MIC 205 - Microbiology Lecture Notes PDF

MIC 205 - Microbiology Lecture 1: “Back to the Future” Ch. 1 History of Microbiology Ch. 4 Classification Lecturer: Patrick Daydif Office: UCENT 356 Phone: (602) 496-0599 Email: [email protected] Office Hours: See Canvas (or by appointment) The...

MIC 205 - Microbiology Lecture 1: “Back to the Future” Ch. 1 History of Microbiology Ch. 4 Classification Lecturer: Patrick Daydif Office: UCENT 356 Phone: (602) 496-0599 Email: [email protected] Office Hours: See Canvas (or by appointment) The best way to contact me and answer your questions is Face to Face. 1 Lecture Task Think of a situation in which you may have “interacted” with microorganisms today, yesterday, or in the past week. What changes to the world would occur if there were NO microorganism on the planet? Introduce yourself to the folks around you and attempt to name as many interactions/changes as your group can. Here is a great opportunity to exchange contact information with a classmate. Collection for grade? No (5 points) 2 2 Major Classes of Microorganisms data:image/jpeg;base64,/9j/4AAQSkZJRgABAQAAAQABAAD/2wCEAAkGBxMTEhQUEhQUFRQQFRUQDw8UFBQPFBUQFBUWFhQUFBQYHCggGBolHBQVITEhJSkrLi4uFx80ODMsNygtLisBCgoKDg0OGhAQGiwkHyQsLC0sLCwsLCwsLCwsLCwsLCwsLCwsLCwsLCwsLCwsLCwsLCwsLCwsLCwsLCwsLCwsLP/AABEIAMIBAwMBIgACEQEDEQH/xAAcAAACAwEBAQEAAAAAAAAAAAAEBQIDBgABBwj/xABBEAABAwIEAwYDBQUGBwEAAAABAAIRAwQFEiExQVFhBhMicYGRFDKxUqHB0fAjQmJy8QcVFpKi4TNDU3OTstIk/8QAGgEAAwEBAQEAAAAAAAAAAAAAAAEDAgQFBv/EACQRAAICAgIDAAMBAQEAAAAAAAABAhEDEiExBBNBFCIyYaEF/9oADAMBAAIRAxEAPwD5QulScFUVQ5iYKkHKqV6 Ebola Virus Ebola – Small infectious agent can replicate only inside the living cells of organisms. – There are unique viruses that Influenza Virus will infect Animal cells Plant cells Bacterial cells data:image/jpeg;base64,/9j/4AAQSkZJRgABAQAAAQABAAD/2wCEAAkGBxMTEhQUEhQUFRQQFRUQDw8UFBQPFBUQFBUWFhQUFBQYHCggGBolHBQVITEhJSkrLi4uFx80ODMsNygtLisBCgoKDg0OGhAQGiwkHyQsLC0sLCwsLCwsLCwsLCwsLCwsLCwsLCwsLCwsLCwsLCwsLCwsLCwsLCwsLCwsLCwsLP/AABEIAMIBAwMBIgACEQEDEQH/xAAcAAACAwEBAQEAAAAAAAAAAAAEBQIDBgABBwj/xABBEAABAwIEAwYDBQUGBwEAAAABAAIRAwQFEiExQVFhBhMicYGRFDKxUqHB0fAjQmJy8QcVFpKi4TNDU3OTstIk/8QAGgEAAwEBAQEAAAAAAAAAAAAAAAEDAgQFBv/EACQRAAICAgIDAAMBAQEAAAAAAAABAhEDEiExBBNBFCIyYaEF/9oADAMBAAIRAxEAPwD5QulScFUVQ5iYKkHKqV6CgC Influenza Influenza data:image/jpeg;base64,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 Canines Parvovirus.jpg Parvo Parvo 3 T4Phage Corona 3 1  Major Classes of Microorganisms Virus Algae – Unicellular or multicellular – Photosynthetic (Phototroph), but not necessarily green! – Simple reproductive structures – Categorized based of pigmentation, storage products, and composition of cell wall 4 4 Major Classes of Microorganisms Virus Algae Fungi – Eukaryotic (have a membrane- bound nucleus) – Obtain energy (food) from other organisms via breaking chemical bonds (chemotroph) – Possess cell walls – Composed of: – Molds – multicellular; have hyphae (filaments); reproduce by sexual and asexual spores – Yeasts – unicellular; reproduce asexually by budding; some produce sexual spores 5 5 Major Classes of Microorganisms Virus Algae Fungi Protozoa – Single-celled eukaryotes – Similar to animals in cell structure and nutrition (chemotroph), needs – Typically live in water; some live inside animal hosts – Most reproduce asexually; some reproduce sexually – Some have two life stages Trophozoite: active stage Cysts: immature stage – Most are capable of locomotion using... Pseudopodia – “false feet;” extensions of the internal guts of a cell Cilia – hair-like projections used for movement Flagella – long, filament-like “tails” used for swimming 6 6 2  Major Classes of Microorganisms Virus Algae Fungi Protozoa Bacilli Prokaryotic (Bacteria) – Unicellular, lack nuclei, possess unique shapes – Much smaller than eukaryotes – Found everywhere there is sufficient moisture; some found in extreme environments – Reproduce asexually Cocci – Two kinds Bacteria (eubacteria or true bacteria) – – cell walls contain peptidoglycan; some lack cell walls; – Some cause disease, but most do not. – Some are beneficial to the human body as normal flora Archaea – – cell walls composed of polymers other than peptidoglycan Spirillum – Many live in extreme environments 7 » High heat ( 60 ˚C +), high pressure, high salt 7 A Brief Look at History of Microbiology Era of Speculation – 5000 BC to 1600. – We interacted each day with microorganisms, although they were unknown to us. Foods – Bread, Wine Diseases (Bad Spirits!!!!) – Plagues – Syphilis First major biological turning point in knowledge was when humans: Domesticated plants for farming Livestock animals This resulted in sedentary societies. 