Microbial Taxonomy. Classification of living organisms into groups. A group or level of classification

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1 Lec 2 Oral Microbiology Dr. Chatin Purpose Microbial Taxonomy 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 Classification Systems Taxonomy: 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:

2 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 أ.م.د. جتني عز of strains الدين علي properties and differ significantly from other groups Species are identified by comparison with known االسنان type كلية طب strains : تكريت wellcharacterized pure cultures; references for the identification of جامعة 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

3 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) Bacterial Classification a. Names for organisms that may be in common usage, but are not taxonomic names Useful Properties in Classification 1- Colony morphology i. eg: tubercle bacillus (Mycobacterium tuberculosis) ii. meningococcus (Neiserria meningitidis) iii. Group A streptococcus (Streptococcus pyogenes)

4 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 Cell morphology Anaerobes have a greater propensity to cause abscesses أ.م.د. جتني tissue عز affects الدين علي Mycobacterium tuberculosis is an obligate aerobe tropism Acid fast organisms grow slowly - chronic infections Shapes Rod Cocci Spiral Filamentous Associations Individual Diplo- Staphylo-

5 Strepto- Filaments 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

6 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 patient sample, which is not always the case (e.g., stool, sinus, endocarditis) 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

7 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 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

8 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 2-Phylum Firmicutes» Other medically important Proteobacteria include genera Haemophilus, Vibrio, Camphylobacter, Helicobacter, Rickessia, Brucella Low G + C gram-positive bacteria 3-Phylum Actinobacteria 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 High G + C gram-positive bacteria Includes genera Actinomyces, Streptomyces, Corynebacterium, Micrococcus, Mycobacterium, Propionibacterium

9 4-Phylum Chlamidiae 5-Phylum Spirochaetes 5-Phylum Bacteroidetes Small phylum containing the genus Chlamydia 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 Flavobacterium, Includes genera Bacteroides, Phylogeny of domain Eucarya 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