1. Classification of Bacteria

3. Microbial World
A major biologic division separates the eukaryotes and prokaryotes
Cells from animals, plants, and fungi are eukaryotes (Greek for "true nucleus"), whereas bacteria and blue-green algae belong to the prokaryotes (Greek for "primitive nucleus").

4. Prokaryotes - Eukaryotes

5. Prokaryotes - Eukaryotes

6. Taxonomy
Classification, nomenclature, and identification are the three separate but interrelated areas of taxonomy
Classification can be defined as the arrangement of organisms into taxonomic groups (taxa) on the basis of similarities or relationships
Nomenclature is naming an organism by international rules according to its characteristics

7. Taxonomy
Identification refers to the practical use of a classification scheme:
(1) to isolate and distinguish desirable organisms from undesirable ones;
(2) to verify the authenticity or special properties of a culture; or, in a clinical setting,
(3) to isolate and identify the causative agent of a disease.
refers to the classification and grouping of organisms
based on genotypic (genetic) and phenotypic (observable) similarities and differences

8. Taxonomy Phenotypic Classification of Bacteria:
Microscopic morphology
Macroscopic morphology
Biotyping
Serotyping
Antibiogram patterns
Phage typing
Genotypic Classification of Bacteria:
Guanine plus cytosine ratio
DNA hybridization
Nucleic acid sequence analysis
Plasmid analysis
Ribotyping
Chromosomal DNA fragment analysis

9. The rank of taxonomy can be seen in this table:
Grading
Example
Kingdom
Prokaryote
Division
Gracilicutes
Class
Scotobacteria
Order
Eubacteriales
Family
Enterobacteriaceae
Genus
Escherichia
Species
coli

10. Nomenclature provides naming assignments for each organism
family name is capitalized and has an-aceae ending (e.g., Micrococcaceae)
genus name is capitalized and followed by the species name, begins with a lowercase letter; should be italicized in print but underlined in the script (e.g., Staphylococcus aureus or Staphylococcus aureus)

11. Nomenclature
using the first letter of the genus followed by a period and the species epithet (name) (e.g., S. aureus)
Species abbreviated sp. (singular) or spp. (plural) is used when the species is not specified
When referred to as a group, their names are neither capitalized nor underlined (e.g., staphylococci)
The plural of genus is genera (e.g., Enterobacteriaceae family)

12. Nomenclature
strain or variety – a culture derived from a single parent that differs in structure or metabolism from other cultures of that species (biovars, morphovars)
type – a subspecies that can show differences in antigenic makeup (serotype or serovar), susceptibility to bacterial viruses (phage type) and in pathogenicity (pathotype)

13. Four Groups Based on Cell Wall Composition
Gram-positive cells
Gram-negative cells
Bacteria without cell walls
Bacteria with chemically unique cell walls

14. Peptidoglycan
N-acetylmuramic acid
(NAM)
Macromolecule composed of a repeating framework of long chains cross-linked by short peptide fragments
Unique to Bacteria
Composed of 2 sugars: NAG & NAM
Sugars alternate in the backbone
Rows linked by polypeptides
Provides strong, flexible support to keep bacteria from bursting or collapsing because of changes in osmotic pressure
N-acetylglucosamine
(NAG)

16. Gram Positive Cell Wall
Consists of
A thick, homogenous sheath of peptidoglycan nm thick
Tightly bound acidic polysaccharides, including teichoic acid and lipoteichoic acid
Retains crystal violet with iodine as a mordant

17. Gram Negative Cell Wall
Consists of
An outer membrane containing lipopolysaccharide (LPS)
Thin shell of peptidoglycan between inner and outer membranes
Periplasm
Inner membrane
Loses crystal violet-iodine complex when cells are exposed alcohol (decolorization step) and stains red with safranin counterstain

18. Be able to identify all the parts of a Gram + & - cell wall for the next exam

19. Bacteria with Chemically Unique Cell Walls
Acid-Fast Cells
Mycobacterium species
Gram + type of cell wall
Unique lipid
Mycolic acid – waxy substance
Does not decolorize

