How to Write E. coli: Nomenclature, Culture, and Genetic Notation

By Dr. Zubair Khalid, DVM, MS, PhD · 2026-08-11

Introduction to E. coli Nomenclature

Escherichia coli is a Gram-negative, facultatively anaerobic rod-shaped bacterium that serves as the workhorse of molecular biology. It is the most widely studied prokaryotic organism, and its proper written representation is a matter of scientific precision, not mere convention. When you write "E. coli" in a lab report, a grant application, or a manuscript, you are communicating a specific biological entity with a defined taxonomic position, a particular genetic background, and a set of experimental conditions. Sloppy notation obscures that information and can lead to genuine experimental confusion.

The rules governing how to write E. coli are established by the International Code of Nomenclature of Prokaryotes for species names, by community consensus for strain designations, and by standardized genetic nomenclature for gene and protein symbols. These rules are not arbitrary. They allow a reader to distinguish between the species E. coli and a specific laboratory strain such as E. coli K-12 MG1655, and to understand whether you are referring to the lacZ gene, the LacZ protein, or a lacZ mutant allele. This article provides a comprehensive guide to writing E. coli correctly across all contexts you will encounter as an undergraduate: from informal lab notebook entries to formal scientific papers.

Why correct notation matters

Scientific writing is a form of precise communication. When you write "E. coli" without italics, you are technically writing a nonsensical hybrid that violates binomial nomenclature. When you write "E. Coli" with a capital C, you are implying that coli is a genus name, which it is not. When you write "the E. coli bacteria" you are using a plural verb with a singular species designation, which is grammatically and biologically incorrect. Each of these errors, while seemingly minor, signals to a reader that the author does not understand the organism they are working with. In a formal setting—a journal submission, a grant proposal, or a thesis—such errors undermine credibility.

More importantly, genetic notation carries functional information. The difference between lacZ (the gene), LacZ (the protein), and lacZ (a mutant allele) is the difference between the blueprint, the product, and a defective version of the blueprint. Writing these incorrectly can lead a reader to misinterpret your experimental design or results. For example, a strain described as "lacZ minus" is ambiguous: does it lack the gene, carry a mutation, or fail to produce the enzyme? Proper notation—lacZ or ΔlacZ—removes that ambiguity.

Overview of the article

This article covers the full spectrum of writing E. coli correctly. It begins with the binomial nomenclature rules for the species name, moves to strain and genetic notation, then addresses practical contexts such as culture media and protocols, and finally covers formal writing in papers and textbooks. A section on common pitfalls and a quick-reference checklist follow, and the article concludes with answers to frequently asked questions.

Writing the Species Name: Italics and Abbreviation

The species name Escherichia coli follows the standard rules of binomial nomenclature established by Carl Linnaeus and codified in the International Code of Nomenclature of Prokaryotes. The genus name Escherichia is capitalized and italicized. The species epithet coli is lowercase and italicized. When the full name is used, both words are always written together: Escherichia coli.

The genus name honors Theodor Escherich, the German-Austrian pediatrician who first described the bacterium in 1885. The species epithet coli derives from the Latin word for the colon, reflecting the organism's natural habitat in the lower intestine of warm-blooded animals. Understanding this etymology helps you remember that coli is not a proper noun and must never be capitalized.

Full name vs. abbreviated form

After the first mention of the full name in a document, you may abbreviate the genus to a single letter followed by a period: E. coli. The abbreviation is always italicized because it represents the genus name. The period after the "E" is not italicized, though some style guides differ on this fine point; the most common convention in molecular biology journals is to italicize the "E" and the period together, or to italicize only the "E" and leave the period roman. The latter is more common in modern journals. The species epithet coli is always written in full and italicized.

The abbreviation rule applies only after the full name has been introduced. In a paper, the first mention should read Escherichia coli, and all subsequent mentions should read E. coli. In a lab notebook, where the organism is used repeatedly, it is acceptable to write E. coli from the first mention if the full name is written at the top of the page or in the materials section. In a figure legend, the abbreviation is acceptable if the full name appears in the main text or in a previous figure legend.

