Bacterial names follow a two-part (binomial) system: a capitalized genus name followed by a lowercase species epithet, with both words italicized. Writing Escherichia coli rather than Escherichia Coli or escherichia coli is not a matter of personal style; it reflects an internationally governed naming code that journals, reviewers, and databases rely on to keep biology intelligible. The rules are straightforward once you learn them, but the details around abbreviation, higher ranks, provisional names, and recent reclassifications trip up even experienced researchers.
The Two-Part Name
Every bacterial species is identified by a binary combination: a genus name and a specific epithet. The genus always begins with a capital letter. The specific epithet is always lowercase, even when it derives from a proper noun. Both words are set in italics in print or underlined in handwritten text. So it is Staphylococcus aureus, never Staphylococcus Aureus or Staphylococcus aureus (without italics).1Writing Intensive Curriculum Program, Oregon State University. Microbiology Writing Guide: Scientific Style
A species name is never just the epithet on its own. You would not write “aureus” in isolation and expect a reader to know you mean Staphylococcus aureus rather than some other organism. The epithet only has meaning when it accompanies its genus.1Writing Intensive Curriculum Program, Oregon State University. Microbiology Writing Guide: Scientific Style This is a point people who work with common pathogens sometimes forget in casual writing, because names like “aureus” or “coli” feel self-explanatory in context. In formal scientific writing, though, the genus must always be present, either spelled out or abbreviated.
The naming rules for prokaryotes (bacteria and archaea) are set by the International Committee on Systematics of Prokaryotes, or ICSP, and codified in the International Code of Nomenclature of Prokaryotes (ICNP).1Writing Intensive Curriculum Program, Oregon State University. Microbiology Writing Guide: Scientific Style Viruses follow an entirely different naming system, and fungi and plants have their own codes. So the conventions described here apply specifically to bacteria and archaea.
Abbreviating the Genus After First Use
Once you have spelled out the full name of a bacterium, you can abbreviate the genus to its initial letter followed by a period. Staphylococcus aureus becomes S. aureus. The abbreviation still gets italicized, and the period after the initial is required. This shorthand is standard in research papers, lab reports, and textbooks.2Oregon State University. Microbiology Writing Guide: Scientific Style
There is an important catch: the abbreviation only works if no other genus in the same document starts with the same letter. If your paper discusses both Staphylococcus aureus and Streptococcus pyogenes, writing S. aureus and S. pyogenes creates ambiguity. In that situation, you either spell out the full genus each time or use a longer abbreviation that distinguishes them, such as Staph. aureus and Strep. pyogenes.2Oregon State University. Microbiology Writing Guide: Scientific Style
The ICSP also recommends that abstracts or summaries spell out the full name again, even if the name has already been abbreviated in the body of the paper. The logic is that many readers encounter only the abstract, whether through database searches or quick scans of a journal issue, and they need the full name without having to hunt through the main text.2Oregon State University. Microbiology Writing Guide: Scientific Style
Using “sp.” and “spp.”
Sometimes you need to refer to a species within a genus without naming it specifically. The designation “sp.” (singular) after a genus means you are referring to one unidentified or unnamed species. The designation “spp.” (plural) means more than one unnamed species. Salmonella spp. indicates multiple species of Salmonella, while Salmonella sp. points to a single species whose identity has not been determined.2Oregon State University. Microbiology Writing Guide: Scientific Style
A detail that trips people up: “sp.” and “spp.” are not italicized, because they are not part of the organism’s formal Latin name. They are abbreviations for the Latin word “species” used as a placeholder. So you would write Bacillus sp. with the genus in italics and the “sp.” in roman (upright) type. This also applies when you see “subsp.” for subspecies.
When you are listing several species in the same genus, it is acceptable to name the genus only once and then list the epithets. For example: Streptococcus pneumoniae, S. pyogenes, and S. agalactiae. Some style guides allow this even if the later species have not been individually introduced earlier, as long as the genus context is clear.2Oregon State University. Microbiology Writing Guide: Scientific Style
Writing Names Above the Species Level
Species and genus are the ranks you will encounter most often, but bacterial classification extends upward through family, order, class, and phylum. The formatting for these higher ranks differs from species-level names in one practical way: while they are still formally Latinized, not all style guides require italicization above the genus level. Many journals do italicize all formal taxonomic names; others italicize only genus and species. Check the target journal’s author guidelines.
