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Bacterial names: Writing them correctly

There is no "official" classification of bacteria.bacterial classifications are devised for microbiologists, not for the entities being classified. Bacteria show little interest in the matter of their classification.

J. T. Staley, N. R. Krieg


Introduction
Initially, bacteria were placed in the kingdom Monera, based on the five-kingdom concept proposed by Whittaker in 1969. This five-kingdom structure recognizes Monera (prokaryotes) and four eukaryotic kingdoms: Animalia (Metazoa), Plantae, Fungi, and Protista. Archebacteria and Eubacteria are treated as subkingdoms of Monera under this system.

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Less than ten years after the creation of the five-kingdom system of classification, microbiologist Carl Woese established a new system of classification, which a little over ten years later became the three-domain system. It classifies Archaea, Bacteria, and Eubacteria as major groupings (called domains) above the kingdom level.

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The rules governing the naming of prokaryotes are established by the International Committee on Systematics of Prokaryotes (ICSP). Names often carry the superscript AL meaning that the name is on the approved list.

The Bible of bacterial identification is a book called Bergey's Manual of Determinative Bacteriology. The first edition of this book was initiated by the action of the Society of American Bacteriologists (now called the American Society for Microbiology). To date, the American Society for Microbiology continues to revise and publish the book.

There is a second book called Bergey's Manual of Systematic Bacteriology that is the final authority on bacterial classification (Systematics is another word for taxonomy).

Two links that can be used for checking the validity of organism names are http://www.dsmz.de/bactnom/bactname.htm and http://www.bacterio.cict.fr/.
Genus and Species Names
The universal convention followed for the representation of bacteria, or any microorganism, is the use of binary names consisting of a generic name and a specific epithet. Simply put, the binomial name of a microorganism is its genus name followed by the species name.

Example
Staphylococcus aureus, where "Staphylococcus" is the genus and "aureus" the specific epithet.

The binary name is italicized; the initial letter of the genus name is uppercased (Staphylococcus), while that of the species is lowercased (aureus). The binary name is italicized at all occurrences and spelled out in full at its first mention in the document. Thereafter, the generic name may be abbreviated to the initial capital letter (e.g., S. aureus ), provided it does not create a confusion with other genera used in the paper. Thus, Staphylococcus aureus can be safely abbreviated to S. aureus in the event that there is no mention of any other genera starting with the letter "S" (e.g., Streptococcus). No other partial abbreviations are acceptable. Thus, S. aureus is acceptable but Staph aureus or St. aureus are unacceptable.

In AMA publications, periods (.) are not used in scientific terms and abbreviations. Thus, E. coli would be represented as E coli. Genus and species names should be expanded and italicized in the title or subtitle and an initial capital letter should be used for the genus but not the species name, just as in the text.

  • Genera starting with the same initial letter
    Ideally, microbiologic publications prefer that the genus names be spelled out to avoid confusion under such circumstances.

    Example
    Incorrect: Heterologous expression of human TLR2 fibroblasts conferred responsiveness to S. aureus and S. pneumoniae.
    Correct: Heterologous expression of human TLR2 in fibroblasts conferred responsiveness to Staphylococcus aureus and Streptococcus pneumoniae.

    Some journals specify their own rules regarding the abbreviation of organism names. Therefore, the instructions regarding nomenclature in the journal guidelines should be followed very carefully.
  • Organisms of the same genus
    Once the binary name of a microorganism has been introduced in the manuscript, other organisms belonging to the same genus may be introduced in their abbreviated form, i.e., without expanding the name of the genus.

    Example
    Wound cultures were positive for Clostridium botulinum, C. perfringens, and C. tetani.

    However, the AMA says that the genus name can be abbreviated (without a period) when used with the species, except when the species is other than that given at the first mention. Simply put, the AMA publications abbreviate the genus to its initial capital letter only if the complete binomial name (genus and species), and not just the genus, has been introduced.

    Example
    Staphylococcus aureus and Staphylococcus epidermidis may be components of normal flora or pathogens, although S aureus is the more serious of the two.

    The example mentioned above follows the AMA style and the genus name is thus abbreviated to its initial capital letter only after the organism has been introduced in its binomial form. (Staphylococcus has been spelled out in full when mentioned with the specific epithet "epidermidis" because the previous mention of the genus was with the specific epithet "aureus." Note that the genus name has been abbreviated to "S" at a subsequent mention with "aureus.")
  • Points to remember
    • The specific epithet is never abbreviated.
    • The specific epithet is in lowercase letters and italicized, even if it is derived from the name of a person. For example, Shigella boydii Ewing 1949 (named after Sir John Boyd).
    • The word "species" is both singular and plural
    • The binary name should be written in full the first time it is mentioned in the Title, Abstract, and subsequently, at its first mention in the text.
    • The names are either italicized or underlined. Underlined means italics to a printer. Either representation can be used depending on what the journal guidelines specify. If no specification is given, italics should be used.
Genus Name Alone
The genus name can be used alone and is always italicized.