Common mistakes in italics and punctuation

The most frequent errors in writing the species name are:

1. Missing italics: Writing "E. coli" or "Escherichia coli" in roman type. This is the single most common error. In handwritten work, italics are indicated by underlining.
2. Capitalizing the species epithet: Writing "E. Coli" or "Escherichia Coli." The species epithet is always lowercase.
3. Omitting the period: Writing "E coli" without the period after the abbreviated genus.
4. Italicizing the period: Writing "E. coli" with the period italicized. Most style guides recommend a roman period, though this is a minor point.
5. Using the abbreviation before the full name: Writing "E. coli" without first introducing Escherichia coli.

A useful mnemonic: the genus name is a proper noun (a person's name), so it is capitalized; the species epithet is an adjective or noun in apposition, so it is lowercase. Both are italicized because they are Latinized binomials.

Strain Designations and Genetic Notation

The species name E. coli refers to the entire species, which encompasses a vast diversity of strains. When you work with E. coli in the laboratory, you are almost always working with a specific strain, and that strain must be identified precisely. Strain designations follow conventions that are distinct from species nomenclature.

Strain naming conventions

A strain is a genetic variant of a species that has a defined, heritable phenotype and genotype. Laboratory strains of E. coli are typically derived from a few ancestral isolates. The most common laboratory strains are derivatives of K-12, B, and W. Each strain has a unique designation that includes a collection identifier and a strain number.

The K-12 strain was isolated in 1922 from a patient in Palo Alto, California, and has been the subject of decades of genetic manipulation. Common K-12 derivatives include:

• MG1655: The wild-type K-12 strain, sequenced in 1997. It is the reference strain for most E. coli genomics work.
• DH5α: A K-12 derivative engineered for high-efficiency transformation and blue-white screening. It carries mutations in recA1 and endA1.
• BL21(DE3): A B-strain derivative used for high-level protein expression. It lacks the Lon and OmpT proteases and carries a chromosomal copy of the T7 RNA polymerase gene under the control of the lacUV5 promoter.

Strain names are written in roman type (not italicized) and are not abbreviated. The strain designation follows the species name: E. coli K-12, E. coli MG1655, E. coli BL21(DE3). Note that the strain name is not part of the binomial nomenclature, so it is not italicized. The parentheses in BL21(DE3) are part of the strain name and indicate that the strain carries a lysogenized λ phage derivative (DE3) that provides T7 RNA polymerase.

When you write a strain designation, be precise. "E. coli K-12" is not the same as "E. coli MG1655," even though MG1655 is a K-12 derivative. If you used MG1655, write MG1655. If you used DH5α, write DH5α. The Greek letter α in DH5α is part of the strain name and should be written correctly, not as "DH5a" or "DH5 alpha."

Gene symbols and protein products

Genetic notation in E. coli follows a standardized system established by the Demerec committee and maintained by the E. coli Genetic Stock Center (CGSC). The rules are:

• Gene names: Three lowercase italicized letters, often followed by a capital letter to distinguish different genes in the same pathway. For example, lacZ encodes β-galactosidase, lacY encodes lactose permease, and lacA encodes thiogalactoside transacetylase. The entire gene symbol is italicized.
• Protein products: The same three letters, but with the first letter capitalized and the entire symbol in roman type. LacZ is the protein product of the lacZ gene. The protein symbol is not italicized.
• Mutant alleles: A mutant allele is indicated by a superscript or by a descriptive suffix. For example, lacZ is a mutant allele of lacZ (the superscript minus sign indicates loss of function). A deletion is indicated by Δ: ΔlacZ. A temperature-sensitive allele is indicated by ts: lacZts. The allele designation is italicized along with the gene symbol.
• Phenotypes: Phenotypes are written with a capital letter and a superscript plus or minus, in roman type: Lac⁺ means the ability to utilize lactose, Lac⁻ means the inability. The phenotype is not italicized.

