PHD213 Microbiology Introduction To Microbiology PDF

FACULTY OF PHARMACY UiTM CAWANGAN PULAU PINANG BERTAM CAMPUS P H D 2 1 3 MICROBIOLOGY LECTURE NOTES F I R S T E D I T I O N S E P T E M B E R 2 0 1 7  PHD213 – MICROBIOLOGY: INTRODUCTION TO MICROBIOLOGY...

FACULTY OF PHARMACY UiTM CAWANGAN PULAU PINANG BERTAM CAMPUS P H D 2 1 3 MICROBIOLOGY LECTURE NOTES F I R S T E D I T I O N S E P T E M B E R 2 0 1 7  PHD213 – MICROBIOLOGY: INTRODUCTION TO MICROBIOLOGY Course information PHD213 – MICROBIOLOGY COURSE DESCRIPTION The aim of this course is towards an understanding of the fundamentals of microbiology including history of microbiology, classifications and identification of microorganisms, physiology (nutrition, metabolism and growth), genetic and microbial pathogenesis. COURSE OUTCOMES (COs) At the end of this course, students should be able to: CO1 - Discuss the basic principles of microbiology including history, characteristic, classification and importance of microorganisms. CO2 - Describe the cell structure, identification, metabolic processes, nutrition and growth, microbial genetic and control of microorganisms. CO3 - Explain the interactions between microbes and humans and factors that may contribute to human diseases. CO4 - Perform appropriate laboratory skills and techniques related to isolation, staining, identification and control of microorganisms. ASSESSMENT Students will be assessed as follows:- 1. Continuous assessment i. Assignment 1 1 5% ii. Assignment 2/ Group Project 1 5% Report & Presentation iii. 4 Quizzes 4 10% iv. Lab reports 5 10% v. Tests (Test 1 & test 2) 2 10% 2. Final examination 60% 100% REFFERENCES 1. Tortora, G. J., Funke, B. R., and Case, C. L. (2012). Microbiology: An Introduction, 11th Ed. Pearson / Benjamin Cummings. 2. Talaro K. P & Chess B. (2012). Foundation in Microbiology: Basic Principle, 8th Ed. McGraw-Hill. 3. Madigan, M. T., Martinko J. M. Stahl D. And Clark D. P. (2010). Brock: Biology of Microorganisms, 13th ed. Prentice-Hall. 4. Wiley J. M., Sherwood L. M. and Woolverton, C. J. (2010). Microbiology, 8th ed. McGraw-Hill. CONFIDENTIAL - ©SurayaSulaiman (1st edition) Page 1  PHD213 – MICROBIOLOGY: INTRODUCTION TO MICROBIOLOGY FACULTY OF PHARMACY UiTM CAWANGAN PULAU PINANG BERTAM CAMPUS P H D 2 1 3 MICROBIOLOGY INTRODUCTION TO MICROBIOLOGY C H A P T E R 1 1.0 Introduction to microbiology 1.1 Types of microorganisms 1.2 Taxonomy: Organizing, classifying and naming of microorganisms 1.3 The Origin and evolution of microorganisms 1.4 History of microbes 1.5 Importance of microbes 1.5.1 Microbes and human welfare 1.5.2 Microbes and human disease F I R S T E D I T I O N S E P T E M B E R 2 0 1 7 CONFIDENTIAL - ©SurayaSulaiman (1st edition) Page 2  PHD213 – MICROBIOLOGY: INTRODUCTION TO MICROBIOLOGY CHAPTER 1 1.0 INTRODUCTION TO MICROBIOLOGY (CO1) LEARNING OBJECTIVES At the end of this chapter, students should be able to: 1. Name and define the primary areas included in microbiological studies. 2. Describe major groups of microorganisms, characteristics and their habitats. 3. Describe the system of scientific nomenclature used to name microorganisms. 4. Discuss the origin and history of microorganisms. 5. Identify the contributions to microbiology made by Koch, Pasteur, van Leuwenhoek, Lister, Ehrlich, Fleming, Jenner and others. 6. Discuss the roles of microorganisms to human life. OVERVIEW Microbiology is the study of microorganisms. Microorganisms can be found in every ecosystem and in close association with every type of multicellular organism. Microorganisms (or microbes) play a very important role in our lives. Some microbes cause disease but the majority is completely harmless. Majority live a free existence, are relatively harmless and often beneficial. Many microorganisms have close associations with other organisms, for example parasites and hosts. Many microbes are either pathogens or parasitic organisms, both of which can harm humans. Microbes are the oldest form of life on Earth. Some types have existed for billions of years. They may live as individuals or cluster together in communities. Microbes live in the water you drink, the food you eat, and the air you breathe. These single-cell organisms are invisible to the eye, but they can be seen with microscopes. While most microbes are unicellular, some multicellular animals and plants are also microscopic and are therefore broadly defined as "microbes." The term microbe is short for microorganism, which means small organism. Microbes are very small living organisms, so small that most of them are invisible. The majority can only be seen with a microscope, which magnifies their image so we can see them. They are grouped or classified in various ways. Microbes are very diverse and represent all the great kingdoms of life. In terms of numbers, most of the diversity of life on Earth is represented by microbes. Microorganisms live in all parts of the biosphere where there is liquid water, including soil, hot springs, on the ocean floor, high in the atmosphere, and deep inside rocks within the Earth's crust. These microscopic organisms play a key role in maintaining life on earth, fixing gases and breaking down dead plant and animal matter into simpler substances that are used at the beginning of the food chain. Biotechnologists can also exploit the activities of microbes to benefit humans, such as in the production of medicines, enzymes and food. They are also used to breakdown sewage and other toxic wastes into safe matter. CONFIDENTIAL - ©SurayaSulaiman (1st edition) Page 3  PHD213 – MICROBIOLOGY: INTRODUCTION TO MICROBIOLOGY TERMS Microbiology - The study of microorganisms Microorganisms Living organism (such as bacteria too small to be seen - with naked eye but visible under a microscope. Pathogen An agent that causes disease, especially a living - microorganism such as a bacterium, virus, or fungus. Microbiota Microorganisms that live in a particular environment. Microbiome Collection of genes found in all of the microbes