta et al. 2020) and the species Deinococcus murrayi (Ferreira et al. 1997).
In this essay, I intend to provide an overview of the ways scientific names of prokaryotes are formed based on the rules of the ICNP and discuss the future of naming prokaryotes in view of the rapidly increasing rate at which novel species are being discovered and described. The description of novel taxa of yet-uncultivated bacteria and archaea based on genome sequence data increases the need for new names manifold: the little over twenty thousand species described today represent only a small fraction of the total diversity (Sutcliffe et al. 2021), and the uncultivated majority can now be characterized thanks to the rapid advances in the sequencing methodology and bioinformatics.
This article is based in part on a presentation I gave in July 2021 in the framework of the BISMiS Live lectures (Oren 2021a). It presents a contemporary overview of the enduring relevance of the ICNP. The topic would have been of much interest to the late Prof. Murray, who was the Chair of the International Committee on Systematics of Bacteria (ICSB, today the International Committee on Systematics of Prokaryotes, the ICSP) from 1982 to 1990 and thereafter elected a Life Member of the ICSB/ICSP. He served two terms as a member at large of the ICSB executive board (1970–1973, 1978–1982) and twice on the ICSB Judicial Commission (1970–1973, 1978–1982). He also was an editor of the International Journal of Systematic Bacteriology from 1990 to 1994. He originally proposed the name of the kingdom “Procaryotae” (Murray 1968). He was a member of the ad hoc committee on reconciliation of approaches to bacterial systematics that published its important recommendations in 1987 (Wayne et al. 1987). He was instrumental in proposing the emendment to Rule 30 of the ICNP to make the deposition of the type strains of cultivable bacterial species and subspecies in a permanent culture collection mandatory so that they are available for study (Murray 1996). We also owe the concept of “Candidatus” taxa for naming of putative taxa of prokaryotes that could not (yet) be cultivated in pure culture to Bob Murray (Murray and Schleifer 1994; Murray and Stackebrandt 1995).

The International Code of Nomenclature of Prokaryotes—the formal framework for naming bacteria and archaea

There is no official classification of prokaryotes, but there is an official nomenclature of prokaryotes based on internationally agreed-upon rules found in the ICNP. The nomenclature is regulated by the ICSP (http://www.the-icsp.org, accessed 28 December 2022). The currently used revision of the Code (Parker et al. 2019) was approved by the ICSP in 2008. A new revision was endorsed by the ICSP in the spring of 2022 (Oren et al., in press).
An in-depth discussion of the 8 General Considerations, 9 Principles, 65 Rules and Recommendations, and 13 Appendices of the Code is outside the scope of this essay. Here, I will only present a few aspects that deal with the use of Latin-based nomenclature, as these issues are important for future approaches to the naming novel prokaryotic taxa. Principle 3 and Rule 6 state that the scientific names of all taxa are Latin or latinized words treated as Latin, regardless of their origin. They are usually taken from Latin or Greek. Rule 6 is followed by a number of Recommendations. Authors are not obliged to follow these Recommendations; names that contravene Recommendations still can be validly published. Thus, Recommendations 6(1) and 6(2) advise authors to avoid names or epithets that are very long or difficult to pronounce and to make names or epithets that have an agreeable form that is easy to pronounce when latinized. Until recently, the longest names in the prokaryotic nomenclature were the genus Hydrogenoanaerobacterium (24 letters), the epithet saccharoperbutylacetonicum (26 letters) used for a Clostridium species, and Thermoanaerobacterium thermosaccharolyticum (42 letters, genus name and specific epithet combined). These numbers were dwarfed by the recent description of Myxococcus llanfairpwllgwyngyllgogerychwyrndrobwllllantysiliogogogochensis. This “geographical” epithet (63 letters) signifies that the organism was isolated from the Welsh village of Llanfairpwllgwyngyllgogerychwyrndrobwllllantysiliogogogoch (Chambers et al. 2020). Such a name obviously contravenes Recommendations 6(1) and 6(2) of the ICNP, recommendations almost directly derived from aphorism 249 of the Philosophia Botanica by Linnaeus: “Nomina generica sesquipedalia, enuntiatu difficilia, vel nauseabunda, fugienda sunt” (generic names that are a foot and a half long, those that are difficult to pronounce, or are disgusting should be avoided) (Linnaeus 1751). As shown for Baia soyae, Dyella soli, Yania flava, and Vibrio xuii, 9 or 10 letters can be sufficient to name bacterial species. Even shorter is Sala cibi (Song et al. 2022), a name that will be validly published in January 2023.
Recommendation 6(3) of the ICNP calls for avoidance of words from languages other than Latin or classical Greek as long as equivalents exist in Latin or Greek or can be constructed by combining word elements from these two languages. Exceptions are names derived from typical local items such as foods, drinks, or geographical localities for which no Latin or Greek names exist. Thus, we have Leuconostoc miyukkimchii isolated from miyukkimchi, a regional food from Korea. The Code recommends against names such as Mycoplasma simbae, a validly published name formed from the Swahili word simba (lion), as a Latin equivalent is available (leonis) (Trüper 1999). The last i of myukkimchii and the e of simbae are Latin genitive endings so that the names are treated as Latin and comply with Principle 3 and Rule 6.