Here is a summary table:

When describing a strain's genotype, list the relevant genes in a standard order: plasmid replicons, chromosomal markers, and then plasmid-borne markers. For example, a typical genotype might read: E. coli DH5α recA1 endA1 gyrA96 thi-1 relA1 hsdR17 (rK⁻ mK⁺) supE44.

Note that the strain name (DH5α) is roman, while the genotype symbols are italicized. The superscripts in hsdR17 (rK⁻ mK⁺) indicate restriction and modification phenotypes.

Writing E. coli in Culture Media and Protocols

In the laboratory, you will write E. coli constantly: in your notebook, on tube labels, in media recipes, and in protocols. The same rules apply, but there are additional conventions for media and measurements.

Common abbreviations

The most common medium for E. coli culture is LB, which stands for Lysogeny Broth (also historically called Luria-Bertani broth or Luria broth). The abbreviation "LB" is written in roman type, without periods, and is not italicized. The composition of LB is 10 g/L tryptone, 5 g/L yeast extract, and 10 g/L NaCl, adjusted to pH 7.0 with NaOH. LB agar is LB with 15 g/L agar added.

Other common media abbreviations include:

• M9 minimal medium: A defined medium containing M9 salts (Na₂HPO₄, KH₂PO₄, NaCl, NH₄Cl), supplemented with MgSO₄, CaCl₂, and a carbon source such as glucose (0.2% w/v) or glycerol (0.2% v/v).
• TB (Terrific Broth): A rich medium for high-density culture, containing 12 g/L tryptone, 24 g/L yeast extract, 4 mL/L glycerol, and phosphate buffer (0.017 M KH₂PO₄, 0.072 M K₂HPO₄).
• SOC: Super Optimal broth with Catabolite repression, used for recovery after transformation. It contains 2% tryptone, 0.5% yeast extract, 10 mM NaCl, 2.5 mM KCl, 10 mM MgCl₂, 10 mM MgSO₄, and 20 mM glucose.

When you write a medium recipe, specify the components and concentrations precisely. For example: "LB agar supplemented with 100 μg/mL ampicillin and 40 μg/mL X-gal (5-bromo-4-chloro-3-indolyl-β-D-galactopyranoside)." The abbreviation "X-gal" is written in roman type, and the full chemical name should be given at first mention.

Units and measurements

When writing about E. coli culture, you will use standard scientific units. The key measurements are:

• Optical density at 600 nm (OD₆₀₀): A measure of culture turbidity, used to estimate cell density. An OD₆₀₀ of 1.0 for E. coli corresponds to approximately 8 × 10⁸ cells/mL, though this varies with strain and spectrophotometer. Write "OD₆₀₀" with the subscript, not "OD600" or "O.D. 600."
• Colony-forming units per milliliter (CFU/mL): The viable cell count. Write "CFU/mL" with the slash, not "cfu/ml."
• Antibiotic concentrations: Write in μg/mL (micrograms per milliliter) or mg/mL. For example, ampicillin is used at 100 μg/mL, kanamycin at 50 μg/mL, chloramphenicol at 25 μg/mL, and tetracycline at 12.5 μg/mL.
• Temperature: E. coli is typically cultured at 37°C, though some strains or plasmids require lower temperatures (e.g., 30°C for temperature-sensitive plasmids). Write "37°C" with the degree symbol.

In a protocol, use numbered steps for ordered procedures. For example:

1. Inoculate 5 mL of LB broth containing the appropriate antibiotic with a single colony of E. coli from a fresh agar plate.
2. Incubate at 37°C with shaking at 200 rpm for 12–16 hours (overnight culture).
3. Dilute the overnight culture 1:100 into fresh medium (e.g., 1 mL into 100 mL) in a 500 mL Erlenmeyer flask.
4. Grow at 37°C with shaking at 200 rpm until the OD₆₀₀ reaches 0.4–0.6 (mid-log phase), which typically takes 2–3 hours.
5. Induce protein expression by adding isopropyl β-D-1-thiogalactopyranoside (IPTG) to a final concentration of 0.5 mM.
6. Continue incubation for 4 hours at 37°C, then harvest cells by centrifugation at 5,000 × g for 10 minutes at 4°C.

