1. CLASSIFICATION AND STRUCTURE OF MICROORGANISMS.
Chair of Microbiology, Virology, and Immunology
CLASSIFICATION AND STRUCTURE OF MICROORGANISMS.

2. Comparison of the three domains
Characteristic
Eubacteria
Archaea
Eucarya
Cell type
Prokaryote
Eukaryote
Cell wall
Peptidoglycan
Varies
Membrane lipids
Unbranched
Branched
Sensitive to antibiotics?
Yes No
Circular chromosome?
No (except in mitochondria and chloroplasts)
Histones?

3. Prokaryotes

6. Classification Systems in the Procaryotae
Microscopic morphology
Macroscopic morphology – colony appearance
Physiological / biochemical characteristics
Chemical analysis
Serological analysis
Genetic and molecular analysis
G + C base composition
DNA analysis using genetic probes
Nucleic acid sequencing and rRNA analysis

7. Bacterial Taxonomy Based on Bergey’s Manual
Bergey’s Manual of Determinative Bacteriology – five volume resource covering all known procaryotes
classification based on genetic information –phylogenetic
two domains: Archaea and Bacteria
five major subgroups with 25 different phyla

8. Taxonomy
Domain
Kingdom
Phylum
Class
Order
Family
Genus
species

9. Major Taxonomic Groups of Bacteria
Vol 1A: Domain Archaea
primitive, adapted to extreme habitats and modes of nutrition
Vol 1B: Domain Bacteria
Vol 2-5:
Phylum Proteobacteria – Gram-negative cell walls
Phylum Firmicutes – mainly Gram-positive with low G + C content
Phylum Actinobacteria – Gram-positive with high G + C content

10. Microbial Phylogeny Phylogeny of domain Bacteria
The 2nd edition of Bergey’s Manual of Systematic Bacteriology divides domain Bacteria into 23 phyla.

11. Microbial Phylogeny Phylogeny of domain Bacteria (cont.)
Phylum Proteobacteria
The largest group of gram-negative bacteria
Extremely complex group, with over 400 genera and 1300 named species
All major nutritional types are represented: phototrophy, heterotrophy, and several types of chemolithotrophy
Sometimes called the “purple bacteria,” although very few are purple; the term refers to a hypothetical purple photosynthetic bacterium from which the group is believed to have evolved

12. Microbial Phylogeny Phylogeny of domain Bacteria (cont.)
Phylum Proteobacteria (cont.)
Divided into 5 classes: Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, Epsilonproteobacteria

13. Microbial Phylogeny Phylogeny of domain Bacteria (cont.)
Phylum Proteobacteria (cont.)
Significant groups and genera include:
The family Enterobacteriaceae, the “gram-negative enteric bacteria,” which includes genera Escherichia, Proteus, Enterobacter, Klebsiella, Salmonella, Shigella, Serratia, and others
The family Pseudomonadaceae, which includes genus Pseudomonas and related genera
Other medically important Proteobacteria include genera Haemophilus, Vibrio, Camphylobacter, Helicobacter, Rickessia, Brucella

14. Microbial Phylogeny Phylogeny of domain Bacteria (cont.)
Phylum Firmicutes
“Low G + C gram-positive” bacteria
Divided into 3 classes
Class I – Clostridia; includes genera Clostridium and Desulfotomaculatum, and others
Class II – Mollicutes; bacteria in this class cannot make peptidoglycan and lack cell walls; includes genera Mycoplasma, Ureaplasma, and others
Class III – Bacilli; includes genera Bacillus, Lactobacillus, Streptococcus, Lactococcus, Geobacillus, Enterococcus, Listeria, Staphylococcus, and others

15. Microbial Phylogeny Phylogeny of domain Bacteria (cont.)
Phylum Actinobacteria
“High G + C gram-positive” bacteria
Includes genera Actinomyces, Streptomyces, Corynebacterium, Micrococcus, Mycobacterium, Propionibacterium
Phylum Chlamidiae
Small phylum containing the genus Chlamydia

