Ch1 Introduction to Microbiology PDF

Ch1 Introduction to Microbiology Instructor: Dr. Clayton  Objectives Following this lecture, students should be able to: 1-1 List several ways in which microbes affect our lives. 1-2 Define microbiome, normal microbiota, and transient microbiota. 1-3 Recognize the system of sc...

Ch1 Introduction to Microbiology Instructor: Dr. Clayton  Objectives Following this lecture, students should be able to: 1-1 List several ways in which microbes affect our lives. 1-2 Define microbiome, normal microbiota, and transient microbiota. 1-3 Recognize the system of scientific nomenclature that uses two names: a genus and a specific epithet. 1-4 Differentiate the major characteristics of each group of microorganisms. 1-5 List the three domains. 1-6 Explain the importance of observations made by Hooke and van Leeuwenhoek. 1-7 Compare spontaneous generation and biogenesis. 1-8 Identify the contributions to microbiology made by Needham, Spallanzani, Virchow, and Pasteur.  Microbes in Our Lives Microorganisms are organisms that are too small to be seen with the unaided eye Microbes include bacteria, fungi, protozoa, microscopic algae, and viruses  Microbes in Our Lives Few Microbes are actually pathogenic (disease causing) Knowledge of microorganisms allows humans to – Prevent food spoilage – Prevent disease – Understand causes and transmission of disease to prevent epidemics  The Microbiome An adult human is composed of 30 trillion body cells – Harbors another 40 trillion bacterial cells The microbiome is a group of microbes that live stably on/in the human body – Help to maintain good health – Can prevent growth of pathogenic microbes – May help train the immune system to discriminate threats  The Microbiome Normal microbiota is the collection of acquired microorganisms on or in a healthy human being – Begin to be acquired as newborns – May colonize the body indefinitely – May colonize the body fleetingly (making them transient microbiota) Colonization can only occur at body sites that provide nutrients and the right environment for the microbes to flourish  The Microbiome The Human Microbiome Project – Begun in 2007 – Goal of determining the makeup of typical microbiota of various areas of the body – Secondary goal of understanding relationship between changes in microbiome and human diseases The National Microbiome Initiative (NMI) – Begun in 2016 – Explores the role microbes play in different ecosystems What percentage of all the cells in the human body are bacterial cells?  Naming and Classifying Microorganisms Carolus Linnaeus established the system of scientific nomenclature in 1735 Each organism has two names: the genus and the specific epithet  Classification Scientific classification Carolus Linnaeus Domain and Bacteria -Taxonomy Kingdom: Phylum: Firmicutes -Classification system DKPCOFGS Class: Bacilli Order: Bacillales -Grouped based on organism characteristics Family: Bacillaceae Genus: Bacillus *The invention of the microscope Species: B. (Hooke & Leeuwenhoek) led to the anthracis classification of microorganisms Binomial name (to be discussed later) Bacillus anthracis Cohn 1872  Binomial System of Nomenclature Scientific Name Genus species Example: Escherichia coli – Genus = Escherichia; species = coli There can be many species in one genus Always italicize both genus and species!!! E. coli is also correct If handwritten: Staphylococcus aureus is correct  Nomenclature Escherichia coli – Honors the discoverer, Theodor Escherich – Describes the bacterium's habitat—the large intestine, or colon Staphylococcus aureus – Describes the clustered (staphylo-) spherical (coccus) cells – Describes the gold-colored (aureus) colonies Types of Microorganisms Bacteria Archaea Fungi Protozoa Algae Viruses Multicellular Animal Parasites  Figure 1.2 Types of Microorganisms Bacteria Sporangia Food Nerve cell ZikV particle Pseudopod  Bacteria Prokaryotes – “Prenucleus” Single-celled Peptidoglycan cell walls Divide via binary fission Derive nutrition from organic or inorganic chemicals or photosynthesis May “swim” by using moving appendages called flagella Figure 1.2a Types of Microorganisms Bacteria  Archaea Are prokaryotes Lack peptidoglycan cell walls – May lack cell wall entirely Often live in extreme