1. Chapter 11: Characterizing and Classifying Prokaryotes

2. Phylogeny: The Study of Evolutionary Relationships of Living Organisms
Over 1.5 million different organisms have been identified to date.
Many similarities among living organisms:
Made up of cells surrounded by a plasma membrane.
Use ATP as energy source.
Store genetic information as DNA.
Ribosomes are the site of protein synthesis.
Both differences and similarities among organisms are caused by natural selection (Darwin, 1858).
Organisms can be classified into taxonomic categories (taxa), based on the differences and similarities among them.

3. Phylogeny: The Study of Evolutionary Relationships of Living Organisms
Ancient Greeks classified all living organisms into two groups
Kingdom Plantae
Kingdom Animalia
In 1850s bacteria and fungi were incorrectly placed in the Plant Kingdom.
In 1860s Kingdom Protista was proposed to include bacteria, fungi, algae, and protozoa, but many scientists still classified bacteria and fungi as plants.
Intense disagreement over classification of bacteria and fungi persisted over 100 years.

4. Phylogeny: The Study of Evolutionary Relationships of Living Organisms
In 1930s electron microscopy made it clear that bacterial cells lacked a nucleus. The term procaryote was introduced in 1937.
In 1959 Kingdom Fungi was established.
In 1961 the current definition of the term procaryote was established.
In 1968 the Kingdom Procaryotae was accepted by biologists.
In 1969 Robert Whitaker proposed a five-kingdom system of biological classification for all living organisms.

5. Five-Kingdom System of Biological Classification
Proposed in by Robert Whitaker :
1. Kingdom Procaryotae (Monera): Oldest known cells. Lived over 3.5 billion years ago. Lack a nucleus and membrane bound organelles.
The other four kingdoms are eucaryotes. Have a true nucleus and membrane bound organelles.
2. Kingdom Protista: Mostly unicellular, lack tissue organization. Most have flagella during life.
3. Kingdom Fungi: May be unicellular (yeasts) or multicellular (molds). Many are saprotrophs.
4. Kingdom Plantae: Multicellular, photosynthetic.
5. Kingdom Animalia: Multicellular, heterotrophs that ingest food through a mouth or oral cavity.

6. Five-Kingdom Classification System

7. Classification of Organisms Scientific Nomenclature
Scientific nomenclature: Universal system for naming and classifying living organisms. Initially developed in the 18th century by Carl Linnaeus.
Binomial nomenclature: Each organism (species) has a two part name. Names are either italicized or underlined.
Genus name: Always capitalized, always a noun. May use initial.
species name: Always lower case, usually an adjective.
Names are usually derived from Latin (or Greek) or may have latinized endings. Examples:
Homo sapiens (H. sapiens): Human
Penicillium notatum (P. notatum): Mold that produces penicillin
Canis familiaris (C. familiaris): Domestic dog

8. Classification of Organisms Hierarchy of Taxonomic Categories DOMAIN
Kingdom
Phylum or Division (Bacteria)
Class
Order
Family
Genus
species

9. Taxonomic Categories
Division
(Bacteria)

10. Bacterial Groups
The most widely accepted taxonomic classification for bacteria is in Bergey’s Manual of Systematic Bacteriology
Close to 5000 bacterial species identified and classified
Millions of bacterial species have not been isolated or cultured (up to 99.5% of existing species)
Bergey’s Manual is updated regularly. Prokaryotes are grouped into 27 phyla based on ribosomal RNA sequence:
24 Bacteria phyla
3 Archaea phyla
Each phylum is divided into sections according to:
Cell shape, arrangement, and motility
Nutritional and metabolic properties
Each phylum contains one or more Genus (plural Genera) 1 1 1

11. Prokaryotic Taxonomy

12. Survey of Archaea
Have features that distinguish them from most bacteria:
Unique ribosomal RNA (rRNA) sequences
No peptidoglycan in cell walls
Membrane lipids have branched hydrocarbon chains
Initial amino acid in proteins is Methionine (versus N-formylmethionine )
Extremophiles: Require extreme conditions to survive
Thermophiles: Only grow at temperatures above 45oC
Hyperthermophiles: Require temperatures over 80oC (Thermophilus aquaticus)
Halophiles: Need NaCl concentration greater then 9%. Many have red to orange pigments. Live in Dead Sea, Salt Lake, brine vats, salted fish, etc.
Methanogens: Largest group of archaea
Obligate anaerobes that generate methane gas from CO2, H2, and acids
Significant environmental impact by converting waste into methane
Live in ponds, lakes, swamps (“swamp gas”), ocean sediments, and intestinal tract of cows
Methane is a greenhouse gas which contributes to global warming 1 1 1

