Introduction and Classification of Bacteria PDF

Introduction and Classification of bacteria Prepared by Dr. Mohammed Ali Eid 10/10/2024  Introduction Microbiology: Study of microscopic organisms (microbes). It also include the study of a multiple biological area (e.g., genetic...

Introduction and Classification of bacteria Prepared by Dr. Mohammed Ali Eid 10/10/2024  Introduction Microbiology: Study of microscopic organisms (microbes). It also include the study of a multiple biological area (e.g., genetics, microbial physiology, microbial morphology, and immunology) Microbes: Present in all ecosystems and mostly associated with all multicellular organisms. It Evolved over billions of years  Microbes' characteristics Billions of microbes inhabit healthy human and animal bodies (normal flora) Some microbes contribute to body functions (e.g., gut bacteria aiding digestion) Others can cause infections and spread either by producing toxins or directly infect via virulence factors.  Different Kinds of Microbes Bacteria: Unicellular microorganisms with rigid cell walls defining their shape Viruses: Obligate intracellular parasites lacking cellular structure Fungi: Non-photosynthetic, typically saprophytic eukaryotes - Multicellular forms: Molds - Unicellular forms: Yeasts Protozoa: Single-celled, non-photosynthetic eukaryotes which have Varied sizes and shapes. Many protozoa are clinically important human parasites Helminths: they are multicellular eukaryotic parasitic worms with complex body structures Classification of Living Organisms Classification: means; Organizing microorganisms into groups (taxa) based on shared traits Hierarchical classification system means; taxa arranged from most broad (Kingdom) to most narrowed (Species)  Follow Classification of Living Organisms Traditional classification: All prokaryotes in a single domain called (Monerans) Modern analysis separate monerans into two domains:  Bacteria; include Environmental prokaryotes (e.g., cyanobacteria), and Medically relevant heterotrophic bacteria  Archaea (ancient bacteria); include environmental isolates from extreme conditions Eukarya domain:  Includes plants, animals, humans, parasites, protists, and fungi Differences between Prokaryotic Cells and Eukaryotic Cells Follow Differences between Prokaryotic Cells and Eukaryotic Cells Follow Differences between Prokaryotic Cells and Eukaryotic Cells  Classification of bacteria Microbiology labs typically use classification from family level downwards Family: - Groups organisms with common attributes (‫)ﺻﻔﺎت‬ - May contain multiple genera - Named by adding -aceae to a type genus (e.g., Streptococcaceae from Streptococcus) - Exception: Enterobacteriaceae (named after "enteric" bacteria)  Follow classification of bacteria Genus: Contains multiple species with common important features Species within a genus are sufficiently different to maintain individual status Grouping together based on shared genetic and phenotypic characteristics  Follow classification of bacteria Species: - Collection of bacterial strains sharing common physiologic and genetic features - Distinctly different from other microbial species (differences in genetic makeup, biochemical reactions, and morphology) - Abbreviated as sp. (singular) or spp. (plural) - May include subspecies as taxonomic subgroups Follow classification of bacteria Prokaryotic species determined by International Committee for Systematics of Prokaryotes Species definition criteria: DNA profiling Complete 16S rRNA sequence (0-5% difference) Phenotypic traits  Nomenclature Nomenclature involves naming microorganisms based on rules set by the International Code of Nomenclature of Bacteria (ICNB). It provides universally accepted names for organisms. The system used is binomial, assigning each organism a genus and a species, both derived from Latin or Greek.  Genus (first letter capitalized).  Species (first letter lowercase).  Both genus and species names are written in italics or underlined.  