Lecture 5: Microbial Taxonomy Flashcards
Define taxonomy
The science of biological classification
List and define the 3 parts of taxonomy
1) Classification: based upon a selected scheme
2) Nomenclature: Assignment into taxa using rules
3) Identification: Determining where each organism fits
What are the 4 main reasons for classifying organisms?
1) Establish relationships, and to differentiate
2) We have only scratched the surface
3) Serves as valuable reference
4) Opens line of communication
How did Carl von Linne classify organisms?
-Used mainly anatomical characteristics
-Used 2 kingdoms and latinized names
How did Carl von Nageli classify organisms?
Bacteria and fungi into plant kingdom
What did Ernst Haeckel do for taxonomy?
He proposed Kingdom Protista
Edouard Chatton proposed the term ‘________’
prokaryote
Who founded the 5 kingdom system of taxonomy?
Robert H. Witaker
Who proposed the idea of 3 domains? What were they based on, and in what other three ways did they differ?
1) Carl Woese
2) Based on rRNA sequences
3) Also differ in membrane lipid structure, tRNA, and antibiotic sensitivity
Define phylogeny
The evolutionary development of a species
Name the 3 phylogenetic groups and define them
1) Monophyletic: organisms that arose from a single common ancestor
2) Paraphyletic: A common ancestor, but doesn’t include all descendents
3) Polyphyletic: Multiple origins and do not share a common ancestor
The binomial system consists of what 2 things?
Genus + species
True or false: the binomial system always italicizes genus and species
True
Define a strain. What does a strain descend from?
-Defined as a population of organisms that are distinguishable from others of the same species
-Descended from a single organism or pure culture
List the 3 ways strains can vary, and define them
1) Biovars: biochemical and physiological properties
2) Morphovars: morphological properties
3) Serovars: antigenic properties
Describe a type strain
-One of the first strains studied, it is the most characterized strain
-Most species have multiple type strains, depends on how much the species has been studied
-The strain that is the most typical for the species as a whole
What are the 3 broad ways to classify bacteria? Which is the most accurate?
1) Phenotypic classification
2) Analytic classification
3) Genotypic classification
-Genomic is most accurate
Define morphology
The form and structure of an organism or group of identical organisms
Differentiate between microscopic and macroscopic classification
1) Microscopic classification: shape, pattern of groups, staining
2) Macroscopic classification: colony morphology, pigment production
Differentiate between biotyping and serotyping
1) Biotyping: Biochemical markers
2) Serotyping: Detection of specific antigens
Define antibiogram patterns and phage typing
1) Antibiogram patterns: Susceptibility to various antibiotics
2) Phage typing: Susceptibility to viruses that infect bacteria; bacteriophages
Name 7 types of phenotypic classification
1) Morphology
2) Microscopic classification
3) Macroscopic classification
4) Biotyping
5) Serotyping
6) Antibiogram patterns
7) Phage typing
What type of classification requires expensive instrumentation (e.g. mass spectrometry) and is labor intensive?
Analytic classification
Give 4 examples of analytic classification
1) Cell envelope fatty-acid analysis
2) Whole cell lipid analysis
3) Whole cell protein analysis
4) Multilocus enzyme electrophoresis
Give 6 examples of genotypic classification
1) Guanine plus cytosine ratio
2) DNA hybridization
3) Nucleic acid sequence analysis
4) Plasmid analysis
5) Ribotyping
6) Chromosomal DNA fragment analysis
Name 4 groups of classical characteristics used to identify organisms
Morphological, physiological/metabolic, biochemical, and ecological
What are the 2 main types of classical characteristics that can be used to classify organisms?
1) Physiological/ metabolic
2) Ecological
Name 4 physiological/ metabolic characteristics that can be used to classify organisms
1) Motility
2) Luminescence
3) Photosynthetic pigments
4) Energy sources
Name 5 ecological characteristics that can be used to classify organisms
1) Life cycle patterns
2) Symbiotic relationships
3) Ability to cause disease
4) Habitat preference
5) Growth requirements
What are the two main categories of characteristics that can be used to identify organisms?
1) Classical characteristics
2) Molecular characteristics
Name 5 molecular characteristics
1) Nucleic acid base composition
2) Nucleic acid hybridization
3) Nucleic acid sequencing
4) Genomic fingerprinting
5) Amino acid sequencing
Describe nucleic acid base composition
•Usually measures G&C content, which usually only varies by ~10% in a genus
•A molecular characteristic
Describe nucleic acid hybridization
-Complete hybridization can occur if the organisms are identical
-Partial hybridization can occur if they’re related
-No hybridization if they’re not related
-A molecular characteristic
Describe nucleic acid sequencing and when it is best used
-Utilizes small subunit rRNAs (SSU rRNAs)
-Best measure for relatedness
-A molecular characteristic
Describe small subunit rRNAs (SSU rRNAs)
-The molecules of choice for phylogenetics
-Have the same role in all organisms
-Part of complex ribosome structure (intolerant of mutations)
-Very well conserved (change very slowly over time)
What are the molecules of choice for phylogenetics? Why?
SSU rRNAs, because they have the same role in all organisms and they’re very well conserved
1) What does genomic fingerprinting consist of?
2) What type of characteristic is genomic fingerprinting?
1) PCR: polymerase chain reaction
-Amplifies a region of the DNA, can be used to identify causative agents
2) A molecular characteristic
Describe amino acid sequencing; what does it reflect and what can it be differentiated based on?
-Directly reflects mRNA sequences
-Can be differentiated based on charge, immunogenicity, and fragmentation
-It’s a molecular characteristic
Define the root
The last universal common ancestor (LUCA) of the 3 domains
How do we know the eukarya and archaea have common ancestry at some point?
They share key proteins
What 3 considerations should be made for microbial genetic diversity?
1) The world environment(s)
2) The extraterrestrial
3) Microbial mechanisms
-Mutations and gene transfer
