Bacterial Structure PDF - Chapter 1

Chapter 1 Bacterial structure Prepared by Dr. Samir Bloukh Professor College of Pharmacy Ajman University  Assessment Date Sections Marks 1st test 13.2.2025 (1M+3F+4F)...

Chapter 1 Bacterial structure Prepared by Dr. Samir Bloukh Professor College of Pharmacy Ajman University  Assessment Date Sections Marks 1st test 13.2.2025 (1M+3F+4F) 10 marks Mid-term 8th week (1M+3F+4F) 20 marks 3-9 Mar. 2025 2nd test 17.4.2025 (1M+3F+4F) 10 marks SDL 1 24.2.2025 (1M+3F+4F) 5 marks SDL 2 24.3.2025 (1M+3F+4F) 5 marks Practical exam Last 3 weeks Section wise during lab 20 marks Final Exam 5-14 May 2025 (1M+3F+4F) 30 marks Total Marks 100 Around 1.3. 2025 is Ramadan. 24.3-1.4.2025 is Spring vacation. 29.3-1.4.2025 Eid Al Fitr. *Kindly refer to the academic calendar on the Ajman University website for other important dates and events.  Classification of Protista a. Higher Protist (Eukaryotic) 1. Algae except (blue green algae) 2. Protozoa 1cm= 10mm 3. Fungi 1mm= 1000 micro.m = 1 million nano m b. Lower Protist (Prokaryotic) 4. Bacteria T or F ???? 5. Blue green algae Bacteria is an eukaryotic cell. ( ) Blue green algae is prokaryotic. ( ) Algae is prokaryotic cell. Microorganisms can be classified into major groups: - algae, Protists kingdom differentiated from animals and plants - protozoa, Bacteria, unicellular or - fungi, fungi and relatively simple multicellularBrown algae protozoa - bacteria, - viruses and a number of organisms Virus is NOT a cell - intermediate between bacteria and viruses (e.g. rickettsiae, chlamydiae and more recently described mimiviruses - so called as they mimic viruses). Bacteria, fungi and protozoa belong to the kingdom of protists and are differentiated from animals and plants by being unicellular or relatively simple multicellular organisms leading a parasitic existence. - Viruses are unique, acellular, metabolically inert organisms and therefore can replicate only within living cells. (Obligate  Structure. Cells possess a nucleus or, in the case of bacteria, a nucleoid with DNA. This is surrounded by the cytoplasm where: - energy is generated and Mitochondria - proteins are synthesized. Ribosome viruses Obligate intracellular rickettsiae bacteria parasite chlamydiae In viruses the inner core of genetic material is either DNA or RNA, but they have no cytoplasm and hence depend on the host for their - energy and - proteins (i.e. they are metabolically inert)  Reproduction. Bacteria reproduce by binary fission (a parent cell divides into two similar cells), but viruses disassemble, produce copies of their nucleic acid and proteins, and then reassemble to produce another generation of viruses. As viruses are metabolically inert they must replicate within host cells. Bacteria, however, can replicate extracellularly (except rickettsiae and chlamydiae, which are - Viruses bacteria that also require living cells for- growth). Obligate Viruses: Disassemble- produce copies- reassembleintracellular rickettsiae and (Obligate intracellular parasite). parasite - chlamydiae  - Attachment - Entry, - Uncoating, - Transcription/ mRNA production, - Synthesis of virus components, - Virion assembly and release but viruses disassemble, produce copies of their nucleic acid and proteins, and then reassemble to produce another  Infected cell Spike peplomers  Bacteria divide by binary fission dsDNA 1 ssDNA Pinch off in the center dsDNA dsDNA Bacteria divide by binary fission 2  The major characteristics of bacteria, mycoplasmas, rickettsiae, chlamydiae and viruses are given in Table 2.1. EUKARYOTES AND PROKARYOTES Another way of classifying cellular organisms is to divide them into prokaryotes and eukaryotes (Greek karyon: nucleus). Fungi, protozoa and humans, for instance, are eukaryotic, whereas bacteria are prokaryotic. In prokaryotes the bacterial genome, or chromosome, is a single, circular molecule of double-stranded DNA, lacking a nuclear membrane (smaller, single or multiple circular DNA molecules called plasmids may also be present in bacteria), whereas the eukaryotic cell has a true nucleus with multiple chromosomes surrounded by a nuclear membrane. The main genome, or chromosome archaebact Eukaryotes true nucleus differences between prokaryotes eria and eukaryotes Prokaryotic Fungi, are