Example: Streptococcus pneumoniae. Training questions 1. Which of the following is NOT mentioned as a type of microbe? A) Bacteria B) Viruses C) Fungi D) Prions E) Helminths Training questions 2. What characteristic distinguishes viruses from other microorganisms? A) They have a rigid cell wall B) They are obligate intracellular parasites C) They are always multicellular D) They are photosynthetic E) They have a true nucleus Training questions 3. In the modern classification system, prokaryotes are divided into which two domains? A) Bacteria and Eukarya B) Archaea and Protista C) Bacteria and Archaea D) Monerans and Protista E) Fungi and Bacteria Training questions 4. Which of the following is NOT a criterion used for prokaryotic species definition? A) DNA profiling B) 16S rRNA sequence C) Phenotypic traits D) Protein shape E) Less than 0-5% difference in 16S rRNA sequence Training questions 5. What is the correct way to write a species name according to the binomial nomenclature system? A) ESCHERICHIA COLI B) escherichia coli C) Escherichia Coli D) Escherichia coli E) escherichia Coli Training questions 6. Which taxonomic level is described as "a collection of bacterial strains that share common physiologic and genetic features"? A) Domain B) Kingdom C) Family D) Genus E) Species Training questions 7. What is the main reason microbiology labs typically use classification from family level downwards? A. Higher taxa are too complex to identify B. Family and lower levels provide more clinically relevant information C. It's impossible to classify bacteria at higher taxonomic levels D. The International Committee for Systematics of Prokaryotes forbids using higher taxa E. Higher taxa are only used in viral classification Training questions 8. Which of the following is true about the Archaea domain? A) It includes all types of bacteria B) It contains mostly pathogenic microorganisms C) It includes strains were isolated from extreme conditions D) It's part of the Eukarya domain E) It's synonymous with the Bacteria domain Training questions 9. What is the standard suffix used for naming bacterial families? A) -aceae B) -ales C) -idae D) -phyta E) -bacteria  Lecture 2 Prokaryotic Cells: Structure, and Function By Prof. Dr. Mohammed Ali Ahmed Eid 17/10/2024  1. Procaryotic cells are the smallest, simplest, and most abundant cells on earth. 2. Representative procaryotes include bacteria and archaea, both of which lack a nucleus and organelles but are functionally complex. Procaryotic cells 3. The structure of bacterial cells is Characteristics compact and capable of adaptations to a myriad of habitats. 4. The cell is encased in an envelope that protects, supports, and regulates transport. 5. Bacteria have special structures for motility and adhesion to the environment.  6. Bacterial cells contain genetic material in a single chromosome, and ribosomes for synthesizing proteins. 7. Bacteria have the capacity for reproduction, nutrient storage, Procaryotic cells dormancy, and resistance to adverse conditions. Characteristics 8. Shape, size, and arrangement of bacterial cells are extremely varied. 9. Bacterial taxonomy and classification is based on their structure, metabolism, and genetics.  Bacterial Morphology Most bacteria are classifying according to shape: 1. Bacillus (pl. bacilli)= rod shaped 2. Coccus (pl. cocci … sounds like cox eye ))= spherical 3. Spiral shaped a. Spirillum (pl. spirilla )= spiral with rigid cell wall, flagella b. Spirochete (pl. spirochetes)= spiral with flexible cell wall, axial filament Bacterial Morphology Pleomorphism when cells of a single species vary to some extent in shape and size There are many more shapes beyond these basic ones. 1. Coccobacilli = elongated coccal form 2. Filamentous = bacilli that occur in long threads 3. Vibrio = short, slightly curved rods 4. Fusiform = bacilli with tapered ends. Bacterial Morphology (Cell- Arrangement)  Parts of prokaryotic cell  Appendages 1. Flagella It is long, thin, whip-like structures that many bacteria use for movement. It is composed of a protein called flagellin and can rotate to push the bacterium through liquid environments.  Structure of flagella A. Basal Body: The basal body is the anchoring structure of the flagellum. It's embedded in the cell envelope and consists of several rings: 1. Fli (Motor Switch Protein) and Motor proteins 2. C-ring: Located in the cytoplasm 3. S-M ring: Embedded in the cell membrane 4. P-ring: Found in the peptidoglycan layer (in gram-negative bacteria) 5. L-ring: Located in the outer membrane (in gram-negative bacteria)  Follow Structure of flagella B. Hook-like Structure: The hook is a short, curved structure that connects the basal body to the flagellar filament. It acts as a universal joint, allowing the rigid filament to rotate relative to the cell body. The hook is made of a single protein called FlgE. C. Flagellar Filament: This is the longest part of the flagellum, extending out from the cell. It's composed of thousands of flagellin protein subunits arranged in a hollow, cylindrical structure. The filament can be several times longer than the bacterial cell itself.  