Note the use of "× g" for relative centrifugal force, not "rpm," unless you specify the rotor radius. The abbreviation "IPTG" is written in roman type and should be defined at first mention.

E. coli in Textbooks and Scientific Papers

Formal scientific writing imposes additional conventions for presenting E. coli. These rules apply to journal articles, textbooks, theses, and grant proposals.

First mention and subsequent use

In a scientific paper, the full binomial Escherichia coli must appear at the first mention in the abstract and again at the first mention in the main text. Subsequent mentions use the abbreviation E. coli. For example:

• Abstract: "We examined the role of the Escherichia coli chaperone DnaK in protein folding."
• Main text: "The Escherichia coli chaperone DnaK is a member of the Hsp70 family. ... We therefore tested whether E. coli DnaK could rescue the folding defect."

Some journals require the full name at the first mention in each section (Introduction, Methods, Results, Discussion), while others allow the abbreviation after the first mention in the abstract. Check the journal's instructions to authors.

When E. coli is used as an adjective, the abbreviation is still written with italics: "an E. coli culture," "E. coli cells." The species name is singular; "E. coli" refers to the species, not to individual bacteria. You should write "E. coli cells" or "E. coli bacteria," not "E. coli" as a plural noun. For example, "The E. coli were grown" is incorrect; "The E. coli cells were grown" is correct.

Citing strains and sources

When you use a specific strain in a paper, you must cite its source. The first mention of a strain should include the strain name, its genotype, and a citation to the original publication or to the strain collection from which it was obtained. For example:

"E. coli K-12 strain MG1655 (CGSC #6300) was used for all experiments."

The CGSC number refers to the E. coli Genetic Stock Center at Yale University, which maintains a curated collection of strains. Other major collections include the American Type Culture Collection (ATCC) and the Coli Genetic Stock Center. When you obtain a strain from a colleague, cite their publication or acknowledge them.

For plasmids, the notation includes the plasmid name (e.g., pET28a, pUC19) written in roman type, followed by the selectable marker and any relevant features. For example: "The expression plasmid pET28a (Novagen) carries an N-terminal His₆ tag and confers kanamycin resistance." The plasmid name is not italicized, but the gene symbols within it are.

Common Pitfalls in Writing E. coli

Despite the clarity of the rules, errors are common. This section catalogs the most frequent mistakes and explains why they are wrong.

Capitalization errors

The most common capitalization error is writing "E. Coli" with a capital C. This is incorrect because coli is the species epithet, not a genus name. In binomial nomenclature, only the genus is capitalized. Another error is writing "Escherichia Coli" with a capital C. The same rule applies.

A subtler error is writing "E. coli" with a lowercase "e" at the start of a sentence. The genus name is always capitalized, even in the middle of a sentence, and the abbreviation "E." is always capitalized. If a sentence begins with the abbreviation, it is written "E. coli," not "e. coli."

Italics and punctuation mistakes

The most common italics error is writing the species name in roman type. This is so widespread that many students do not realize it is an error. In any formal document, Escherichia coli and E. coli must be italicized. In handwritten work, underline the name to indicate italics.

Another common error is italicizing the strain name. Strain designations (K-12, MG1655, BL21) are not italicized. Only the genus and species are italicized. For example, "E. coli K-12" has italics only on "E. coli," not on "K-12."

A related error is italicizing gene symbols when they should be roman, or vice versa. Remember: genes are italicized (lacZ), proteins are roman (LacZ), phenotypes are roman (Lac⁺), and strain names are roman (DH5α).

Misuse of 'strain' vs. 'species'

The terms "strain" and "species" are often confused. A species is a taxonomic category; a strain is a genetic variant within a species. You cannot write "the E. coli species K-12" because K-12 is a strain, not a species. You also cannot write "E. coli K-12 species" for the same reason. The correct phrasing is "the E. coli species" or "the E. coli strain K-12."

Similarly, "E. coli" alone refers to the species, not to a specific strain. If you say "we used E. coli," you have not told the reader which strain you used. You must specify the strain: "we used E. coli K-12 strain MG1655."

