Microbiology and Microbes

Topics of study
• Introduction and Clasification of microbes

• Bacteria of Dental Diseases
• Characteristic of Deep Caries Lesion
• Intracanal & Periapical Infection
• Pathogenesis of Dental Infections
• Diagnostic microbiology and lab. methods
• Cross infection and control
Microbiology
• Study about microbes

• Microbes cannot be seen with unaided
eye
Loops, microscopes
Microbes and our live
Virus
AIDS SPOILED
BACTERIA
FOOD
FUNGI
INFECTION
1. Food Industry
2. Medical Field
3. Chemical
A. Taxonomy
B. Naming
C. Identification
Taxonomy & Phylogeny
Taxonomy: put organisms in to categories, or taxa
(singular: taxon), to show degrees of similarities among
organisms.
These similarities are due to relatedness- , all organisms
are related through evolution.
Systematics, or phylogeny, is the study of the

evolutionary history of organisms. The hierarchy of taxa
reflects evolutionary, or phylogenetic, relationships.
A. Phenotypic Taxonomy
• Morphology (cocci, bacilli, spirochaetes)
• Staining properties (Gram-positive, Gram-negative)
• cultural requirements (aerobic, facultative anaerobic,
anaerobic)
• Biochemical reactions (saccharolytic and asaccharolytic,
according to sugar fermentation reactions)
• Antigenic structure (serotypes).
B. Genotypic Taxonomy
• Genotypic classification and speciation of organisms →
becoming increasingly important and useful
• Genotypic taxonomy exploits the genetic characteristics,
which are more stable than the sometimes transient
phenotypic features of organisms
• These methods essentially evaluate the degree of DNA
homology of organisms in order to speciate them
• Examples: molecular guanine and cytosine (GC) content,
ribotyping, random amplification of polymorphic DNA (RAPD)
analysis and pulsed-field gel electrophoresis (PFGE).
How do organisms get their names?
Taxonomic Rank:
• Kingdom
• Divisi
• Klas
• Ordo
• Famili
• Genus
• Species
Hierarchical ranks in classification of organisms
• Every organism is assigned two names (binomial).
These names are the genus name and specific epithet
(species), and both names are printed underlined or
italicized.
• The genus name is always capitalized and is always a
noun. The species name is lowercase and is usually an
adjective.
• Because this system gives two names to each
organism, the system is called binomial nomenclature.
Scientific nomenclature (Carolus Linnaeus; 1735):
• First name: genus, Capitalized
• Second name: specific ephitet, not capitalized
→ Can be abbreviated with the initial of genus followed
by special ephitet.
→ Both name are italicized.
→ Discribing microbes: to honor researcher, to identify
the habitat or the color or the shape.
Ex.
• Streptococcus mutans ----- S. mutans
• Staphycococcus aureus ----- S. aureus
• Candida albicans ------ C. albicans
In 1978, Carl Woese devided a system of classification based
on the cellular organization of organisms. It groups all
organisms in three domains as follows:
1. Bacteria (cell walls contain a protein-carbohydrate complex called
peptidoglycan)
2. Archaea (cell walls, if present, lack peptidoglycan)
3. Eukarya, which includes the following:
• Protists (slime molds, protozoa, and algae)
• Fungi (unicellular yeasts, multicellular molds, and mushrooms)
• Plants (includes mosses, ferns, conifers, and flowering plants )
• Animals (includes sponges, worms, insects, and vertebrates)
Microorganisms:
• Prokaryotes
• Bacteria
• Archaea
• Eukaryotes
• Fungi
• Protozoa
• Algae
• Viruses
• Multicellular animal parasites
Prokaryotes
vs
Eukaryotes:
Prokaryotes & Eukaryotes:
• Chemically similar, in the sense that they both

