Taxonomy and Classification of Microbes (Especially Prokaryotes) The Three Domains and What Distinguishes Them Review of Characteristics of Prokaryotes, Eukaryotes, Viruses The Taxonomic Hierarchy and Species Definitions Characteristics Used to Classify Prokaryotes Nine Medically Important Groups of Prokaryotes Dichotomous Keys and Microbe Identification

Three Domain System Eubacteria Archaea Eucarya Protista Animalia Fungi Plantae Gram positives Gram negatives Spirochetes Cyanobacteria Methanogens Halophiles Thermoacidophiles Circular DNA chromosome Prokaryotic cell type Peptidoglycan cell walls Straight chain phospholipids Antibiotic sensitive F-methionine for first aa Circular DNA chromosome Prokaryotic cell type No peptidoglycan in cell walls Branched chain phospholipids Antibiotic insensitive Methionine for first aa Linear DNA chromosomes Eukaryotic cell type Cell walls variable if present Straight chain phospholipids Antibiotic insensitive Methionine for first aa

The Three-Domain System Figure 10.1

Taxonomy and Classification of Microbes (Especially Prokaryotes) The Three Domains and What Distinguishes Them Review of Characteristics of Prokaryotes, Eukaryotes, & Viruses The Taxonomic Hierarchy and Species Definitions Characteristics Used to Classify Prokaryotes Nine Medically Important Groups of Prokaryotes Dichotomous Keys and Microbe Identification

Bacteria Archaea Protista Animalia Plantae Fungi Viruses Cell type Chromo- somes Cell wall? Uni/multi cellular Energy source Example organism Review Chart of Cell Characteristics Domain Domain Domain Eukarya Non- living

Eubacteria Archaea Protista Animalia Plantae Fungi Viruses Cell type Chromo- somes Cell wall? Uni/multi cellular Energy source Example organism Review Chart of Cell Characteristics Domain Domain Domain Eukarya Non- living prokaryotic prokaryotic eukaryotic eukaryotic eukaryotic eukaryotic no cells

Eubacteria Archaea Protista Animalia Plantae Fungi Viruses Cell type Chromo- somes Cell wall? Uni/multicell ular Energy source Example organism Review Chart of Cell Characteristics Domain Domain Domain Eukarya Non- living prokaryotic prokaryotic eukaryotic eukaryotic eukaryotic eukaryotic no cells 1 Circular DNA 1 Circular DNA Linear DNA Linear DNA Linear DNA Linear DNA DNA or in nucleoid in nucleoid in nucleus in nucleus in nucleus in nucleus RNA

Eubacteria Archaea Protista Animalia Plantae Fungi Viruses Cell type Chromo- somes Cell wall? Uni/multicell ular Energy source Example organism Review Chart of Cell Characteristics Domain Domain Domain Eukarya Non- living prokaryotic prokaryotic eukaryotic eukaryotic eukaryotic eukaryotic no cells 1 Circular DNA 1 Circular DNA Linear DNA Linear DNA Linear DNA Linear DNA DNA or in nucleoid in nucleoid in nucleus in nucleus in nucleus in nucleus RNA yes, most of none or none none yes, of yes, of no murein pseudomurein cellulose chitin

Eubacteria Archaea Protista Animalia Plantae Fungi Viruses Cell type Chromo- somes Cell wall? Uni/multicell ular Energy source Example organism Review Chart of Cell Characteristics Domain Domain Domain Eukarya Non- living prokaryotic prokaryotic eukaryotic eukaryotic eukaryotic eukaryotic no cells 1 Circular DNA 1 Circular DNA Linear DNA Linear DNA Linear DNA Linear DNA DNA or in nucleoid in nucleoid in nucleus in nucleus in nucleus in nucleus RNA yes, most of none or none none yes, of yes, of no murein pseudomurein cellulose chitin unicellular unicellular unicellular multicellular multicellular uni & multi no cells multicell