Example
The coagulase test is a useful test for differentiating Staphylococcus species.

The species name is never used alone. This is important because the species name is frequently descriptive and sometimes organisms from different genera might have the same species name. For example, Streptococcus pneumoniae, Mycoplasma pneumoniae, and Chlamydia pneumoniae are all very different organisms that merely have the capacity to cause the same disease. If you used the species name for any of these without the genus name, it would be impossible to determine which organism was being referred to.

Example
Incorrect: A heavy growth of pneumoniae was recovered from the patient's sputum.
Correct: A heavy growth of S. pneumoniae was recovered from the patient's sputum.

When a Genus Is Not a Genus

Sometimes, the genus is referred to indirectly as a noun or as an adjective, and in such situations, the first letter is not a capital and the word is neither underlined nor italicized.
  • Derived adjectives
    Adjective forms such as enterococcal, streptococcal, and mycobacterial are adjective forms derived from the root (genus) names Enterococcus, Streptococcus, and Mycobacterium, respectively. These adjective forms should be neither capitalized nor italicized. English nouns derived from scientific names should not be capitalized or italicized (e.g., pneumocystis pneumonia).

    Example
    Incorrrect: The Mycobacterial lipoglycans lipomannan (LM) and lipoarabinomannan (LAM) are potent immunomodulators in tuberculosis.
    Correct: The mycobacterial lipoglycans lipomannan (LM) and lipoarabinomannan (LAM) are potent immunomodulators in tuberculosis.
  • Plural generic designations
    Traditional plural generic designations are not capitalized and italicized. If the correct generic plural cannot be determined, add the word "organisms" or "species" to the italicized genus name (e.g., Escherichia organisms).

    Genus
    Chlamydia
    Escherichia
    Mycobacterium
    Proteus
    Pseudomonas
    Salmonella
    Staphylococcus
    Streptococcus
    Treponema
    Plural Noun Form
    chlamydiae
    Escherichia organisms
    mycobacteria
    Proteus organisms
    pseudomonads
    salmonellae
    staphylococci
    streptococci
    treponemes

    Example

    Incorrect: PAHs have been found to be degraded by a wide range of Pseudomonads and Vibrios.
    Correct: PAHs have been found to be degraded by a wide range of pseudomonads and vibrios.
  • Vernacular names
    Some organisms acquire common names that are sometimes convenient to use. For example, Neisseria meningitidis is often referred to as the meningococcus, and Streptococcus pneumoniae is often referred to as the pneumococcus. Such common names are neither italicized nor capitalized at the beginning.
  • Points to remember
    • Use of the word "bacillus" or "bacilli" should be avoided if there might be confusion as to whether the genus Bacillus or a nonspecific rod-shaped bacterium is meant (The word "bacilli" in italics and capitalized, is never correct). Organisms in the genus Treponema can be designated as "treponema" (singular) and "treponemas" or "treponemata" (plural).
    • The genus name is not treated as a genus also when used as laboratory media (brucella agar). Note that capitalization, in such cases, indicates a product name (Haemophilus ID Quad agar). This should not be confused with the laboratory tests that use organism names, e.g., Limulus lysate test. This is an assay using the amebocyte lysate of Limulus polyphemus. Here, the genus name Limulus is capitalized and italicized.
Taxa Above the Genus Level
  • Family and other taxa
    The representation of taxonomic divisions above the genus level, such as the phylum, class, order, family, and tribe, is unclear. The ASM journals and the CBE italicize names above the genus level, while taxa above the genus level are not italicized in AMA publications. Subranks and superranks follow the same style. However, the names (of these taxa) are always capitalized.

    Example
    In 1959, Krassilnikov (13) affiliated N. ramosa with the genus Gallionella (family, Ferribacteriaceae; order, Ferribacteriales).
    Or
    In 1959, Krassilnikov (13) affiliated N. ramosa with the genus Gallionella (family, Ferribacteriaceae; order, Ferribacteriales).
  • Overlap of names (identification and capitalization)
    A few terms have more than one meaning, which may create difficulties in determining whether they should be capitalized. "Metazoa" and "Protozoa" should be capitalized when they are used as the names of divisions. The plurals of their vernacular designations—metazoan and protozoan—are "metazoa" and "protozoa," respectively. The rule is as follows. When they refer to the members of the division and not the division itself, they should be in lowercase. When the division is being referred to, they should be uppercased. A similar problem arises with the word "archaea," which was lately awarded the Domain status. Thus, when referring to the domain, it should be uppercased (Archaea), and when referring to the members of the domain, it is lowercased (archaea).