listed in Table 2.2. plasmids eubacteria and Bacteria protozoa and multiple chromosomes humans single, circular nuclear membrane lacking a nuclear membrane molecule of double-stranded DNA  Electron microscope electron microscope intracellular only intracellular only intracellular only Either DNA or RNA - Has no cell wall Stop them but cannot kill them no cell wall 30S antibiotics of choice no ribosome Totally different budding  nucleoid No nucleus, no nuclear membrane (Haplo id) - Conjugation Zygote - Transduction - Transformation No any of these  Prokaryotes Eukaryotes No LPS and no teichoic acid ATP (No mitochondria) ATP produced in mitochondria Blue-green algae, (cyanobacteria) Hopanoids are a diverse group of pentacyclic triterpenoid lipids mainly produced by bacteria, which have been widely used as biomarkers for different bacterial group productivity in ancient and modern environments (50S and 30S) (60S and 40S) No cell wall for Human cell Archaebacteria: lack peptidoglycan, still form Pla Fungi  9+0 9+2 Theodor Svedberg was awarded the 1926 Nobel Prize for chemistry for his work in colloid chemistry, but his name is best known for the “Svedberg unit,” the unit of measurement of the velocity of sedimentation and, thus, the molecular weight of proteins. S: Svedberg (50S) 60S PROKARYOTES 70S (50S and 30S EUKARYOTES 80S (60S and 40S (30S) 40S  Prokaryotes can again be divided into eubacteria and archaebacteria (synonym: archaea). - Eubacteria comprise the vast majority of human pathogens, whilst eubacteria majority of human pathogens Prokaryotes rarely to cause human disea archaebacteriaHuman mouth also - archaebacteria appear extreme Human mouth also - rarely to cause human disease and environments - live in extreme environments (e.g. high temperature or salt concentrations). Archaebacteria received little attention traditionally as they cannot be easily cultured in the laboratory. Interestingly, recent studies have uncovered the presence of cannot be easily cultured in the laboratory archaebacteria rchaebacteria in the oral cavity. Their role, if any, in oral present Their role in oral healthyet to be determined ????????????? health or disease in the oral cavity is yet to be determined. MORPHOLOGY Shape and size The shape of a bacterium is determined by its rigid cell wall. Bacteria are classified by shape into three basic groups (Fig. 2.1): coccal 4. pleomorphic and forms I. cocci (spherical) bacillary 2. bacilli (rod-shaped) 3. spirochaetes (helical). Some bacteria with variable shapes, 1mm=appearing both as coccal 1000 μ (micro.m) and bacillary forms, are called pleomorphic (pleo: many, morphic: shaped) in appearance. Yeast RBC The size of bacteria ranges from about 0.2 to 5 /μ 7μ (micro.meter) 7μ  Fig. 2.1 Common bacterial forms. A coccus; coccus flagellated bacillus B capsulated diplococci; staphylococcus C, D cocci in chains (e.g. streptococcus) and clusters (e.g. staphylococcus); E bacillus; F, G capsulated and ba flagellated bacillus (e.g. c ill Vibrio spp us Escherichia coli); capsulated diplococci H curved bacilli (e.g. Vibrio spp.); capsulated bacillus I spore-bearing bacilli (e.g. spore-bearing Clostridium tetani); st re pt bacilli J spirochaete. oc oc cu s streptococcus A- coccus spirocha E- bacillus ete - spirochete  capsulated diplococci Arrangement Bacteria, whichever shape they may be, arrange themselves (usually according to the plane of successive cell division) as: - pairs (diplococci), - chains (streptococci), - grape-like clusters (staphylococci), or as staphylococci - angled pairs or palisades (corynebacteria). Fence Palisade ‫ سياج‬Palisade: Fence streptococcus  Gram-staining characteristics Bacteria is classified into two subgroups according to the staining characteristics of their cell walls. The stain is Gram ‫دانيماركي‬ stain (first developed by a Danish physician, Christian Gram), divides the bacteria into - Gram-positive (purple) and - Gram-negative (pink) groups. The Gram-staining property of bacteria is useful both for their - identification and in the - therapy of bacterial infections because, in general, Gram-positive bacteria are more susceptible: to penicillins Gram-positive bacteriaare than Gram-negative more susceptible: to penicillins bacteria.  