environments Include: – Methanogens – Extreme halophiles – Extreme thermophiles Generally not known to cause disease in humans  Fungi Eukaryotes – Distinct nucleus surrounding DNA genetic material Chitin cell walls Absorb organic chemicals for energy Yeasts are unicellular Molds and mushrooms are multicellular – Molds consist of masses of mycelia, which are composed of filaments called hyphae Figure 1.2b Types of Microorganisms Sporangia  Protozoa Eukaryotes Absorb or ingest organic chemicals May be motile via pseudopods, cilia, or flagella Free-living or parasitic (derive nutrients from a living host) – Some are photosynthetic Reproduce sexually or asexually Figure 1.2c Types of Microorganisms Food particle Pseudopod  Algae Eukaryotes Cellulose cell walls Found in freshwater, saltwater, and soil Use photosynthesis for energy – Produces oxygen and carbohydrates Sexual and asexual reproduction possible Figure 1.2d Types of Microorganisms  Viruses Acellular Consist of DNA or RNA core Core is surrounded by a protein coat – Coat may be enclosed in a lipid envelope Are replicated only when they are in a living host cell – Inert outside living hosts Figure 1.2e Types of Microorganisms Nerve cell ZikV  Multicellular Animal Parasites Eukaryotes Multicellular animals Not strictly microorganisms Parasitic flatworms and roundworms are called helminths – Some microscopic stages in their life cycles  Classification of Microorganisms Developed by Carl Woese in 1978 Three domains based on cellular organization – Bacteria – Archaea – Eukarya ▪Protists ▪Fungi ▪Plants ▪Animals  Check Your Understanding Check Your Understanding  1-3 Distinguish a genus from a specific epithet.  1-4 Which groups of microbes are prokaryotes? Which are eukaryotes?  1-5 What are the three domains? Pioneers of Microbiology Robert Hooke (1660s) 1665 Hooke published Micrographia describing microscopic and telescopic observations Coined the term “cell” for describing biological organisms Marked the beginning of cell theory: All living things are composed of cells Antony van Leeuwenhoek Prosperous Dutch linen merchant Developed interest in microscopes In 1676 described spherical, rod, & spiral bacteria and protozoa (animalcules); later published by the Royal Society in England Also described red blood cells, sperm cells, and yeast cells Antony van Leeuwenhoek  Small Life Forms & Fundamental Nature of Life Fundamental disagreement: where do organisms come from? Two different ideas emerged: – Biogenesis: life comes from pre-existing life – Spontaneous generation (abiogenesis): life can come from non-living sources Spontaneous Generation Skeptics Francesco Redi (1668)-Decaying Meat John Needham (1745)-Boiled Nutrient Broth, covered flask Lazzarro Spallanzi (1765)-Boiled Nutrient Broth, sealed flask Rudolf Virchow (1858)-Cells arise from preexisting cells Louis Pasteur (1859)-microbes in the air From where did the microbes come? Spontaneous generation or biogenesis flies and maggots, this was a good case against spontaneous generatio The argument over microbial origins continued for over 100 years. Disproving Spontaneous Generation: Louis Pasteur French chemist 1859 - disproved spontaneous generation by experiments with swan- necked flasks 1864 - invented pasteurization Foundation Figure 1.4 Disproving Spontaneous Generation Fig. 01.02 A. Tilt flask Quality Control: Break off top of flask  Check Your Understanding Check Your Understanding  1-7 What evidence supported spontaneous generation?  1-8 How was spontaneous generation disproved?  A Brief History of Microbiology Learning Objectives 1-9 Explain how Pasteur's work influenced Lister and Koch. 1-10 Identify the importance of Koch's postulates. 