How many prokaryote species have been named?

The publication of the Approved Lists of Bacterial Names (Skerman et al. 1980) signified a new starting point for the nomenclature of prokaryotes. The Approved Lists contained names of nearly 1800 species. For new names to become validly published, they must be published in original articles in the International Journal of Systematic and Evolutionary Microbiology (IJSEM; before 2000: the IJSB) or in the validation lists that are periodically published in that journal (for names effectively published in other journals) (see Rules 24b and 27 of the ICNP). Thus, the number of validly published names of species, genera, and higher taxa is known at any given time.
The website “List of Prokaryotic names with Standing in Nomenclature” (LPSN; lpsn.dsmz.de; bacterio.net; accessed 28 December 2022) (Parte et al. 2020) is an excellent source for updated information on names of prokaryotic taxa, both validly and effectively published. In addition, information is found on Candidatus taxa, whose nomenclature is not regulated by the rules of the ICNP (see below). For each taxon, the literature source is given and the etymology of the name. For species and subspecies, culture collection accession numbers are provided, as well as links to 16S rRNA gene sequences in GenBank. It is important to note that LPSN is not an official document endorsed by the ICSP and cannot replace the authoritative lists published in the IJSEM. As of 28 December 2022, LPSN listed 22 919 validly published names of species, classified in 3898 genera, 663 families, 280 orders, and 154 classes. Without synonyms, these numbers were 18 912, 3597, 556, 222, and 100, respectively. In addition, LPSN listed 1924 Candidatus species.
In the years 1990–1994, the average annual number of prokaryotic species named was 150. This number increased to 250 for 1995–2000, 408 for 2001–2005, and 624 for 2006–2012 (Oren and Garrity 2014). In the years 2017–2021, 950 new species names and 176 new genus names were validly published annually on average (data from LPSN; lpsn.dsmz.de; bacterio.net; accessed 28 December 2022).

What fraction of the prokaryotic species has been cultivated and named?

The above-quoted numbers of prokaryotes described and named are small when compared to the numbers of known eukaryotic species. The Orchidaceae (the orchid family, being the largest plant family) has about 28 000 known species, more than the bacteria and archaea together, and nearly one million species of insects have been documented. The total number of species described is over two million (https://www.catalogueoflife.org/2022/08/30/release; accessed 28 December 2022) (Hobern et al. 2021).
Cultivation-independent studies based on the sequencing of 16S rRNA genes retrieved from DNA isolated from the environment and (or) assembly of genomes from metagenomics data or single-cell amplified genomes have shown that the cultivated ∼23 000 species of prokaryotes represent only a small fraction of the true diversity in nature. Examination of the complete or draft genomes of bacteria and archaea accessible from the Genome Taxonomy Database (Chaumeil et al. 2020) (317 542 genomes listed in Release 07-RS207 of April 2022; https://gtdb.ecogenomic.org; accessed 28 December 2022) shows that less than half are derived from cultivated organisms and that Latin names could be assigned only to one quarter of them. The fraction of uncultivated and unnamed species-level taxa is expected to increase dramatically in the coming years due to the advances in sequencing technology and bioinformatics. Describing the uncultivated majority is therefore a major task for the future. The currently practiced way in which new species are documented in the literature is poorly suitable for the description of numbers that are several orders of magnitude higher (Sutcliffe et al. 2021).
Estimates of the true number of different species-level taxa of prokaryotes on Earth (based on the currently accepted way of delineating species) vary widely. Based on a global-scale compilation of data, it was predicted that our planet is home to as many as one trillion (1012) microbial species (Locey and Lennon 2016). Other estimates are much lower, in the order of millions (Amann and Rosselló-Móra 2016; Schloss et al. 2016; Sutcliffe et al. 2021). In either case, the need remains to assign suitable names to numbers of bacteria and archaea that are several orders of magnitude higher than the current ∼23 000 names of prokaryotes with standing in the nomenclature based on the rules of the ICNP.