16. Microbial Phylogeny Phylogeny of domain Bacteria (cont.)
Phylum Spirochaetes
The spirochaetes
Characterized by flexible, helical cells with a modified outer membrane (the outer sheath) and modified flagella (axial filaments) located within the outer sheath
Important pathogenic genera include Treponema, Borrelia, and Leptospira
Phylum Bacteroidetes
Includes genera Bacteroides, Flavobacterium, Flexibacter, and Cytophyga; Flexibacter and Cytophyga are motile by means of “gliding motility”

17. Procaryotae Kingdom has 4 Divisions according to the structure of cell wall and Gram staining:
Gracilicutes (gracilis - thin, cutis - skin) – Gram-negative bacteria,
Firmicutes (firmus - firm) – Gram-positive bacteria,
Tenericutes (tener – soft, tender) – microbes without cell wall,
Mendosicutes (mendosus - mistaket) – microbes with atipical peptidoglican

18. Bacterial Nomenclature
Binomial naming system
Two word naming system
First word is genus name
Always capitalized
Escherichia
Second word is species name
Not capitalized
coli
When writing full name genus usually abbreviated
E. coli
Full name always italicized
Or underlined

19. Species is population of microbes, which have the only source of origin, common genotype, and during the present stage of evolution are characterized by similar morphological, biochemical, physiological and other signs

20. Infrasubspecies subdivisions
If deviations from the typical species properties are found on examination of the isolated bacteria, then culture is considered a subspecies.
Infrasubspecies subdivisions
serovar (antigenic properties)
morphovar (morphological properties)
chemovar (chemical properties)
biovar (biochemical or physiological properties)
pathovar (pathogenic properties)
phagovar (relation to phages)

21. The term clone was applied to population of cells derived from a single cell
Population is an elementary evolutional unit (structure) of a definite species
The term strain designates a microbial culture obtained from the different sources or from one source but in different time
Or: A subgroup within a species with one or more haracteristics that distinguish it from other subgroups in the species

22. Morphological Classification of Bacteria
Bacteria (Gk. bakterion - small staff) are unicellular organisms lacking chlorophyll.
Morphological Classification of Bacteria
Morphologically, bacteria possess four main forms:
spherical (cocci)
rod-shaped (bacteria, bacilli, and clostridia)
spiral-shaped (vibrios, spirilla and spirochaetes)
thread-shaped (non-pathogenic)

24. Cocci groupings Coccus Tetrad Diplococcus Sarcinae Streptococcus
Staphylococcus
Streptococcus

25. Cocci (Gk. kokkos berry)
Cocci (Gk. kokkos berry). These forms of bacteria are spherical, ellipsoidal, bean-shaped, and lanceolate. Cocci are subdivided into six groups according to cell arrangement, cell division and biological properties
Micrococci (Micrococcus). The cells are arranged singly or irregularly. They are saprophytes, and live in water and in air ( M. roseus, M. luteus, etc.).

26. Diplococci (Gk. diplos double) divide in one plane and remain attached in pairs. These include: Meningococcus (causative agent of epidemic cerebrospinal meningitis, and gonococcus, causative agent of gonorrhoea and blennorrhoea) Pneumococcus (causative agents of pneumonia)

27. Streptococci (Gk. streptos curved, kokkos berry) divide in one plane and are arranged in chains of different length. Some streptococci are pathogenic for humans and are responsible for various diseases.

28. Tetracocci (Gk. tetra four) divide in two planes at right angles to one another and form groups of fours. They very rarely produce diseases in humans.