Protoplast: (cytoplasmic membrane, cytoplasm, nucleus and cell organ Structure Bacteria have a rigid cell wall protecting a fluid protoplast. Comprising a cytoplasmic membrane and a variety of other components (described below). - Flagella Patterns monotrichous amphitrichous Structures external to the cell wall: - Fimbriae and pili. of lophotrichous - Glycocalyx (slime layer). flagella - Capsule. peritrichous - Flagella. Flagella are whip-like filaments which act as propellers and guide the bacteria toward nutritional and other sources. (Organ of locomotion: motility) The filaments are composed of many subunits of a single protein, flagellin. mono - monotrichous, a single polar flagellum; - amphitrichous, single flagellum attached to each end, - lophotrichous, tufts of flagella at one or both end or - peritrichous all over the outer surface. lopho lopho Spirochaetes Many bacilli (rods) amphi have flagella, but most cocci do not and are  Capsule - d.s DNA Cell wall - Genome Cell membrane -Plasma membrane Chromosome- Mesosome - Plasmid - Transposon - - Cytoplasm - Nucleoid DNA - Ribosomes - Flagellum Structures Pilus external -to the cell wall Flagella - Fimbriae and pili - Glycocalyx (slime layer) Transposon - Capsule Fig 2.2 Anatomy of Bacterial cell  Spirochete axial filament Fixed at this end Fixed at this end  adhesion of bacteria pilin Common pilus found mainly on Gram -ve first step in infection - Fimbriae and pili. sex pilus conjugation Fimbriae and pili are fine, hair-like filaments, shorter than flagella, that extend from the cell surface. Pili, found mainly on Gram-negative organisms, are composed of subunits of a protein, pilin, and mediate the adhesion of bacteria to receptors on the human cell surface a necessary first step in F the initiation of infection. A specialized type of pilus, the sexM pilus, forms the attachment between the male (donor) and the female (recipient) bacteria during conjugation, when genes are transferred from one bacterium to another. - Glycocalyx (slime layer). - oral Themucosa, glycocalyx is a protect the bacteria cells - teeth, polysaccharide from: coating that covers the outer surfaces of - heart valves and many bacteria - antibiotics and and allows the bacteria to adhere firmly to - catheters  Glycocalyx (slime layer). This is especially true in the case of Streptococcus mutans, a major cariogenic organism, which has the ability to produce vast quantities of extracellular polysaccharide in the presence Cause tooth caries of dietary sugars without defined shapesuch as sucrose. - polysaccharide, and Jelly like sometimes determine Bacillus anthracis the serological type - protein Capsule. An amorphous, gelatinous layer (usually more substantial Bacillus anthracis than the glycocalyx) surrounds the entire bacterium; it is composed of - polysaccharide, and sometimes - protein (e.g. Bacillus anthracis: anthrax disease). The sugar components (1-84) of the polysaccharide vary in different bacterial species and frequently determine the serological type within a species  reptococcus pneumoniae Streptococcus Streptococcus Streptococcus 1st animal pneumoniae 2nd animal pneumoniae 3rd animal pneumoniae 4th animal act polysaccharide capsule and inject to 4 lab. animal on several occasions h one will be injected every time with the same capsular antigen (sugar) h Lab. animal will develop antibodies against one capsule antigen in the blood blood from each Lab. animal separately, centrifuge the blood to collect the serum or the plasm um or the plasma of each animal will contain different type of antibodies ibodies of the 1st animal will recognize only the capsule of the 1st animal Antibodies of the 2nd animal will recognize only the capsule of the 2nd animal and so on his is called serological typing of Streptococcus pneumoniae 84 different antibodies are used for serotyping this  Mediates adhesion of bacteria human tissues or prosthesis The capsule is important because: virulence such as Anti-phagocytosis: dentures Laboratory identification (Quellung or implants reaction) Antigens in certain vaccines (S. pneumonia) (Hib vaccine It mediates the adhesion of bacteria to human tissues or prosthesis such as dentures or implants - a prerequisite for colonization and infection It hinders or inhibits phagocytosis; hence, the presence of a Anti-phagocytosis: