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Biological Nomenclature

Chapter:
Nomenclature
Author(s):

AMA Manual of Style Committee

Biological Nomenclature

Scientific and Vernacular Names.

Scientific names are labels used in place of lengthy descriptions. A scientific name corresponds to a set of formally defined attributes. The meanings of scientific names are internationally understood.2

Vernacular names or common names are also labels. Vernacular names seen in medical publications include fungi, prokaryotes, meningococcus, and St John’s wort. Vernacular names cannot be assumed to correspond to formally defined sets of attributes and vary by region and language.

In scientific writing, scientific names should be used when the labeled entity verifiably corresponds to the set of attributes associated with the scientific name, at least at first mention. Subsequently vernacular names (including collective genus terms, described later in this section) may be used.

Parenthetic mention of the vernacular name when the scientific name is used, and vice versa, is helpful. For instance:

First Mention

Subsequent Mention

Vernacular name

St John’s wort (Hypericum perforatum)

St John’s wort; eg, “participants who reported taking St John’s wort tablets”

Scientific name

Hypericum perforatum (St John’s wort)

H perforatum, or St John’s wort, depending on context; eg, “participants given tablets prepared from a pure extract of H perforatum”

Biological Nomenclature.

Biological nomenclature is the scientific naming of organisms and is the source of scientific names. Taxonomy comprises the principles and practices of classifying organisms2 to reflect their relatedness. Nomenclature “is the assignment of names to the taxonomic groups according to international rules.”3(p27)

Biological nomenclature—the nomenclature of living things—derives from the paradigm of the 18th-century taxonomist Linnaeus, who used 2-word labels to replace the long descriptive Latin phrases appended to the genus name.4,5 Since Linnaeus’ time, international bodies have continued to formalize biological nomenclature, resulting in the current principal codes:

Code

Content

International Code of Zoological Nomenclature1

animals, including protozoa and parasites

International Code of Botanical Nomenclature6

fungi and noncultivated plants, including algae

International Code of Nomenclature of Bacteria7

bacteria

International Code of Nomenclature for cultivated plants8

cultivated plants

International Code of Virus Classification and Nomenclature

viruses (see 15.14.3, Organisms and Pathogens, Virus Nomenclature)

The codes contain principles, rules, and recommendations for name derivations, priority, validity, and spelling. For a name to have international standing, the codes stipulate valid publication according to specific requirements.

An effort has been made to unify biological nomenclature for all organisms with a single code, the BioCode, under the auspices of the International Committee on Bionomenclature (a joint committee of the International Union of Microbiological Societies and the International Union of Biological Sciences).5,9-11 Another proposed unifying code is the PhyloCode, which is meant to reflect phylogeny and to be used concurrently with the extant codes, at least initially.12,13

“The essence of the Linnaean revolution was the recognition that the function of the specific ‘name’ was merely to label a concept rather than to describe an entity.”5(p5) Scientific names change when taxonomy changes, but not when new knowledge indicates that the original name is no longer an apt descriptor. (For instance, it was learned several decades after its discovery that the bacterium Haemophilus influenzae did not cause influenza,14 but the name was not changed.7) The stability of names is crucial, and name changes may cause harm5(p75),6(preamble) (see “perilous name” in the bacteriologic code7).

Resources.

A useful source of names of organisms available on the Web, particularly plant and animal names, is the Index to Organism Names.15 Other resources are available at the National Center for Biotechnology Information Entrez Taxonomy Homepage (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=taxonomy).16

Style for Scientific Names.

This section presents style that applies to scientific names. The nomenclature codes differ in some style recommendations, but most publications, when possible, will apply style consistently for all scientific names, eg, will use abbreviations in the same way for animals, plants, and bacteria. Therefore, style applied to animals, plants, and bacteria is presented together in this section. (See also 15.14.2, Bacteria: Additional Terminology, and 15.14.3, Virus Nomenclature.)

Organisms are classified in taxonomic groups, also called taxa (singular: taxon), within different ranks, eg:

Rank

Taxon

genus

Homo

species

Homo sapiens

Major ranks, from most inclusive to most specific, are kingdom, domain (bacteria), phylum (animals, fungi, and bacteria) or division (plants and bacteria), class, order, family, genus, and species.