29. Staphylococci (Gk. staphyle cluster of grapes) divide in several planes resulting in irregular bunches of cells, sometimes resembling clusters of grapes. Some species of Staphylococci cause diseases in man and animals

30. Sarcinae (L. sarcio to tie) divide in three planes at right angles to one another and resemble packets of 8, 16 or more cells. They are frequently found in the air. Virulent species have not been encountered

31. Rods. Rod-shaped forms are subdivided into: bacteria, bacilli,
clostridia
Bacteria include those microorganisms which, as a rule, do not produce spores (colibacillus, and organisms responsible for enteric fever, paratyphoids, dysentery, diphtheria, tuberculosis, etc.).
Bacilli and clostridia include organisms the majority of which produce spores (hay bacillus, bacilli responsible for anthrax, tetanus, anaerobic infections, etc.)

32. According to their arrangement, cylindrical forms can be subdivided into three groups:
monobacteria
monobacilli
C. tetani
E. coli
Y. pestis
C. botulinum

33. diplobacteria
diplobacilli
K. pneumoniae

34. streptobacteria
streptobacilli
Haemophilus ducreyi
(chancroid)
Bacillus anthracis
(anthrax)

35. Spiral-shaped bacteria
Vibriones (L. vibrio to vibrate) are cells which resemble a comma in appearance. Typical representatives of this group are Vibrio cholerae, the causative agent of cholera, and aquatic vibriones which are widely distributed in fresh water reservoirs.

36. Spirilla (L. spira coil) are coiled forms of bacteria exhibiting twists with one or more turns. Only one pathogenic species is known {Spirillum minus} which is responsible for a disease in humans transmitted through the bite of rats and other rodents (rat-bite fever, sodoku)

37. Spirochaetes (L. spira curve, Gk
Spirochaetes (L. spira curve, Gk. chaite cock, mane) differ from bacteria in structure with a corkscrew spiral shape
Borrelia. Their cells have large, obtuse-angled, irregular spirals, the number of which varies from 3 to 10. Pathogenic for man are the causative agents of relapsing fever transmitted by lice (Borrelia hispanica), and by ticks (Borrelia persica, etc.). These stain blue-violet with the Romanowsky-Giemsa stain

39. Leptospira (Gk. leplos thin, speira coil) are characterized by very thin cell structure. The leptospirae form 12 to 18 coils wound close to each other, shaping small primary spirals. The organisms have two paired axial filaments attached at opposite ends (basal bodies) of the cell and directed toward each other.
Leptospira interrogans which is pathogenic for animals and man cause leptospirosis

40. Treponema (Gk. trepein turn, nema thread) exhibits thin, flexible cells with 6-14 twists. The micro-organisms do not appear to have a visible axial filament or an axial crest when viewed under the microscope
A typical representative is the causative agent of syphilis Treponema pallidum

41. Properties of prokaryotes and eukaryotes
The nucleoid has no membrane separating it from the cytoplasm
Karyoplasm is separated from the cytoplasm by membrane
Chromosome is a one ball of double twisted DNA threads. Mitosis is absent
Chromosome is more than one, There is a mitosis
DNA of cytoplasm are represented in plasmids
DNA of cytoplasm are represented in organelles
There aren’t cytoplasmic organelle which is surrounded by membrane
There are cytoplasmic organelle which is surrounded by membrane
The respiratory system is localized in cytoplasmic membrane
The respiratory system is localized mitochondrion
There are ribosome 70S in cytoplasm
There are ribosome 80S in cytoplasm
Peptidoglycan are included in cell’s wall (Murein)
Peptidoglycan aren’t included in cell’s wall

42. The structure of procaryotes

44. Nucleus. The prokaryotic nucleus can be seen with the light microscope in stained material. It is Feulgen-positive, indicating the presence of DNA. Histonelike proteins have recently been discovered in bacteria and presumably play a role similar to that of histones in eukaryotic chromatin
The DNA is seen to be a single, continuous, "giant" circular molecule with a molecular weight of approximately 3 X 109. The unfolded nuclear DNA would be about 1-3 mm long (compared with an average length of 1 to 2 µm for bacterial cells)

