Process of systemics - ANSWER-Isolation → Identification → Classification →
Nomenclature
Taxonomy hierarchy - ANSWER-Domain → Phylum → Class → Order → Family →
Genus → Species
Nomenclature - ANSWER-Genus + species
Phenotypic characteristics: - ANSWER-Morphology
Physiology:
- ex: Temperature, pH, salinity, Oxygen relationships, H2/H2S production, Fermentation
products, Antibiotic resistance
Metabolism:
- ex: Carbon and nitrogen sources
Genomic characteristics - ANSWER-GC content
DNA similarity
16S rRNA sequences/18s rRNA sequence (eukaryotes)
Multi-locus sequence analysis (MLSA)
Genome sequence
Plasmids
Strain - ANSWER-genetic variant or subtype within a species
Different strains can have different traits
Phylum - ANSWER-a major taxonomic group above class
Groups organisms based on broad evolutionary relationships
Type strain - ANSWER-Well-characterized reference strain that defines a species
Used as the standard for comparison
Core genome - ANSWER-genes present in ALL strains of a species
Essential functions
Accessory genome - ANSWER-genes NOT present in all strains
, Variable, flexible
Often include = antibiotic resistance, virulence factors
Pan-genome - ANSWER-total gene set of all strains in a species
Core genome + accessory genome
Uncultivated bacteria - ANSWER-bacteria that cannot be grown in pure (axenic) culture
- Can be obtained in consortia (groups of microbes working together) and symbiotic
relationships
- Cannot survive alone, depend on environment or other microbes
How do we know about uncultivated bacteria? - ANSWER-through metagenomics
DNA sequencing directly from environment (ex: soil, human gut)
What is cell differentiation - ANSWER-Process where cells become morphologically or
physiologically different
Triggered by environmental cues
Controlled by intra and/or intercellular signaling
3 types of cell differentiation - ANSWER-1) Cell divides to produce two daughter cells
that can be distinguished morphologically and/or physiologically
Ex: Swarmer cells differentiate into stalked cells
2) Cell acquires morphological and physiological changes, clearly differentiates from
precursor cell
Ex: Endospore formation
3) Multicellular development → cells interact to form specialized structures
Ex: biofilms
Endospores - ANSWER-dormant, highly resistant structure formed in cells
- Not reproductive
- Extremely resistant
- Triggered by environmental cues
Why do bacteria make endospores? - ANSWER-Survival under stress conditions
Starvation
Heat
pH stress
Biofilms key features - ANSWER-structured communities of microbes that attach to
surfaces
Enclosed in a self-produced matrix
Can consist of consortia of several species or single-species
Biofilm structure - ANSWER-Can be monolayer, stratified, complex 3D with channels
Biofilm formation - ANSWER-1) attachment (reversible → irreversible)
Reversible → bacteria briefly stick to a surface through weak interactions
Irreversible → cells start producing sticky substances using pili and flagella to attach
Flagella are turned OFF or lost
2) Growth and division
Attached cells begin to divide and form small clusters
3) Matrix production (EPS)
Cells produce EPS (extracellular polymeric substances)
Forms a protective slime layer
4) Maturation (3D structure)
5) Dispersal
Nomenclature
Taxonomy hierarchy - ANSWER-Domain → Phylum → Class → Order → Family →
Genus → Species
Nomenclature - ANSWER-Genus + species
Phenotypic characteristics: - ANSWER-Morphology
Physiology:
- ex: Temperature, pH, salinity, Oxygen relationships, H2/H2S production, Fermentation
products, Antibiotic resistance
Metabolism:
- ex: Carbon and nitrogen sources
Genomic characteristics - ANSWER-GC content
DNA similarity
16S rRNA sequences/18s rRNA sequence (eukaryotes)
Multi-locus sequence analysis (MLSA)
Genome sequence
Plasmids
Strain - ANSWER-genetic variant or subtype within a species
Different strains can have different traits
Phylum - ANSWER-a major taxonomic group above class
Groups organisms based on broad evolutionary relationships
Type strain - ANSWER-Well-characterized reference strain that defines a species
Used as the standard for comparison
Core genome - ANSWER-genes present in ALL strains of a species
Essential functions
Accessory genome - ANSWER-genes NOT present in all strains
, Variable, flexible
Often include = antibiotic resistance, virulence factors
Pan-genome - ANSWER-total gene set of all strains in a species
Core genome + accessory genome
Uncultivated bacteria - ANSWER-bacteria that cannot be grown in pure (axenic) culture
- Can be obtained in consortia (groups of microbes working together) and symbiotic
relationships
- Cannot survive alone, depend on environment or other microbes
How do we know about uncultivated bacteria? - ANSWER-through metagenomics
DNA sequencing directly from environment (ex: soil, human gut)
What is cell differentiation - ANSWER-Process where cells become morphologically or
physiologically different
Triggered by environmental cues
Controlled by intra and/or intercellular signaling
3 types of cell differentiation - ANSWER-1) Cell divides to produce two daughter cells
that can be distinguished morphologically and/or physiologically
Ex: Swarmer cells differentiate into stalked cells
2) Cell acquires morphological and physiological changes, clearly differentiates from
precursor cell
Ex: Endospore formation
3) Multicellular development → cells interact to form specialized structures
Ex: biofilms
Endospores - ANSWER-dormant, highly resistant structure formed in cells
- Not reproductive
- Extremely resistant
- Triggered by environmental cues
Why do bacteria make endospores? - ANSWER-Survival under stress conditions
Starvation
Heat
pH stress
Biofilms key features - ANSWER-structured communities of microbes that attach to
surfaces
Enclosed in a self-produced matrix
Can consist of consortia of several species or single-species
Biofilm structure - ANSWER-Can be monolayer, stratified, complex 3D with channels
Biofilm formation - ANSWER-1) attachment (reversible → irreversible)
Reversible → bacteria briefly stick to a surface through weak interactions
Irreversible → cells start producing sticky substances using pili and flagella to attach
Flagella are turned OFF or lost
2) Growth and division
Attached cells begin to divide and form small clusters
3) Matrix production (EPS)
Cells produce EPS (extracellular polymeric substances)
Forms a protective slime layer
4) Maturation (3D structure)
5) Dispersal