Stylistic hallmarks of biological nomenclature differentiate scientific names from vernacular names.2,4 These hallmarks are latinization, italics, and a 2-word term for species: the binomial, also called binary or binominal, eg, Homo sapiens. (Within a code, the names of ranks above species usually must be unique; the same species designator, however, can be used with multiple genera, eg, Klebsiella pneumoniae, Streptococcus pneumoniae. Across codes, names may be the same at any rank, eg, the bacterial genus Bacillus, the stick and leaf insect genus Bacillus.)

According to the international codes, initial capitals are used for all taxa, except for the second portion of the binomial. (That portion is called the specific name in the zoological code and the specific epithet in the botanical and bacteriological codes.) Italics are always used for the genus and species components of the binomial. Diacritical marks (accents) and ligatures (eg, æ) are not used. Hyphens occasionally may be used in the specific epithet, eg, the butterfly Polygonia c-album, which has a c-shaped wing mark.2

All codes capitalize scientific names of taxa but differ on italicizing higher taxa. The bacterial code recommends italicizing all scientific names but recognizes that journals may wish to style all organism names similarly. In JAMA and the Archives Journals, taxa above genus are not italicized. The following examples of taxonomic classification according to the 3 codes illustrate style in JAMA and the Archives Journals for capitalization and italicization (see also 10.3.6, Capitalization, Proper Nouns, Organisms). The suffixes are typical and specified in each code (eg, family: -idae [animals], -aceae [plants and bacteria]), although exceptions are found:

Animal

Fungi

Bacteria

Rank

Taxon

Rank

Taxon

Rank

Taxon

kingdom

Animalia

kingdom

Fungi (Mycota)

kingdom

Procaryotae

phylum

Chordata

phylum

Ascomycota

division

Firmicutes

class

Mammalia

class

Ascomycetes

class

Firmibacteria

order

Primates

order

Onygenales

order

(not applicable in example; ending: -ales)

family

Hominidae

family

Onygenaceae

family

Bacillaceae

genus

Homo

genus

Ajellomyces

genus

Staphylococcus

species

Homo Sapiens

species

Ajellomyces capsulatus

species

Staphylococcus aureus

(Another scheme for bacterial taxonomic rank uses domain and phylum, rather than kingdom and division.4)

Subranks and superranks follow the same style, eg:

Animal

Fungi

Rank

Taxon

Rank

Taxon

subphylum

Vertebrata

subclass

Peronosporomycetidae

suborder

Anthropoidea

superfamily

Hominoidea

(See also the sections “Subgenus” and “Subspecific Ranks, Ternary Names,” below.)

Abbreviation of Genus and Other Abbreviations.

As described in 14.11, Abbreviations, Clinical, Technical, and Other Common Terms, treat each manuscript portion (title, abstract, text, etc) separately. After first mention of the binomial species name, abbreviate the genus portion of the name. (JAMA and the Archives Journals do not use a period.) Do not abbreviate the specific name. Do not begin a sentence with an abbreviated genus name; either expand or reword.

Staphylococcus aureus is a common cause of hospital-acquired infection. Nosocomial S aureus infection is also a source of community-acquired infection.

When the genus name is repeated but used with a new specific name, do not abbreviate the genus name until subsequent mention.

Staphylococcus aureus and Staphylococcus epidermidis may be components of normal flora or pathogens in clinically significant infections, although S aureus is the more serious pathogen of the two.

Do not abbreviate the specific name, and do not abbreviate the genus name when used alone.