8 8 A Brief Look at History of Microbiology How does one understand a Biological organism? At this point, we studied the only organism that we can see. Increase in size over time (Growth) – Reproduce* – Responds to environment** – Movement – Metabolism (Ability to extract energy from a molecule)** – Complex & exhibit organized structure** *Depends on the organism ** Technology is needed to measure Theory of Spontaneous Generation – Explains reproduction of small organisms 9 9 3  Theory of Spontaneous Generation Can you think of other theories that were commonplace that are false today? Greek philosophers, With weeks of no rain After rain such as Aristotle 10 10 A Brief Look at History of Microbiology Spontaneous Generation originated with the Greek philosophers in the middle ages. – It was well accepted and commonplace regarding smaller life forms such as flies or fleas. The Church and religious leaders influenced people and governments. – People were sick due to bad spirits. Galileo was threaded death for believing the Earth was not the center of the universe. Some individuals have asked other questions such as, – Is there a link between disease and the environment? – Why could people who once had a disease not fall ill again after contact? – Why does one need to add a little old 12 wine to make grape juice into wine? 12 Connections “Environment & Diseases” Pakistan/ India 2700 BC, Rome 315 AD – Were the first to make the connection. Rome – Inventions of Water pipes/Elaborate aqueducts Toilets Sewers Public fountains Commissioner Quarantine Some recognize that some diseases were COMMUNICABLE, but few made the connection of spoiled food/ dirty water and microbes, WHY? 13 No one could see them!!! 13 4  Suitable Tools “Era of Observation” Antoni van Leeuwenhoek (Dutch, mid-17th century,~1675) – Began making and looking through simple microscopes – Often made new microscope for each specimen – Examined water and visualized tiny animals, fungi, algae, and single-celled protozoa; “animalcules.” – By the end of the 19th century, these organisms were called “microbes.” Leeuwenhoek is known as “Father of Protozoology” and “Father of Bacteriology.” 14 14 How Can Life Be Classified? Early Taxonomy – String together descriptive terms that would would vary from each scientist and their country of origin. Carolus Linnaeus (Swedish, mid-18th century) – Taxonomy consists of classification (grouping similar organisms together), nomenclature (naming), and identification similar organisms together. – Grouped Leeuwenhoek’s microorganisms into five categories: Small animals, Fungi, Protozoa, Algae, Prokaryotes Nomenclature – Genus and species categories together constitute a binomial nomenclature for every organism. – Gives each microbe 2 names: Genus - noun, always capitalized species - adjective, lowercase – Both italicized or underlined Staphylococcus aureus (S. aureus) Escherichia coli (E. coli) 15 15 Linnaean Taxonomic Scheme Linnaeus provided a hierarchical system that standardized the classification of organisms. This used shared characteristics to organize large amounts of information about organisms and make predictions based on knowledge of similar organisms More – Kingdom Inclusive – Phylum (Broader) – Class – Order – Family – Genus Less – Species Inclusive Typically, microbiologist may identify subspecies such as 16 E.coli O157H7 ……“O157H7” is the strain name. 16 5  What is a VARIANT! Remember! Typically, microbiologist may identify subspecies such as E.coli O157H7 ……“O157H7” is the strain name. Variant is just a subspecies of a subspecies, and a maybe a 17 subspecies! 17 Taxonomic Categories Linnaeus’s goal was classifying and naming organisms as a means of cataloging them – Linnaeus proposed only two kingdoms system Animalia and Plantae – Some bacteria was placed with the Plants???? – 1965: Whitaker proposed a taxonomic approach based on five kingdoms: Animalia, Plantae, Fungi, Protista, and Prokaryotae (widely accepted) Some photosynthesizing bacteria was placed with the Plants???? 18 18 Domains (Modern Taxa) Modern goal is to understand relationships among groups of organisms – Develop Phylogenetic hierarchy/ Evolutionary relationship – Comparisons of organisms’ genetic material led to the formation of organism “domains.” 