associated with a particular host. MAJOR FIELDS OF MICROBIOLOGY Among the many specialized fields of microbiology: Bacteriology - The study of prokaryotic microbes or bacteria. Virology - The study of acellular and intracellular parasites (virus) Mycology - The study of fungi like yeasts molds and mushrooms The study of parasites (usually focused on protozoa and Parasitology - helminths (worms) Epidemiology The study and analysis of the patterns, causes, and - effects of health and disease conditions in defined populations The study of the relationships between host body, Immunology - pathogen and immunity Phycology - The study of algae. The study of technology and any life form like microbes, Biotechnology plants animals in the sense to improve quality of life and develop new technology. Microbial genetics The study of how microbes inherit traits Genomics The study of an organism’s genes CONFIDENTIAL - ©SurayaSulaiman (1st edition) Page 4  PHD213 – MICROBIOLOGY: INTRODUCTION TO MICROBIOLOGY GENERAL CHARACTERISTICS OF MICROORGANISMS - Living things which individually are too small to be seen with the naked eye. - Has habitat - Germ-rapidly growing cell - Live in population (not alone) - Communities are either swimming freely or attached to a surface (biofilm) - Interact between communities; may either be o harmful (because of waste product) o beneficial (cooperative feeding efforts - waste & nutrient) - Two types based on cell line: o Two cell lines  Prokaryote – microscopic, unicellular organisms, lack nuclei and membrane-bound organelles  Eukaryote – unicellular (microscopic) and multicellular, nucleus and membrane-bound organelles o Acellular  Viruses, parasitic particles composed of a nucleic acid and protein Figure 1.1 Basic structure of cells and viruses CONFIDENTIAL - ©SurayaSulaiman (1st edition) Page 5  PHD213 – MICROBIOLOGY: INTRODUCTION TO MICROBIOLOGY A microorganism or microbe is a microscopic organism, which may be single-celled or multicellular. Most microbes are unicellular and small enough that they require artificial magnification to be seen. However, there are some unicellular microbes that are visible to the naked eye, and some multicellular organisms that are microscopic. An object must measure about 100 micrometers (µm) to be visible without a microscope, but most microorganisms are many times smaller than that. For some perspective, consider that a typical animal cell measures roughly 10 µm across but is still microscopic. Bacterial cells are typically about 1 µm, and viruses can be 10 times smaller than bacteria (Figure 1.2). Figure 1.2: The relative sizes of various microscopic and non-microscopic objects. CONFIDENTIAL - ©SurayaSulaiman (1st edition) Page 6  PHD213 – MICROBIOLOGY: INTRODUCTION TO MICROBIOLOGY 1.1 TYPES OF MICROORGANISMS Microorganisms are divided into six types: bacteria (eubacteria, archaebacteria), protozoa, algae (microscopic algae), fungi (yeasts, molds), viruses, and multicellular animal parasites (helminths/ parasitic worm). Each type has a characteristic cellular composition, morphology, mean of locomotion, and reproduction. BACTERIA Bacteria (Plural)/ Bacterium (Singular) Cellular organization - Prokaryotes - unicellular organisms Contain cytoplasm, lack of special structures such as nucleus and organelles nucleus membrane doesn’t available in the cells (no nucleus); only genetic material most bacteria has peptidoglycan cell walls Size - Size - 1-2 μm, average 1 μm (micrometer) Nutrition - Use a wide range of chemical substances for their nutrition - Utilize organic/ inorganic chemicals, or photosynthesis to obtain energy Reproduction - Divide by binary fission i) Eubacteria/ - Peptidoglycan cell walls bacteria - Common shapes include spherical (coccus), rod-shaped (bacillus), or curved (spirillum, spirochete, or vibrio). - Locomotion - may possess flagella - Can be classified as either Gram-positive or Gram- negative when using the Gram staining. - For energy, use organic chemicals, inorganic chemicals, or photosynthesis - Examples: Staphylococcus aureus, Bacillus subtilis, Escherichia coli Figure 1.3 Different type of bacteria shape CONFIDENTIAL - ©SurayaSulaiman (1st edition) Page 7  PHD213 – MICROBIOLOGY: INTRODUCTION TO MICROBIOLOGY ii) Archaebacteria - Lack or no peptidoglycan in cell wall - Many are found in extreme environments - such as hot springs and salt lakes - Use different energy source like hydrogen gas, carbon dioxide and Sulphur. Some use sunlight to make energy. - Examples: Methanogens, Extreme halophiles, Extreme thermophiles Figure 1.4 Different extreme conditions CONFIDENTIAL - ©SurayaSulaiman (1st edition) Page 8  PHD213 – MICROBIOLOGY: INTRODUCTION TO MICROBIOLOGY FUNGI Fungi (singular: fungus). Fungi (mushroom, molds, and yeasts) are eukaryotic cells; can be found in any habitat Celllular organization - Eukaryotes (with a true nucleus) Some multicellular fungi, such as mushrooms, resemble plants, but are actually quite different. Fungi are not photosynthetic, Cell walls are usually made out of chitin Size - microscopic to visible; yeasts - 5-12 μm; molds - 5-12 μm diameter up to 25 μm length Nutrition - Use organic chemicals for energy - absorbing organic material from their environment (decomposers), through symbiotic relationships with plants (symbionts), or harmful relationships with a host (parasites). Reproduction - Asexual and sexual reproduction i) Yeasts - Unicellular fungi (lost ability to form hypha yet some pathogens can form filaments) - Shape: oval cells – 5 μm diameter - Reproduce by budding - Beneficial uses: brewing, baking, industrial fermentations, food supplements - Examples: Saccharomyces cerevisiae (baker's yeast), Candida albicans (pathogenic yeast) Figure 1.5 Yeast structure CONFIDENTIAL - ©SurayaSulaiman (1st edition) Page 9  PHD213 – MICROBIOLOGY: INTRODUCTION TO MICROBIOLOGY ii) Molds - Molds are multicellular - Consist masses of mycelia, which are composed of filaments called hyphae - Filamentous tubes are called hyphae