1-11 Identify the importance of Jenner's work. 1-12 Identify the contributions to microbiology made by Ehrlich and Fleming. The Golden Age of Microbiology 1857–1914 Beginning with Pasteur's work, discoveries included the relationship between microbes and disease, immunity, and antimicrobial drugs Copyright © 2019 Pearson Education, Inc. All Rights Reserved The Golden Age of Microbiology Pasteur showed that microbes are responsible for fermentation Fermentation is the microbial conversion of sugar to alcohol in the absence of air Microbial growth is also responsible for spoilage of food and beverages Bacteria that use air spoil wine by turning it to vinegar (acetic acid) Copyright © 2019 Pearson Education, Inc. All Rights Reserved The Golden Age of Microbiology Pasteur demonstrated that these spoilage bacteria could be killed by heat that was not hot enough to evaporate the alcohol in wine Pasteurization is the application of a high heat for a short time to kill harmful bacteria in beverages Copyright © 2019 Pearson Education, Inc. All Rights Reserved Figure 1.5 Milestones in the Golden Age of Microbiology An asterisk (*) indicated a Nobel Laureate. The Germ Theory of Disease states that many diseases are caused by microorganisms. Copyright © 2019 Pearson Education, Inc. All Rights Reserved The Germ Theory of Disease 1835: Agostino Bassi showed that a silkworm disease was caused by a fungus 1865: Pasteur showed that another silkworm disease was caused by a protozoan 1840s: Ignaz Semmelweis advocated handwashing to prevent transmission of puerperal fever from one obstetrical patient to another Copyright © 2019 Pearson Education, Inc. All Rights Reserved The Germ Theory of Disease 1860s: Applying Pasteur's work showing that microbes are in the air, can spoil food, and cause animal diseases, Joseph Lister used a chemical antiseptic (phenol) to prevent surgical wound infections Is a theory trivial? Copyright © 2019 Pearson Education, Inc. All Rights Reserved The Germ Theory of Disease 1876: Robert Koch discovered that a bacterium causes anthrax and provided the experimental steps, Koch's postulates, to demonstrate that a specific microbe causes a specific disease Copyright © 2019 Pearson Education, Inc. All Rights Reserved Vaccination 1796: Edward Jenner inoculated a person with cowpox virus, who was then immune to smallpox Years after Jenner, Pasteur discovered why Vaccination is derived from the Latin word vacca, meaning cow The protection is called immunity Copyright © 2019 Pearson Education, Inc. All Rights Reserved Check Your Understanding-7 Check Your Understanding  Summarize in your own words the germ theory of disease. 1-9  What is the importance of Koch's postulates? 1-10  What is the significance of Jenner's discovery? 1-11 Copyright © 2019 Pearson Education, Inc. All Rights Reserved The Birth of Modern Chemotherapy: Dreams of a “Magic Bullet” Treatment of disease with chemicals is called chemotherapy Chemotherapeutic agents used to treat infectious disease can be synthetic drugs or antibiotics Antibiotics are chemicals produced by bacteria and fungi that inhibit or kill other microbes Copyright © 2019 Pearson Education, Inc. All Rights Reserved The First Synthetic Drugs Quinine from tree bark was long used to treat malaria Paul Ehrlich speculated about a “magic bullet” that could destroy a pathogen without harming the host – 1910: Ehrlich developed a synthetic arsenic drug, salvarsan, to treat syphilis 1930s: Sulfonamides were synthesized Copyright © 2019 Pearson Education, Inc. All Rights Reserved A Fortunate Accident—Antibiotics 1928: Alexander Fleming discovered the first antibiotic (by accident) Fleming observed that Penicillium fungus made an antibiotic, penicillin, that killed S. aureus 1940s: Penicillin was tested clinically and mass- produced Copyright © 2019 Pearson Education, Inc. All Rights Reserved Figure 1.6 The Discovery of Penicillin Normal bacterial colony Area of inhibited bacterial growth Penicillium colony Copyright © 2019 Pearson Education, Inc. All Rights Reserved Problems with Antimicrobial Chemicals Overuse can lead to resistance Some drugs can be toxic to humans – Especially antivirals Research used to overcome these problems has ushered in a Third Golden Age of Microbiology from the late 1980s to the present Copyright © 2019 Pearson Education, Inc. All Rights Reserved Modern Developments in Microbiology Learning Objectives 1-13 Define bacteriology, mycology, parasitology, immunology, and virology. 