45. Plasmids: R, Col, Hly, Ent, Sal
small circular, double-stranded DNA
free or integrated into the chromosome
duplicated and passed on to offspring
not essential to bacterial growth & metabolism
may encode antibiotic resistance, tolerance to toxic metals, enzymes & toxins
used in genetic engineering- readily manipulated & transferred from cell to cell
There may be several different plasmids in one cell and the numbers of each may vary from only one to 100s in a cell
Plasmids: R, Col, Hly, Ent, Sal

46. Prokaryotic Ribosome
A ribosome (70 S) is a combination of RNA and protein, and is the site for protein synthesis
Composed of large (50S) and small (30S) subunits
S = Svedverg unit, measures molecular size
The 80S ribosomes of eukaryotes are made up of 40S and 60S subunits.

47. Inclusions, granules Storage granules Gas vesicles
Metachromatic granules
Polysaccharide granules
Lipid inclusions
Sulfur granules
Carboxyzomes
Magnetosomes
Gas vesicles

48. Corynebacterium diphtheriae
Volutin granules
Corynebacterium diphtheriae
Neisser's staining
Loeffler's technique

49. Cell Envelope Composted of A. The cytoplasmic membrane
To act as a physical barrier btw cytoplasm and environments and selectively controls the movement of substaces into and out of the cell
“Semipermeable”
B. Cell wall
The rigid layer that protect the fragile cytoplasmic membrane from rupturing
To maintains cell’s shape
C. Capsule or slime layer (glycocalyx)

50. Cell membrane
Bacterial plasma membrane are composed of 40 percent phospholipid and 60 percent protein.
The phospholipids are amphoteric molecules with a polar hydrophilic glycerol "head" attached via an ester bond to two nonpolar hydrophobic fatty acid tails, which naturally form a bilayer in aqueous environments. Dispersed within the bilayer are various structural and enzymatic proteins which carry out most membrane functions.
Peripheral
Membrane
Protein
Phospholipid
Integral
Membrane
Protein
Peripheral
Membrane
Protein

51. Mesosome

52. The predominant functions of bacterial membranes are:
1. Osmotic or permeability barrier;
2. Location of transport systems for specific solutes (nutrients and ions);
3. Energy generating functions, involving respiratory and photosynthetic electron transport systems, establishment of proton motive force, and transmembranous, ATP-synthesizing ATPase;
4. Synthesis of membrane lipids (including lipopolysaccharide in Gram-negative cells);
5. Synthesis of murein (cell wall peptidoglycan);
6. Assembly and secretion of extracytoplasmic proteins;
7. Coordination of DNA replication and segregation with septum formation and cell division;
8. Chemotaxis (both motility per se and sensing functions);
9. Location of specialized enzyme system.

53. Cell wall Unique chemical structure
Distinguishes Gram positive from Gram-negative
bacteria and archaea bacterial species
Rigidity of cell wall is due to peptidoglycan (PTG)
Compound found only in bacteria
Archaea –psudomurein or other sugars, proteins, glycoproteins
Many antimicrobial interfere with synthesis of PTG
Penicillin; Lysozyme

54. Structure of peptidoglycan
Basic structure of peptidoglycan
Alternating series of two subunits
N-acetylglucosamin (NAG)
N-acetylmuramic acid (NAM)
Joined subunits form glycan chain
Glycan chains held together by string of four amino acids
Tetrapeptide chain:
L-ala-D-glu-DAP-D-ala
L-ala-D-glu-Lys-D-ala
Interpeptide bridge

55. Structures associated with gram-positive and gram-negative cell walls.
Differences of cell wall structure in Gram-positive and Gram negative cells
Structures associated with gram-positive and gram-negative cell walls.