that help absorb material. - The collection of hyphae is called mycelium. - Reproduction - Usually asexual by producing spores (resistant can cause allergic reactions) or sexual by hyphal cell fusion/ sexual spores - Examples: Aspergillus niger, Figure 1.6 Molds CONFIDENTIAL - ©SurayaSulaiman (1st edition) Page 10  PHD213 – MICROBIOLOGY: INTRODUCTION TO MICROBIOLOGY PROTOZOA The largest group of organisms in the world in terms of numbers, biomass, and diversity. Classified under kingdom Protists. Celllular organization - Eukaryotes have nucleus & complex organelles Cell walls are made up of cellulose. Classified according to their means of locomotion Size - Most parasitic protozoa in humans are less than 50 μm in size. - The smallest (mainly intracellular forms) are 1 to 10 μm long, but Balantidium coli may measure 150 μm. Habitat - Live in a wide variety of moist habitats including fresh water, marine environments and the soil. Nutrition - Obtain nourishment (organic chemicals) by absorption or ingestion through specialized structures. Reproduction - The most common form of reproduction is asexual - Binary fission; multiple asexual divisions occur in some forms. - Both sexual and asexual reproductions occur in the Apicomplexa. Locomotion - May move using pseudopods, cilia or flagella - Flagellates produce their own food and use their whip- like structure to propel forward, - Ciliates have tiny hair that beat to produce movement, - Amoeboids have false feet or pseudopodia used for feeding and locomotion - Sporozoans are non-motile. Examples - Amoeba proteus, Paramecium caudatum, Toxoplasma gondii, Plasmodium falciparum, Figure 1.7 Amoeba CONFIDENTIAL - ©SurayaSulaiman (1st edition) Page 11  PHD213 – MICROBIOLOGY: INTRODUCTION TO MICROBIOLOGY Figure 1.8 Paramecium sp. ALGAE Algae are almost ubiquitous throughout the world and can be categorized ecologically by their habitats. Classified under kingdom Protists. Celllular organization - Unicellular/multicellular eukaryotes Cellulose cell walls Size - From microscopic Micromonas species to giant kelps that reach 60 metres (200 feet) in length. Habitat - Live in water, damp soil, and rocks and produce oxygen and carbohydrates used by other organisms. Nutrition - Obtain nourishment by photosynthesis for energy Reproduction - Asexual and sexual reproduction - Most green algae reproduce both asexually (by mitosis) and sexually. - The green algae also reproduce by vegetative method - by fragmentation. - Larger algae reproduce by spores. Locomotion - Flagella, gliding, buoyancy Examples - Free-floating phytoplankton, Euglenophyta (euglenoids), Chrysophyta (golden-brown algae), Rhodophyta (red algae), Chlorophyta (green algae), diatoms. CONFIDENTIAL - ©SurayaSulaiman (1st edition) Page 12  PHD213 – MICROBIOLOGY: INTRODUCTION TO MICROBIOLOGY Figure 1.9 Algae CONFIDENTIAL - ©SurayaSulaiman (1st edition) Page 13  PHD213 – MICROBIOLOGY: INTRODUCTION TO MICROBIOLOGY VIRUSES A virus is a small infectious agent that replicates only inside the living cells of other organisms. Celllular organization - Acellular Consist of a nucleic acid core (DNA or RNA) surrounded by a protein coat. Size - 1/10 to 1/1000 the size of an ordinary bacterial cell. Reproduction/ - Viruses are replicated only when they are in a living host Nutrition cell. Viruses cannot reproduce outside a host cell and cannot metabolize on their own. - Lytic and lysogenic cycle Examples - HIV virus, Influenza virus, Herpes Simplex virus, Figure 1.9 Viruses CONFIDENTIAL - ©SurayaSulaiman (1st edition) Page 14  PHD213 – MICROBIOLOGY: INTRODUCTION TO MICROBIOLOGY MULTICELLULAR ANIMAL PARASITES Helminths - large enough to be easily seen with the naked eye but live a part of their life cycle in microscopic form. Celllular organization - Eukaryotes/ Multicellular Characterized by elongated, flat or round bodies. Habitat - They can live inside humans and other animals. Nutrition - Living in and feeding on living hosts, receiving nourishment and protection while disrupting their hosts' nutrient absorption, causing weakness and disease. Reproduction - Microscopic stages in life cycles - develop through egg, larval (juvenile), and adult stages. Examples - Taenia saginata, Flukes (Trematodes), Tapeworms (Cestodes), Roundworms (Nematodes) Hook worm Pin worm Figure 1.10 Helminthes CONFIDENTIAL - ©SurayaSulaiman (1st edition) Page 15  PHD213 – MICROBIOLOGY: INTRODUCTION TO MICROBIOLOGY 1.2 TAXONOMY: ORGANIZING, CLASSIFYING AND NAMING OF MICROORGANISMS TERMS Taxonomy - The science of classifying organisms Taxa - The groups making up the classification hierarchy Nomenclature - Assigning names Microbial nomenclature - Naming microorganisms Classification General process related to categorization, the process in which ideas and objects are recognized, - differentiated, and understood. Orderly arrangement of organisms into groups. Identification Determining and recording traits of organisms for - placement into taxonomic schemes Phylogeny The history of the evolution of a species or group, - especially in reference to lines of descent and relationships among broad groups of organisms. 1.2.1 Taxonomy - Taxonomy: organizing, classifying, and naming living things - Formal system originated by Carl von Linné - Consists of classifying new organisms or reclassifying existing ones. - Concerned with classification, nomenclature and identification. - Classification of microorganisms has been largely aided by studies of fossils and recently by DNA sequencing. - The most widely employed methods for classifying microbes are morphological characteristics, differential staining, biochemical testing, DNA fingerprinting or DNA base composition, polymerase chain reaction, and DNA chips. 