1-14 Explain the importance of microbial genetics, molecular biology, and genomics. Copyright © 2019 Pearson Education, Inc. All Rights Reserved Bacteriology, Mycology, and Parasitology Bacteriology is the study of bacteria Mycology is the study of fungi Parasitology is the study of protozoa and parasitic worms Copyright © 2019 Pearson Education, Inc. All Rights Reserved Figure 1.8 Parasitology: The Study of Protozoa and Parasitic Worms Copyright © 2019 Pearson Education, Inc. All Rights Reserved Immunology Immunology is the study of immunity – Vaccines and interferons are used to prevent and cure viral diseases A major advance in immunology occurred in 1933 when Rebecca Lancefield classified streptococci based on their cell wall components Copyright © 2019 Pearson Education, Inc. All Rights Reserved Figure 1.9 Rebecca Lancefield (1895– 1981) Rebecca Lancefield (1895–1981), who discovered differences in the chemical composition of a polysaccharide in the cell walls of many pathogenic streptococci. Copyright © 2019 Pearson Education, Inc. All Rights Reserved Virology Virology is the study of viruses Dmitri Iwanowski in 1892 and Wendell Stanley in 1935 discovered the cause of mosaic disease of tobacco to be a virus Electron microscopes have made it possible to study the structure of viruses in detail Copyright © 2019 Pearson Education, Inc. All Rights Reserved Molecular Genetics Microbial genetics: the study of how microbes inherit traits Molecular biology: the study of how DNA directs protein synthesis Genomics: the study of an organism's genes; has provided new tools for classifying microorganisms Recombinant DNA: DNA made from two different sources – In the 1960s, Paul Berg inserted animal DNA into bacterial DNA, and the bacteria produced an animal protein Copyright © 2019 Pearson Education, Inc. All Rights Reserved Molecular Genetics 1941: George Beadle and Edward Tatum showed that genes encode a cell's enzymes 1944: Oswald Avery, Colin MacLeod, and Maclyn McCarty showed that DNA is the hereditary material 1953: James Watson and Francis Crick proposed a model of DNA structure 1961: François Jacob and Jacques Monod discovered the role of mRNA in protein synthesis Copyright © 2019 Pearson Education, Inc. All Rights Reserved Figure 1.5 Milestones in the Golden Age of Microbiology (4 of 4) Copyright © 2019 Pearson Education, Inc. All Rights Reserved Figure 1.7 Milestones in the Second and Third Golden Ages of Microbiology Copyright © 2019 Pearson Education, Inc. All Rights Reserved Check Your Understanding-9 Check Your Understanding  1-13 Define bacteriology, mycology, parasitology, immunology, and virology.  1-14 Differentiate microbial genetics, molecular biology, and genomics. Copyright © 2019 Pearson Education, Inc. All Rights Reserved Microbes and Human Welfare Learning Objectives 1-15 List at least four beneficial activities of microorganisms. 1-16 Name two examples of biotechnology that use recombinant DNA technology and two examples that do not. Copyright © 2019 Pearson Education, Inc. All Rights Reserved Recycling Vital Elements Microbial ecology is the study of the relationship between microorganisms and their environment Bacteria convert carbon, oxygen, nitrogen, sulfur, and phosphorus into forms used by plants and animals Copyright © 2019 Pearson Education, Inc. All Rights Reserved Sewage Treatment: Using Microbes to Recycle Water Sewage is 99.9% water, with a few hundredths of 1% suspended solids Treatment of sewage removes undesirable components so water can be released or reused – Large solids are removed physically – Microbes are used to convert left over liquid and organic materials into by-products such as carbon dioxide Copyright © 2019 Pearson Education, Inc. All Rights Reserved Bioremediation: Using Microbes to Clean Up Pollutants Bacteria degrade organic matter in sewage Bacteria degrade or detoxify pollutants such as oil and mercury Copyright © 2019 Pearson Education, Inc. All Rights Reserved Figure 27.8 Composting Municipal Wastes Copyright © 2019 Pearson Education, Inc. All Rights Reserved Insect Pest Control by Microorganisms Microbes that are pathogenic to insects are alternatives to chemical pesticides – Prevent insect damage to agricultural crops and disease transmission Bacillus thuringiensis infections are fatal in many insects but harmless to animals and plants – The bacteria produce protein crystals toxic to insects – The toxin gene has been inserted into some plants to confer insect resistance Copyright © 2019 Pearson Education, Inc. All Rights Reserved Figure 11.21 Bacillus Toxin Endospore Copyright © 2019 Pearson Education, Inc. All Rights Reserved Biotechnology and Recombinant DNA Technology Biotechnology is the use of microbes for practical applications, such as producing foods and chemicals Recombinant DNA technology enables bacteria and fungi to produce a variety of proteins, vaccines, and enzymes – Missing or defective genes in human cells can be replaced in gene therapy – Genetically modified bacteria are used to protect crops from insects and from freezing Copyright © 2019 Pearson Education, Inc. All Rights Reserved Check Your Understanding-10 Check Your Understanding  1-15 Name two beneficial uses of bacteria.  