13. Four Divisions of Bacteria

14. Division I. Gram-Negative Bacteria
1. Spirochetes
Helical shape. Flexible.
Contain two or more axial filaments (endoflagella).
Move in corkscrew pattern.
Medically important members:
Treponema pallidum: Syphilis
Borrelia burgdorferi.: Lyme disease, relapsing fever
Leptospira: Leptospirosis

15. Gram Negative Bacteria Spirochetes

16. Syphilis is Caused by a Spirochete
Primary syphilitic chancre and secondary rash.
Source: Tropical Medicine and Parasitology, 1997

17. Lyme Disease is Caused by a Spirochete
Lyme Disease early lesion at tick bite site.
Source: Medical Microbiology, 1998

18. 2. Aerobic, Motile, Helical/Vibroid Gram-Negative Bacteria
Rigid helical shape or curved rods.
Lack axial filaments (endoflagella); have polar flagella instead.
Most are harmless aquatic organisms.
Genus Azospirillum fixes nitrogen in soil.
Genus Bdellovibrio attacks other bacteria.
Important pathogens include:
Campylobacter jejuni: Most common bacterial food-borne intestinal disease in the United States (2 million cases/year). Associated with undercooked chicken.
Helicobacter pylori: Causes most gastric ulcers in humans.
Campylobacter fetus: Abortions in domestic animals.

19. Gram Negative Bacteria Aerobic, Motile, Helical/Vibroid Gram-Negative Bacteria

20. Helicobacter pylori causes Gastric Ulcers

21. 4. Gram-Negative Aerobic Rods and Cocci
Contains many medically significant groups.
Genus Pseudomonas: Rods with polar flagella. Many secrete pigments in media.
Pseudomonas aeruginosa: Urinary tract infections (UTIs), septicemia, abcesses, burns, pulmonary infections in cystic fibrosis patients, and meningitis.
Genus Legionella: Rods that live in natural waters. Frequently found in air conditioning systems, humidifiers, showers, spas, and fountains.
Legionella pneumophila: Legionnaires’ disease (pneumonia, 1976) and Pontiac fever.
Genus Neisseria: Diplococci. Frequently found on human mucous membranes. Only grow well around body temperature.
Neisseria gonorrhea: Gonorrhea.
Neisseria meningitidis: Meningitis.

22. Neisseria gonorrhea Diplococci

23. Neisseria gonorrhea Causes Salpingitis

24. Neisseria gonorrhea Causes Neonatal Blindness
Ophtalmia neonatorum caused by Neisseria gonorrheae
Source: Microbiology Perspectives, 1999

25. 4. Gram-Negative Aerobic Rods and Cocci
(Continued)
Genus Acinetobacter: Plump rods or coccbacilli, nonmotile.
Acinetobacter baumannii: Infections (Bone, lung, blood, CSF) in Iraq war veterans, ICU patients. Multiple drug resistance.
Genus Moraxella: Aerobic egg-shaped cocco-bacilli.
Moraxella lacunata: Conjunctivitis.
Genus Brucella: Small nonmotile coccobacilli.
All species are obligate parasites of mammals.
Cause brucellosis. Can survive phagocytosis.
Genus Bordetella: Nonmotile rods. Virulent forms have capsules.
Bordetella pertussis: Whooping cough (P in DPT vaccine).
Genus Francisella: Small pleomorphic bacteria.
Francisella tularensis: Tularemia
Genera Rhizobium and Bradyrhizobium: Form nodules on legume roots and fix nitrogen in soil.

26. 5. Facultative Anaerobic Gram-Negative Rods
Many cause diseases of gastrointestinal tract.
Contains three medically significant families.
I. Family Enterobacteriaceae (Enterics)
Inhabit intestinal tracts of animals.
Motile bacteria with peritrichous flagella or nonmotile.
Many have fimbriae for attachment to mucous membranes and sex pili for exchange of DNA (antibiotic resistance genes)
Most ferment glucose and other sugars.
Genus Escherichia: E. coli is common inhabitant of human intestinal tract. Most strains are not pathogenic, but others can cause UTIs (urinary tract infections), traveler’s diarrhea, and food-borne disease.

27. I. Family Enterobacteriaceae (Continued)
Genus Salmonella: Almost all members are potential pathogens. Common inhabitants of animal GI tract. Can contaminate food (eggs, meat).
Salmonella typhi: Typhoid fever, severe illness.
Salmonella enteritidis: Causes salmonellosis, the second most common bacterial food-borne disease.
Over 1.3 million cases/year in the U.S.
Genus Shigella: Only found in humans. Second most common cause of traveler’s diarrhea.
Genus Klebsiella: Cause respiratory and UTIs.
Klebsiella pneumoniae: Antibiotic resistant strains cause pneumonia and nosocomial infections.
Genus Serratia: Opportunistic respiratory and urinary tract infections.
Serratia marcescens: Produces a red pigment. Important cause of nosocomial infections.