1.2.2 Naming and Classifying Microorganisms - Microorganisms are scientifically recognized using a binomial nomenclature - Linnaeus established the system of scientific nomenclature (Binomial System of Nomenclature) - The names assigned to microorganisms are in Latin. - Each organism has two names: Using two words that refer to the genus and the species/ specific epithet. o Scientific Name: italicized or underlined. o The first letter of the genus name is always Capitalized and the specific epithet is lowercase. CONFIDENTIAL - ©SurayaSulaiman (1st edition) Page 16  PHD213 – MICROBIOLOGY: INTRODUCTION TO MICROBIOLOGY - Naming examples: o Staphylococcus aureus  Staphule - bunch of grapes  Kokkus - berry  aureus - golden o Escherichia coli  Honors the discoverer - Theodor Escherich  Coli - bacterium’s habitat - the large intestine, or colon o Campylobacter jejuni  Kampylos - curved  Bakterion - little rod  Jejunum - part of intestine o Giardia lamblia  Alfred Giard - Fr. Microbiologist  Victor Lambl – Bohemian physician - Common or descriptive names (trivial names), o Example: Group A streptococcus (Streptococcus pyogenes) - For viruses - common names are used o Example: Polio virus, HIV, Influenza virus - For parasites – Either binomial or common names are used o Example: Round worm, Ascaris lumbricoides, A. lumbricoides 1.2.3 Classification of Microorganisms - Three domains o Bacteria - true bacteria o Archaea - odd bacteria that live in extreme environments, high salt, heat, etc. o Eukarya - have a nucleus and organelles  Protists  Fungi  Plants  Animals - Level of classifications: o Domain - Archaea, Bacteria, & Eukarya o Kingdom o Phylum or Division o Class o Order o Family o Genus o Species CONFIDENTIAL - ©SurayaSulaiman (1st edition) Page 17  PHD213 – MICROBIOLOGY: INTRODUCTION TO MICROBIOLOGY Figure 1.11 Classification of organisms 1.2.4 The Five Kingdom Model - Classification by Kingdoms - Traditional Robert Whittaker system of classification (1959) - 5 kingdoms o Animals o Plants o Fungi o Protists o Monera - 2 cell types o Types of Prokaryotes  Bacteria  Archae o Types of Eukaryotes  Protozoa  Algae  Fungi (singular: Fungus)  Viruses  Multicellular animal parasites CONFIDENTIAL - ©SurayaSulaiman (1st edition) Page 18  PHD213 – MICROBIOLOGY: INTRODUCTION TO MICROBIOLOGY Figure 1.12 Traditional Whittaker system of classification. 1.2.5 New Views of Phylogeny - Classification by Domains - Woese-Fox system - 3 domains o Bacteria - true bacteria o Archaea - odd bacteria that live in extreme environments, high salt, heat, etc. o Eukarya - have a nucleus and organelles  Protists  Fungi  Plants  Animals CONFIDENTIAL - ©SurayaSulaiman (1st edition) Page 19 Figure 1.13 Woese-Fox system.  PHD213 – MICROBIOLOGY: INTRODUCTION TO MICROBIOLOGY Figure 1.13 Comparisons of Three Cellular Domains CONFIDENTIAL - ©SurayaSulaiman (1st edition) Page 1  PHD213 – MICROBIOLOGY: INTRODUCTION TO MICROBIOLOGY 1.14 Classification of Microbes CONFIDENTIAL - ©SurayaSulaiman (1st edition) Page 2 1.2.6 Bacterial Taxonomy Based on Bergey’s Manual Bergey’s Manual of Determinative Bacteriology – five volume resource covering all known prokaryotes. - First appeared in 1923 and, at present, is in its 9th edition under the title Bergey’s Manual of Systematic Bacteriology - A major taxonomic treatment of bacteria (prokaryotes). - Has served the community of microbiologists since more than 80 years and is a compendium of information on all recognized species of bacteria (prokaryotes). - Each chapter of this treatise, written by an expert, contains tables, figures, and other systematic information useful for identification of bacteria. - Bergey’s Manual of Systematic Bacteriology (2nd Ed.) is the main resource for determining the identity of prokaryotic organisms, emphasizing bacterial species, using every characterizing aspect. - Classification based on genetic information – phylogenetic - Two domains: o Archaea – primitive, adapted to extreme habitats and modes of nutrition o Bacteria  Phylum Proteobacteria – Gram-negative cell walls  Phylum Firmicutes – mainly gram-positive with low G + C content  Phylum Actinobacteria – Gram-positive with high G + C content - Five major subgroups with 25 different phyla - The current grouping is: o Volume 1: The Archaea and the deeply branching and phototrophic Bacteria o Volume 2: The Proteobacteria o Volume 3: The Firmicutes o Volume 4: The Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes), Acidobacteria, Fibrobacteres, Fusobacteria, Dictyoglomi, Gemmatimonadetes, Lentisphaerae, Verrucomicrobia, Chlamydiae, and Planctomycetes o Volume 5 : The Actinobacteria  PHD213 – MICROBIOLOGY: INTRODUCTION TO MICROBIOLOGY 1.3 THE ORIGIN AND EVOLUTION OF MICROORGANISMS - The Earth is about 4.5 billion years old - The early Earth was anoxic and much hotter. - Analysis of ancient rocks provides evidence for the Earth’s early atmospheric and surface conditions. - Earth was inorganic and its primitive conditions provided an environment conducive to the evolution of organic molecules. The evidence suggests that biologically important molecules could be formed when gaseous mixtures like the primitive - Bacteria-like organisms have existed on earth for about 3.5 billion years Figure 1.15 The origin and evaluation of microorganisms. CONFIDENTIAL - ©SurayaSulaiman (1st edition) Page 1  PHD213 – MICROBIOLOGY: INTRODUCTION TO MICROBIOLOGY 1.4 HISTORY OF MICROBES TERMS Spontaneous generation The hypothesis that living organisms arise from - nonliving matter; a “vital force” forms life Biogenesis The hypothesis that the living organisms arise from - preexisting life The germ theory of States: disease - Many diseases are caused by microorganisms. - Specific microscopic organisms are the cause of specific diseases. Fermentation A metabolic process that converts sugar to acids, gases, or alcohol. It occurs in yeast and bacteria, - and also in oxygen-starved muscle cells, as in the case of lactic acid fermentation. Pasteurization A process that kills microbes (mainly bacteria) in - food and drink, such as milk, juice, canned food, and others. Contamination The presence of an unwanted constituent, - contaminant or impurity in a material, physical body, natural environment, workplace, etc. Koch postulates Guidelines to prove