56. L Forms

57. Glycocalyx Capsule Slime layer Protects bacteria from phagocytic cells
Enable attachment and aggregation of bacterial cells

58. Capsules
Most prokaryotes contain some sort of a polysaccharide layer outside of the cell wall polymer
Only capsule of B. anthracis consist of polypeptide (polyglutamic acid)

59. Capsule The capsule is covalently bound to the cell wall.
Associated with virulence in bacteria.
Example:
Streptococcus pneumoniae

60. Slime Layer The slime layer is loosely bound to the cell.
Carbohydrate rich material enhances adherence of cells on surfaces
Example:
Streptococcus mutans and “plaque formation”

61. Biofilms
The slime layer is associated with cell aggregation and the formation of biofilms
Example:
Staphylococcus epidermidis biofilms on catheter tips

62. General capsule function
Adhesion
Avoidance of immune response
Protection from dehydration
Protection of bacterial cells from engulfment by protozoa or white blood cells (phagocytes), or from attack by antimicrobial agents of plant or animal origin.
They provide virulent properties of bacteria (S. pneumoniae, B. anthracis)

63. Flagella 3 parts rotates 360o 1-2 or many distributed over entire cell
filament – long, thin, helical structure composed of proteins
hook- curved sheath
basal body – stack of rings firmly anchored in cell wall
rotates 360o
1-2 or many distributed over entire cell
functions in motility

64. Flagellar arrangements
1. Monotrichous – single flagellum at one end (cholera vibrio, blue pus bacillus),
2. Lophotrichous – small bunches arising from one end of cell (blue-green milk bacillus, Alcaligenes faecalis)
3. Amphitrichous – flagella at both ends of cell (Spirillum volutans),
4. Peritrichous – flagella dispersed over surface of cell, slowest E. coli, salmonellae of enteric fever and paratyphoids A and B

65. The rotation of the flagella enables bacteria to be motile.
Bacterial Motility
Flagella are important for:
Motility (dispersal)
Antigenic determinant
Number and location species specific
The rotation of the flagella enables bacteria to be motile.

66. Fimbriae are smaller than flagella and are important for attachment
Pili and Fimbriae
Short, hair-like structures on the surfaces of procaryotic cells
Proteinaceuse filaments (~20 nm in diameter)
Very common in Gram-negative bacteria
Functions:
Adherence to surface/ substrates: teeth, tissues
Involved in transfer of genetic information btw cells
Have nothing to do with bacterial movement (Except the twitching movement of Pseudomonas)
Fimbriae are smaller than flagella and are important for attachment

67. Bacterial endospores
Bacterial spores are often called “endospore” (since they are formed within the vegetative cell)
Produced in response to nutrient limitation or extreme environments
Highly resistant
Highly dehydrated (15% water)
Metabolically inactive
Stable for years
Not reproductive
Functions: to survive under an extreme growth conditions such as high temperature, drought, etc.
Bacillus, Clostridium, Sporolactobacillus, Thermoactinomyces, Sporosarcina, Desulfotomaculum species sporulate

68. Spore

69. Spores Key compositions: Structure Dipicolinic acid (DPA)
Calcium (Ca2+)
Structure
Core / Cytoplasm
Plasma membrane
Core wall/ spore wall
Cortex
Spore coat
Exosporium

70. Endospores

71. The sporulation process begins when nutritional conditions become unfavorable, depletion of the nitrogen or carbon source (or both) being the most significant factor. Sporulation involves the production of many new structures, enzymes, and metabolites along with the disappearance of many vegetative cell components.

72. Spores are located: Centrally (B. anthracis);
2) Terminally (С. tetani);
3) Subterminally (C. botulinum, C. perfringens)

74. The spores of certain bacilli are capable of withstanding boiling and high concentrations of disinfectants. They are killed in an autoclave exposed to saturated steam, at a temperature of C, and also at a temperature of C in a Pasteur hot-air oven.

75. Important Point: If you are having trouble
understanding lecture material:
Try reading your text
before attending lectures.
And take the time to read it well!