    Examples
    It was surprising that CysRS has yet to be found in the completely sequenced genome of Methanocaldococcus jannaschii or Methanopyrus kandleri, despite the fact that these archaea are indeed capable of forming Cys-tRNA Cys .

    The biosynthetic conversion of ZMP to IMP in three members of the domain Archaea


    Thus, only when the domain in specifically referred to, the word is capitalized (Archaea).

    Another common error is the incorrect representation of the words streptomycetes and actinomycetes (words commonly used to refer to the members of the genera Actinomyces and Streptomyces, respectively). Thus, follow this rule for the representation of these organisms/genera.
  • Points to remember
    • The adjective or derived forms (e.g., archaeal) should be lowercased.
    • When citing a type of archaea, the word garchaeah is lowercased. For example, methanogenic archaea.
Salmonella Nomenclature
Nomenclature for bacteria in the genus Salmonella is in flux. Salmonella bacteria were originally grouped as species and named accordingly, e.g., Salmonella typhi and Salmonella typhimurium. However, it was subsequently found that what were considered separate species were, in fact, serovars (serotypes).

Although terminology appropriate to serovars is preferred in microbiology settings, the binomial species-like terms predominate in the clinical infectious disease literature.

Examples
Salmonella typhi
or
Salmonella serovar Typhi
(Salmonella serotype Typhi also acceptable)
(Salmonella Typhi acceptable on subsequent mentions)
Salmonella typhimurium
or
(Salmonella serotype Typhimurium also acceptable)
(Salmonella Typhimurium acceptable on subsequent mentions)


When the serotype/serovar form is used, to avoid confusion, it is best to expand Salmonella, rather than following the style for abbreviating genus. Serovars are defined by the O (somatic), Vi (capsular), and H (flagellar) antigens. In practice, and in contrast to E. coli strains, when the serotype is expressed using those antigens, the letters O, H, and Vi are not included in the serotype designation. Colons separate the O, Vi, and H designations, which take a variety of forms (letter, numeric, etc.).

Example
Salmonellae subsp arizonae serovar 50:z1z24

Salmonellae are also allotted to seven subgroups, represented with roman numerals.

Example
Salmonella serotype IIIa 41:z1z2:-

O antigen serotypes are A, B, C 1 , C 2 , D, and E

Example
Salmonella paratyphi B

Names Below the Species Level
Names below the species level include the "subspecies" and infrasubspecific designations such as "pathovars," "serovars," "phagovars," and "strain designations."
  • Subspecies

    The additional name is italicized but the descriptor (the word subspecies) is not.

    Example
    Incorrect: Acinetobacter calcoaceticus subsp. lwoffii
    Correct: Acinetobacter calcoaceticus subsp. lwoffii

    However, if the subspecies level descriptor is only a number or a letter designation, then it is not italicized. In the case of letters, they may be uppercased or lowercased.

    Examples
    Corynebacterium group D2 and Corynebacterium group JK.
    Haemophilus influenzae type b and H. influenzae type c.
  • Below the subspecies level
    Some organisms that cannot be differentiated taxonomically at the subspecies level are given infrasubspecific designations that are not covered in the Code and are therefore excluded from the Approved List. These designations include "pathovars" (pv), "biovars" (bv), "serovars" (sv), "phagovars," "chemovars," and "morphovars." The infrasubspecific designation, but not its abbreviation (e.g., pv), is written in italics.

    Example
    Xanthomonas campestris (Pammel 1895) Dowson 1939 pv. caladiae pv. nov.

    The citation of the name of a pathovar reported previously should bear the name of the author(s) of publication in which the pathovar epithet was proposed formally, followed by the date of publication. Full citation of the publication should include the number of the page in the body of the text (not in the summary or the abstract) where the name was proposed. Xanthomonas campestris (Pammel 1895) Dowson 1939 pv. cannabina Severin 1978, 13 (indicates that the pathovar was proposed by Severin in 1978, and the proposed name can be found on page 13 of the publication cited).

    Another infrasubspecific rank is the biovar (biotype) with special biochemical or physiologic properties.

    Example
    Agrobacterium tumefaciens (Smith and Townsend 1907) Conn 1942 bv. 3

    Serovars (serotypes) have distinct antigenic properties.