virulence capsule correlates with virulence It helps in laboratory identification of organisms (in the presence of antiserum against the 84 capsular polysaccharide different serological the types of S. pneumoniae capsule will swell greatly - a phenomenon called the Quellung reaction) Its polysaccharides aemophilus influenzaeare used as antigens Hibbvaccine type in certain vaccines Streptococcus Capsules and slime layers quellung reaction slime layers  peptidoglycan murein mucopeptide Cell wall The cell wall confers rigidity upon the bacterial cell. It is a multilayered structure outside the cytoplasmic membrane. It is porous and permeable to substances of low molecular weight. Protein + sugar in G-ve not in G+ve The cell wall is made of peptidoglycan and is covered by an outer membrane (in G-ve). The cell wall varies in thickness and chemical composition. (Fig. 2.4). The term 'peptidoglycan' is derived from the peptides and the sugars (glycan) that make up the molecule. (Synonyms Thick in G+ve for peptidoglycan are cell wall peptidoglycan murein and mucopeptide.) Thin in G-ve  :alternating strand of N-acetyl muramic acid and murein) ,N-acetylglucosamin residues (mucopeptide) cross-linked with.peptide subunits G +ve peptidoglycan cytoplasm strandsmultilayered structure cytoplasmic membrane Cell wall  Peptido: peptide cross bridges (N-AGA) Glycan: millions of NAG + NAM forming chains (N-AMA) )Sugars like glucose( N-acetylglucosamin N-acetyl muramic acid peptide cross bridges  much thickerNO outer membrane thinner complex outer membrane periplasmic space Teichoic acid NO periplasmic space Lipoteichoic acid G-ve G+ve -lactamases penicillinase la sm Cytoplasm op t Cy G+ve Outer membrane composed of: G-ve lipopolysaccharide Outer membrane Cell wall Periplasmic space Cytoplasmic (LPS), containing cell wall membrane lipoprotein and Cytoplasmic membrane Cytoplasm Cytoplasm Cytoplasm The cell walls of Gram-positive and Gram-negative bacteria have important structural and chemical differences: The peptidoglycan layer is common to both Gram- porins positive and Gram-negative bacteria but is much thicker in the Gram-positive bacteria In contrast, the Gram-negative organisms have a complex outer membrane composed of lipopolysaccharide (LPS), lipoprotein and phospholipid. Porins, through which hydrophilic molecules are transported in and out of the organism. LPS consists of 0 antigen, core and lipid A embedded in the outer membrane. Lying Outer between the leaflet outer of outer membran - 0 antigen LPS membrane and the cytoplasmic penicillinase membrane lipopolysaccharide (LPS), - Core of Gram- lipoprotein and negative bacteria is the periplasmic phospholipid space. porins - lipidItA is in this space that someperiplasmic bacterial species produce enzymes Enerthat destroy leaflet of outer  porins hydrophilic molecules are transported outer membrane lipoprotein present on the outer leaflet of the outer membrane antibiotics Bacterial lipoproteins are proteins anchored to a membrane by alipoprotein and phospholipid form porins lipid moiety  The LPS of Gram-negative bacteria, which is extremely toxic, has been called the endotoxin. (Hence, no endotoxins in Gram-positive bacteria as they do not have LPS.) fever and endotoxinsResponsible for shock G-ve LPS is only released when bacteria is dead. It is responsible for fever Mycobacterium and shock (see Ch. 5) tuberculosis mycolic acid- acids 60% of its cell wall fast The cell walls of some bacteria (e.g. Mycobacterium tuberculosis) contain lipids called mycolic acids which cannot be Gram-stained, and hence are called acid-fast (i.e. they resist decolorization with acid-alcohol Resist decolorization after with acid-alcohol being trying to stained with carbolfuchsin). remove carbolfuchsin Lying between the outer membrane and the - cytoplasmic membrane of Gram-negative lipopolysaccharide bacteria is the periplasmic (LPS), Periplasmic space - lipoprotein and - phospholipid Outer LPS membrane outer leaflet of cell wall Inner leaflet Peptidoglycan phospholipid Layer of cell wall lipoprotein Cytoplasmic Cytoplasmic membran membrane (Ener membrane)  Lipopolysaccharide :)Outer leaflet( (LPS) Manose-Rhamnose-Galactose Repeat units O antigen Sugars: ketodeoxyoctanoic acid and a heptoses Core phosphorylated