Naming the uncultivated majority

In 2016, Whitman published a formal proposal to expand the type material acceptable for the valid publication of names of species, genera, and higher taxa under the rules of the ICNP to genome sequences and even gene sequences (Whitman 2016). The proposal aimed at changing the rules so that Candidatus taxa (see below), endosymbionts, and uncultivated prokaryotes can be named in the absence of pure cultures required under the current rules of the ICNP. A unified nomenclature for all prokaryotes, cultured as well as uncultured, could thus be established. Whitman et al. (2019) further proposed to grant priority to Candidatus names based upon their date of publication in the IJSEM. A public discussion of these proposals was held online, and these discussions were summarized in an 80-page document (supplementary file 1 of Sutcliffe et al. 2020). Subsequently, the ICSP rejected all amendments to the ICNP proposed by Whitman (2016) and Whitman et al. (2019) (Sutcliffe et al. 2020).
Parallel to the attempts to incorporate the nomenclature of the uncultivated majority under the rules of the ICNP, proposals were made to establish a separate, independent framework for the naming of the yet-uncultivated taxa of prokaryotes. Thus, Konstantinidis and co-workers proposed the implementation of an independent nomenclatural system for uncultivated taxa, following nomenclature rules similar to those for cultured bacteria and archaea but with its own list of validly published names. The ultimate aim was to provide a unified catalog of validly published names, thereby avoiding synonyms and confusion. They proposed the formation of a committee of experts “to govern the new classification system, in a similar way to ICSP” (Konstantinidis et al. 2017). Unfortunately, their proposals suffered from misconceptions about the way the ICNP works. According to Principle 1.4 of the ICNP, “Nothing in this Code may be construed to restrict the freedom of taxonomic thought or action”. Thus, the ICNP does not deal with classification, and the ICSP does not support an “official” classification of the prokaryotes. The nomenclature system for the yet-uncultivated prokaryotes proposed by Konstantinidis and co-workers differs from that of the Candidatus taxa proposed in the mid-1990s where Candidatus names are not validly published and have no priority. How the implementation of an independent nomenclatural system for uncultivated taxa will provide a unified catalog of validly published names, thereby avoiding synonyms and confusion, is not clear. Having two independent systems running in parallel can only be a source of confusion (Oren and Garrity 2018). Similar aspects of the nomenclature and classification of uncultivated prokaryotes were discussed by Rosselló-Móra and Whitman (2019).
Following the decision of the ICNP not to allow valid publication of names of yet-uncultivated prokaryotes characterized mainly or solely by gene or genome sequences, an alternative Code of Nomenclature (the Code of Nomenclature of Prokaryotes Described from Sequence Data, or the SeqCode) was recently prepared to cover the nomenclature of the uncultivated majority (Murray et al. 2020; Hedlund et al. 2022; Whitman et al. 2022). The SeqCode and supplementary information is available online (https://disc-genomics.uibk.ac.at/seqcode/page/publications; accessed 28 December 2022).
The SeqCode resembles the ICNP in many aspects, and names under the SeqCode are also based on classical Latin. Thus, the need for correctly formed names is identical for names under the rules of the ICNP, Candidatus names, and names formed under the SeqCode.

The provisional status Candidatus

In the mid-1990s, Murray and Schleifer (1994) and Murray and Stackebrandt (1995) proposed the establishment of the provisional status Candidatus for naming of putative taxa of prokaryotes that could not (yet) be cultivated in pure culture but for which sufficient information, including gene sequence information, was available to be recognized as separate taxa. This may be considered as one of Bob Murray’s most significant contributions to prokaryotic taxonomy and nomenclature. The Candidatus status is not formally included in the rules of the ICNP. Appendix 11, added in the 2008 revision of the Code (Parker et al. 2019) and improved in the forthcoming 2022 revision of the ICNP (Oren et al., in press), addresses the application of the Candidatus concept (Oren 2021b). When an organism with Candidatus status is later isolated in pure culture, it can be described and named according to the rules of the ICNP. The concept of Candidatus taxa has been widely adopted by journals and databases so that many Candidatus names have achieved de facto standing in the academic literature following description of such taxa in peer-reviewed publications (Pallen 2021). Candidatus names do not have standing in the nomenclature under the rules of the ICNP, but they can now be validated under the SeqCode (Hedlund et al. 2022).
Appendix 11 of the ICNP states that a list in the form of a codified record of organisms of the status Candidatus is kept by the Judicial Commission of the ICSP in cooperation with the Editorial Board of the IJSEM and is published in that journal at appropriate intervals. However, this was never implemented by the Judicial Commission. Curated annotated lists of Candidatus names (not including phyla) have only been published since 2020 (Oren et al. 2020a). List No. 1 (Oren et al. 2020b) contained names of 1091 Candidatus taxa published between 1995 and 2018, including 706 species. List No. 2 (Oren and Garrity 2021), with names published in 2019 and addenda to the first list, had 226 new names, including 110 species, and List No. 3 (Oren and Garrity 2022), with names published in 2020 and addenda to the earlier lists, had 286 new names, including 160 species.
Candidatus List No. 4, (Oren 2022), which included newly added names in 2021, is very long: it contains 1190 new names, including 861 species. As of 8 November 2022, the draft list of new names to be included in Candidatus List No. 5 contained 333 taxa, including 196 species-level Candidatus names. These high numbers are largely due to the publication of two papers that used high-throughput metagenomics to characterize the prokaryotic diversity in the chicken gut and in horse feces. The first added 817 novel Candidatus taxa: 1 family, 159 genera, and 657 species (Gilroy et al. 2021); the second described 48 new Candidatus genera and 101 new Candidatus species (Gilroy et al. 2022). These numbers are dwarfed by the over 65 000 Candidatus names published on 20 September 2022 to name previously unnamed taxa within the Genome Taxonomy Database (https://gtdb.ecogenomic.org; accessed 28 December 2022) (Pallen et al. 2022).