Not:S au is the more serious pathogen…

Not:…the more serious pathogen in the genus S

When organisms with genus names that begin with the same letter are mentioned in the same article, in JAMA and the Archives Journals, genus is abbreviated after first mention, for instance:

hospital infections caused by Staphylococcus aureus and Streptococcus faecalis and bacteriuria with S aureus and S faecalis

Style variations in such instances are permissible (eg, if the editor thinks there is any possibility of confusing genera), and author requests to expand the genus names should be honored. JAMA and the Archives Journals do not use multiletter abbreviations for genus name, eg:

S aureus and S faecalis (not Sta aureus or Str faecalis)

Do not use 2-letter abbreviations for the binomial, eg, do not use SA for Staphylococcus aureus or SE for S epidermidis. However, longer expressions that include the scientific name may be abbreviated:

CoNS

coagulase-negative Staphylococcus species

EHEC

enterohemorrhagic Escherichia coli

MRSA

methicillin-resistant Staphylococcus aureus

Abbreviations such as sp nov (species nova, new species) and gen nov (genus novum, new genus) are used in published proposals of new genus and species designations, eg:

Corynebacterium nigricans sp nov

Roseomonas mucosa sp nov and Roseomonas gilardii subsp rosea subsp nov17

Wigglesworthia glossinidia sp nov18

Wigglesworthia gen nov18

New proposals for higher taxa are indicated as in the following examples19-22:

Cycliophora, new phylum

Eucycliophora, new class

Symbiida, new order

Symbiidae, new family

Symbion gen nov

Symbion pandora sp nov

Pfiesteria piscicida gen et sp nov (Pfiesteriaceae fam nov)

Parachlamydiaceae fam nov and Simkaniaceae fam nov

The “nov” abbreviations should be mentioned prominently in the article, eg, in the title, but need not be included with every mention of the organism name.

Synonyms are expressed as follows:

Fugomyces cyanescens (syn Sporothrix cyanescens, Cerinosterus cyanescens)

Mesocestoides vogae (syn M corti)

Subgenus.

Subgenus is capitalized, italicized, and placed in parentheses, sometimes with the abbreviation “subgen,” eg:

Mus (Mus) musculus

Moraxella (subgen Branhamella) catarrhalis

Parentheses.

For other uses of parentheses within species names, such as name changes, use quotation marks or a qualifier such as “formerly,” eg:

Bartonella (formerly Rochalimaea) henselae

Helicobacter (formerly Campylobacter) pylori

Issatchenkia orientalis (anamorph Candida krusei)

Indicate a change in species name with the entire binomial in parentheses as follows:

Bacteroides ureolyticus (formerly Bacteroides corrodens)

Authorship of the scientific name may be indicated by personal names, which are not italicized, following the species name. Sometimes parentheses are used. Within and among codes, conventions for such references vary. Editors should not restyle such terms but rather should verify with authors that the proper form has been used. “L.” alone is the common abbreviation for “Linneaus,” eg, Culex pipiens L., but “Linnaeus” should be written in full in publications whose readers are unlikely to know of this convention. Examples:

Aedes aegypti (Linnaeus)

Culex pipiens Linnaeus

Escherichia coli (Migula) Castellani and Chalmers

Serratia marcescens Bizio

The parentheses indicate that the organism, after initial description, was transferred into another genus by others, in the case of E coli by Castellani and Chalmers.

Year of published discovery may be included, eg:

Escherichia coli (Migula 1895) Castellani and Chalmers 1919

Serratia marcescens Bizio 1823

Subspecific Ranks, Ternary Names.

Subspecific ranks receive ternary or trinomial names. Subspecific designations are handled differently for animals, plants, and bacteria, as in the following examples. (The term var as a synonym for subspecies was removed from the bacterial nomenclature code in 1990.)

Type of Organism

Subspecific Rank (Designator)

Example

Animal

Higher animal

subspecies (no designator)

Mus musculus domesticus

Protozoon

Trypanosoma brucei gambiense

Fungus

variety (var)

Histoplasma capsulatum var duboisii

 

Bacteria

Bacterium

subspecies (subsp)

Campylobacter fetus subsp fetus Mycobacterium avium subsp paratuberculosis

Plant names may use var, as above, subsp, f (form), and other subspecific epithets, which are not interchangeable, in ternary names, eg:

Satureja parnassica subsp parnassica

Not all 3-word combinations are ternary names:

Ixodes scapularis larvae

Legionella pneumophila pneumonia

Schistosoma mansoni miracidium

Trypanosoma brucei procyclin

Infrasubspecific Subdivisions.