1-16 Differentiate biotechnology from recombinant DNA technology. Copyright © 2019 Pearson Education, Inc. All Rights Reserved Microbes and Human Disease Learning Objectives 1-17 Define resistance. 1-18 Define biofilm. 1-19 Define emerging infectious disease. Copyright © 2019 Pearson Education, Inc. All Rights Reserved Normal Microbiota Microbes normally present in and on the human body are called normal microbiota – Normal microbiota prevent growth of pathogens – Normal microbiota produce growth factors such as vitamins B and K Resistance is the ability of the body to ward off disease Resistance factors include skin, stomach acid, and antimicrobial chemicals Copyright © 2019 Pearson Education, Inc. All Rights Reserved Biofilms Microbes attach to solid surfaces and grow into masses They will grow on rocks, pipes, teeth, and medical implants Biofilms can cause infections and are often resistant to antibiotics Copyright © 2019 Pearson Education, Inc. All Rights Reserved Figure 1.10 Biofilm on a Piece of Plastic Serratia liquefaciens Capsular material Plastic Copyright © 2019 Pearson Education, Inc. All Rights Reserved Emerging Infectious Diseases When a pathogen invades a host and overcomes the host's resistance, disease results Emerging infectious diseases (EIDs): new diseases and diseases increasing in incidence Copyright © 2019 Pearson Education, Inc. All Rights Reserved Emerging Infectious Diseases Zika virus disease – Virus discovered in 1947 in Uganda – Human epidemics in Micronesia 2007, then in French Polynesia and Brazil in 2013–2015 – Spread by bite of an infected Aedes mosquito; also transmitted by sexual contact – Infection during pregnancy can result in severe birth defects Copyright © 2019 Pearson Education, Inc. All Rights Reserved Emerging Infectious Diseases Middle East respiratory syndrome (MERS) – Caused by Middle East respiratory syndrome coronavirus (MERS-CoV) – Common to SARS ▪Severe acute respiratory syndrome – 1,800 confirmed human cases and 630 deaths since 2014 Copyright © 2019 Pearson Education, Inc. All Rights Reserved Emerging Infectious Diseases H1N1 influenza – Also known as swine flu – First detected in the United States in 2009 ▪ Declared a pandemic, or worldwide large-scale outbreak, by WHO in 2009 Avian influenza A (H5N1) – Influenza A virus – Primarily in waterfowl and poultry – Sustained human-to-human transmission has not yet occurred Copyright © 2019 Pearson Education, Inc. All Rights Reserved Figure 13.3b Morphology of an Enveloped Helical Virus Spikes Copyright © 2019 Pearson Education, Inc. All Rights Reserved Emerging Infectious Diseases Methicillin-resistant Staphylococcus aureus (MRSA) – 1950s: Penicillin resistance developed – 1980s: Methicillin resistance – 1990s: MRSA resistance to vancomycin reported ▪VISA: vancomycin-intermediate S. aureus ▪VRSA: vancomycin-resistant S. aureus Copyright © 2019 Pearson Education, Inc. All Rights Reserved Emerging Infectious Diseases Ebola hemorrhagic fever (EHF) – Ebola virus – Causes fever, hemorrhaging, and blood clotting – Transmitted via contact with infected blood or body fluids – First identified near Ebola River, Congo – 2014 outbreak in Guinea; over 28,000 infected over 2 years, with 1/3 of those infected dead Copyright © 2019 Pearson Education, Inc. All Rights Reserved Figure 23.21 Ebola Hemorrhagic Virus Copyright © 2019 Pearson Education, Inc. All Rights Reserved Check Your Understanding-11 Check Your Understanding  1-17 Differentiate normal microbiota and infectious disease.  1-18 Why are biofilms important?  1-19 What factors contribute to the emergence of an infectious disease? Copyright © 2019 Pearson Education, Inc. All Rights Reserved Sizes in Microbe World