Taxonomy

Question 1

Taxonomy

Answer 1

the science of biological classification

Question 2

Nomenclature

Answer 2

the devising or choosing of names for things

Question 3

Phylogeny

Answer 3

the evolutionary development and history of a species or higher taxonomic grouping of organisms

Question 4

Oligonucleotide

Answer 4

short single-stranded DNA or RNA molecules

Question 5

Species

Answer 5

collection of organisms that share the same sequences in their core housekeeping genes

Question 6

Strain

Answer 6

a genetic variant descended from a single, pure, microbial culture

Question 7

Biovars

Answer 7

a genetic variant that differs biochemically and physiologically

Question 8

Morphovars

Answer 8

A genetic variant that differs morphologically

Question 9

Serovars

Answer 9

a genetic variant that differs in antigenic properties

Question 10

Clade

Answer 10

a group consisting of a common ancestor and its descendants.

Question 11

Parsimony

Answer 11

adoption of the simplest assumption in the formulation of a theory or in the interpretation of data

Question 12

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

Answer 12

Binomial nomenclature is the naming system created by Carl Linneaus that describes an organism by its genus (capitalized and italicized) and its species (italicized). After naming the full organism once, i.e., Escherichia coli, you can just shorten it to E. Coli

Question 13

List taxon categories used in the classification of organisms

Answer 13

A taxon (plural: taxa) is a unit of any rank (i.e. kingdom, phylum, class, order, family, genus, species) designating an organism or a group of organisms

Taxonomic categories:
Life
Domain
Kingdom
Phylum
Class
Order
Family
Genus
Species

Collection of organisms that share the same sequences in their core housekeeping genes
Core housekeeping genes = genes that are essential for life (organism can’t survive without it)
Ex: Gram - bacteria requires LPS, other bacteria don’t → therefore, not the same species

Question 14

Biovars, Morphovars, Serovars, Clade

Answer 14

Biovars → differ biochemically & physiologically
Morphovars → differ morphologically (phenotypically)
Serovars → differ in antigenic properties
Clade → group consisting of an organism and its descendants
Ex: HIV, HIV 1, HIV2

Question 15

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 15

The three domains are Eukarya, Archaea, and Bacteria
The six kingdoms are Animale, Plante, Protista, Fungi, Archaebacteria, and Eubacteria
For microbiology, all domains and kingdoms are studied except plante. There are examples of all other kingdoms and domains in microbiology.

Question 16

Describe traditional and modern methods used to classify microorganisms

Answer 16

Phenetic Classification
Groups organisms together based on mutual similarity of phenotypes→ observable traits
Can reveal evolutionary relationships, but not dependent on genetic analysis
Phylogenetic Classification
Newer, recent approach
Also called phyletic classification
Phylogeny
Evolutionary development of a species
Usually based on direct comparison of genetic material and gene products
Using genes to find similarities

Question 17

Describe traditional and modern methods used to classify microorganisms

Answer 17

Taxonomy consists of three separate by interrelated principles:
Classification → arrangement of organisms into groups (taxa/taxon)
Nomenclature → assignment of names to taxa
Identification: determination of taxon to which an isolate belongs
Traditional (older) method for classification :
Phenetic Classification
Groups organisms together based on mutual similarity of phenotypes
Can reveal evolutionary relationships, but not dependent on genetic analysis
Modern (newer) approach:
Phylogenetic Classification
Phylogeny = evolutionary development of a species
Usually based on direct comparison of genetic material and gene products
Gives evolutionary relationships/development
SSU rRNA = small subunit rRNAs (16S for prokaryotes)
Highly conserved (least changes) so it is good for determining ancestors → genes encoding SSU rRNAs are the most frequently used sequence in phylogenetics
Comparative analysis of 16S rRNA sequences
When comparing rRNA sequences between 2 organisms, their relatedness is represented by percent sequence homology → 70% cutoff value for species definition

Question 18

Phylogenetic trees

Answer 18

Show inferred evolutionary relationships in the form of multiple branching lineages connected by notes
Identified sequences at tip of branches
Nodes represent divergence event
Length of branch represents the number of molecular changes between two nodes