Subdivisions below the subspecies level (infrasubspecific subdivisions) include the serovar (serologically differentiated) and the biovar (biochemically or physiologically differentiated). The suffix -type is most often used in the clinical literature, eg, biotype, serotype. But to avoid confusion with nomenclatural type (“the element of the taxon with which the name is permanently associated”7[p17]), the suffix -var is often preferred in microbiological literature.

Infrasubspecific subdivisions are designated with various numbers, letters, or terms; follow author usage:

Brucella suis biovar 4

Cryptococcus neoformans serovar A

Fusarium oxysporum f sp radicis lycopersici [f sp: forma specialis]

Haemophilus influenzae biotype I

H influenzae biotype VII

Pseudomonas fluorescens biovar I

Staphylococcus aureus subsp aureus biotype A

S simulans biovar staphylolyticus

Ureaplasma urealyticum parvo biovar

U urealyticum T960 biovar

Yersinia enterocolitica serovar O:8

Anglicized and Vernacular (Trivial, Common) Terms.

In medical publications, uncapitalized anglicized forms are often used for taxa in ranks above genus (see also 9.4, Plurals, Microorganisms)23:

Anglicized Term

Formal Term

vertebrates

Vertebrata

primates

Primates

hominids

Hominidae

fungi

Fungi

moniliaceous molds

Moniliaceae

prokaryotes

Procaryotae

mycobacteria

Mycobacteriaceae

chlamydiae

Chlamydiales

Collective Genus Terms.

Many organisms possess traditional generic plural designations, which are verifiable in the dictionary. Some also have special adjectival forms. It is also acceptable to add the word organisms or species to the italicized genus name. See the examples below.

Genus

Plural Noun Form

Adjectival Form

Cryptococcus

Cryptococcus species

cryptococcal

Escherichia

Escherichia organisms

Legionella

legionellae

Macaca

macaques

Mycobacterium

mycobacteria

mycobacterial

Pseudomonas

pseudomonads

pseudomonal

Salmonella

salmonellae

Staphylococcus

staphylococci

staphylococcal

Streptococcus

streptococci

streptococcal

Treponema

treponemes

treponemal

Trypanosoma

trypanosomes

trypanosomal

a novel Yersinia species

Loxosceles species (brown recluse) spider venom

group A streptococcal infection

viridans streptococcal endocarditis

Genus names often qualify other terms, eg:

Candida endocarditis

Lactobacillus serogroups

Legionella pneumonia

Unspecified Species.

The name of a genus used alone implies the genus as a whole:

Toxocara infections are frequently acquired from household pets.

The term species is used in cases in which the genus is certain but the species cannot be determined. For instance, if an author knew that a skin test reaction indicated presence of Toxocara organisms but was unsure whether the reaction resulted from Toxocara canis infection or Toxocara cati infection, the author might write:

The source of the patient’s infection was Toxocara species.

In the latter example, Toxocara organisms would also be acceptable, but Toxocara alone would be incorrect.24,25

Name Changes.

Two recent new names have been adopted more readily by microbiologists than clinicians: Chlamydophila (see 15.14.2, Bacteria: Additional Terminology) and Pneumocystis jiroveci.26-29

The fungal genus Pneumocystis now includes 2 authentic species. The name of the species infective of rats is P carinii. The human pathogen was transitionally named P carinii f sp hominis and is now known as P jiroveci.26,27 The familiar abbreviation PCP may be retained for Pneumocystis pneumonia in human and nonhuman hosts.26

When a name is very new or in dispute, authors are advised to include both versions at first mention:

Chlamydophila (formerly Chlamydia) pneumoniae

Chlamydia pneumoniae (proposed new name Chlamydophila pneumoniae)

Usage.

In text dealing with infectious conditions, it is important to distinguish between the infectious agent and the condition. Infectious agents, infections, and diseases are not equivalent.

Incorrect:

Legionella pneumophila may be serious or subclinical.

Preferred:

Infection with Legionella pneumophila may be serious or subclinical.

 

 

Incorrect:

Legionella pneumophila may be severe.

Preferred:

Legionella pneumophila pneumonia may be severe.

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