    Example
    Erwinia chrysanthemi Burkholder et al. 1953 sv. IV

    Phagovars (phagocytes) are designed for bacteria susceptible to viruses that can lyse bacteria. Phage designations can be letters or numbers, but they are not italicized unless they are written in Latin or they designate genes.

    Examples
    Azotobacter vinalandii Lipman 1903 phagovar A41 ATCC 12518-B10
    Bacillus cereus Frankland and Frankland 1887 phagovar Phagus pertinax ATCC 12826-B1


    Other examples of phage designations are "Charon," "lambda," "mu," and "P1 vir."

    Morphovars (morphotypes) have special morphologic features, and chemovars (chemotypes) have special chemical features.
  • Strain designations
    These follow the genus and species and may be a combination of letters and numbers.

    Example
    Escherichia coli O157:H7, where O157:H7 designates the particular antigenic strain of E. coli.

    Bacterial strains can be designated by letters and numbers. Both are printed either solid or with a space, depending on the collection.

    Examples
    Clostridium argentinense Suen et al. 1988 Type ATCC 27322
    Vibrio furnissii Brenner et al. 1984 Type strain CDCB3215


    The strain designation should be written with the full binomial.

    Example
    Pseudomonas aeruginosa ATCC 10145

    If the specific epithet is missing, the word "strain" should be inserted.

    Example
    Pseudomonas strain B 13 [or] Pseudomonas sp. strain B 13.
  • Point to remember
    • The term "variety" or "var." as a synonym for subspecies was removed from the bacterial nomenclature code in 1990. Therefore, it is not used in bacterial nomenclature.
Species, sp., and spp.
The words species, spp., and sp. are often used to refer to the species of a particular genus in cases where the precise species name is unknown. For example, the sentence "Currently, no vaccines are available for Campylobacter spp." implies that vaccines are not available for any species in the genus Campylobacter.

Alternatively, the author may sometimes want to refer to a particular species in a genus even though the identity of the species is unknown.

Example
The patient was hospitalized following isolation of Mycobacterium sp. from the lung.

In this case, a particular species of Mycobacterium (as opposed to multiple or all species in the previous example) was isolated, but it cannot yet be named completely as the complete identity is yet to be established.

Some authors describe infections caused by organisms as follows:

Toxocara infections are frequently acquired from household pets.

The terms "sp." and "spp." should be followed by a period and should not be italicized. Further, AMA publications do not use the abbreviated forms "sp." or "spp." in place of species.

In such cases, if you wish to convey that the infections are caused by Toxocara organisms but you are uncertain whether the species was Toxocara canis or Toxocara cati, you may write as follows:

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

In this example, Toxocara organisms would also be acceptable, but Toxocara alone would be incorrect.
Writing-specific Issues
  • Subject-verb
    The binomial taxonomic term is always singular.

    Example
    Escherichia coli (Migula 1895) Castellani and Chambers 1919 was.
    [but]
    E. coli strains were.


    When spelled out, the word "species" may take both the singular and plural form (similar to the word data). Thus, the word "specie" as the singular is incorrect.

    Examples
    This species is highly subdivided.
    The species are adapting to a rugged multipeaked fitness landscape.


    The terms "sp." and "spp." are singular and plural abbreviations of the word "species." Therefore, "sp." should have "is" as the verb, while "spp." should have "are."

    Example
    Pseudomonas sp. is believed to have caused the infection in two of the three subjects.
    Pseudomonas spp. are known to cause nosocomial or hospital-borne infections.
  • Word choice (in infectious conditions)
    It is important to distinguish between the infectious agent and the condition. Infectious agents, infections, and diseases are not equivalent.

    Examples
    Incorrect: Haemophilus influenzae may be a life-threatening disease.
    Correct: Haemophilus influenzae infection may be life threatening.
    Preferred: Infection with Haemophilus influenzae may be a life-threatening disease.

    Incorrect: Chlamydia trachomatis is often an overlooked disease.
    Awkward: Chlamydia trachomatis disease is often overlooked.
    Preferred: The disease caused by Chlamydia trachomatis is often overlooked.
  • Miscellaneous
    When referring to a species, the name of the author should follow the specific epithet with a date but without punctuation. Further, "and" is used in place of "et" or the ampersand (&) for two authors.

    Erwinia quercina Hildebrand and Schroth 1967

    If there are more than two authors for a taxon, "et al." can be used instead of the complete list of authors.

    Example
    Legionella pittsburghensis Pasculle, feeley, Gibson, Cordes, Myerowitz, Patton, Gorman, Carmack, Ezzel, and Dowling 1980 [or]
    Legionella pittsburghensis Pasculle et al. 1980