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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 جتني عز الدين علي.د.م.أ 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 الدين علي جتني عز.د.م.أ • 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) جتني عز الدين علي.د.م.أ 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 الدين– علي عزtissue جتني.د.م.أ 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 جتني عز الدين علي.د.م.أ 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 جتني عز الدين علي.د.م.أ 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 جتني عز الدين علي.د.م.أ 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 جتني عز الدين علي.د.م.أ 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