Lipid A disaccharide, )Endotoxin( attached to it chains of fatty acids ,inner leaflet of it is composed of (phospholipids and proteins)  LPS O Antigen ,phosphorylated disaccharide attached to it chains of O Antigen fatty acids Lipid A Core ndotoxin) phosphate phosphate Lipid A Endotoxin monosacchar disaccharide monosacchar Fatty acids Lipid A (E complex outer membrane - 0 antigen - Core - lipid A Myristoxymyristic acid Lauroxymyristic acid 2Hydroxymyristic acid.phosphorylated disaccharide, attached to it chains of fatty acids Lipopolysaccharide (LPS) :)Outer leaflet( Bacteria with defective cell walls. Some bacteria can survive without or with defective cell walls. - Mycoplasmas do not possess a cell wall and do not need hypertonic media for their survival. They occur in nature and can of G+ve are protoplasts Mycoplasmas pneumoniae cause human L-forms disease of G-ve are (e.g. pneumonia). L-forms spheroplasts of G+ve are protoplasts - L-forms are usually produced in the laboratory and may totally or partially lack L-forms of cell G-ve arewalls. They may be produced in spheroplasts patients treated with penicillin. L- L-forms of G-ve - spheroplasts (derived from Gram-negative formscondition bacteria) require hypertonic and - protoplasts (derived from Gram-positive bacteria) - lack cell walls, - cannot replicate on laboratory media and are - unstable and osmotically fragile. They require hypertonic  Eukaryotic: Cytoplasmic membrane (phospholipid bilayer) sterols Prokaryotes: no sterols The cytoplasmic membrane lies just inside the peptidoglycan layer of the cell wall and is composed of a phospholipid bilayer similar in appearance to that of eukaryotic cells. However, eukaryotic membranes contain sterols, whereas prokaryotes generally do not. The membrane has the following major functions: eukaryotic cytoplasmic membranes contain sterols (cholesterol) active transport and selective prokaryotes diffusion generally do not of molecules and solutes into and out of the cell electron transport and oxidative phosphorylation, in aerobic species synthesis of cell wall precursors secretion of enzymes and toxins Attractants (periplasmic space: - and repellents bind to receptors lactamases (penicillinase) heads in this membrane. 20 different chemorecep supporting the receptors and other proteins of the Tails In the membrane of E.coli. heads  Mesosome. This is a convoluted invagination of the cytoplasmic membrane which functions as the origin of the transverse septum that divides the cell in half during cell division. It is also the binding site of the DNA which will nucleoid composed of DNA become the genetic containsmaterial of each amorphous ribosomes, nutrient daughter matrix granules, cell. metabolites Cytoplasm without and various ions defined shape‫مصفوفة‬ The cytoplasm comprises an inner, nucleoid region (composed of DNA) which is surrounded by an amorphous matrix that contains ribosomes, nutrient granules, metabolites and various ions. - Nuclear material or nucleoid. Bacterial DNA comprises a single, supercoiled, circular chromosome that contains about 2000 genes, approximately I mm long in the unfolded Haploid state. (It isreplication semiconservative analogous to a single, haploid chromosome.) bi-directionally Diploid During cell division it undergoes semiconservative  DNA replication takes place in a semiconservative Y.manner Replication fork - semiconservative Y replication - bi-directionally from a fixed point 43 DNA replication Replication: 1,000 nucleotides per second replication fork Leading strand DNA helicase The two strands separate. each Replaces then acts as a DNA polymerase III new DNA template for SSBP the synthesis of a complementary 3′ 5′ 5 ′→3′ Gyrase 3′ 5′ 3′ 5′ RNA primase RNA Primer Links Replaces Okazaki fragments Okazaki DNA polymerase I RNA primers fragments DNA ligase Lagging strand ssDNA BINDING PROTEINS 44 - Ribosomes. are the sites of protein synthesis. prokaryotes Bacterial ribosomes differ from those of eukaryotic cells in both 50 70S prokaryotes S - size and 30 - chemical composition. prokaryotes S They are organized in units of ribosomesribosomes eukaryotic of 70S 60S 40S - 70S, compared with eukaryotic 'S' refers to Svedberg's unit for ribosomes of 80S of sedimentation - 80S. These differences are