that a disease is caused by a - specific organism. Sterilization Any process that eliminates, removes, kills, or deactivates all forms of life and other biological agents (such as fungi, bacteria, viruses, spore - forms, prions, etc.) present in a specified region, such as a surface, a volume of fluid, medication, or in a compound such as biological culture media. Vaccination The administration of antigenic material (a Vaccination vaccine) to stimulate an individual's immune - system to develop adaptive immunity to a pathogen. Recombinant DNA DNA that has been formed artificially by combining - constituents from different organisms. CONFIDENTIAL - ©SurayaSulaiman (1st edition) Page 2  PHD213 – MICROBIOLOGY: INTRODUCTION TO MICROBIOLOGY 1.4.1 Hypothesis of the Origin of the Microorganism - Two hypothesis attempted to explain the origin of the microbes: o Biogenesis – They arose only from other living things of their same kind. o Theory of Spontaneous Generation – They arose spontaneously from something non-living. - The debate over Spontaneous Generation o Until the mid – 1880s, many people believed in spontaneous generation, the idea that living organisms could arise from nonliving matter. o Experimentation by Francesco Redi in the seventeenth century presented the first significant evidence refuting spontaneous generation. Francesco Redi demonstrated that maggots appear on decaying meat only when flies are able to lay eggs on the meat. o Prominent scientists designed experiments and argued both in support of (John Needham) and against (Lazzaro Spallanzani) spontaneous generation. o Louis Pasteur demonstrated that microorganisms are in the air everywhere and offered proof of biogenesis by using various shapes of swan necked flasks. - Louis Pasteur is credited with conclusively disproving the theory of spontaneous generation with his famous swan-neck flask experiment. He subsequently proposed that “life only comes from life.” THEORY OF SPONTANEOUS GENERATION - The hypothesis that living organisms arise from nonliving matter; a “vital force” forms life. - Proposed by Aristotle. - Evidence: He noted several instances of the appearance of animals from environments previously devoid of such animals, such as the seemingly sudden appearance of fish in a new puddle of water. FRANCESCO REDI’S EXPERIMENT - Italian physician Francesco Redi (1626–1697), performed an experiment in 1668 that was one of the first to refute the idea that maggots (the larvae of flies) spontaneously generate on meat left out in the open air. - He predicted that preventing flies from having direct contact with the meat would also prevent the appearance of maggots. - Redi left meat in each of six containers (Figure 1). o Two were open to the air, o Two were covered with gauze o Two were tightly sealed. - His hypothesis was supported when maggots developed in the uncovered jars, but no maggots appeared in either the gauze-covered or the tightly sealed jars. - Conclusion: maggots could only form when flies were allowed to lay eggs in the meat, and that the maggots were the offspring of flies, not the product of spontaneous generation. CONFIDENTIAL - ©SurayaSulaiman (1st edition) Page 3  PHD213 – MICROBIOLOGY: INTRODUCTION TO MICROBIOLOGY Figure 1.16 Francesco Redi’s experiment JOHN NEEDHAM’S EXPERIMENT - In 1745, John Needham (1713–1781) published a report of his own experiments. - He briefly boiled broth infused with plant or animal matter, hoping to kill all preexisting microbes. - He then sealed the flasks. - After a few days, Needham observed that the broth had become cloudy and a single drop contained numerous microscopic creatures. - He argued that the new microbes must have arisen spontaneously. - In reality, however, he likely did not boil the broth enough to kill all preexisting microbes. LAZZARO SPALLANZANI’S EXPERIMENT - Lazzaro Spallanzani (1729–1799) did not agree with Needham’s conclusions. - He performed hundreds of carefully executed experiments using heated broth. - Broth in sealed jars and unsealed jars was infused with plant and animal matter. - Spallanzani’s results contradicted the findings of Needham: o Heated but sealed flasks remained clear, without any signs of spontaneous growth, unless the flasks were subsequently opened to the air. - This suggested that microbes were introduced into these flasks from the air. CONFIDENTIAL - ©SurayaSulaiman (1st edition) Page 4  PHD213 – MICROBIOLOGY: INTRODUCTION TO MICROBIOLOGY LOUIS PASTEUR’S EXPERIMENT - Disproved Spontaneous Generation - Pasteur made a series of flasks with long, twisted necks (“swan-neck” flasks), in which he boiled broth to sterilize it. - His design allowed air inside the flasks to be exchanged with air from the outside, but prevented the introduction of any airborne microorganisms, which would get caught in the twists and bends of the flasks’ necks. - If a life force besides the airborne microorganisms were responsible for microbial growth within the sterilized flasks, it would have access to the broth, whereas the microorganisms would not. - He correctly predicted that sterilized broth in his swan-neck flasks would remain sterile as long as the swan necks remained intact. - However, should the necks be broken, microorganisms would be introduced, contaminating the flasks and allowing microbial growth within the broth. Figure 1.17 Louis Pasteur’s experiment CONFIDENTIAL - ©SurayaSulaiman (1st edition) Page 5  PHD213 – MICROBIOLOGY: INTRODUCTION TO MICROBIOLOGY 1.4.2 The First Observation - 1665 - Robert Hooke observed the plant material was composed of ‘little boxes’; he introduced the term cell. - Hooke’s observations were the groundwork for development of the cell theory, the concept that all living things are composed of cells. - Cell theory: All living things are composed of cells and come from preexisting cells - 1858: Rudolf Virchow said cells arise from preexisting cells - The first microbes were observed in 1673 by Anton Van Leeuwenhoek, using a simple microscope, was