20. Rickettsia – Chemically Unique Cell Wall
Stains Gram -
Cell wall contains diaminopimelic acid & lacks teichoic acid
0.25 m in diameter
Obligate intracellular pathogens
Encapsulated
Enter cell by induced phagocytosis
Divide rapidly once inside
Pathogens that alternate between mammals and fleas, lice or ticks
Rickettsia rickettisii – Rocky Mountain spotted fever
Rickettsia prowazekii – epidemic typhus
Coxiella burnetti – Q fever

21. Chlamydia – Chemically Unique Cell Wall
Obligate intracellular parasites
0.3 and 1.0 m in diameter
Cell wall contains an outer lipopolysaccharide membrane but lacks peptidoglycan
Contains cysteine-rich proteins that are assumed to be the functional equivalent of peptidoglycan
Stains Gram -
Chlamydia trachomatis
The most common sexually transmitted disease
Chlamydia psittaci
Ornithosis, parrot fever
Chlamydia pneumoniae
Lung infection

22. Bacteria without Cell Walls - Mycoplasma
Lack a rigid cell wall during their entire life cycle
Smallest known organisms – smallest genomes (other than viruses)
Diameter ranges from 0.15 m to 0.30 m
Do not stain with the Gram stain
Pleomorphic
Tiny pleomorphic cocci, short rods, short spirals, and sometimes doughnut shape
Mycoplasma pneumoniae
Atypical pneumonia in humans

23. Bergey’s Manual of Systematic Bacteriology.
Most widely accepted taxonomic classification for bacteria is Bergey’s Manual of Systematic Bacteriology.
5000 bacterial species identified, 3100 classified.
Bacteria are divided into four divisions (phyla) according to the characteristics of their cell walls.
Gram-Negative Bacteria (Division I)
Gram-Positive Bacteria (Division II)
Wall-Less Bacteria (Division III)

24. Bergey’s Manual of Systematic Bacteriology.
Each division is divided into sections according to:
Gram stain reaction
Cell shape
Cell arrangements
Oxygen requirements
Motility
Nutritional and metabolic properties
Each section contains several genera. 1 1 1

25. Bergey’s Manual of Systematic Bacteriology.
Gram-Negative Bacteria (Division I)
Gram-Positive Bacteria (Division II)
Wall-Less Bacteria (Division III)

26. Bergey’s Manual of Systematic Bacteriology.
Gram-Negative Bacteria (Division I)
a. Spirochetes
Helical shape. Flexible.
Contain two or more axial filaments (endoflagella).
Move in corkscrew pattern.
Medically important members:
Treponema pallidum: Syphilis
Borrelia spp.: Lyme disease, relapsing fever
Leptospira: Leptospirosis
Borrelia Burgdorferi
Treponema pallidum
Leptospira spp.

27. Bergey’s Manual of Systematic Bacteriology.
Gram-Negative Bacteria (Division I)
b. 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.

28. Bergey’s Manual of Systematic Bacteriology.
Gram-Negative Bacteria (Division I)
c. Gram-Negative Aerobic Rods and Cocci
Contains many medically significant groups (Genera).
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.
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.
Neisseria: Diplococci. Frequently found on human mucous membranes. Only grow well around body temperature.
Neisseria gonorrhea: Gonorrhea.
Neisseria meningitidis: Meningitis.

29. Bergey’s Manual of Systematic Bacteriology.
Gram-Negative Bacteria (Division I)
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.

30. Bergey’s Manual of Systematic Bacteriology.
Gram-Negative Bacteria (Division I)
d. Facultative Anaerobic Gram-Negative Rods
Many cause diseases of gastrointestinal tract;
Contains three medically significant families.
1) 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.

31. Bergey’s Manual of Systematic Bacteriology.
Gram-Negative Bacteria (Division I)
d. Facultative Anaerobic Gram-Negative Rods
1) Family Enterobacteriaceae (Enterics) Lanjutan
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.
S. 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.