the basis of the selective action of some antibiotics that inhibit bacterial, but not human, protein- synthesis. (Tetracycline 30S) - Cytoplasmic inclusions. The cytoplasm contains different types of inclusions, which serve as sources of stored energy; examples include Not every bacteria have a spore Favorable conditions Bacterial spores Germinate Unfavorable conditionssporulate vegetative spore Spores are formed in response to adverse conditions by the medically important bacteria that belong Bacillus to the; anthracis Bacillus stearothermophilus - genus Bacillus (which includes the agent of anthrax) and the - genus Clostridium (which includes the agents of tetanus and botulism). These bacteria sporulate (form spores) when - nutrients, such as sources of carbon and nitrogen, are scarce (Fig. 2.6). spore The spore develops at the expense of the vegetative contains cell and contains - bacterial DNA, - a small amount of cytoplasm, vegetative - cell membrane, peptidoglycan, spore Spore formation Spore forming bacteria grow as vegetative cells and divide by binary fission when nutrients are.available and environmental conditions are not adverse.When nutrients are depleted or conditions become adverse spore formation is initiated.The DNA condenses and aligns it self in the center of the cell The vegetative cell is now referred to as mother cell. Next, the DNA divides into two complete copies and the mother cell membrane invaginates to form the developing fore spore. The mother cell membrane continues to grow and engulfs the developing spore and the developing spore is now surrounded by two.membrane layers Next , peptidoglycan is laid down between the two membranes of the developing spore to form the.cortex The dipiclonic acid is formed inside the spore and calcium enter from the outside and water is.removed to the outside.A protein coat is formed exterior to the cortex and spore becomes mature.Some spores forms additional layer called the exosporium.A mature spore is resistant to environmental conditions.Finally, lytic enzymes destroy the mother cell and the mature spore is released This coat, which contains a high concentration of calcium dipicolinate, is remarkably resistant to - heat, metabolically inert - dehydration, resistantDormant: to sleeping phase - radiation and - chemicals. many years Once formed, the spore is metabolically inert and can remain dormant for many years. Spores are called either Central, terminal or subterminal, depending on their position in relation to the cellterminal Central, wall of the bacillus from which or subterminal they developed. When appropriate conditions supervene (i.e. water, nutrients) there is enzymic degradation of the coat and the spore transforms itself into a metabolizing, reproducing metabolize Germinate bacterial cell once again (Fig. 2.6). reproduce sporul Dormant: sleeping phase Central, terminal or subterminal central subterminal terminal spherical oval Endospores terminal (spores) terminal central subterminal central Clinical relevance of bacterial spores The clinical importance of spores lies in their extraordinary resistance- heat, to Spores not killed by boiling but by autoclaving only - heat and -dehydratio - evaluating the - chemicals.n, spores used for sterilization - radiation efficacy of stearothermophil and Bacillus Because of -this, autoclaves chemicals. - sterilization cannot be easily achieved by boiling; - Sterilization by autoclaving, steam under pressure (autoclaving), autoclav are required to ensure the sterility of products ing used for surgical purposes. Bacterial spores are used for evaluating the sterilization efficacy of autoclaves; spores of Bacillus THE END  2nd semester Year 2024-2025-2 Around March 1 1 test st Thurs 13.2.2025 (1M+3F+4F) Ramadan 24-28 March spring (10 marks) vacation 29.3-1.4.2025-2 Eid Al Fitr Mid-term Thurs 13-March 2025 (1M+3F+4F) (20 marks) 2nd test Thurs 17.4.2025 (1M+3F+4F) (10 marks) May 2. 2024 Last Day of Classes TOTAL = 40 MARKS Practical & SDL1, 2 Spring break: 24-28 March, Eid Al Fitr: 29.3-1.4. 2025 10+20 = 30 marks (30.3-11.4.2024) Final Exam: (May 5-14.2025) TOTAL= 70 MARKS (30 marks) 1. 2. Assignment 1 Assignment 2 1- Dental Caries 3. 2- Periodontal diseases 4. Supervised by Dr. 5. Samir Bloukh By: 6. Sondos…………….. I.D…………………………. 