1980’s Carl Woese – Taxonomists compare DNA sequences of very stable rRNA molecules (very few changes over time). – Proposed three domains based on three basic types of cells as determined by ribosomal RNA sequences Bacteria (Eubacteria) – true bacteria, peptidoglycan (cell wall) Archaea – odd bacteria that live in extreme environments, high salt, heat, etc. (usually called extremophiles) Eukarya – have a nucleus & organelles (humans, animals, plants) 19 19 6  Modern Classification of Prokaryotes 1. Macroscopic morphology - Colony appearance 2. Microscopic morphology Cell shape 3. Nucleic acid techniques (NAT) G + C base composition DNA/RNA analysis to identify genetic sequences 4. Physiological / Chemical / Biochemical characteristics 5. Serological analysis (Immunology) -Antibodies / Antigens 20 20 Carl Woese’s Classification System WAIT! Where are the Viruses? Humans 21 21 Era of Cultivation The Golden Age of Microbiology – Late 19th to early 20th century Scientists searched for answers to four questions – Is the spontaneous generation of microbial life possible? – What causes fermentation? – What causes disease? – How can we prevent infection and disease? These questions based upon historical challenges facing society – Food and wine spoilage – Flu, smallpox, and plague epidemics 22 22 7  Is Spontaneous Generation Possible? Aristotle (350 BC) proposed spontaneous generation – living things can arise from nonliving matter Redi’s Experiments (Late 1600’s): – Established doubt of Spontaneous Generation 23 23 Spontaneous Generation John Needham (mid-1750’s) – Worked with boiled Beef and Hay infusions. – “…..there must be a life force that causes inanimate matter to come to life spontaneously….” Spallanzani (1799) – Concluded that Microorganisms exist in the air and can contaminate experiments Spontaneous generation of microorganisms does not occur – Critics said sealed vials did not allow enough air for organisms to survive and that prolonged heating destroyed “life force.” Louis Pasteur (1850’s) – Swan neck flask 24 24 Pasteur’s Experiments 25 25 8  What Causes Fermentation? Spoiled wine threatening the livelihood of vintners, so they funded research into how to promote the production of alcohol but prevent spoilage by acid during fermentation Some believed air caused fermentation reactions, while others insisted living organisms caused fermentation This debate is also linked to the debate over spontaneous generation. 26 26 The Scientific Method Debate over spontaneous generation led to the development of the scientific method – A group of observations leads scientist to ask a question about some phenomenon – The scientist generates a hypothesis (potential answer to a question) – The scientist designs and conducts an experiment to test a hypothesis – Based on observed results of an experiment, scientist either accepts, rejects, or modifies the hypothesis 27 27 Pasteur and Pasteurization 28 28 9  Pasteur and Pasteurization 29 29 Pasteur (Father of Microbiology) Fermentation Spontaneous generation Diseases of BEER and wine Disease of silkworm Virus & Vaccines Rabies 30 30 What Causes Disease? Louis Pasteur developed the germ theory of disease Robert Koch studied causative agents of disease – Anthrax Examined colonies of microorganisms – Koch’s postulates Because of his achievements, Koch is considered the Father of the Microbiological Laboratory Simple staining technique First photomicrograph of bacteria First photomicrograph of bacteria in diseased tissue Techniques for estimating CFU/ml Use of steam to sterilize media Use of Petri dishes Aseptic techniques 31 Bacteria as distinct species 31 10  Koch’s Postulates 1. A suspected causative agent must be found in every case of the disease and be absent in healthy hosts 2. Agent must be isolated and grown outside the host 3. The isolated agent is to be introduced into a healthy susceptible host, and the host must get the same disease as the original host 4. Same agent must be reisolated from the diseased host 32 32 Limitations of Koch’s Postulates Limitations Viral pathogens Not all microorganisms can be cultured (grown) outside the host. Synergy Two or more organisms work together to cause disease. State of the immune system of the health host There is no animal model of infection with that pathogen for a human disease 33 33 Disease Prevention (1800-1950) Ignaz Semmelweis – Observed the mortality rate of childbirth – Implemented hand washing during childbirth Joseph Lister – Antisepsis in healthcare settings Florence Nightingale – Introduced cleanliness into the nursing practice. Edward Jenner – Vaccine – Cowpox protected against smallpox. John Snow – Epidemiology Alexander Fleming – Antibiotics 34 34 11