Chapter 1 - Summary Microbiology: an Introduction PDF

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Chapter 1 1.1.1

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Microbes/microorganisms: minute living things that individually are usually too small to be seen with the unaided eye  Group includes bacteria, fungi (yeasts and molds), protozoa, and microscopic algae. Also includes viruses (non-cellular entities straddling life and non-life). Microorganisms also have both destructive and more beneficial uses  Destructive: used to make specialized types of gunpowder  Minority of them are pathogenic  Beneficial: used in the food industry to create a variety of substances  Yogurt, cheese, vinegar, etc.  Also used in the synthesis of some vitamins (Riboflavin, B12)  Decompose organic waste  Are primary producers for a lot of life --> transform vital elements into something usable by other organisms  Produce industrial chemicals Microorganisms exist everywhere --> are ubiquitous! Even in extreme habitats, they are only limited by the availability of water. Pathogenicity  Most do not cause disease (less than 1%), and are actually beneficial to humans  Pathogen: are microorganisms (bacteria, viruses, etc.) that can cause disease  Pathogenesis: the origination and development of disease.  Virulence: refers to the severity of a disease or poison Interest in MB fields dependent on broader objectives --> medical MB to achieve medical goals. 1.1.2 Nomenclature  Genus: is the first name of an organism and is ALWAYS capitalized  Specific epithet: is the species name that follows and is not capitalized.  Both are underlined or italicized  Names are also "Latinised"  Initial conventions --> S. Aureus  Scientific names also denote various things  Can honour researcher, describe the species or identify the habitat 1.1.3 Bacteria

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Relatively simple, single celled organisms. Genetic material not enclosed in a nuclear membrane, therefore bacterial cells are called prokaryotes (Greek word meaning nucleus). Prokaryotes are both bacteria and archaea. Shapes  Bacillus or rod-like  Coccus: spherical or ovoid  Spiral: corkscrew or curved  Some can be star shaped or squared  Can form chains, pairs or other groups which are indicative of the species of bacteria Cell walls largely composed of carb and protein complex peptidoglycan Can reproduce by dividing into two equal cells --> process called binary fission Use organic chemicals for nutrition Many can swim by using appendages called flagella Seen everywhere in nature in almost every conceivable environment Simple cellular organization sets them apart from other cellular entities Archaea Consist of prokaryotic cells BUT lack peptidoglycan in cell walls that you see with bacteria Often found in extreme environments Divided into three main groups  Methanogens: produce methane as waste product from respiration  Extreme halophiles (halo = salt; phillic= loving) --> live in extremely salty environments  Extreme thermophiles: live in hot sulfurous water, such as hot springs. Are NOT known to cause disease to humans Fungi Are eukaryotes which are organisms whose cells have a distinct nucleus which houses their genetic material, surrounded by a special envelope called the nuclear membrane May be unicellular OR multicellular  Large multicellular fungi like mushrooms may look like plants, but unlike them, they cannot carry out photosynthesis Cell walls composed of substance called chitin Unicellular forms of fungi (yeasts) are oval in shape --> bigger than bacteria Most typical fungi are molds

Form visible masses called mycelia which are composed of long filaments (hyphae) that branch and intertwine  Ex: cottony growths on bread are mold mycelia Can reproduce sexually or asexually Obtain nourishment by absorbing solutions of organic material from environment Organisms called slime molds have characteristics of both fungi and amebae Medically important as both agents of disease and as sources of antibiotics Protozoa Are unicellular eukaryotic microbes with at least one nucleus and numerous intracellular structures Move by pseudopods, flagella or cilia.  Amebae move by using extensions of their cytoplasm called pseudopods (false feet)  Others have long flagella or numerous shorter appendages for locomotion called cilia. Have variety of shapes and live either as free entities or as parasites (those that derive nutrients from a living host) that absorb or ingest organic compounds from environment Some are photosynthetic and use light as a source of energy and carbon dioxide as their chief source of carbon to produce sugars Can reproduce sexually or asexually Algae Alga (singular) are photosynthetic eukaryotes with a wide variety of shapes Both sexual and asexual forms Algae of interest are usually unicellular Cell walls composed of carb called cellulose Abundant in fresh water and saltwater, soil and in association with plants As photosynthesizers, they need water, light and carbon dioxide for food production and growth, but usually don't need organic compounds from environment Through p synthesis, they produce oxygen and carbs that are used by other organisms --> so play an important role in balance of nature Viruses Are very different from the other microbial groups mentioned So small that most can only be seen with electron microscope Are acellular (not cellular) Structurally very simple. One virus particle contains a core made of only one type of nucleic acid, either DNA or RNA. 