Is it possible to find enough new names for all newly discovered prokaryotes?

The massive discovery of new bacteria and archaea, cultivated as well as uncultivated, requires their naming based on the rules of a code of nomenclature. For cultivated taxa, the rules of the ICNP apply, and the same rules are applied for Candidatus taxa (Appendix 11 of the ICPN). The SeqCode also calls for names based on Latin and uses similar orthography rules (Hedlund et al. 2022).
The recent paper in which 159 novel Candidatus genera and 698 novel species of prokaryotes were described from chicken feces (41 cultivated and 657 with Candidatus status) (Gilroy et al. 2021) shows the need for many more new names that must meet the requirements of the nomenclature codes. That paper also shows how this can be achieved by a scalable combinatorial system in which a small number of word elements from Latin and Greek are used to create compound names in a mix-and-match approach while using the guidelines of Appendix 9 of the ICNP on how to correctly form such names. In the case of the microbiome of the chicken gut, examples of words used are avis, gallus, gallina, and pullus (Latin) and alektryon, kottos, and ornis (Greek) for bird or chicken; intestinum (Latin) and enteron (Greek) for intestine; and egeries, excrementum, faex, merda, and stercus (Latin) and aphodos and kakke (Greek) for excrement. These can then be combined with suffixes such as -cola, -microbium, -monas, -morpha, -plasma, -soma, -vivens, etc. to yield a large number of names. Addition of prefixes such as allo-, alteri-, meta-, neo-, novi-, paeni-, para-, pseudo-, etc. further increases the number of names that can be created. This approach can be automated so that new, linguistically correct names can be created en masse by computer, even before they are tied to taxa, based on stocks of Latin or Greek roots with relevant meanings. For this purpose, a Python program named GAN (the “Great Automatic Nomenclator”) was created (Telatin 2020; Pallen et al. 2021). The GAN program can be linked to the “Protologger” program (automatic description of novel bacteria; www.protologger.de; accessed 28 December 2022), a bioinformatic tool that generates all the necessary readouts for writing detailed protologues for high-throughput and comprehensive description of novel prokaryotes, thus reducing the time needed to gather the information for describing novel taxa (Hitch et al. 2021). A different approach is the automated generation of thousands of arbitrary names. Using this approach, over 65 000 previously unnamed taxa within the Genome Taxonomy Database (https://gtdb.ecogenomic.org; accessed 28 December 2022) were named. Examples of such meaningless but basically well-formed names are “Candidatus Cofrixana mapaxosa”, “Candidatus Didresosa oboposa”, and “Candidatus Sufrabetta lutexaria” (Pallen et al. 2022). The future will show whether such names indeed are memorable linguistic labels as claimed by the authors.

Machine-made names: advantages and disadvantages

The obvious advantage of automatically generated names as the output of a well-written computer program is that the names are correctly formed. No manual quality control by expert linguists is needed if the program is written so that it processes all relevant information on how to find the stems of the words extracted from the Latin and Greek dictionaries and the rules that apply for the formation of compound names as found in section A(1) of Appendix 9 of the ICNP. These rules include the use of -i- as the connecting vowel following a word element of Latin origin and -o- when the preceding word element is of Greek origin. A connecting vowel is dropped when the following word element starts with a vowel. Section A(2) of Appendix 9 lists a few exemptions from these regulations, and these can also be incorporated in nomenclature computer programs.
The disadvantage of such machine-made names is that they are formed according to a highly standardized pattern, are uninteresting, often long, and are unlikely to arouse the general interest in prokaryotic nomenclature. The rules of the ICNP provide many opportunities to create names that are more interesting. I recently compiled a selection of such names based on my personal preferences. Here are three examples. A predatory bacterium assigned to the existing genus Vampirococcus was named Vampirococcus lugosii (Moreira et al. 2021), named after Bela Lugosi, who portrayed Count Dracula in the 1931 film. One may argue that such a name contravenes Recommendation 12c (3), which in the 2022 revision of the ICNP (Oren et al. 2021; Oren et al., in press) reads, “Specific epithets should not honour … any persons not connected with microbiology or at least with natural science”. However, a clear connection does exist, and in my personal opinion, the creation of such names should be encouraged. Another interesting name is “Candidatus Desulforudis audaxviator”, an organism from the deep subsurface (Chivian et al. 2008). The epithet audaxviator, “the audacious traveler”, was derived from Jules Verne’s Voyage au centre de la Terre. A third example is Dehalogenimonas lykanthroporepellens (Moe et al. 2009). The epithet means “repelling werewolves”: the organism produces a garlic aroma, garlic being said to repel werewolves in fiction literature. The formation of such names takes some effort, as well as the ability to use the lexicon of classical Greek and Latin, but it may boost the interest of microbiologists and also of the general public in biological nomenclature (Oren 2020).