32. Bergey’s Manual of Systematic Bacteriology.
Gram-Negative Bacteria (Division I)
d. Facultative Anaerobic Gram-Negative Rods
1) Family Enterobacteriaceae (Enterics) Lanjutan
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..

33. Bergey’s Manual of Systematic Bacteriology.
Gram-Negative Bacteria (Division I)
d. Facultative Anaerobic Gram-Negative Rods
2) 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.

34. Bergey’s Manual of Systematic Bacteriology.
Gram-Negative Bacteria (Division I)
d. Facultative Anaerobic Gram-Negative Rods
3) 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.

35. Bergey’s Manual of Systematic Bacteriology.
Gram-Negative Bacteria (Division I)
e. 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.

36. Bergey’s Manual of Systematic Bacteriology.
Gram-Negative Bacteria (Division I)
f. Sulfur-Reducing Bacteria
Obligate anaerobes that release H2S into the atmosphere.
Found in soil and intestinal tract of animals.
Ecologically important.

37. Bergey’s Manual of Systematic Bacteriology.
Gram-Negative Bacteria (Division I)
g. Anaerobic Gram-Negative Cocci
Nonmotile cocci typically found in pairs.
Genus Veillonella: Cause dental plaque

38. Bergey’s Manual of Systematic Bacteriology.
Gram-Negative Bacteria (Division I)
h. 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).
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.

39. Bergey’s Manual of Systematic Bacteriology.
Gram-Negative Bacteria (Division I)
Gram-Positive Bacteria (Division II)
Wall-Less Bacteria (Division III)

40. Bergey’s Manual of Systematic Bacteriology.
Gram-Positive Bacteria (Division II)
a. 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.
Antibiotic resistance is big problem.
Vancomycin is last line of defense against antibiotic resistant strains.

41. Bergey’s Manual of Systematic Bacteriology.
Gram-Positive Bacteria (Division II)
a. 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, puerperal fever, glomerulonephritis.

42. Bergey’s Manual of Systematic Bacteriology.
Gram-Positive Bacteria (Division II)
b. 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.
Clostridium perfringens: Causes gas gangrene and foodborne diarrhea.

43. Bergey’s Manual of Systematic Bacteriology.
Gram-Positive Bacteria (Division II)
b. 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.
Clostridium perfringens: Causes gas gangrene and foodborne diarrhea.

44. Bergey’s Manual of Systematic Bacteriology.
Gram-Positive Bacteria (Division II)
d. Irregular Nonsporing Gram-Positive Rods
Club shaped (Corynebacteria); Pleomorphic; May be anaerobic or aerobic.
Corynebacterium diphtheriae
Important pathogens; Cause diphtheria (D in DPT vaccine);
Propionibacterium acnes: Causes acne.

45. Bergey’s Manual of Systematic Bacteriology.
Gram-Positive Bacteria (Division II)
e. Mycobacteria
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

46. Bergey’s Manual of Systematic Bacteriology.
Gram-Positive Bacteria (Division II)
f. Nocardioforms
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

47. Bergey’s Manual of Systematic Bacteriology.
Gram-Positive Bacteria (Division II)
g. Actinomycetes
Gram-positive, filamentous, resemble molds.
Common in soil.
Genus Streptomyces:
Live in soil.
Give soil its musty odor.
Produce hundreds of antibiotics

48. Bergey’s Manual of Systematic Bacteriology.
Gram-Negative Bacteria (Divisi I)
Gram-Positive Bacteria (Divisi II)
Wall-Less Bacteria (Divisi III)

49. Bergey’s Manual of Systematic Bacteriology.
Wall-Less Bacteria (Division III)
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).
Very small cells: 0.1 to 0.25 mm in diameter.
Can pass through bacterial filters.
Most important human pathogen:
Mycoplasma pneumoniae: Walking pneumonia.