Understanding the International Code of Nomenclature of Prokaryotes
In the vast world of microbiology, precision is everything. To ensure that scientists across the globe are talking about the same organism, a standardized system of naming is essential. This is where the International Code of Nomenclature of Prokaryotes (ICNP), also known as the Prokaryotic Code, comes into play. The ICNP provides the definitive set of rules for naming taxa (groups of one or more populations of an organism) of Bacteria and Archaea—the two primary domains of prokaryotes, which are single-celled organisms that lack a cell nucleus.
Formerly known as the International Code of Nomenclature of Bacteria (ICNB) or the Bacteriological Code (BC), this system ensures that scientific names are unique, stable, and universally accepted. It serves as one of the primary nomenclature codes in biology, preventing the chaos of multiple names for a single species.
ไม่มีภาพประกอบThe Governance and Evolution of the Code
The ICNP is not a static document but an evolving set of guidelines. It is maintained by the International Committee on Systematics of Prokaryotes (ICSP), previously known as the International Committee on Systematic Bacteriology (ICSB). While an early version of the code was approved in 1947, it was eventually discarded in favor of more robust systems.
Historically, bacteria were managed under the International Code of Botanical Nomenclature. However, by the 1975 International Botanical Congress, references to bacteria were removed from the botanical code to allow for a specialized bacteriological approach. Today, the baseline for all bacterial names is the "Approved Lists," which established a starting point in 1980.
While the 1990 Revision was the last version printed as a book, it no longer represents the current rules. Modern updates, including the 2008 and 2022 Revisions, are published in the International Journal of Systematic and Evolutionary Microbiology (IJSEM). For a new bacterial name to be considered validly published, it must be reviewed by the ICSP for conformity and published within the IJSEM.
The Role of the Type Strain
A cornerstone of prokaryotic nomenclature is the type strain. Since 2001, any description of a new bacterial or archaeal species must designate a type strain, which is a living culture to which the scientific name is formally attached.
To ensure the name is validly published, the type strain must be deposited in public culture collections in at least two different countries. This redundancy ensures that the reference material remains available to the scientific community even if one collection is lost. Interestingly, while there is only one type strain per species, different collections may assign it different identification numbers. For example, the type strain of E. coli is known as ATCC 11775 in the United States, DSM 30083 in Germany, JCM 1649 in Japan, and LMG 2092 in Belgium.
Naming the Unculturable: Candidatus and SeqCode
Not all prokaryotes can be grown in a laboratory. When a species cannot be cultivated, it cannot be deposited in a culture collection, making traditional valid publication impossible. In these cases, the organism is given a provisional Candidatus name.
Until recently, these names were not considered validly published. However, starting in 2024, a "pro-valid" publication mechanism was introduced. This allows Candidatus names to become "pro-legitimate" and "pro-correct" if they meet most publication requirements, replacing the living culture requirement with alternatives such as:
- A preserved specimen.
- A sequenced genome deposited on the International Nucleotide Sequence Database Collaboration (INSDC).
- A single-gene sequence deposited on the INSDC.
Before this update, the validation of sequence-based names was handled by the SeqCode (Code of Nomenclature of Prokaryotes Described from Sequence Data), published in 2022 by the International Society for Microbial Ecology, an organization separate from the ICSP.
The Cyanobacteria Controversy
Cyanobacteria (oxygen-producing photosynthetic bacteria) presented a unique challenge because they fell under both the botanical and bacteriological codes starting in 1999. This overlap created significant nomenclatural confusion.
By 2020, three potential solutions were proposed: excluding them from the bacteriological code, applying the bacteriological code exclusively, or accepting botanical publications as valid under the bacteriological code. In 2021, the ICSP voted in favor of the third option, effectively bridging the two codes for these specific organisms.
ICNP vs. the Botanical Code: Key Differences
While both systems aim for organization, the ICNP has specific rules that differ from the Botanical Code:
Formatting and Orthography
- Hyphenation: Hyphens are strictly forbidden. Any previously hyphenated names or new compound names must be joined into a single word.
- Diacritics: Accents or special marks (diacritics) are not allowed; they are replaced by fixed two-letter combinations.
- Italicization: While the ICNP recommends differentiating scientific names (e.g., using italics), it is not mandatory. However, the IJSEM and the ICNP text itself italicize all scientific names, except for specific Candidatus formatting.
Citation Practices
The ICNP uses specific terms for author citations. The term ex is used in parentheses—for example, "Taxon (ex Earlier) Later"—to denote authorship. Similarly, the term non is parenthesized when indicating that a name is not the same as a previously used one.
Summary of ICNP Revisions
The following table outlines the progression of the prokaryotic nomenclature codes.
| Year | Version/Revision | Publication Method |
|---|---|---|
| 1947 | Proposed Bacteriological Code | Iowa State College Press |
| 1958 | International Code of Nomenclature of Bacteria and Viruses | Iowa State College Press |
| 1975 | International Code of Nomenclature of Bacteria (1975 Revision) | American Society of Microbiology |
| 1990 | Bacteriological Code (1990 Revision) | ASM Press (Book form) |
| 2008 | Prokaryotic Code (2008 Revision) | IJSEM |
| 2022 | Prokaryotic Code (2022 Revision) | IJSEM |
Key Facts
- Governing Body: The International Committee on Systematics of Prokaryotes (ICSP).
- Official Journal: The International Journal of Systematic and Evolutionary Microbiology (IJSEM).
- Baseline: The Approved Lists of Bacterial Names (1980).
- Type Strain Rule: Must be deposited in at least two different countries' public collections since 2001.
- Candidatus: A provisional name for unculturable prokaryotes, now eligible for "pro-valid" publication as of 2024.
- Cyanobacteria: Valid publications under the botanical code are now accepted under the bacteriological code (decided 2021).
Frequently Asked Questions
What is the difference between a validly published name and a Candidatus name?
A validly published name meets all ICNP requirements, including the deposition of a living type strain in two public collections. A Candidatus name is provisional and used for organisms that cannot yet be cultured in a lab, though some can now achieve "pro-valid" status via genomic data.
Why does the same type strain have different names in different collections?
While there is only one biological type strain for a species, different culture collections (such as ATCC in the US or DSM in Germany) use their own internal cataloging systems to assign unique identification numbers to that strain.
Are scientific names required to be italicized under the ICNP?
Italicization is recommended as a way to differentiate scientific names from the surrounding text, but it is not strictly mandatory. However, most major publications, including the IJSEM, follow the practice of italicizing all scientific names.
How are hyphenated names handled in the Prokaryotic Code?
Hyphenation is not permitted in the ICNP. Any names that were previously hyphenated or any new compound names must be written as a single, joined word.
What is the SeqCode?
The SeqCode is a separate nomenclatural system published in 2022 by the International Society for Microbial Ecology. it specifically handles the naming of prokaryotes that are described solely from sequence data.