Chapter 6: Taxonomy

Question 1

Explain binomial nomenclature and how to properly identify organisms in this format

Answer 1

Devised by Carolus Linnaeus

Each organism has two names
– genus name and species epithet
-Abbreviated after first use (e.g., E. coli)
-New species of bacteria cannot be recognized until it has been published in the International Journal of Systematic and Evolutionary Microbiology

Question 2

List taxon categories used in the classification of organisms

Answer 2

Classification: arrangement of organisms into groups (taxa; s., taxon)

Nomenclature: assignment of names to taxa

Identification: determination of taxon to which an isolate belongs

Question 3

Describe the 3 domains and the 6 kingdoms of organisms.

Explain the key differences between organisms in each group.

Identify the domains and kingdoms containing organisms within the purview of microbiology

Answer 3

3 Domains:
○ Eukarya, Archaea, Bacteria

6 Kingdoms:
○ Animalia (no cell walls, multicellular)
○ Plantae (cellulose, multicellular)
○ Fungi (chitin, MOSTLY unicellular)
○ Protista (cellulose, MOSTLY unicellular

○ Archaebacteria (prokaryotes, unicellular, no peptidoglycan in cell walls)

○ Eubacteria (prokaryotes, unicellular, peptidoglycan)

Question 4

Describe traditional and modern methods used to classify microorganisms

Answer 4

Phenetic Classification: relied on phenotypic/morphological similarities. Can be insightful, but also obscured true relationships bc it didn’t rely on actual inheritable material (genome).

Phylogeny: The evolutionary development and history of a species or higher taxonomic grouping of organisms. Tracing a taxon through the ages based on genetic relatedness and bioinformatic predictions. Phylogenetic groupings now rely on sequence similarity.

Question 5

Describe the difference between a species and a strain.

Answer 5

Species: Collection of organisms that share the same sequences in their
core housekeeping genes

Strain: A genetic variant descended from a single, pure microbial culture
-Clinical vs. lab strains
– Can have multiple strains with a species
– More exclusive term than species
– May vary between each other by virulence factors and metabolites

Question 6

Phylogenetic Trees

Answer 6

Show inferred evolutionary
relationships in the form of multiple
branching lineages connected by
nodes.

Identified sequences at tip of
branches.

Operational taxonomic unit.

Nodes represent a divergence event

Length of branch represents number
of molecular changes between two
nodes – the longer the branch, the
more genetic difference

Node and everything branching from it = clade

Question 7

Creating Phylogenetic Trees from Molecular Data

Answer 7

• Align sequences
• Determine number of positions that are different
• Express difference
  – e.g., evolutionary distance
• Use measure of difference to create tree
  – Organisms clustered based on relatedness
  – Parsimony
• Fewest changes from ancestor to organism in question
• Simplest theory is usually the best one – the fewer the genetic differences, the
  more likely the organisms are to be related

Question 8

Sequencing Technologies

Answer 8

Whole genome sequencing (WGS) has revolutionized how we think about evolution and organism relatedness

We can also use smaller bits of the genome for differentiating between
species/strains (Housekeeping genes).

Use multilocus sequencing technology (MLST) to take a look at
multiple gene loci (sites) in the genome

SSU rRNA sequencing

Question 9

SSU rRNA

Answer 9

Small subunit rRNAs (SSU
rRNAs)
The smaller of the two main RNA components of a ribosome
– 16S rRNA prokaryotes (50+30 = 70S)
– 18S rRNA eukaryotes (60+40 = 80S)

It’s a widely used genetic marker because it is present in all living cells (core housekeeping genes— the genes that every single organism needs to live), has conserved and variable regions, and contains important evolutionary information.

Especially for identifying different
genera.

Due to its ancient origin and slow rate of evolution, the SSU rRNA gene functions like a molecular clock, providing a way to measure evolutionary distances between species.

Question 10

Strain Characterization

Answer 10

Biovars
– differ biochemically and physiologically
– Have the same housekeeping genes – different environments call for different gene expression

Morphovars
– differ morphologically – size, shape, color

Serovars
– differ in antigenic properties – how immune system builds antibodies

Clade
– a group consisting of an organism and its descendants

Question 11

Viral Taxonomy

Answer 11

• Use ICTV system for Order, Family, Genus, and specific epithet
• Naming of strains/variants differ by virus
  – Sometimes named by antigens (e.g. H1N1 for flu)
  – Sometimes named by host organism
  – Sometimes named by pandemic year/location
• Always refer to ICTV for official naming system