Flagellar Arrangements: A. Polar: Flagella are located at one or both ends (poles) of the bacterial cell. Monotrichous: Single flagellum at one pole (e.g., Vibrio cholerae) Lophotrichous: Multiple flagella at one pole of the bacterial cell. (e.g., Helicobacter pylori) Amphitrichous: Single or multiple flagella at each pole (e.g., Spirillum volutans) B. Peritrichous: Multiple flagella distributed all around the bacterial cell surface. Example: Escherichia coli, Salmonella Flagellar Rotation Patterns: A. Counterclockwise (CCW) Rotation: In peritrichous bacteria (e.g., Escherichia coli), flagella bundle together when rotating counterclockwise, resulting in a smooth, forward swimming motion called a "run.“ The CCW rotation aligns the flagella and propels the cell in a relatively straight direction. B. Clockwise (CW) Rotation: When the flagella rotate clockwise, the bundle disassembles, causing the bacterium to "tumble" or change direction. This allows the cell to reorient itself in response to environmental stimuli, such as chemical gradients (chemotaxis). Flagellar movement  Fimbriae Structure Short, thin, and numerous (hundreds to thousands). Typically, 3-10 nanometers in diameter. Composed of pilin protein subunits. They tend to cover the entire surface of the bacterial cell, giving the appearance of a rough texture.  Fimbriae Function 1. Primarily involved in adhesion to surfaces, host tissues, or other bacteria. This adhesion is crucial in the early stages of infection or biofilm formation. 2. They help bacteria attach to host cells, increasing their pathogenic potential, and to non-living surfaces, such as rocks or medical devices, aiding in biofilm formation. 3. They are especially important in urinary tract infections (e.g., E. coli uses fimbriae to adhere to epithelial cells in the urinary tract). 4. Fimbriae do not play a significant role in motility or genetic exchange. Pili Structure: Long, thick, and fewer in number compared to fimbriae. Usually, 6-15 nanometers in diameter and may extend longer than fimbriae. Also composed of pilin protein, but with a more specific structure depending on the type of pilus.  Pili Function: Can serve multiple roles depending on the type: 1. Conjugative pili (or sex pili): These are used for bacterial conjugation, where they mediate the transfer of genetic material (plasmids) between bacterial cells, a form of horizontal gene transfer. 2. Type IV pili: Involved in twitching motility (a form of surface motility), adhesion to host cells, and biofilm formation. 3. Adhesion: Like fimbriae, pili also play a role in adhering to host tissues and surfaces, although their adhesive function is less emphasized compared to fimbriae. Twitching motility Differences between Fimbriae and Pili External Structures Many pathogenic bacteria have glycocalyces The Glycocalyx 1. A coating of repeating polysaccharide, protein, or both 2. Protects bacterial cell against phagocytes 3. Can help the cell adhere to the environment Slime layer: a loose shield that protects some bacteria from loss of water and nutrients Capsule: when the glycocalyx is bound more tightly to the cell and is denser and thicker Slime Layer The slime layer is important in the formation of biofilms. For example, the slime layer of Streptococcus mutans forms a biofilm that eventually leads to a buildup of plaque. This slime allows the bacteria to accumulate on tooth enamel, which in turn causes other bacteria in the mouth to become trapped in the slime.  Capsule Polysaccharides firmly attached to the cell wall. Capsules adhere to solid surfaces and to nutrients in the environment. Adhesive power of capsules is a major factor in the initiation of some bacterial diseases. Capsule also protect bacteria from being phagocytized by cells of the hosts immune system.  