Week 1 Lec 2 Microbiology Lecture Notes PDF

BIOL341/BIOL982: Week 1 Introduction to Microbiology Part 2 Dr Emma-Jayne Proctor [email protected] Introduction to Microbiology Lecture 2 Outline (Textbook, Pommerville Fundamentals of Microbiology chapters 4 and 15): Microorganisms: diversity Pathogenic Microorganisms...

BIOL341/BIOL982: Week 1 Introduction to Microbiology Part 2 Dr Emma-Jayne Proctor [email protected] Introduction to Microbiology Lecture 2 Outline (Textbook, Pommerville Fundamentals of Microbiology chapters 4 and 15): Microorganisms: diversity Pathogenic Microorganisms Structural features of Bacteria Structural features of Viruses Assumed Knowledge: BIOL103, BIOL215, BIOL340 2 Learning Outcomes  Be aware of the techniques used to study microbial diversity  Knowledge of basic bacterial structure  Knowledge of basic viral structure  Understand some techniques used to classify bacteria and viruses What do you know about Microorganisms?  Definition?  What are the 5 types of microorganisms?  What proportion of microorganisms affecting humans are pathogenic?  What are the 10 most dangerous microorganisms to human health? Microorganisms  Colonise every habitat or environment on and in the earth = ubiquitous  Profound influence on all aspects of life  Bacteria, fungi, algae, protozoa and viruses  Vast numbers  Very diverse  Not always harmful but pathogens driving force for much microbiology development 5 Microbial Diversity  Metagenomics is the study of the total number of genomes in a sample  Estimates are conducted by PCR amplification of 16S or 23S rRNA genes because many bacterial Genera are non-culturable by known techniques….  Oceans may support over 2 million bacterial Genera  Half a ton of soil may contain over 4 million bacterial Genera  Human skin houses approximately 2 x 109 bacteria  Human gut content contains approximately 1 x 1014 bacteria Microbial Diversity  Whole genome sequencing becoming more standard  Challenges of computational power, bioinformatics tools and mix of biological and mathematical skillsets. Microbial Diversity  The vast majority of microorganisms are benign and do not cause disease. In fact, most microorganisms are beneficial;  Niche occupation, preventing pathogens gaining entry into gut, lungs, skin etc.  Performing digestion functions in the gut  Turning over nitrogen and carbon compounds in the soil  Photosynthesis  Biotechnology Pathogenic organisms are present in all 5 kingdoms e.g. helminths- worms e.g. red algae e.g. Trichophyton BACTERIA Ring worm VIRUSES e.g. protozoa e.g. bacteria 9 Prokaryotes  Hereditary material – DNA  Complex biochemical processes  Reproduce to produce new generations  Evolutionary adaptation in response to other organisms and the environment  Complex and regulated responses to stimuli Often described as “simple single-cell” organisms, but are they really? Bacterial Cells Have an Organised Structure Figure 4.3: Bacterial cell * structure. * * * *not in all bacteria * 11 The Bacterial Cell Wall  Covers entire cell surface  Serves as exoskeleton  Provides structural integrity  Anchors cellular appendages  Protects the cell from injury  Maintains water balance and prevents cell Figure 4.9: Cell rupture (lysis). rupture The Bacterial Cell Wall Structure  Bacteria are classified into two major groups: Gram-positive or Gram- negative following staining  Gram stain results reflect the thickness of the peptidoglycan layer in the bacterial cell wall.  Gram-positive bacteria stain purple/blue whilst Gram-negative bacteria stain pink. Staphylococcus aureus Escherichia coli The cell wall governs the shape of the bacterium : cocci, rod or spiral shaped. 13 www.cat.cc.md.us Gram-Positive and Gram-Negative Bacterial Cells  Gram-positive bacteria:  Thick peptidoglycan cell walls containing teichoic acid. Figure 4.10B1: Gram- positive cell wall.  Gram-negative bacteria:  Two-dimensional peptidoglycan layer and no teichoic acid.  Outer membrane containing porins separated from the cell membrane by the periplasmic space. Figure 4.10C1: Gram-14 negative cell wall. Bacterial Cell Wall Structure The structure of the Gram-positive cell wall: Peptidoglycan chains - alternating units of 2 amino containing sugars; N acetyl glucosamine (NAG) and N acetyl muramic acid (NAM) 15 www.cat.cc.md.us Bacterial Cell Wall Structure The structure of the Gram-negative cell wall: 16 www.cat.cc.md.us  Courtesy of Elliot Juni, Department of Microbiology The Glycocalyx Serves and Immunology, The University of Michigan. Several Functions  The glycocalyx is a sticky layer of polysaccharides secreted externally to the cell wall. Figure 4.8A: The bacterial  Capsule: Thick, firmly bound layer. glycocalyx in Acinetobacter cells.  