Eubacteria Archaea Protista Animalia Plantae Fungi Viruses Cell type Chromo- somes Cell wall? Uni/multi cellular Energy source Example organism Review Chart of Cell Characteristics Domain Domain Domain Eukarya Non- living prokaryotic prokaryotic eukaryotic eukaryotic eukaryotic eukaryotic no cells 1 Circular DNA 1 Circular DNA Linear DNA Linear DNA Linear DNA Linear DNA DNA or in nucleoid in nucleoid in nucleus in nucleus in nucleus in nucleus RNA yes, most of none or none none yes, of yes, of no murein pseudomurein cellulose chitin unicellular unicellular unicellular multicellular multicellular uni & multi no cells heterotrophic hetero, chemo heterotrophic heterotrophic autotrophic heterotrophic none chemotrophic autotrophic

Eubacteria Archaea Protista Animalia Plantae Fungi Viruses Cell type Chromo- somes Cell wall? Uni/multi cellular Energy source Example organism Review Chart of Cell Characteristics Domain Domain Domain Eukarya Non- living prokaryotic prokaryotic eukaryotic eukaryotic eukaryotic eukaryotic no cells 1 Circular DNA 1 Circular DNA Linear DNA Linear DNA Linear DNA Linear DNA DNA or in nucleoid in nucleoid in nucleus in nucleus in nucleus in nucleus RNA yes, most of none or none none yes, of yes, of no murein pseudomurein cellulose chitin unicellular unicellular unicellular multicellular multicellular uni & multi no cells hetero, chemo, hetero, chemo heterotrophic heterotrophic autotrophic heterotrophic none autotrophic autotrophic (autotrophic) Staphylococcus Sulfolobus Entamoeba Canis Tsuga Saccharomyces HIV aureus histolytica domestica heterophylla cerevesiae

Taxonomy and Classification of Microbes (Especially Prokaryotes) The Three Domains and What Distinguishes Them Review of Characteristics of Prokaryotes, Eukaryotes, Viruses The Taxonomic Hierarchy and Species Definitions Characteristics Used to Classify Prokaryotes Nine Medically Important Groups of Prokaryotes Dichotomous Keys and Microbe Identification

Taxonomic Hierarchy Figure 10.5

Domain Eubacteria Kingdom Prokaryotae (?) Phylum Gram Positive Class Scotobacteria Order Spirochaetales Family Spirochaetaceae Genus Treponema Species pallidum Scientific name: Treponema pallidum or Treponema pallidum No common name except “syphilis bacteria” Classification of a Particular Bacterium

The “Species Definition” Varies By Microbial Type A eukaryotic species is: –A group of closely related organisms that breed among themselves A prokaryotic species is: –A population of cells with similar characteristics  A clone is a population of cells derived from a single cell  A strain is composed of cells of a species with minor identifiable differences  A serovar is a strain identified by serological (antibody-identified) means A viral species is: –A population of viruses with similar characteristics that occupies a particular ecological niche

Taxonomy and Classification of Microbes (Especially Prokaryotes) The Three Domains and What Distinguishes Them Review of Characteristics of Prokaryotes, Eukaryotes, Viruses The Taxonomic Hierarchy and Species Definitions Characteristics Used to Classify Prokaryotes Nine Medically Important Groups of Prokaryotes Dichotomous Keys and Microbe Identification

Characteristics Used to Classify Prokaryotes Morphology Cell shape Cell wall anatomy (staining characteristics)

Characteristics Used to Classify Prokaryotes Morphology Cell shape Cell wall anatomy (staining characteristics) Physiology Spore-forming ability Motility (how many flagella and where attached) Fruiting or budding ability Ability to live with or without oxygen

Characteristics Used to Classify Prokaryotes Morphology Cell shape Cell wall anatomy (staining characteristics) Physiology Spore-forming ability Motility (how many flagella and where attached) Fruiting or budding ability Ability to live with or without oxygen Metabolic abilities Use of carbohydrates, proteins, lipids