the first to observe microorganisms. Anton van Leeuwenhoek described live microorganisms 1.4.3 The Golden Age of Microbiology - 1857-1914 (about 50 years) - Beginning with Pasteur’s work, discoveries included relationship between microbes and disease, immunity, and antimicrobial drugs THE GERM THEORY OF DISEASE - 1835: Agostino Bassi showed that a silkworm disease was caused by a fungus - 1865: Pasteur believed that another silkworm disease was caused by a protozoan - 1840s: Ignaz Semmelweis advocated hand washing to prevent transmission of puerperal fever from one OB patient to another - 1860s: Applying Pasteur’s work showing that microbes are in the air, can spoil food, and cause animal diseases, Joseph Lister used a chemical disinfectant to prevent surgical wound infections - 1876: Robert Koch proved that a bacterium causes anthrax and provided the experimental steps, Koch’s postulates, to prove that a specific microbe causes a specific disease IGNAZ SEMMELWEISS - A Hungarian physician- decided that doctors in Vienna hospitals were spreading childbed fever while delivering babies. - He started forcing doctors under his supervision to wash their hands before touching patients. CONFIDENTIAL - ©SurayaSulaiman (1st edition) Page 6  PHD213 – MICROBIOLOGY: INTRODUCTION TO MICROBIOLOGY ROBERT KOCH - German bacteriologist was the first to cultivate anthrax bacteria outside the body using blood serum at body temperature. Identified a bacterium as cause of anthrax - Introduced agar, inoculating loop to transfer bacteria and prepare pure cultures. - Introduced “Koch’s Postulates” and the concept that a disease is caused by a single organism; demonstrated the first direct role of a bacterium in disease - Koch's postulates (a sequence of experimental steps that verified the germ theory): o The agent must be present in every case of the disease. o The agent must be isolated and cultured in vitro. o The disease must be reproduced when a pure culture of the agent is inoculated into a susceptible host. o The agent must be recoverable from the experimentally-infected host. - This eventually led to: o Development of pure culture techniques o Stains, agar, culture media, petri dishes - Identified cause of anthrax, TB, and cholera - Developed pure culture methods KOCH EXPERIMENT 1. Microorganisms are isolated from a dead animal and identified. - The microorganism must be found in abundance in all organisms suffering from the disease, but should not be found in healthy animals. 2. Microorganisms are grown in pure culture. - The microorganism must be isolated from a diseased organism and grown in pure culture. 3. Microorganisms are injected into a healthy animal. - The cultured microorganism should cause disease when introduced into a healthy organism. 4. Disease reproduced in the second animal; microorganisms are isolated, grown in pure culture; the microorganisms are identical to the # 1. - The microorganism must be reisolated from the inoculated, diseased experimental host and identified as being identical to the original specific causative agent. Figure 1.18 Koch’s experiment. CONFIDENTIAL - ©SurayaSulaiman (1st edition) Page 7  PHD213 – MICROBIOLOGY: INTRODUCTION TO MICROBIOLOGY MARTINUS BEIJERINCK (1884 - 85) - Discovered “viruses” (toxins, poisons). - Infectious agents in tobacco plant fluids. PAUL EHRLICH (1910) - Introduced concept of chemotherapy. - Use of salvarsan for the treatment of syphilis. ALEXANDER FLEMING (1928) - Discovered the first antibiotic - penicillin. - Fleming observed that Penicillium fungus made an antibiotic, penicillin, that killed S. aureus - 1940s: Penicillin was tested clinically and mass produced. Figure 1.19 Antibiotic discovery - The birth of modern chemotherapy CONFIDENTIAL - ©SurayaSulaiman (1st edition) Page 8  PHD213 – MICROBIOLOGY: INTRODUCTION TO MICROBIOLOGY EDWARD JENNER AND SMALLPOX - 1800’s inoculated own son with cowpox blister from milkmaids. - Vaccination is derived from Vacca (cow) = virus name and vaccine - Before this the only prevention for smallpox = variolation (ground up smallpox blister blown up nose) - Jenner’s experiment: o Observation: Milkmaids who contracted cowpox never became ill with smallpox. o Hypothesis: Cowpox infection prevented smallpox infection. o Experiment: Infect a boy with cowpox, the smallpox. o Results: Boy did not develop smallpox. - NOTE: This experiment is highly unethical! LOUIS PASTEUR'S (1822-1895) - Famous experiments with swan-necked flasks - Disproved spontaneous generation of microorganisms - Demonstrated what is now known as Germ Theory of Disease o Pasteur fought to convince surgeons that germs existed and carried diseases, and dirty instruments and hands spread germs and therefore disease. - Developed pasteurization o Pasteur's pasteurization process killed germs and prevented the spread of disease. o Pasteurization is the application of a high heat for a short time - Showed microbes caused fermentation and spoilage o Fermentation - conversion of sugar  alcohol = beer and wine o Microbial growth is also responsible for spoilage of food o Bacteria that use alcohol and produce acetic acid spoil wine by turning it to vinegar (acetic acid) o Pasteur demonstrated that these spoilage bacteria could be killed by heat that was not hot enough to evaporate the alcohol in wine 1.4.4 Recombinant DNA Technology - Recombinant DNA: DNA made from two different sources. - 1960s: Paul Berg inserted animal DNA into bacterial DNA, and the bacteria produced an animal protein - 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 was the hereditary material - 1961: Francois Jacob and Jacques Monod discovered the role of mRNA in protein synthesis CONFIDENTIAL - ©SurayaSulaiman (1st edition) Page 9  PHD213 – MICROBIOLOGY: INTRODUCTION TO MICROBIOLOGY CONTRIBUTIONS: - Microscopy - Defense or Control of Microbes o 1677 Antony Leeuwenhoek o 1796 Edward Jenner o 1882 Paul Ehrlich o 1850 Ignaz Semmelweis o 1884 Christian Gram o 1867 Joseph Lister o 1885 Louis Pasteur - Culture