Download Microbial Taxonomy

Lec 2
Oral Microbiology
Dr. Chatin
Microbial Taxonomy
 Purpose
 Classification Systems provide an easy way grouping of diverse and huge
numbers of microbes
 To provide an overview of how physicians think when confronted with a
bacterial infection so To alert you to the importance of bacterial
classification in treatment
 The importance of knowing the etiology of organ system based infection
and the Gram stain
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Classification Systems
 Taxonomy:
‫جامعة تكريت – كلية طب االسنان‬
• Classification of living organisms into groups
1- Phylogenetic Classification System:
• Groups reflect genetic similarity and evolutionary relatedness
2- Phenetic Classification System:
• Groups do not necessarily reflect genetic similarity or evolutionary
relatedness. Instead, groups are based on convenient, observable
characteristics.
Levels of Classification
 Taxon:
• A group or “level” of classification
•
broad divisions are divided up into smaller divisions:
– Kingdom (Not used by most bacteriologists)
– Phylum (Called “Division” by botanists)
– Class
– Order
– Family
– Genus (plural: Genera)
– Species (Both singular & plural)
Definition of “species” in microbiology:
• Classic definition: A collection of microbial strains that share many
properties and differ significantly from other groups
of strains
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• Species are identified by comparison with known
strains”:
well-‫جامعة‬
‫“االسنان‬type
‫كلية طب‬
– ‫تكريت‬
characterized pure cultures; references for the identification of
unknowns
• There are several collections of type strains, including the American
Type Culture Collection (ATCC)
Strain: A population of microbes descended from a single individual or pure
culture
– Different strains represent genetic variability within a species
– Biovars: Strains that differ in biochemical or physiological
differences
– Morphovars: Strains that vary in morphology
– Serovars: Stains that vary in their antigenic properties
Nomenclature
1- Scientific name (Systematic Name)
Binomial System of Nomenclature
• Genus name + species name
– Italicized or underlined
– Genus name is capitalized and may be abbreviated
– Species name is never abbreviated
– A genus name may be used alone to indicate a genus group; a
species name is never used alone
– eg: Bacillus subtilis
B. subtilis
2- Common or descriptive names
(trivial names)
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‫جامعة تكريت – كلية طب االسنان‬
a. Names for organisms that may be in common usage, but are not
taxonomic names
i. eg: tubercle bacillus
(Mycobacterium tuberculosis)
ii. meningococcus
(Neiserria meningitidis)
iii. Group A streptococcus
(Streptococcus pyogenes)
Bacterial Classification
Useful Properties in Classification
1- Colony morphology
2- Cell shape & arrangement
3- Cell wall structure (Gram staining)
4- Special cellular structures
5- Biochemical characteristics
6- Metabolic behavior (e.g., oxygen)
7- DNA sequence (G + C content)
Metabolic properties
May influence the type of disease caused, but not necessarily
 Anaerobes have a greater propensity to cause abscesses
 Mycobacterium tuberculosis is an obligate aerobe
affects
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‫عز‬tissue
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tropism
‫جامعة تكريت – كلية طب االسنان‬
 Acid fast organisms grow slowly - chronic infections
Cell morphology
 Shapes
– Rod
– Cocci
– Spiral
– Filamentous
 Associations
– Individual
– Diplo– Staphylo-
– Strepto– Filaments
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‫جامعة تكريت – كلية طب االسنان‬
Classification and Disease
Gram-positive cocci - pyogenic
 Streptococcus pyogenes
 Staphylococcus aureus
Gram-negative cocci - pyogenic
 Neisseria gonorrhoeae
 Neisseria meningitidis
Spirals - chronic infections
 Treponema pallidum
 Borrelia burdorferi
 Leptospira
How a physician approaches bacterial diseases
1- Organ system approach
 Which bacteria cause disease in a certain location :The "usual
suspects"
2- Gram stain approach
a. The Gram stain is used to treat empirically before cultures are
completed
b. Requires that one is able to get a Gram stain directly from a
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patient sample, which is not always the case (e.g., stool, sinus,
endocarditis)
‫جامعة تكريت – كلية طب االسنان‬
The combination of these is ideal
Serological Tests
• Use group specific antiserum isolated from the plasma of animals
that have been sensitized to the organism
1- The antiserum contains antibody proteins that react with
antigens on the unknown organism.
2- The reaction can be detected by examining agglutination or by
using sera labeled with colorimetric or fluorescent labels
• Advantages:
1- Highly specific
2- Does not usually require the organism to be isolated into pure
culture
3- Can be used to identify organisms that can’t be grown on
medium
Nucleic acid hybridization
• By mixing ssDNA from two different species and determining the
percentage of the DNA that can form dsDNA hybrids
• The greater the percent hybridization, the closer the species
Microbial Phylogeny
 Domains
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‫جامعة تكريت – كلية طب االسنان‬
• Based on the research of Woese and others in the 1980s and 1990s,
most biologists divide all living organisms into 3 domains:
1- Domain Archaea
2- Domain Bacteria
3- Domain Eucarya
• Many microbiologists reject the “kingdom” designation.
• Each domain is divided into phyla, phyla into classes. etc.
Phylogeny of domain Bacteria
• The 2nd edition of Bergey’s Manual of Systematic Bacteriology
divides domain Bacteria into 23 phyla.
• The most medicaly important
1-Phylum Proteobacteria
 Significant groups and genera include:
» The family Enterobacteriaceae, the “gramnegative 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
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2-Phylum Firmicutes
‫جامعة تكريت – كلية طب االسنان‬
 “Low G + C gram-positive” bacteria
 Divided into 3 classes
» Class I – Clostridia; includes genera Clostridium
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, Enterococcus,
Listeria, Staphylococcus, and others
3-Phylum Actinobacteria
 “High G + C gram-positive” bacteria
 Includes genera Actinomyces, Streptomyces,
Corynebacterium, Micrococcus, Mycobacterium,
Propionibacterium
4-Phylum Chlamidiae
 Small phylum containing the genus Chlamydia
5-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
5-Phylum Bacteroidetes
• Includes genera Bacteroides, Flavobacterium, ‫ جتني عز الدين علي‬.‫د‬.‫م‬.‫أ‬
Phylogeny of domain Eucarya
‫جامعة تكريت – كلية طب االسنان‬
• The domain Eucarya is divided into four kingdoms by most biologists:
1- Kingdom Protista, including the protozoa and algae
2- Kingdom Fungi, the fungi (molds, yeast, and fleshy fungi)
3- Kingdom Animalia, the multicellular animals
4- Kingdom Plantae, the multicellular plants