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All living cells have both, can carry out chemical reactions and can reproduce as self-sufficient units (viruses cannot) Core surrounded by protein coat, which is sometimes encased by lipid membrane called an envelope Viruses can only reproduce by using cellular machinery of other organisms  So considered to be living only when multiplying inside host cell, so they are parasites of other forms of life.  On other hand, not considered alive because they are inert when outside a living host. Multicellular animal parasites Animal parasites are eukaryotes Two major groups are the flatworms and the round worms, collectively called helminths During some stages of life cycle, helminths are microscopic in size Recap (which are prokaryotes vs eukaryotes) Prokaryotes: bacteria and archaea Eukaryotes: fungi, algae, protozoa and multicellular parasites 

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Classification based on cellular organization of organisms --> grouped all organisms into three domains  Bacteria (peptidoglycan cell walls)  Archaea (cell walls, if present, lack peptidoglycan)  Eukarya which include  Protists (slime, mold, protozoa, and algae)  Fungi (unicellular yeasts, multicellular molds and mushrooms)  Plants (mosses, ferns, conifers, and flowering plants)  Animals (sponges, worms, insects and vertebrates) 1.1.5 o Robert Hooke and his discovery of cells spurred cell theory--> theory that all living things are composed of cells  Anton Van Leeuwenhoek discovered the microbial world as he was the first person to accurately observe and describe microorganisms with his own microscope  Drew his "animalcules" which were really representations of bacteria and protozoa ---> found them on material from surface of teeth, feces and rainwater  Probably the first to see live organisms through his simple single lenses microscope 1.1.6

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Only have known that disease can arise from viral, bacterial or fungal infections for about 120yrs. Those that first introduced the concept were seen as crazy o Some believed that life could arise spontaneously from non living matter through a hypothetical process known as Spontaneous germination  Redi's experiments set out to challenge that flies and maggots generated spontaneously --> two jars with meat, no maggots but one exposed to air --> BUT AIR IS NEEDED FOR SG, so new experiment with fine net over jar, allowing air in --> no maggots.  Case for SG strengthened by John Needham --> chicken broth experiments/cooled solutions soon teaming with microorganisms after being heated --> Spallanzani replies with microorganisms from air probably entered Needham's solutions after they were boiled ---> demonstrated that no MO developed if the solution was heated after being sealed in a flask o Rudolph Virchow challenged SG with the concept of biogenesis, hypothesizing that living cells arise only from pre-existing living cells  Could provide no proof though o Louis Pasteur  demonstrated MO present in air can contaminate sterile solutions, but air itself did no create microbes  Filled short necked flasks with beef broth, boiled contents.  Some left open and allowed to cool  In a few days, the open flasks became contaminated with microbes ---> lead him to reason that it must be microbes in the air causing the contamination  The others sealed after boiling were free of microbes  He then placed the broth in open-ended, long necked flasks ---> the contents were then boiled and cooled  But the broth in these flasks also did not become contaminated  The curved flask allowed air in, but trapped microbes so broth at the end of the flask was not contaminated  Showed MO can be in non-living matter, on solids, liquids and in air  Showed the MO life can be killed off by heat and that methods can be devised to block MO to nutrient environments --> discovery which formed basis of aseptic techniques, procedures that prevent contamination by unwanted MO which are now standard practice in labs and medical procedures  Proved it wasn't mystical SG, but SG in some form probably lead to life on earth --> but it doesn't happen today o Recap  Evidence in favour of SG --> John Needham o

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SG disproved by Pasteur and his curved flasks