7. Section…………. 8.  diagnostic microbiology knowledge of taxonomy ‫التصنيف‬ studies in epidemiology useful for TAXONOMY pathogenicity The systematic classification and categorization of organisms into ordered groups are called taxonomy. The knowledge of taxonomy is useful for diagnostic microbiology and for studies in epidemiology and pathogenicity. Bacterial classification is somewhat artificial in that they are categorized according to phenotypic (as opposed to genotypic) features, which facilitate their laboratory identification. phenotypicsomewhat according to phenotypic features artificial genotypic realistic, stable TAXONO classical phenotypic classification meth MY Bacterial classification: Genotypic taxonomy Phenotypic taxonomy These phenotypic features comprise: morphology (cocci, bacilli, spirochaetes) staining properties (Gram-positive, Gram-negative) cultural requirements (aerobic, facultative anaerobic, anaerobic) Ferment sugar Do not Ferment sugar G+ve biochemical reactions (saccharolytic and G-ve asaccharolytic, according to sugar fermentation reactions) antigenic structure (serotypes). Most of the medically and dentally important bacteria are classified according to their - Morphology (cocci, bacilli, spirochetes), - Gram-staining characteristics (G+ or G-) and - atmospheric requirements. A simple classification of  (Gram +ve or –ve), (Cocci/bacilli), (aerobe/anaerobe), ………..etc. Gram +ve Gram +ve.7 A simple classification of Gram-positive bacteria  Gram -ve Gram -ve g. 2.8 A simple classification of Gram-negative bacteria.  Periodontal disease 2.8 A simple classification of Gram-negative bacteria. exploits the genetic characteristics Genotypic taxonomy which are more stable Genotypic classification and speciation of organisms are becoming increasingly important and useful. Genotypic taxonomy exploits the genetic characteristics, which are more stable than phenotypic features of organisms. These methods essentially analyze bacterial DNA to speciate them, Phenotypic taxonomy for example by: morphology - Bacterial DNA sequence AGTCCCTTAATACGATGC staining properties (G+ & G-) - assessing molecular guanine and cytosine (GC) content, cultural requirements biochemical  Additionally, recent research indicates that endogenous bacterial habitats in humans, including the oral cavity, harbour a flora that cannot be cultured using routine laboratory techniques. These so-called unculturable bacteria comprise mostly archaebacteria, mentioned before 1980:1791 and can only be detected by molecular S: Svedberg 30S species subunit oftechniques ribosome (e.g. now: 8168 direct amplification of 16S rRNA). species50S The role of these totally new phylotypes of bacteria recent research indicates that 30S including in either disease or health endogenous bacterial habitats awaits clarification. in humans including oral cavity harbour a flora that cannot be cultured mostly archaebacteria 30S subunit of ribosome can only be detected by molecular technique (e.g. direct amplification of 16S rRNA).  ‫نظام‬ How do organisms get their ‫هرمي‬ names? (a hierarchical system) Organisms are named according to a hierarchical system, beginning with the taxonomic rank kingdom, followed by ‫ثنائي التسميه‬ division, subdivision, order, family, genus and species (Table 2.3). The scientific name of an organism is classically a binomial of the last two ranks, i.e. a combination of the generic name followed by the species name, e.g. Streptococcus salivarius (note that the species name does not begin with a capital letter). The name is usually written in italics with the generic name abbreviated (e.g. S. salivarius).kingdom division, When bacterial Streptococcus names are used salivarius adjectivally or collectively subdivision, the names written arewith in italics not italicized S. salivariusand do not begin with order,a capital the family, letter (e.g. staphylococcal enzymes, staphylococci, generic name genus and  hierarchical system Classification of E. coli: Domain: Bacteria, Kingdom: Procaryotae, division: proteobacteria Order: Enterobacteriales, Lactobacillales Family: Enterobacteriaceae, Genus: Escherichia, genus and species S. salivarius Species: E. coli. S. salivarius The name is usually written in italics with the generic name abbreviated