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BioAtlas

Chapter 4

Naming and classification

Every organism gets two words, and both of them are load-bearing. Written correctly the name tells you the group and the organism; written carelessly it costs a mark on a paper that gives them out sparingly.

The three domains

Carl Woese proposed these in 1978 from ribosomal RNA sequences, which is why the split does not follow what the cells look like.

DomainCell typeCell wallNote
BacteriaProkaryoticPeptidoglycanEverything clinically important in this course.
ArchaeaProkaryoticNo peptidoglycanExtremophiles. No known human pathogens.
EukaryaEukaryoticCellulose, chitin or noneFungi, protozoa, algae, plants and animals.

Archaea are not bacteria

They are prokaryotic and they look like bacteria down a microscope, but their walls have no peptidoglycan and their ribosomal RNA puts them closer to us than to E. coli. No archaeon is a known human pathogen.

Why rRNA?

Ribosomal RNA does the same job in every living thing, so it changes very slowly. Two organisms whose rRNA sequences differ have been separated for a long time — which makes it a clock rather than a description.

The eight ranks

Domain down to species, broad to narrow. Only the last two are used in a name.

  1. 01

    Domain

    Broadest — three of them

  2. 02

    Kingdom

    Intermediate rank

  3. 03

    Phylum

    Intermediate rank

  4. 04

    Class

    Intermediate rank

  5. 05

    Order

    Intermediate rank

  6. 06

    Family

    Intermediate rank

  7. 07

    Genus

    First word of the name

  8. 08

    Species

    Second word of the name

Staphylococcus aureus in full: Bacteria, Firmicutes, Bacilli, Bacillales, Staphylococcaceae, Staphylococcus, aureus. Only the last two are written when the organism is named.

Writing the name

Five rules, and each one has a matching way to get it wrong.

  1. 01Two parts: the genus first, then the species epithet.
  2. 02The genus is capitalised; the species epithet is not.
  3. 03Both parts are italicised, or underlined when written by hand.
  4. 04After the first use the genus may be abbreviated to its initial — E. coli.
  5. 05The species epithet is never used on its own.
WrongRightBecause
staphylococcus aureusStaphylococcus aureusThe genus is capitalised.
Staphylococcus AureusStaphylococcus aureusThe species epithet is not capitalised, ever.
Staphylococcus aureusStaphylococcus aureusBoth parts are italicised, or underlined by hand.
aureusS. aureusThe species epithet is never used on its own.
S. aureus (first mention)Staphylococcus aureusAbbreviate only after the genus has been written out once.

Names carry meaning worth knowing: Staphylococcus is “bunch of grapes, round”, aureus is “golden”. Escherichia honours Theodor Escherich; coli says where it lives.