Linguistic skills should be a part of the education of any taxonomist

There is no lack of review papers and book chapters that provide guidance on how to use Latin and Greek to form appropriate names for new taxa. The chapter on “Nomenclatural literacy” by MacAdoo (1993) is delightful. The review paper by Trüper (1999), on which much of Appendix 9 of the ICNP is based, is excellent. In addition, the chapters by Oren (2011, 2019a, 2019b) may prove useful.
The IJSEM, being the official journal of the ICSP and the only journal in which names of new cultured prokaryotic taxa can be validly published, has a team of experienced nomenclature reviewers who ensure that new names published in the journal meet the requirements of the ICNP (https://www.microbiologyresearch.org/content/journal/ijsem?page=editorial-board; accessed 28 December 2022). Editors of a few other journals have the names submitted for effective publication checked by nomenclature experts. Unfortunately, the number of experts in the field is small, and there is an urgent need for younger colleagues to learn the trade and continue the work to ensure that the current high level of quality control can be maintained in the future (Oren et al. 2015).
In spite of the ability of computers to take over part of the naming process for new taxa of prokaryotes, Latin and Greek skills remain indispensable to provide proper quality control for names that need to meet the requirements of the ICNP. The International Code of Nomenclature for algae, fungi, and plants (Turland et al. 2018) and the International Code of Zoological Nomenclature (International Commission on Zoological Nomenclature 1999) have similar strict rules for naming taxa based on Latin and Greek. Therefore, basic linguistic skills should be a part of the education of any taxonomist, in addition to handling of DNA and mastery of modern bioinformatics tools. A perfect command of the classical languages is not needed to create names of genera and species that conform to the rules of the ICNP. Appendix 9 of the ICNP can guide those describing new taxa on how to propose correctly formed names.
In his autobiographical essay ‘A structured life’, Bob Murray wrote, “My association with the International Committee for Systematic Bacteriology and the International Journal of Systematic Bacteriology has brought experience in the additional stringencies of monitoring the description of bacteria and the application of rules of bacterial nomenclature. There is a great need to help authors in a field unfamiliar to most of them” (Murray 1988). Today, the number of experts in the application of the rules of prokaryote nomenclature who can help authors is probably even smaller than at the time those words were written. Educating and assisting the community of microbial taxonomists is as important today as it was then.

Acknowledgements

The author thanks Iain C. Sutcliffe (Northumbria University) for helpful comments.