28. I. Family Enterobacteriaceae (Continued)
Genus Proteus: Actively motile. Cause UTIs, wound infections, and infant diarrhea (nosocomial).
Genus Yersinia:
Yersinia pestis: Causes bubonic plague (black death). Transmitted by fleas, respiratory droplet, and contact with animals.
Genus Erwinia: Important plant pathogens.
Genus Enterobacter: Cause UTIs and nosocomial infections.

29. 5. Facultative Anaerobic Gram-Negative Rods
II. Family Vibrionaceae
Found in aquatic habitats.
Straight or slightly curved rods
Genus Vibrio: Slightly curved rods.
Vibrio cholerae: Cholera, profuse & watery diarrhea.
Vibrio parahaemolyticus: Gastroenteritis. Shellfish.

30. Cholera is Caused by Vibrio cholerae
Rice-water stool of cholera.
Source: Tropical Medicine and Parasitology, 1995

31. 5. Facultative Anaerobic Gram-Negative Rods
III. Family Pasterellaceae
Found in aquatic habitats.
Straight or slightly curved rods
Genus Pasteurella: Pathogens of domestic animals.
Genus Hemophilus: Important pathogens that inhabit mucous membranes of upper respiratory tract, mouth, vagina, and intestinal tract. Require blood in culture.
Hemophilus influenzae: Causes meningitis, ear infections, bronchitis, arthritis, and pneumonia in children.
H. ducreyi: Cause of sexually transmitted chancroid.
Genus Gardnerella: Not assigned to any family.
G. vaginalis causes common form of vaginitis.

32. 6. Anaerobic Gram-Negative Rods
May be straight, helical, or curved.
Genus Bacteroides: Nonmotile. Live in human intestinal tract (1 billion/gram of feces) and gum crevices. Cause peritonitis, abscesses, and deep tissue infections.
Genus Fusobacterium: Long slender rods with pointed tips. Found in gingival crevices, cause dental abscesses.
7. Sulfur-Reducing Bacteria
Obligate anaerobes that release H2S into the atmosphere.
Found in soil and intestinal tract of animals. Ecologically important.

33. Gram negative bacteria.
8. Anaerobic Gram-Negative Cocci
Nonmotile cocci typically found in pairs.
Genus Veillonella: Cause dental plaque.
9. Rickettsias and Chlamydias
Gram negative bacteria.
Obligate intracellular parasites.
Rickettsias: Rod shaped bacteria or coccobacilli, highly pleomorphic. Transmitted to humans by insects and ticks (except for Coxiella burnetti which causes Q fever).
Genus Ehrlichiae: Live in white blood cells.
Genus Rickettsia: Cause spotted group fevers (Rocky mountain spotted fever, endemic typhus).

34. Rickettsias are Intracellular Parasites

35. Chlamydias: Cocci shaped bacteria
Chlamydias: Cocci shaped bacteria. Transmitted to humans by interpersonal contact or by airborne respiratory routes.
Unique life cycle: Form a reticulate and elementary bodies in infected cells.
Three species:
Chlamydia trachomatis: Causes blindness in humans and nongonococcal urethritis (most common STD in U.S.).
C. psittaci: Parrot fever.
C. pneumoniae: Mild pneumonia.

36. Division II. Gram-Positive Bacteria
17. Gram-Positive Cocci
Non-spore forming cocci.
Aerobic to strictly anaerobic.
Pyogenic (pus-forming)
Genus Staphylococcus: Tend to form grape-like clusters. Grow well under high osmotic pressure and low moisture.
Very common infections, because almost always found on skin and in nasal mucous membranes.
Staphylococcus aureus: (aureus = golden) Yellow pigmented colonies. Produce several toxins. Cause pimples, sties, skin abscesses, toxic shock syndrome, food poisoning, and nosocomial infections.
MRSA (Methicillin Resistant S. aureus): Antibiotic resistant S. aureus is a growing problem.
Vancomycin is last line of defense against antibiotic resistant strains.