contain nucleic acids, proteins, lipids, and
carbohydrates.
• They use the same kinds of chemical reactions
to metabolize food, build proteins, and store
energy.
Prokaryotes:
1. Their DNA is not enclosed within a membrane and is usually a
singular circularly arranged chromosome. (Some bacteria, such
as Vibrio cholerae, have two chromosomes)
2. Their DNA is not associated with histones (special chromosomal
proteins found in eukaryotes)
3. They lack membrane-enclosed organelles.
4. Their cell walls almost always contain the complex
polysaccharide peptidoglycan.
5. They usually divide by binary fission. During this process, the
DNA is copied, and the cell splits into two cells. Binary fission
involves fewer structures and processes than eukaryotic cell
division.
Eukaryotes:
1. Their DNA is found in the cell's nucleus, which is separated from
the cytoplasm by a nuclear membrane, the DNA is found in
multiple chromosomes.
2. Their DNA is consistently associated with chromosomal proteins
called histones and with nonhistones.
3. They have a number of membrane-enclosed organelles,
including mitochondria, endoplasmic reticulum, Golgi complex,
lysosomes, and sometimes chloroplasts.
4. Their cell walls, when present, are chemically simple.
5. Cell division usually involves mitosis, in which chromosomes
replicate and an identical set is distributed into each of two
nuclei.
Bacteria:
• Bacteria (singular: bacterium) are relatively simple,
single-celled (unicellular) organisms
• Cell wall contain a protein-carbohydrate complex
(peptidoglycan)
• Its genetic material is not enclosed in a special nuclear
membrane --- prokaryote
• Bacterial cells generally appear in one of several
shapes. Bacillus (rodlike), coccus (spherical or ovoid),
and spiral (corkscrew or curved) or square (rare)
Archaea:
• As bacteria, archaea consist of prokaryotic cells, but
if they have cell walls, the walls lack peptidoglycan
• Often found in extreme environments
• Main groups:
• Methanogene
• Extreme halophile
• Extreme thermophile
☞ Differentiate among the major characteristics of each group of microorganisms.
Archaea:
1. The methanogens, strict anaerobes that produce
methane (CH.) from carbon dioxide and hydrogen.
2. Extreme halophiles, which require high
concentrations of salt for survival.
3. Hyperthermophiles, which normally grow in
extremely hot environments.
Fungi:
• Fungi (singular: fungus) are eukaryotes, organisms
whose cells have a distinct nucleus containing the
cell's genetic material (DNA), surrounded by a
special envelope called the nuclear membrane.
• Fungi may be unicellular (yeast) or multicellular
(mould ex. mushroom)
• Have cell walls composed primarily of a substance
called chitin.
• Fungi can reproduce sexually or asexually
Protozoa:
• Unicellular eukaryotic microbes
• May move using pseudopods, flagella, or cilia
• Amoebas move by using extensions of their
cytoplasm called pseudopods (false feet).
• Other protozoa have long flagella or numerous
shorter appendages for locomotion called cilia.
Algae:
• Photosynthetic eukaryotes with a wide variety of shapes
and both sexual and asexual reproductive forms
• Usually unicellular
• The cell walls of many algae, are composed of a
carbohydrate called cellulose.
• Algae are abundant in fresh and salt water, in soil, and in
association with plants
• algae produce oxygen and carbohydrates that are then
utilized by other organisms
Viruses:
• Acellular
• Very small and can only be seen by an electron
microscope
• Simple structure: contains only one type of nucleic
acid either DNA or RNA
• Surrounded by a protein coat
• Viruses can reproduce only by using the cellular
machinery of other organisms.
Microbe and Human Welfare
• Recycling vital elements
• Sewage Treatment: Using microbes to
recycle water
• Bioremediation: Using microbes to clean
up pollutants
• Insect pest control by microorganisms
• Modern biotechnology and recombinant
DNA Technology
Normal Flora in Our Body
Normal Flora
• The microorganism (m.o) that establish

more or less permanent residence
(colonize) but do not produce disease
under normal conditions
• Benefit the host by preventing the
overgrowth of harmful m.o
Normal Flora
Protecs cell host by:

• Competing for nutrients
• Producing substances harmful to the
invading m.o
• Affecting condition of environment
➢ pH
➢ Available oxygen
Normal Flora
Figure: Distribution of
the resident human
microflora. The
predominant groups of
microorganism at some
distinct anatomical sites
Marsh and Martin, 2009

Normal Flora in Oral Cavity
• The mouth is an ideal environment that supports very large
and diverse microbial populations on the tongue, cheeks,
teeth and gums
• However, biting, chewing, tongue movements and salivary
flow dislodge microbes. Saliva contain several antimicrobial
substances.
Streptococcus, Staphylococcus, Lactobacillus,

Actinomyces, Bacteriodes, Veillonella, Neisseria,
Haemophilis, Fusobacterium, Treponema,
Corynebacterium, and Candida (fungus)
REFERENSI
• Marsh, P.D., and Martin, M.P., 2009, Oral Microbiology,
Churchill Livingstone Elsevier, Philadelphia
• Samaranayake, L., 2012, Essential Microbiology for
Dentistry, 4th Ed., Churchill Livingstone Elsevier, Toronto
• Tortora, G.J, Funke, B.R, and Case, C.L, 2010,
Microbiology, An Introduction, Pearson, Toronto
• Fouod, A.F., 2017, Endodontic Microbiology, 2nd Ed.,
Wiley, Nort Carolina

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Topics of study

• Introduction and Clasification of microbes

• Study about microbes

Systematics, or phylogeny, is the study of the

• Chemically similar, in the sense that they both

• The microorganism (m.o) that establish

Protecs cell host by:

Marsh and Martin, 2009

Streptococcus, Staphylococcus, Lactobacillus,

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