References

Amann R., Rosselló-Móra R. 2016. After all, only millions? mBio, 7: e00999–e00916.
Chambers J., Sparks N., Sydney N., Livingstone P.G., Cookson A.R., Whitworth D.E. 2020. Comparative genomics and pan-genomics of the Myxococcaceae, including a description of five novel species: Myxococcus eversor sp. nov., Myxococcus llanfairpwllgwyngyllgogerychwyrndrobwllllantysiliogogogochensis sp. nov., Myxococcus vastator sp. nov., Pyxidicoccus caerfyrddinensis sp. nov. and Pyxidicoccus trucidator sp. nov. Genome Biol. Evol. 12: 2289–2302.
Chaumeil P.A., Mussig A.J., Hugenholtz P., Parks D.H. 2020. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics, 36: 1925–1927.
Chivian D., Brodie E.L., Alm E.J., Culley D.E., Dehal P.S., Desantis T.Z. 2008. Environmental genomics reveals a single-species ecosystem deep within Earth. Science, 322: 275–278.
Ferreira A.C., Nobre M.F., Rainey F.A., Silva M.T., Wait R., Burghardt J., et al. 1997. Deinococcus geothermalis sp. nov. and Deinococcus murrayi sp. nov., two extremely radiation-resistant and slightly thermophilic species from hot springs. Int. J. Syst. Bacteriol. 47: 939–947.
Gilroy R., Ravi A., Getino M., Pursley I., Horton D.L., Alikhan N.-F., et al. 2021. Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture. PeerJ, 9: e10941.
Gilroy R., Leng J., Ravi A., Adriaenssens E.M., Oren A., Baker D., et al. 2022. Metagenomics investigation of the equine faecal microbiome reveals extensive taxonomic and functional diversity. PeerJ, 10: e13084.
Gupta R.S., Patel S., Saini N., Chen S. 2020. Robust demarcation of 17 distinct Bacillus species clades, proposed as novel Bacillaceae genera, by phylogenomics and comparative genomic analyses: description of Robertmurraya kyonggiensis sp. nov. and proposal for an emended genus Bacillus limiting it only to the members of the Subtilis and Cereus clades of species. Int. J. Syst. Evol. Microbiol. 70: 5753–5798.
Hansen T.A., Imhoff J.F. 1985. Rhodobacter veldkampii, a new species of phototrophic purple nonsulfur bacteria. Int. J. Syst. Bacteriol. 35: 115–116.
Hedlund B.P., Chuvochina M., Hugenholtz P., Konstantinidis K.T., Murray A.E., Palmer M., et al. 2022. SeqCode: a nomenclatural code for prokaryotes described from sequence data. Nat. Microbiol. 7: 1702–1708.
Hitch T.C.A., Riedel T., Oren A., Overmann J., Lawley T., Clavel T. 2021. Automated analysis of genomic sequences facilitates high-throughput and comprehensive description of prokaryotes. ISME Commun. 1: 16.
Hobern D., Barik S.K., Christidis L., Garnett S.T., Kirk P., Orrell T.M., et al. 2021. Towards a global list of accepted species VI: The Catalogue of Life checklist. Org. Divers. Evol. 21: 677–690.
International Commission on Zoological Nomenclature. 1999. International Code of Zoological Nomenclature. 4th ed. The International Trust for Zoological Nomenclature, London. Available from https://www.iczn.org/the-code/the-code-online/ [accessed 28 December 2022].
Konstantinidis K.T., Rosselló-Móra R., Amman R. 2017. Uncultivated microbes in need of their own taxonomy. ISME J. 11: 2399–2406.
Kushmaro A., Banin E., Loya Y., Stackebrandt E., Rosenberg E. 2011. Vibrio shiloi sp. nov., the causative agent of bleaching of the coral Oculina patagonica. Int. J. Syst. Evol. Microbiol. 51: 1383–1388.
Linnaeus C. 1751. Philosophia botanica. G. Kiesewetter, Stockholm.
Locey K.J., Lennon J.T. 2016. Scaling laws predict global microbial diversity. Proc. Natl. Acad. Sci. U.S.A. 113: 5970–5975.
MacAdoo T.O. 1993. Nomenclatural literacy. In Handbook of new bacterial systematics. Edited by M. Goodfellow, A.G. O'Donnell. Academic Press, London. pp. 339–360.
McInerney M.J., Bryant M.P., Hespell R.B., Costerton J.W. 1981. Syntrophomonas wolfei gen. nov. sp. nov., an anaerobic, syntrophic, fatty acid-oxidizing bacterium. Appl. Environ. Microbiol. 41: 1029–1039.
Moe W.M., Yan J., Nobre F., da Costa M.S., Rainey F.A. 2009. Dehalogenimonas lykanthroporepellens gen. nov., sp. nov., a reductively dehalogenating bacterium isolated from chlorinated solvent-contaminated groundwater. Int. J. Syst. Evol. Microbiol. 59: 2692–2697.
Moreira D., Zivanovic Y., López-Archilla A.I., Iniesto M., López-García P. 2021. Reductive evolution and unique predatory mode in the CPR bacterium Vampirococcus lugosii. Nat. Commun. 12: 2454.
Murray R.G.E. 1968. Microbial structure as an aid to microbial classification and taxonomy. Spisy Fac. Sci. Univ. Purkyne (Brno), 43: 245–252.
Murray R.G.E. 1988. A structured life. Annu. Rev. Microbiol. 42: 1–34.
Murray R.G.E. 1996. Taxonomic note: a rule about the deposition of type strains. Int. J. Syst. Bacteriol. 46: 831.
Murray R.G.E., Schleifer K.H. 1994. Taxonomic notes: a proposal for recording the properties of putative taxa of procaryotes. Int. J. Syst. Bacteriol. 44: 174–176.
Murray R.G.E., Stackebrandt E. 1995. Taxonomic note: implementation of the provisional status Candidatus for incompletely described procaryotes. Int. J. Syst. Bacteriol. 45: 186–187.
Murray A.E., Freudenstein J., Gribaldo S., Hatzenpichler R., Hugenholtz P., Kämpfer P., et al. 2020. Roadmap for naming uncultivated Archaea and Bacteria. Nat. Microbiol. 5: 987–994.
Oren A. 2011. How to name new taxa of prokaryotes? In Taxonomy of prokaryotes—methods in microbiology. Elsevier/Academic Press, Amsterdam. pp. 438–463.
Oren A. 2019a. Prokaryotic nomenclature. In Bergey’s manual of systematics of archaea and bacteria. John Wiley & Sons, Inc.
Oren A. 2019b. How to name new taxa of archaea and bacteria. In Bergey’s manual of systematics of Archaea and Bacteria. John Wiley & Sons, Inc. .
