Infection and Immunity
Characteristics used in taxonomy: Characteristic used in taxonomy:
Microbial Taxonomy: Morphology (appearance):
• Generally structural features
Genetic analysis:
• Genomics – full sequence
• Depend on expression of many genes • Point mutations
Systematics: • Thus genetically stable. Also show limited variation from • But beware plasmid problems
• Taxonomy – science of biological classification environmental influences
• Classification – arrangement of organisms into groups or taxa Characteristic used in taxonomy:
• Nomenclature – branch of systematics concerned with Molecular characteristics:
assignment of names • Proteins. Amino acid sequence/antibodies
• Lipid composition of membrane
• Nucleic acid base composition/mole %G+C
Taxonomic ranks: • Nucleic acid hybridization
• Kingdom, division, class, order, family, genera. Species, (strain/ • Nucleic acid sequencing. rRNA
variety)
• Species – group of interbreeding or potentially interbreeding Recent developments:
natural populations that are reproductively isolated from other Numerical Taxonomy:
groups • Requires determination of the presence or absence of selected
characters in the group of organisms under study
• Requires 50 – 100 characteristics to be used
• Requires a range of different data: morphological, biochemical
and physiological
• Aim to determine a measurement of agreement between
characteristics possessed by two organisms
• Simple matching coefficient (SSM) is most commonly used
Species definition: • SSM is the proportion of characters which match regardless of
• But many microbes do not reproduce sexually. Thus we use whether the attribute is present or absent
phenotypic and genotypic features
Characteristic used in taxonomy:
• A microbial species is a collection of strains that share many Physiological and metabolic features: Classical groupings:
stable properties but differ significantly from other groups of • Usually relate to enzyme activity Simple matching coefficient (SSM)
strains • Often protein based
• Strain – a population of microbes that descends from a single • Are a direct expression of genes
• For microorganisms is often based on ability to grow on
microbe or pure culture isolate metabolised specific nutrients
• Morphovar – morphological differences
• Biovar – biochemical or physiological differences Characteristic used in taxonomy:
• Serovar – antigenic differences Ecological:
• Genovar – differences in DNA sequence • Preferred habitats – pH and temp optima
• Life cycles
• Community relations and interactions with other organisms
(including parasitism and symbiosis)
Characteristic used in taxonomy:
Serology:
• Relates to protein structure and so indirectly to gene sequence
• Antibody reactions can be very sensitive to small differences in
proteins
• Allows species and strains to be distinguished
• Often applied as ELISA tests
Characteristics used in taxonomy: Characteristic used in taxonomy:
Microbial Taxonomy: Morphology (appearance):
• Generally structural features
Genetic analysis:
• Genomics – full sequence
• Depend on expression of many genes • Point mutations
Systematics: • Thus genetically stable. Also show limited variation from • But beware plasmid problems
• Taxonomy – science of biological classification environmental influences
• Classification – arrangement of organisms into groups or taxa Characteristic used in taxonomy:
• Nomenclature – branch of systematics concerned with Molecular characteristics:
assignment of names • Proteins. Amino acid sequence/antibodies
• Lipid composition of membrane
• Nucleic acid base composition/mole %G+C
Taxonomic ranks: • Nucleic acid hybridization
• Kingdom, division, class, order, family, genera. Species, (strain/ • Nucleic acid sequencing. rRNA
variety)
• Species – group of interbreeding or potentially interbreeding Recent developments:
natural populations that are reproductively isolated from other Numerical Taxonomy:
groups • Requires determination of the presence or absence of selected
characters in the group of organisms under study
• Requires 50 – 100 characteristics to be used
• Requires a range of different data: morphological, biochemical
and physiological
• Aim to determine a measurement of agreement between
characteristics possessed by two organisms
• Simple matching coefficient (SSM) is most commonly used
Species definition: • SSM is the proportion of characters which match regardless of
• But many microbes do not reproduce sexually. Thus we use whether the attribute is present or absent
phenotypic and genotypic features
Characteristic used in taxonomy:
• A microbial species is a collection of strains that share many Physiological and metabolic features: Classical groupings:
stable properties but differ significantly from other groups of • Usually relate to enzyme activity Simple matching coefficient (SSM)
strains • Often protein based
• Strain – a population of microbes that descends from a single • Are a direct expression of genes
• For microorganisms is often based on ability to grow on
microbe or pure culture isolate metabolised specific nutrients
• Morphovar – morphological differences
• Biovar – biochemical or physiological differences Characteristic used in taxonomy:
• Serovar – antigenic differences Ecological:
• Genovar – differences in DNA sequence • Preferred habitats – pH and temp optima
• Life cycles
• Community relations and interactions with other organisms
(including parasitism and symbiosis)
Characteristic used in taxonomy:
Serology:
• Relates to protein structure and so indirectly to gene sequence
• Antibody reactions can be very sensitive to small differences in
proteins
• Allows species and strains to be distinguished
• Often applied as ELISA tests