Lecture 3 Bacterial Cell Envelope By Prof. Dr. Mohammed Ali Ahmed Eid 24/10/2024 Bacterial Cell Envelope Most bacteria have a chemically complex external covering, termed the cell envelope, that lies outside of the cytoplasm. It is composed of two basic layers known as the cell wall, and the cell membrane. The layers of the envelope are stacked one upon another and are often tightly bonded together like. Although each envelope layer performs a distinct function, together they act as a single protective unit. The envelope is extensive and can account for one-tenth to one-half of a cell’s volume.  Bacterial Cell wall Immediately below the glycocalyx lies a second layer, the cell wall. Importance of the bacterial cell wall: 1. It determines the shape of a bacteria. 2. It save the bacterium from bursting or collapsing because of changes in osmotic pressure (osmotic lysis). 3. It might have components that contribute to pathogenicity. 4. The cell wall can protect the bacterial cell from toxic substances 5. It is the site of action of several antibiotics. 6. Cell wall composition helps identify bacterial species.  Christian Gram 1884 Christian Gram (1853-1938) was a Danish (‫)ﻣن اﻟدﻧﻣﺎرك‬ bacteriologist who made a fundamental contribution to microbiology through the development of the Gram staining technique in 1884, which revolutionized bacterial classification. He found that certain bacteria retained crystal violet dye after iodine fixation. This led to classification of bacteria as: – Gram-positive (retain ‫ ﺗﺳﺗﺑﻘﻲ‬the crystal violet stain) – Gram-negative (don't retain the crystal violet stain) This discovery helped advance understanding of bacterial infections, and contributed to development of targeted treatments Gram-positive: Gram-negative: Thick peptidoglycan layer (20-80 nm) Thin peptidoglycan layer (2-7 nm) (90%) (10%) No outer membrane Has outer membrane Contains teichoic acids Contains lipopolysaccharides (LPS) Single lipid membrane Double lipid membrane More susceptible to penicillin More resistant to antibiotics Sensitive to lysozyme Protected by outer membrane Peptidoglycan structure Sugar derivatives N-acetylglucosamine (NAG) N-acetylmuramic acid (NAM); NAG-lactic acid. Tetra peptide chain L-alanine D-glutamic acid meso-diaminopimelic acid D-alanine. Peptidoglycan structure Peptidoglycan Cross-Links Gram-positive bacteria: Uses interpeptide bridge (pentaglycine bridge; 5 glycine molecules) Gram-negative bacteria: Direct cross-linking No interpeptide bridge needed Peptidoglycan Teichoic acids structure Teichoic acids Polymers of glycerol or ribitol joined by phosphate Ribitol Amino acids such as D-alanine or sugars like glucose are attached to the glycerol and ribitol groups It is connected covalently with N- acetylmuramic (NAM) acid or to plasma membrane lipids (Lipoteichoic acid). Glycerol Peptidoglycan structure Gram positive cell wall Gram negative cell wall Outer Membrane Proteins: Porins: Other Proteins: Lipoproteins (Braun's lipoprotein)  Gram Negative cell wall Lipopolysaccharide (LPS) Structure Lipid A: Glucosamine disaccharide backbone 6-7 fatty acid chains Phosphate groups at positions 1 and 4’ Core Polysaccharide: Inner core: KDO (3-deoxy-D-manno-octulosonic acid) Heptose Outer core: Glucose Galactose N-acetylglucosamine O-antigen: Repeating oligosaccharide units Variable length (0-40 repeats) Strain-specific structure Function of outer membrane 1. Serve as a protective barrier 2. It prevents or slows the entry of antibiotics (Ex. Beta lactam class like penicillin and cephalosporin , and other toxic substances. 3. It contains porin proteins: Create channels for passive diffusion, and control permeability of outer membrane 4. It prevents the loss of constituents like periplasmic enzymes  Periplasmic Space: This is the region between the inner (cytoplasmic) membrane and the outer membrane in Gram-negative bacteria. It contains a gel-like matrix called the periplasm, Periplasm contains several proteins that allows for various Periplasmic biochemical processes, such as: 1. It contains hydrolytic enzymes that break down nutrients. space and 2. It contains transport proteins for nutrients and ions from the periplasm outer membrane into the cell. 3. It contains enzymes involved in cell wall and peptidoglycan biosynthesis. 4. It contains enzymes that can degrade harmful substances before they enter the cytoplasm such as β-lactamases, which can degrade antibiotics like penicillin. 5. It contains chaperones and enzymes that fold proteins, ensuring that secreted proteins are properly folded and functioning.  