Practical Summary: Quick Reference for Writing E. coli

This section provides a concise checklist for writing E. coli correctly in various contexts.

Checklist for students

1. First mention: Write the full binomial Escherichia coli in italics.
2. Subsequent mentions: Use E. coli in italics, with a roman period after the "E."
3. Strain names: Write in roman type after the species name: E. coli K-12, E. coli MG1655.
4. Gene symbols: Italicize three-letter gene names with a capital letter suffix: lacZ, recA, gyrA.
5. Protein symbols: Use roman type with a capital first letter: LacZ, RecA, GyrA.
6. Mutant alleles: Use superscripts or Δ: lacZ, ΔlacZ, lacZts.
7. Phenotypes: Use roman type with superscript plus or minus: Lac⁺, Lac⁻.
8. Media: Write LB, M9, TB, SOC in roman type, without periods.
9. Measurements: Write OD₆₀₀, CFU/mL, μg/mL, 37°C with correct symbols.
10. Never: Capitalize coli, omit italics, italicize strain names, or use "E. coli" as a plural noun.

Final tips

• Keep a style guide handy. The ASM Journals style manual and the Cold Spring Harbor Protocols style guide both provide detailed rules for microbial nomenclature.
• When in doubt, check a recent issue of a molecular biology journal (e.g., Journal of Bacteriology, Molecular Microbiology) to see how E. coli is written in published work.
• In your lab notebook, write the full name Escherichia coli at the top of the first page where you use the organism, then use E. coli throughout.
• If you are writing by hand, underline E. coli to indicate italics. Do not use quotation marks or bold.

Frequently Asked Questions

How do you write E. coli correctly?

Write E. coli with the "E" capitalized and italicized, followed by a roman period, then "coli" in lowercase italics. The full name is Escherichia coli, with both words italicized and only the genus capitalized.

Should E. coli be italicized?

Yes. E. coli is a binomial species name and must be italicized in all formal writing. In handwritten work, underline it. The strain designation that follows (e.g., K-12) is not italicized.

Is it E. coli or E coli?

It is E. coli with a period after the "E." The period indicates that "E" is an abbreviation for Escherichia. Omitting the period is incorrect.

How do you write E. coli in a lab report?

In a lab report, write the full name Escherichia coli at first mention, then use E. coli thereafter. Specify the strain (e.g., E. coli DH5α) and describe the culture conditions, including medium, temperature, and any antibiotics used. Italicize the species name throughout.

What is the full name of E. coli?

The full name is Escherichia coli. The genus Escherichia honors Theodor Escherich, and the species epithet coli refers to the colon, the bacterium's natural habitat.

Do you capitalize coli in E. coli?

No. The species epithet coli is always lowercase. Only the genus name Escherichia (or its abbreviation "E.") is capitalized.

How do you write E. coli in a scientific paper?

In a scientific paper, write Escherichia coli at the first mention in the abstract and again at the first mention in the main text. Thereafter, use E. coli. Specify the strain and its genotype, and cite the source of the strain. Follow the journal's instructions for italicization and abbreviation.

Key Takeaways

• Escherichia coli is the full binomial name; E. coli is the standard abbreviation. Both are italicized, with only the genus capitalized.
• Strain designations (K-12, MG1655, BL21) are written in roman type and follow the species name.
• Gene symbols are italicized (lacZ), protein products are roman (LacZ), and phenotypes are roman with superscripts (Lac⁺).
• In culture protocols, use standard abbreviations (LB, OD₆₀₀, CFU/mL) and specify concentrations and temperatures precisely.
• In formal writing, introduce the full name at first mention, then use the abbreviation; always specify the strain and its source.
• Common errors include missing italics, capitalizing coli, italicizing strain names, and confusing strain with species.
• Always write E. coli as a singular species name; refer to "E. coli cells" or "E. coli bacteria," not "E. coli" as a plural noun.

Related Topics

• E. coli Bacteria
• E. coli Definition
• E. coli Transformation
• E. coli Expression System
• E. coli Protein Expression

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