Oren A. 2020. Prokaryotic names: the bold and the beautiful. FEMS Microbiol. Lett. 367: fnaa096.
Oren A. 2021a. Naming new taxa of prokaryotes in the 21th century. Lecture, 17 July 2021. BISMiS Live. Available from https://www.youtube.com/watch?v=254Uh9YZ514&t=11s  [accessed 28 December 2022].
Oren A. 2021b. Nomenclature of prokaryotic Candidatus taxa: establishing order in the current chaos. New Microbes and New Infect. 44: 100932.
Oren A. 2022. Candidatus List No. 4: lists of names of prokaryotic Candidatus taxa. Int. J. Syst. Evol. Microbiol. 72: 005545.
Oren A., Garrity G.M. 2014. Then and now—a systematic review of the systematics of prokaryotes in the last 80 years. Antonie van Leeuwenhoek, 106: 43–56.
Oren A., Garrity G.M. 2018. Uncultivated microbes—in need of their own nomenclature? ISME J. 12: 309–311.
Oren A., Garrity G.M. 2021. Candidatus List No. 2. Lists of names of prokaryotic Candidatus taxa. Int. J. Syst. Evol. Microbiol. 71: 004671.
Oren A., Garrity G.M. 2022. Candidatus List No. 3. Lists of names of prokaryotic Candidatus taxa. Int. J. Syst. Evol. Microbiol. 72: 005186.
Oren A., Schink B., Garrity G.M. 2015. Wanted: microbiologists with basic knowledge of Latin and Greek to join our ‘nomenclature quality control’ team. Int. J. Syst. Evol. Microbiol. 65: 3761–3762.
Oren A., Garrity G.M., Trujillo M.E. 2020a. Registration of names of prokaryotic Candidatus taxa in the IJSEM. Int. J. Syst. Evol. Microbiol. 70: 3955.
Oren A., Garrity G.M., Parker C.T., Chuvochina M., Trujillo M.E. 2020b. Lists of names of prokaryotic Candidatus taxa. Int. J. Syst. Evol. Microbiol. 70: 3956–4042.
Oren A., Arahal D.R., Rosselló-Móra R., Sutcliffe I.C., Moore E.R.B. 2021. Preparing a revision of the International Code of Nomenclature of Prokaryotes. Int. J. Syst. Evol. Microbiol. 71: 004598.
Oren A., Arahal D.R., Göker M., Moore E.R.B., Rosselló-Móra R., Sutcliffe I.C. International Code of Nomenclature of Prokaryotes. Prokaryotic Code (2022 Revision). Int. J. Syst. Evol. Microbiol. 73: 005585. (in press).
Pallen M.J. 2021. The status Candidatus for uncultured taxa of Bacteria and Archaea: SWOT analysis. Int. J. Syst. Evol. Microbiol. 71: 005000.
Pallen M.J., Telatin A., Oren A. 2021. The next million bacterial names. Trends Microbiol. 29: 289–298.
Pallen M.J., Rodriguez-R L.M., Alikhan N.-F. 2022. Naming the unnamed: over 65,000 Candidatus names for unnamed Archaea andBacteria in the Genome Taxonomy Database. Int. J. Syst. Evol. Microbiol. 72: 005482.
Parker C.T., Tindall B.J., Garrity G.M. 2019. International Code of Nomenclature of Prokaryotes. Prokaryotic code (2008 revision). Int. J. Syst. Evol. Microbiol. 69: S1–S111.
Parte A.C., Sardà Carbasse J., Meier-Kolthoff J.P., Reimer L.C., Göker M. 2020. List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. Int. J. Syst. Evol. Microbiol. 70: 5607–5612.
Rosselló-Móra R., Whitman W.B. 2019. Dialogue on the nomenclature and classification of prokaryotes. Syst. Appl. Microbiol. 42: 5–14.
Schloss P.D., Girard R.A., Martin T., Edwards J., Thrash J.C. 2016. Status of the archaeal and bacterial census: an update. mBio, 7: e00201–e00216.
Skerman V.B.D., Sneath P.H.A., McGowan V. 1980. Approved lists of bacterial names. Int. J. Syst. Bacteriol. 30: 225–420.
Song H.S., Kim J., Kim Y.B., Lee S.H., Whon T.W., et al. 2022. Sala cibi gen. nov., sp. nov., an extremely halophilic archaeon isolated from solar salt. J. Microbiol. 60: 899–904.
Sutcliffe I.C., Dijkshoorn L., Whitman W.B. 2020. Minutes of the International Committee on Systematics of Prokaryotes online discussion on the proposed use of gene sequences as type for naming of prokaryotes, and outcome of vote. Int. J. Syst. Evol. Microbiol. 70: 4416–4417.
Sutcliffe I.C., Rosselló-Móra R., Trujillo M.E. 2021. Addressing the sublime scale of the microbial world: reconciling an appreciation of microbial diversity with the need to describe species. New Microbes New Infect. 43: 100931.
Telatin A. 2020. GAN: the Great Automatic Nomenclator. Available from https://github.com/telatin/gan [accessed 28 December 2022].
Trüper H.G. 1999. How to name a prokaryote? Etymological considerations, proposals and practical advice in prokaryote nomenclature. FEMS Microbiol. Rev. 23: 231–249.
Turland N.J., Wiersema J.H., Barrie F.R., Greuter W., Hawksworth D.L., Herendeen P.S., et al. (Editors). 2018. International Code of Nomenclature for algae, fungi, and plants (Shenzhen Code) adopted by the Nineteenth International Botanical Congress Shenzhen, China, July 2017. Regnum Vegetabile 159. Koeltz Botanical Books, Glashütten. Available from https://www.iapt-taxon.org/nomen/main.php. [accessed 28 December 2022].
Wayne L.G., Brenner D.J., Colwell R.R., Grimont P.A.D., Kandler O., Krichevsky M.I., et al. 1987. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int. J. Syst. Bacteriol. 37: 463–464.
Whitman W.B. 2016. Modest proposals to expand the type material for naming of prokaryotes. Int. J. Syst. Evol. Microbiol. 66: 2108–2112.
Whitman W.B., Sutcliffe I.C., Rossello-Mora R. 2019. Proposal for changes in the International Code of Nomenclature of Prokaryotes: granting priority to Candidatus names. Int. J. Syst. Evol. Microbiol. 69: 2174–2175.
Whitman W.B., Chuvochina M., Hedlund B.P., Hugenholtz P., Konstantinidis K.T., Murray A.E., et al. 2022. Development of the SeqCode: a proposed nomenclatural code for uncultivated prokaryotes with DNA sequences as type. Syst. Appl. Microbiol. 45: 126305.