What is consistent, and increasingly standardized, is the use of suffixes to denote rank. Family names end in -aceae, orders in -ales, classes in -ia, and phyla now end in -ota. The phylum suffix is relatively recent: the ICSP adopted -ota as part of a broader effort to bring phylum-level nomenclature under the formal rules of the ICNP.3International Journal of Systematic and Evolutionary Microbiology. Proposal of the suffix –ota to denote phyla. Addendum to ‘Proposal to include the rank of phylum in the International Code of Nomenclature of Prokaryotes’ This replaced the older, somewhat inconsistent -aeota ending and brought phylum names in line with other ranks.
In practice, the shift to -ota has been a headache. Long-familiar phylum names like Proteobacteria, Firmicutes, and Actinobacteria now formally become Proteobacteriota, Firmicuteota, and Actinobacteriota under the new rules.4PubMed Central. Harmonizing Prokaryotic Nomenclature: Fixing the Fuss over Phylum Name Flipping You will still see the older names widely used in textbooks and papers published before the change, and many microbiologists continue using them out of habit. If you are writing a new manuscript, the safest approach is to use the current valid name and note the older synonym in parentheses on first mention so readers who learned the old names can follow along.
These standardized suffixes are not just housekeeping. They make it possible for databases and text-mining algorithms to automatically identify the rank at which a scientific name is being used, which matters for large-scale genomic and ecological studies. The one weak spot is the class-level suffix -ia, which also appears in some genus names, creating occasional ambiguity for automated systems.5SpringerLink / Current Microbiology. Standardised Suffixes in the Nomenclature of the Higher Taxa of Prokaryotes an Aid to Data Mining, Database Administration and Automatic Assignment of Names to Taxonomic Ranks
How to Handle “Candidatus” Names
Genomic sequencing has revealed an enormous number of bacteria that have never been grown in a laboratory. These organisms are known from their DNA alone, and because traditional naming requires a cultured type strain, they cannot be formally validated under the ICNP. The workaround, introduced in the mid-1990s, is the “Candidatus” designation, which signals that a name is provisional and does not have formal standing in the nomenclature.6Europe PMC. Nomenclature of prokaryotic ‘Candidatus’ taxa: establishing order in the current chaos
Formatting a “Candidatus” name looks like this: “Candidatus Pelagibacter ubique.” The word “Candidatus” is not italicized and is enclosed in quotation marks along with the rest of the name, or only the genus and epithet are italicized while “Candidatus” stays in roman type, depending on the journal’s preferred style. The most common convention you will see in recent papers is: Candidatus Liberibacter solanacearum (with “Candidatus” sometimes placed in quotes but always visually distinct from the binomial). Styles vary, and this is one area where consistency within a document matters more than which exact convention you pick. The key point is that “Candidatus” must always appear, signaling the name’s provisional status. Dropping it and writing the name as if it were a validly published species is incorrect.
The sheer number of organisms known only from sequences has created pressure to reform this system. Automated approaches for generating valid names from genomic data have been proposed, which would relieve the bottleneck of having to culture every organism before it can be formally named.7Europe PMC. Bacterial nomenclature in the era of genomics For now, though, if you are writing about an uncultured organism, “Candidatus” is the accepted label.
When Bacterial Names Change
Bacterial taxonomy is not static. As genomic data accumulates, organisms get reclassified. Genera are split, merged, or renamed. If you work in clinical microbiology or infectious disease, you have probably encountered situations where a well-known pathogen is suddenly reported under an unfamiliar name. These changes are scientifically necessary, but they create real practical problems for clinicians, diagnostic laboratories, and electronic health records.
Implementing a name change in a clinical lab, for instance, is not as simple as updating a label. It affects everything from automated reporting systems to antimicrobial stewardship protocols. Infectious disease clinicians, infection prevention teams, and information technology staff all need to be involved in the transition, and the decision about whether to adopt a new name depends on the expected clinical impact, existing infrastructure, and accreditation requirements.8Oxford University Press. Change of Plans: Overview of Bacterial Taxonomy, Recent Changes of Medical Importance, and Potential Areas of Impact
For writing purposes, the practical advice is this: use the currently accepted name and, on first mention, give the former name in parentheses. If the older name is far more widely recognized (as is sometimes the case for recently reclassified clinical pathogens), you might note the synonym prominently so your readers can find related older literature. Journal editors will generally expect you to use the valid name at time of publication, but they also appreciate clarity for readers who may only know the older name.
The pace of naming new species has itself accelerated. A single institution in Marseille reported the isolation of 468 new bacterial species, accounting for roughly 3% of all bacterial species isolated worldwide at the time of their report.9Europe PMC. Naming microorganisms: the contribution of the IHU Méditerranée Infection, Marseille, France That kind of output, multiplied across research groups globally, means the landscape of valid names shifts constantly. Keeping up is genuinely difficult, which is one reason databases like the List of Prokaryotic names with Standing in Nomenclature (LPSN) exist.