37. Diseases Caused by Staphylococcus aureus
Scalded Sty Toxic Shock
Skin Syndrome Syndrome

38. 17. Gram-Positive Cocci
Genus Streptococcus: Most are pathogens. Tend to appear in chains or pairs. Do not use oxygen, but most are aerotolerant. Classified based on their effect on red blood cells (hemolysis).
Cause a wide range of diseases: Strep throat, respiratory infections, abscesses, puerperal fever, and opportunistic infections.
A flesh eating Streptococcus strain emerged in 1994 and After initial infection, bacteria live on dead flesh, produce toxins, and are not treatable by antibiotics.
Streptococcus pneumoniae: Bacterial pneumonia, ear infections, meningitis, and sinus infections.
Streptococcus pyogenes: Strep throat, scarlet fever, rheumatic fever, impetigo, skin infections, erysipelas, childbirth (puerperal) fever, glomerulonephritis, and flesh eating infections.

39. Scarlet Fever is Caused by a Strain of Streptococcus pyogenes

40. Flesh-Eating Streptococcus pyogenes
Necrotizing fasciitis with blood filled vesicles.
Source: Perspectives in Microbiology, 1995

41. Erysipelas is Caused by Strep. pyogenes
Erysipelas on face due to S. pyogenes infection
Source: Color Guide to Infectious Diseases, 1992

42. 18. Endospore-Forming Gram-Positive Rods and Cocci
Aerobic to strictly anaerobic.
Motile and nonmotile.
Survive harsh environmental conditions.
Genus Bacillus: Rod shaped bacteria.
Bacillus anthracis: Causes anthrax a disease of cattle. Large (4-8 um) nonmotile facultative anaerobe.
Bacillus thuringiensis: Kills insects, used by gardeners.
Genus Clostridium: Rod shaped bacteria, obligate anaerobes.
Clostridium tetani: Causes tetanus (T in DPT vaccine).
Clostridium botulinum: Causes botulism (source of Botox).
Clostridium perfringens: Causes gas gangrene and foodborne diarrhea.
Clostridium dificile: Causes diarrhea, especially after antibiotics.

43. Tetanus is Caused by Clostridium tetani
Neonatal Tetanus (Wrinkled brow and risus sardonicus)
Source: Color Guide to Infectious Diseases, 1992

44. Gangrene Caused by Clostridium perfringens
Severe gangrene caused by Clostridium perfringens.
Source: Tropical Medicine and Parasitology, 1997

45. 19. Regular Nonsporing Gram-Positive Rods
Genus Lactobacillus: Produce lactic acid which inhibits the growth of other bacteria. In humans live in vagina, intestinal tract, and mouth. Used commercially to make yogurt, pickles, sauerkraut, and buttermilk.
Genus Listeria: Contaminates dairy products.
Listeria monocytogenes: Survives in phagocytic cells and grows in refrigerators.
Causes listeriosis.
Infection of pregnant women can cause stillbirth or severe damage to fetus.

46. 20. Irregular Nonsporing Gram-Positive Rods
Club shaped (Corynebacteria), pleomorphic.
May be anaerobic or aerobic.
Important pathogens:
Corynebacterium diphtheriae: Cause diphtheria (D in DPT vaccine).
Propionibacterium acnes: Causes acne.

47. 21. Mycobacteria Important pathogens: Aerobic, non-spore-forming rods.
Stain Gram-positive, but cell wall structure is more similar to Gram-negative bacteria.
Waxy cell wall with mycolic acids (instead of peptidoglycan).
Acid-fast, drug resistant, resistant to drying, and pathogenic due to waxy cell wall.
Grow very slowly.
Tend to cause chronic infections.
Important pathogens:
Mycobacterium tuberculosis: Causes tuberculosis.
Mycobacterium leprae: Causes leprosy.

48. Mycobacterium leprae Causes Leprosy
Source: Tropical Medicine and Parasitology, 1995

49. Mycobacterium leprae Causes Leprosy
Severe bone destruction in advanced leprosy
Source: Diagnostic Pictures in Infectious Diseases, 1995

50. 22. Nocardioforms 25. Actinomycetes
Gram-positive, filamentous, aerobic.
Many are acid fast.
Common in soil.
Genus Nocardia: Form filaments which fragment into short rods to reproduce.
Nocardia asteroides: Pulmonary infections, mycetoma, abscesses.
25. Actinomycetes
Gram-positive, filamentous, resemble molds.
Genus Streptomyces: Live in soil. Give soil its musty odor. Produce hundreds of antibiotics.

51. Division III. Wall-Less Bacteria
30. Mycoplasmas
Do not form cell walls.
Most are aerobes or facultative anaerobes.
Highly pleomorphic.
Can produce filaments that resemble fungi.
Produce very small colonies (1 nm in diameter).
Smallest free-living cells: 0.1 to 0.25 mm in diameter.
Can pass through bacterial filters.
Most important human pathogen:
Mycoplasma pneumoniae: Walking pneumonia.