Methods o 1900 Walter Reed o 1882 Robert Koch o 1910 Paul Ehrlich o 1887 R. J. Petri o 1928 Alexander Fleming - Germ Theory of Disease - Molecular Methods o 1860 Louis Pasteur o 1977 W. Gilbert & F. Sanger o 1867 Joseph Lister o 1983 Kary Mullis o 1876 Robert Koch o 1995 The Institute for Genome Research (TIGR) announced that - Virology it had sequenced the genomes of o 1892 Dmitri Iosifovich Ivanovski not one but two species of o 1899 Martinus Beijerinck bacteria using the whole genome shotgun method. HISTORY OF MICROBIOLOGY (TIMELINE) 1677 - Observed "little animals" (Antony Leeuwenhoek) 1796 First scientific Small pox vaccination (Edward Jenner) Advocated washing hands to stop the spread of disease (Ignaz 1850 Semmelweis) 1861 Disproved spontaneous generation (Louis Pasteur) 1862 Supported Germ Theory of Disease (Louis Pasteur) 1867 Practiced antiseptic surgery (Joseph Lister) First proof of Germ Theory of Disease with B. anthracis discovery 1876 (Robert Koch) 1881 Growth of Bacteria on solid media (Robert Koch) 1881 Outlined Kochs postulates (Robert Koch) 1882 Developed acid-fast Stain (Paul Ehrlich) 1884 Developed Gram Stain (Christian Gram) 1885 First Rabies vaccination (Louis Pasteur) 1887 Invented Petri Dish (R.J. Petri) 1892 Discovered viruses (Dmitri Iosifovich Ivanovski) Recognized viral dependence on cells for reproduction (Martinus 1899 Beijerinck) 1900 Proved mosquitoes carried the yellow fever agent (Walter Reed) 1910 Discovered cure for syphilis (Paul Ehrlich) 1928 Discovered Penicillin (Alexander Fleming) 1977 Developed a method to sequence DNA (W. Gilbert & F. Sanger) 1983 Polymerase Chain Reaction invented (Kary Mullis) 1995 First microbial genomic sequence published (H. influenzae) CONFIDENTIAL - ©SurayaSulaiman (1st edition) Page 10  PHD213 – MICROBIOLOGY: INTRODUCTION TO MICROBIOLOGY 1.5 IMPORTANCE OF MICROBES Microorganism is important in the maintenance of an ecological balance on earth. Microbes have an important place in most higher-order multicellular organisms as symbionts, and they are also exploited by people in biotechnology, both in traditional food and beverage preparation, and in modern technologies based on genetic engineering. Pathogenic microbes are harmful, however, since they invade and grow within other organisms, causing diseases that kill humans, animals, and plants. 1.5.1 Microbes and Human Welfare i) Microorganisms as a decomposer - Recycle nutrients stored in organic matter to an inorganic form. - Decompose organic waste - Microorganisms degrade dead plants and animals and recycle chemical elements to be used by living plants and animals. - Decomposition releases the mineral nutrients (e.g., N, P, K) bound up in dead organic matter in an inorganic form that is available for primary producers to use. Without this recycling of inorganic nutrients, primary productivity on the globe would stop. - For examples, bacteria are used to decompose organic matter in sewage and microbes decompose food into simple molecules. ii) Microorganisms as a nitrogen fixer - Some bacteria live in nodules on a plant roots. Atmospheric nitrogen compounds that the plants can use for growth. N2 → NH3 Nitrogen fixer bacteria iii) Microbes and agriculture - Sustaining agriculture - Rumen microbes help digest grass and hay in cows, sheep etc - Through their roles in recycling nitrogen, carbon, and sulfur, microorganism are able to convert these essential elements into forms that can be used by plants in their growth. They are also essential in enabling ruminant animals such as cows and sheep to digest cellulose from the grasses they eat. - Biological Insecticides - Microbes that are pathogenic to insects are alternatives to chemical pesticides in preventing insect damage to agricultural crops and disease transmission. o Bacillus thuringiensis infections are fatal in many insects but harmless to other animals, including humans, and to plants iv) Microorganism and Food Production/ Industry - Many food products employ microorganisms in their production. These include the microbial fermentation processes used to produce yogurt, buttermilk, cheeses, alcoholic beverages, leavened breads, sauerkraut, pickles, and kimchi. - Industry: o Prevent spoilage (tempeh, salted fish) o Assist in manufacturing of food CONFIDENTIAL - ©SurayaSulaiman (1st edition) Page 11  PHD213 – MICROBIOLOGY: INTRODUCTION TO MICROBIOLOGY v) Microorganism and Manufacturing - Play role in industry (e.g. fermentation to produce ethanol and acetone) - Textile: Stone-washing: Trichoderma; Cotton: Gluconacetobacter; Debleaching: Mushroom peroxidase; Indigo: E. coli - Plastic: Bacterial polyhydroxyalkanoate - Leather products – the hard skin of an animal is separated from its tissues by decomposing bacteria to produce leather. Leather for clothing is soften using protease (enzyme) from bacteria. vi) Energy production - Natural gas - Methane, or natural gas, is a product of methanogenic microorganisms. Many aquatic microbes capture light energy and store it in molecules used as food then used by other organisms. - Biofuels - Animal wastes, domestic refuse, biomass, and grain can be converted to biofuels such as ethanol and methane by microorganisms. vii) Oxygen Cycle - Generate Oxygen in the Atmosphere. - Microorganisms such as the cyanobacteria are thus considered producers of atmospheric oxygen. Microorganisms are also involved in the removal of oxygen from the atmosphere (i.e., they are consumers of oxygen). The process of respiration uses oxygen to produce energy. viii) Cleaning up the environment - Through a process called bioremediation, some pollutants such pesticides, solvents, and oil spills can be cleaned up with the aid of microbes. - Bacteria degrade organic matter in sewage, or detoxify pollutants such as oil and mercury ix) Production of useful natural gene products or products from bioengineering. - Genetic engineering - Biotechnology, the use of microbes to produce foods and chemicals. - Examples include specific enzymes, antibiotics, vaccines, and