Slime layer: Diffuse, water-soluble layer. © George Musil/Visuals Unlimited.  It protects cells from the environment and allows them to attach to surfaces.  Also helps pathogens evade immune system. Figure 4.8B: The17 glycocalyx of E. coli. Cell-Surface Structures Interact with the Environment  Pili are short protein fibers extending from the surface of many gram-negative bacteria.  Type I: Contain adhesins that attach cells to surfaces. Figure 4.4A: Bacterial pili on E. coli.  Actas virulence factor in pathogenic bacteria.  Type IV: Provide “twitching motility” to cells.  Conjugation pili: Used to transfer genetic material between cells. 18 Neisseria gonorrhoeae http://textbookofbacteriology.net Flagella Provide Motility  Prokaryotic flagella are very long corkscrew appendages extending from the cell surface at one or more points.  Bacterial flagella are used for locomotion and chemotaxis (moving up or down chemical gradients). Courtesy of Dr. Jeffrey Pommerville.  Flagella differences are used to classify bacterial strains Figure 4.5A: Bacterial flagella on Proteus vulgaris. 19 Bacterial Spores  Bacterial spores survive desiccation and heating. Spores “germinate” to form vegetative cells eg. Bacillus anthracis.  Vegetative cells usually are destroyed at 60oC while spores require heating to 121oC for 15 min. 20 http://www.wired.com Viruses Have a Simple Structural Organisation  Viruses are tiny infectious agents that are obligate intracellular parasites.  They lack the machinery for generating energy/large molecules and need a host cell to replicate. Figure 15.3: Size relationships Figure 15.4: The viral among cells and viruses. replication cycle. 21 Viruses  Viruses have either a DNA or RNA genome  single- or double-stranded  Viruses are typically less than 1 um (1/1000 mm) in size HIV virus  Viruses lack metabolic enzymes, DNA replication enzymes, ribosomes etc…  Viruses infect all classes and types of living organisms (animals, plants, fungi, bacteria) 22 Viral Structure  The major components of viruses include:  Capsid (or core) which is the protein shell of the virus.  The genome which can be either single- or double-stranded DNA or RNA.  Many animal viruses contain an envelope, which is made up of host cell membrane and viral proteins. Figure 15.5: The components of viruses. 23 Viral Structure  Viruses can be grouped by their shape:  Those with a rod or filament shape have helical symmetry.  Viruses with a capsid that has 20 triangular sides have isocahedral symmetry.  Other viruses are classified as having complex symmetry. 24 Figure 15.6: Viral shapes. Bacterial Viruses  Bacteriophage (or coliphage) T4 infects E. coli.  Many bacteriophage contain a tail structure, which is used like a syringe to inject the bacteriophage genome into the host cell. 25 biologyonline.us Dr Graham Beards via wikimedia.commons Eukaryotic viruses  Eukaryote viruses are usually rod-shaped, oblong or round  These viruses do not possess a “tail” structure Influenza virus Rotavirus 26 http://web.uct.ac.za  Viruses Can Be Classified by Their Genome Figure 15.7: A classification for the medically relevant 27 human viruses. Figure 15.9: Diversity of viruses. Diversity of Viruses 28 Pie charts modified from Small Things Considered (January 2016). Viral Abundance and Diversity. Detection of Viruses  Detection of viruses is critical to disease identification: © Dennis Kunkel Microscopy/Science Source.  Some diseases have specific symptoms, such as mumps or measles.  Light microscopes look for cytopathic effects (e.g., syncytia or giant cells in RSV).  Electron microscopes examine cellular Figure 15.17: Cells and viruses. components.  Serology looks for antibodies.  PCR 29  Cultivation of Viruses  In a primary cell culture, cells form a monolayer in a culture dish and cytopathic effects are noted.  Viruses can also be identified by the formation of plaques—clear zones within the monolayer—and phage typing of the plaques, as specific strains create characteristic plaques. © James King-Holmes/Science Source. Courtesy of Giles Scientific Inc., CA, Courtesy of Greg Knobloch/CDC. www.biomic.com. Figure 15.18: Infection of cells in embryonated eggs and cell culture. 30 Today’s Tools to Study Microbiology  Advanced microscopes  High throughput technologies  Automation  Advanced computer analysis systems, data storage, data retrieval etc… (bioinformatics)  Model systems  The “OMICS” - 31 Summary  Basic bacterial and viral structures and their function  Host immune response differs between microbes  Modern tools for the study of microbiology 32