Chapter 9.

Microbial Taxonomy
and Classification
Terminology
• Taxonomy: Science of classification. Taxa are groups of organisms.
• Phylogeny/Phylogenetic Tree: Evolutionary history or relatedness of organisms.
Clade/Lineage: a sub-tree
• Systematics/Phylogenetic Classification: Classification of living matters should
be according to their phylogeny
• Homology: Common ancestry. Homology is NOT Similarity. This is because the
same trait can evolve independently (non-homologously) in separate evolutionary
lineages ("Evolutionary Convergence"; e.g., independent origin of wings in birds,
reptiles, and mammals). Conversely, closely related (or the same) species can
evolve different traits ("Evolutionary Divergence"; e.g., bacterial surface proteins,
breeds of dogs). Both convergence and divergence are evidence of natural
selection and species adaptation.
• Biological Species Concept (BSC): Members of the same species can interbreed
and produce fertile offspring. Speciation creates permanent gaps between taxa,
because no gene flow is possible after reproductive barrier is created. BSC does
NOT apply to bacteria because bacteria reproduce asexually. Thus, bacterial
species are mostly working definitions, not biological species.

Taxonomic hierarchy
• Three Domains: Eukarya are eukaryotes (their cells contain a nucleus). Archaea
(living in extreme environments) and Bacteria are prokaryotes (their cells have
no nucleus). The three-domain classification is based on a "tree of life" (the
evolutionary tree of all existing cellular organisms), reconstructed according to
the similarities of ribosomal RNA sequences (i.e., species with similar rRNA
sequences are grouped together).

• Five Kingdoms:

o Monera: All prokaryotes. Examples are archaeobacteria (Archaea), Gram-positive

bacteria, cyanobacteria, spirochetes, Gram-negative bacteria, rickettsias
o Protists: Single-celled eukaryotes. Plasmodium species cause malaria.
o Fungi: Multi- or uni-cellular eukaryotes living by absorption of nutrients.
Examples are molds, yeasts, and mushrooms.
o Plants: Not relevant to microbiology.
o Animals: Helminths (flat and round worms) are human pathogens. Many
arthropod, including insects (six-legged) and arachnid (eight-legged), species do
NOT cause diseases themselves but act as vectors of many infectious diseases.
 Examples of arthropods serving as disease vectors are ticks (Lyme disease),
mosquito (malaria) and flea (plague).

• Classification of bacteria

o Hierarchy: phylum-class-order-family-genus-species-strains (strains are sub-

groups of bacteria belonging to the same species; e.g. E. coli O157:H7 is a
pathogenic strain of E. coli)
o Bacterial species are classified and identified based on their morphology,
differential staining of cell walls, biochemical and physiological tests of oxygen
and nutrient requirements, serology (antibody-antigen reactions), (G+C)% of DNA
(GC% is species-specific), phage typing (bacterial viruses are often species-
specific), and DNA sequences.
o Bergey's Manuals: Bergey's Manual of Systematic Bacteriology classifies bacterial
groups based on their evolutionary relatedness derived from rRNA sequence
similarities. Bergey's Manual of Determinative Bacteriology is used for
identification of bacterial species based on criteria such as morphology, Gram
staining, oxygen requirements.

• Non-cellular infectious agents

o Viruses: Viruses are obligate intra-cellular parasites (non-free-living).
Viruses consists of a DNA or RNA (not both) as the genetic material and
a protein coat. Viruses are classified by their genetic material and shape.
o Viroids: Virus-like particles, having only a small RNA (no protein).
o Prions (Proteinaceous infectious particle): normal proteins in a misfolded
conformation, causing e.g., mad cow disease in cattle.

Molecular Phylogenetic Methods

• Comparison of Morphology-based and Molecular methods: Morphology is more
subject to evolutionary convergence due to adaptation. DNA sequences are less
subject to adaptive convergence. However, horizontal gene transfer of DNA
between different bacterial species can lead to mis-informed phylogeny.
• DNA sequences used as phylogenetic markers: rRNA sequences are (a)
universally present and (b) evolve slowly. Therefore, rRNA genes are good
phylogenetic marker for building evolutionary relationships between bacterial
species. However, rRNA sequences evolve too slowly to be useful for distinguish
between different strains of the same bacterial species. For strain differentiation,
fast-evolving loci (e.g., repetitive sequences) are needed.
• How to read a phylogenetic tree: Nodes represent species, either existing species
(at the tip) or ancestral species (represented internal nodes). A branch represents
the number of evolutionary changes or divergence time since the last ancestor. A
phylogenetic tree can be depicted in a variety of shapes (triangular or tree-like
form, rectangular form), but still describing the same evolutionary relationship.
At each level of tree, one ancestor gives rise to two descendant species. To find
the evolutionary distance between two species, trace back one ancestor at a time
 until the most recent common ancestor of the two species. Species sharing a more
recent common ancestor are more closely related than those sharing a more
distant ancestor.
• Molecular methods: Amplification of DNA using PCR (Polymerase Chain
Reaction, using the heat-resistant Taq DNA polymerase -- isolated from a hot-
spring Archaea species) and DNA sequencing