Common Formatting Mistakes and How to Avoid Them
Certain errors show up so regularly in student papers, grant applications, and even published manuscripts that they are worth listing explicitly:
- Capitalizing the epithet: Escherichia Coli is wrong. The specific epithet is always lowercase, no matter where it falls in a sentence.
- Forgetting italics: Escherichia coli without italics (or underlining) is technically incorrect in formal writing. Some word processors auto-correct to roman type, so double-check after formatting.
- Using the epithet alone: Writing “coli” or “aureus” without the genus (or genus abbreviation) breaks the binomial convention. The epithet has no standing on its own.
- Italicizing “sp.” or “spp.”: These abbreviations are not part of the organism’s Latin name and should stay in roman type.
- Abbreviating on first mention: S. aureus should not appear before Staphylococcus aureus has been written out at least once in the document.
- Ambiguous abbreviation: If your text discusses Staphylococcus and Streptococcus, abbreviating both to “S.” makes them indistinguishable. Spell out or use longer abbreviations.
Many of these errors survive peer review, so do not assume that a published paper’s formatting is always correct. Journals have different levels of copyediting rigor, and nomenclatural formatting is one of the things that slips through. When in doubt, the ICNP rules as summarized by the ICSP are the authoritative reference.
Formatting Differences Across Journals and Style Guides
Although the core conventions (capitalization, lowercase epithet, italics, abbreviation after first mention) are universal, you will encounter minor variations depending on where you are publishing. Some biomedical journals follow the AMA Manual of Style, which aligns closely with ICNP conventions but has its own preferences for things like whether to italicize names above genus rank. Ecology journals often follow the CSE (Council of Science Editors) style, which can differ on small points like punctuation around “Candidatus.” Microbiology-specific journals tend to be the most rigorous about nomenclatural formatting, because their readership notices.
One area where style guides genuinely differ is the treatment of common names derived from bacterial taxa. Words like “staphylococcal,” “streptococcal,” or “pseudomonad” are adjectives or common nouns derived from genus names. They are not italicized and are not capitalized (unless they start a sentence), because they are not the formal taxonomic name. Similarly, informal group terms like “enterics” or “mycobacteria” (when used loosely to refer to the group rather than the genus Mycobacterium) are written in roman type and lowercase. This distinction between the formal name and the vernacular derivative is one of the subtleties that marks careful scientific writing.
Strain Designations and Subspecies
Below the species level, you will sometimes need to refer to specific strains or subspecies. Subspecies names follow the species epithet and are also italicized and lowercase: Mycobacterium tuberculosis subsp. tuberculosis. The abbreviation “subsp.” is in roman type, just like “sp.” and “spp.”
Strain designations, on the other hand, are not italicized at all. They are alphanumeric identifiers that follow the species name in roman type. For example, Escherichia coli K-12 or Bacillus subtilis 168. The strain name is essentially a label for a particular isolate held in a culture collection, not a formal taxonomic rank. Mixing up the formatting of subspecies and strains is another common mistake: “subsp.” with its Latinized epithet gets partial italics, but a strain code like ATCC 25922 is always roman.
Type strains deserve a quick mention because they are central to how bacterial species are defined. A type strain is the reference culture against which a species description is anchored. When you see a superscript “T” after a strain designation (e.g., DSM 20543T), it means that strain is the nomenclatural type. You are unlikely to need this notation in most writing, but it comes up in species descriptions and taxonomic papers.
Writing for Audiences Outside Microbiology
If you are writing for a clinical, environmental, or popular audience, the rules do not change, but the expectations around how much context you provide do. A paper in the Journal of Bacteriology can refer to B. subtilis and assume every reader knows the genus. A report for a hospital infection-control committee should spell out Burkholderia cepacia complex in full and might add a plain-language note about what the organism does. A science journalism piece will spell out the full name, probably skip the italics if the publication does not support them, and add a short gloss like “a common gut bacterium.”
The italics convention is particularly worth thinking about in non-traditional formats. Slide presentations, posters, social media posts, and informal communications do not always support italics. When italics are not available, underlining is the accepted substitute. If even underlining is impractical (as in a plain-text email), the convention is to at least capitalize and format the name correctly, and most readers will understand. The goal is always clarity: the reader should be able to tell that you are referring to a specific organism by its formal scientific name, not using an English word.
Regardless of audience, the principle that a species epithet never stands alone remains. Even in contexts where everyone knows “coli” means E. coli, writing the bare epithet in any document that might be read outside its immediate context risks confusion. Bacteria are named in a system designed to be universal. Using that system correctly, even in informal writing, is what keeps it useful.