Lecture 4 Bacterial Cell Membrane and Internal Structure By Prof. Dr. Mohammed Ali Ahmed Eid 31/10/2024  Bacterial Cell Membrane The bacterial cell membrane is an interesting structure built from phospholipids that form an amphipathic bilayer. 1. Phospholipid Structure: Each phospholipid molecule has two distinct ends: – A polar head (hydrophilic) - "water- loving“ – Nonpolar tails (hydrophobic) - "water- hating“  Bacterial Cell Membrane 2. Bilayer Formation: The phospholipids organize themselves into two layers because of how they interact with water: The hydrophilic (polar) heads face outward, interacting with water both inside and outside the cell The hydrophobic (nonpolar) tails face inward, away from water, creating a protected inner zone This arrangement is about 5-10 nanometers thick Bacterial Cell Membrane Why phospholipid bilayer Works: 1.The hydrophilic heads can interact favorably with the watery environments inside and outside the cell 2.The hydrophobic tails cluster together, away from water, creating a stable barrier 3.This arrangement creates a selective barrier that helps control what enters and exits the cell  Fluid mosaic model 1. Peripheral Proteins: Loosely attached to membrane surface Easy to remove with gentle treatments Water-soluble (can exist in aqueous solutions) Make up 20-30% of membrane proteins Functions: 1. Often involved in cell signaling 2. Can act as enzymes 3. May be temporary regulatory proteins 4. Help anchor other proteins  Fluid mosaic model 2. Integral Proteins: Deeply embedded in membrane Require harsh treatments to remove Water-insoluble Comprise 70-80% of membrane proteins Amphipathic (have both hydrophobic and hydrophilic regions) Functions: 1. Transport proteins 2. Channel proteins 3. Receptor proteins 4. Structural proteins  Fluid mosaic model 3. Carbohydrates: Attached to outer surface only Often linked to proteins (glycoproteins) Also linked to lipids (glycolipids) Functions: 1. Cell recognition 2. Cell-cell communication 3. Immune system recognition 4. Protection The term "Fluid Mosaic" refers to how these components: Move freely within the membrane (fluid) Create a complex pattern of different molecules (mosaic) Function of the Cytoplasmic Membrane 1. It retains the cytoplasm 2. It serves as a selectively permeable barrier 3. It is the location of a variety of crucial metabolic processes: respiration, photosynthesis, the synthesis of lipids and cell wall constituents 4. It contains special receptor molecules that help bacteria detect and respond to chemicals in their surroundings. Internal Structure 1. Nucleoid: This is the region where the bacterial chromosome (a single, circular DNA molecule) is located. It is not surrounded by a membrane, but DNA is compacted within this area Internal Structure 2. Plasmids: Small, circular DNA molecules separate from the chromosomal DNA. Plasmids often carry genes for antibiotic resistance, virulence factors, or metabolic capabilities and can be exchanged between bacteria. Internal Structure 3. Ribosomes: These are responsible for protein synthesis and are made of RNA and proteins. Bacterial ribosomes (70S) are smaller than eukaryotic ribosomes and serve as targets for certain antibiotics  Internal Structure 4. Inclusion Bodies: These are storage granules containing nutrients or building blocks such as glycogen, lipids, sulfur, or polyphosphate. Some bacteria also store gas vesicles in inclusion bodies to regulate buoyancy. Internal Structure 5. Cytoskeleton: Though simpler than the eukaryotic cytoskeleton, bacteria have proteins (e.g., MreB, FtsZ) that help: 1. Maintain cell shape, 2. Aid in cell division, 3. Facilitate intracellular organization. Internal Structure Cytoplasm Cytoplasm: The fluid matrix within the cell that contains water, enzymes, ions, and various molecules. It is the site of many metabolic reactions, including glycolysis and other biochemical pathways. Internal Structure 7. Endospores: Certain bacteria, such as Bacillus and Clostridium species, produce endospores as a survival mechanism. Endospores are highly resistant to extreme environmental conditions and allow bacteria to endure unfavorable environments. Possible Location of Endospores Common locations within the cell include: 1. Central (middle of the cell) 2. Subterminal (near one end) 3. Terminal (at one end) 4. Terminal spore with swollen sporangium. The specific location of an endospore can be a characteristic feature used for bacterial identification.