Characteristics Used to Classify Prokaryotes Morphology Cell shape Cell wall anatomy (staining characteristics) Physiology Spore-forming ability Motility (how many flagella and where attached, gliding) Fruiting or budding ability Ability to live with or without oxygen Metabolic abilities Use of carbohydrates, proteins, lipids Serology (recognition by blood antibodies) Phage Typing (recognition by specific viruses) DNA sequencing (similarities in gene sequences)

Groups of Prokaryotes      Escherichia coli Haemophilus influenzae Pseudomonas aeruginosa Staphylococcus aureus Streptococcus pneumoniae Clostridium tetani Mycobacterium teuberculosis Corynebacterium diptheriae Mitochondria in eukaryotes Chloroplasts in eukaryotes

References Bergey’s Manual of Determinative Bacteriology Provides identification schemes for identifying bacteria and archaea Morphology, differential staining, biochemical tests Bergey’s Manual of Systematic Bacteriology Provides phylogenetic information on bacteria and archaea Based on rRNA sequencing Approved Lists of Bacterial Names Lists species of known prokaryotes Based on published articles

Taxonomy and Classification of Microbes (Especially Prokaryotes) The Three Domains and What Distinguishes Them Review of Characteristics of Prokaryotes, Eukaryotes, Viruses The Taxonomic Hierarchy and Species Definitions Characteristics Used to Classify Prokaryotes Nine Medically Important Groups of Prokaryotes Dichotomous Keys and Microbe Identification

Spirochetes Long, helical bacteria which swim by spinning like corkscrews Treponema pallidum causes syphilis Borrelia burgdorferi causes Lyme disease Leptospira interrogans causes leptospirosis

Gram negative, facultatively anaerobic rods Escherichia coli (urinary tract infections) Salmonella (typhoid fever, food poisoning) Shigella sonnei (shigellosis diarrhea) Vibrio cholerae (cholera diarrhea) Haemophilus influenzae (ear infections, meningitis) Serratia marcescens (urinary, resp tract infections)

Gram negative aerobic rods and cocci Pseudomonas aeruginosa (burn, wound, & other infections) Neisseria gonorrhoeae (gonorrhea) Bordatella pertussis (pertussis/whooping cough)

Rickettsias and Chlamydias obligate intracellular parasites Rickettsia prowazekii (typhus) Chlamydia trachomatis (urethritis - most common STD)

Mycoplasmas Mycoplasma pneumoniae (“walking pneumonia”) No cell wall, intracellular parasite, small size, unusual sterols in cell membrane

Gram positive cocci Staphylococcus aureus Streptococcus pyogenes Streptococcus pneumoniae

Endospore forming bacteria Bacillus anthracis Clostridium tetani Clostridium botulinum

Mycobacteria Mycobacterium tuberculosis Mycobacterium leprae Thick waxy lipids in cell wall (acid fast)

Groups of Prokaryotes      Escherichia coli Haemophilus influenzae Pseudomonas aeruginosa Staphylococcus aureus Streptococcus pneumoniae Clostridium tetani Mycobacterium teuberculosis Corynebacterium diptheriae Mitochondria in eukaryotes Chloroplasts in eukaryotes

Archaea (Archaebacteria) Many are morphologically part of the Gram-negative Aerobic Rods and Cocci group Halobacterium in salt lake Sulfulobus in Yellowstone hot springs

Taxonomy and Classification of Microbes (Especially Prokaryotes) The Three Domains and What Distinguishes Them Review of Characteristics of Prokaryotes, Eukaryotes, Viruses The Taxonomic Hierarchy and Species Definitions Characteristics Used to Classify Prokaryotes Nine Medically Important Groups of Prokaryotes Dichotomous Keys and Microbe Identification

Dichotomous Key