Information & Authors

Information

Published In

cover image Canadian Journal of Microbiology
Canadian Journal of Microbiology
Volume 69Number 4April 2023
Pages: 151 - 157

History

Received: 28 December 2022
Revised: 26 January 2023
Revised: 26 January 2023
Accepted: 26 January 2023
Accepted manuscript online: 28 February 2023
Version of record online: 28 February 2023

Notes

Dedicated to the memory of Prof. Robert G.E. Murray (1919–2022). This paper is a part of the tribute collection entitled "Dr. Robert Murray: Strong roots in Canadian microbiology - Strong global leadership and vision"

Data Availability Statement

Not applicable.

Permissions

Request permissions for this article.

Key Words

  1. nomenclature
  2. International Committee on Systematics of Prokaryotes
  3. International Code of Nomenclature of Prokaryotes
  4. SeqCode
  5. Candidatus taxa

Authors

Affiliations

Department of Plant and Environmental Sciences, The Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem 9190401, Israel
Author Contributions: Conceptualization, Writing – original draft, and Writing – review & editing.

Author Contributions

Conceptualization: AO
Writing – original draft: AO
Writing – review & editing: AO

Competing Interests

The author declares that he has no competing interests.

Funding Information

The author declares no specific funding for the work.

Metrics & Citations

Metrics

Other Metrics

Citations

Cite As

Export Citations

If you have the appropriate software installed, you can download article citation data to the citation manager of your choice. Simply select your manager software from the list below and click Download.

There are no citations for this item

View Options

View options

PDF

View PDF

Get Access

Login options

Check if you access through your login credentials or your institution to get full access on this article.

Subscribe

Click on the button below to subscribe to Canadian Journal of Microbiology

Purchase options

Purchase this article to get full access to it.

Restore your content access

Enter your email address to restore your content access:

Note: This functionality works only for purchases done as a guest. If you already have an account, log in to access the content to which you are entitled.

Media

Media

Other

Tables

Share Options

Share

Share the article link

Share on social media

Cookies Notification

We use cookies to improve your website experience. To learn about our use of cookies and how you can manage your cookie settings, please see our Cookie Policy.
×