medications such as human insulin, interferons, and growth hormones. x) Medicine - Dead bacteria and viruses are used to produce vaccine for disease such as chicken pox and measles. - Insulin produced by genetically engineered bacteria is used to treat diabetes mellitus. - Antibiotics are produced by microorganisms as a byproduct which they excrete and they are used mainly in the treatment of bacterial diseases. Examples: o Penicillin is obtained from fungi o Streptomycin and tetracycline are obtained from bacteria. xi) The human microbiota and microbiome - Microbes normally present in and on the human body are called normal microbiota. CONFIDENTIAL - ©SurayaSulaiman (1st edition) Page 12  PHD213 – MICROBIOLOGY: INTRODUCTION TO MICROBIOLOGY - Normal microbiota prevent growth of pathogens - Normal microbiota produces growth factors such as folic acid and vitamin K. - Resistance is the ability of the body to ward off disease - Resistance factors include skin, stomach acid, and antimicrobial chemicals - The microbiome aids in the following: o Food digestion - The digestion of many foods, especially plant polysaccharides that would normally be indigestible by humans. o The regulation of many host metabolic pathways. o Regulation of Immunity 1.5.2 Microbes and Human Disease - Bacteria are single-celled organisms that cannot be seen with the human eye except through a microscope. Some kinds of bacteria are the most dangerous microorganisms. - Some microorganisms can cause disease and infections in humans and other living things - Different diseases are caused by different types of microorganisms. - A pathogen is a microorganism that has the potential to cause disease. - Microbes can invade the host body and caused infection. - An infection is the invasion and multiplication of pathogenic microbes in an individual or population. - Disease is when the infection causes damage to the individual’s vital functions or systems. Microbes cause infectious diseases such as flu and measles. - An infection does not always result in disease. 1.5.3 Harmful Effect/ Disadvantages of Microorganism i) Biological warfare. - Bioterrorism is terrorism involving the intentional release or dissemination of biological agents. - These agents are bacteria, viruses, or toxins, and may be in a naturally occurring or a human-modified form. For the use of this method in warfare. ii) Disease causing bacteria - Bacteria: Causes various diseases such as typhoid, diarrhea, and cholera. - Fungi: Causes a large number of diseases in plants and in animals such as rust diseases in plants, fruit rot in apple, red rot in sugar cane and ring worm disease in human beings. - Algae: Algal boom in water (rapid growth of algae) causes poisonous effect after they die, which in turn results in the death of aquatic organisms. - Protozoa: Causes Amoebic dysentery, pyorrhea and sleeping sickness etc. - Virus: Cause small fox, common cold, influenza, herpes, hepatitis, polio and rabies. iii) Spoilage of food - they can leave toxic waste products behind even if they are eradicated from the contaminated material. Also can cause food poisoning. CONFIDENTIAL - ©SurayaSulaiman (1st edition) Page 13  PHD213 – MICROBIOLOGY: INTRODUCTION TO MICROBIOLOGY TERMS Decomposition - The process by which organic substances are broken down into simpler matter. The process is a part of nutrient cycle and is essential for recycling the finite matter that occupies physical space in the biosphere. Fermentation - Chemical process by which molecules such as glucose are broken down using microorganisms (yeasts or bacteria) under anaerobic conditions. Biofuel - Fuel that is produced through contemporary biological processes, such as agriculture and anaerobic digestion, rather than a fuel produced by geological processes such as those involved in the formation of fossil fuels, such as coal and petroleum, from prehistoric biological matter. Bioremediation - A process that uses living organisms, mostly microorganisms and plants, to degrade and reduce or detoxify waste products and pollutants. Bioengineering - The “biological or medical application of engineering principles or engineering equipment – also called biomedical engineering.” Biotechnology - The use of living systems and organisms to develop or make products, or - "any technological application that uses biological systems, living organisms, or derivatives thereof, to make or modify products or processes for specific use" Microbiota - The microscopic organisms of a particular environment or - An "ecological community of commensal, symbiotic and pathogenic microorganisms" found in and on all multicellular organisms studied to date from plants to animals. - A microbiota includes bacteria, archaea, protists, fungi and viruses. Microbiome - A community of microorganisms (such as bacteria, fungi, and viruses) that inhabit a particular environment and especially the collection of microorganisms living in or on the human body. Infection - The invasion of an organism's body tissues by disease- causing agents, their multiplication, and the reaction of host tissues to these organisms and the toxins they produce. Bioterrorism - The use of hazardous agents (biological agents - bacteria, viruses, or other germs) to harm people. Pathogen - An agent that causes disease, especially a living microorganism such as a bacterium, virus, or fungus. CONFIDENTIAL - ©SurayaSulaiman (1st edition) Page 14  PHD213 – MICROBIOLOGY: INTRODUCTION TO MICROBIOLOGY REFFERENCES 1. Tortora, G. J., Funke, B. R., and Case, C. L. (2012). Microbiology: An Introduction, 11th Ed. Pearson / Benjamin Cummings. 2. Talaro K. P & Chess B. (2012). Foundation in Microbiology: Basic Principle, 8th Ed. McGraw-Hill. 3. Madigan, M. T., Martinko J. M. Stahl D. And Clark D. P. (2010). Brock: Biology of Microorganisms, 13th ed. Prentice-Hall. 4. Wiley J. M., Sherwood L. M. and Woolverton, C. J. (2010). Microbiology, 8th ed. McGraw-Hill. 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