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Fermentation: a process whereby microorganisms called yeasts convert sugars into alcohol in the absence of air.  Process discovered by Pasteur when asked about the reasons why wine was spoiling. However, Pasteur also discovered that the microorganisms responsible for the spoiling was bacteria, who in the presence of air, change the alcohol to vinegar. Solution? Heat the beer and wine just enough to kill most of the bacteria causing spoilage --> pasteurization. Now is a common practice Discovery that yeast could lead to physical and chemical changes in organic materials lead to germ theory of disease which postulated that microorganisms may be responsible for illness Theory further corroborated by physician Ignaz Semmelweis who knew that certain alcohol killed bacteria --> started to wash hands with it before surgeries, and this reduced incidence of infection First real proof that bacteria cause disease came from Robert Koch  Was racing to discover cause of anthrax  Discovered rod celled bacteria in blood of cattle that had died of anthrax  Isolated bacteria and injected it into healthy cattle  When they died, examined their blood and compared with isolated bacteria --> the blood had the original bacteria  Established Koch's postulates which were a sequence of experimental steps for directly relating a specific microbe to a specific disease. Jenner and cowpox  Inoculated girl with cowpox --> found she had developed immunity to small pox Pasteur found that Bacteria that have lost their virulence after being grown in lab were able to inoculate people against bacteria's virulent counterparts  Used term vaccine for cultures of avirulent microorganisms used for preventive inoculation 1.1.11 Treatment of disease by using chemical substances is called chemotherapy  May be derived from natural sources or may be synthetic Chemicals produced naturally by bacteria and fungi to act against other microorganisms are called antibiotics Chemotherapeutic agents prepared from chemicals in the lab are called synthetic drugs Success if chemo treatments is based on fact that some chemicals are more poisonous to microorganism than to the infected host

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Chemo --> magic bullet that finds its target without killing host First anti-bio was discovered by accident --> by Alexander Fleming ---> noticed curious pattern of growth on the plates ---> it was an area where bacterial growth had been inhibited. It was produced by the mold Penicillium chrysogenum Many microbial chemicals kill pathogenic microbes but also damage the infected host --> toxicity to humans has always been a problem Viral growth depends on healthy host cells, thus very few successful antiviral drugs exist as a drug that interferes with viral reproduction would also likely affect uninfected cells of the body 1.1.12 Bacteriology: study of bacteria  Began with Leeuwenhoek's first examination of tooth scrapings  Most thoroughly studied microorganism  Majority are single celled with spherical, rod or spiral shapes  Most too small they need a light microscope to be seen Mycology: study of fungi, includes medical, agricultural and ecological branches  Account for 10% of infections Parasitology: study of protozoa and parasitic worms  Many worms able to be seen with naked eye ---> so their existence has been known for thousands of years  Advances in genomics (study of an organisms genes) have allowed scientists to classify bacteria and fungi according to their genetic relationships with other bacteria, fungi and protozoa. Immunology: is the study of immunity Virology: the study of viruses  Viruses cause many types of disease --> influenza, measles, mumps and colds 1.1.15

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MO can be genetically modified to manufacture large amounts of human hormones and other substances  Paul berg showed that fragments of human or animal DNA that code for important proteins can be attached to bacterial DNA.  The resulting hybrid was the first example of recombinant DNA.  Recombinant DNA (rDNA) technology inserts recombinant DNA into bacteria (or other microbes) to make large quantities of a desired protein.  Field combines elements from two other areas of study: microbial genetics, which studies the mechanisms by which MO inherit traits

And molecular biology, which looks at how genetic information is carried in molecules of DNA and how DNA directs the synthesis of proteins.  Much of our knowledge of how genes determine specific traits found from exp with bacteria.  They are unicellular, simple organisms, which makes them less complex than plants or animals and life cycles last less than an hour --> many can be cultivated in a short period of time Majority of microbes benefit humans in many ways Microbial ecology: they study of the relationship between MO and their environment.  MO responsible for transforming essential elements for life (carbon, Nitrogen, oxygen, etc.) into forms plants and animals can use Other beneficial uses of bacteria  Treatment of sewage  Bacteria which use pollutants as sources of energy --> when used in this way, the process is referred to as bioremediation  Means that toxins can be removed  Insect control --> bacteria which produce toxic substances to insect digestive system Biotechnology: refer to the practical application of microbiology  Has become a lot more sophisticated through the advent of recombinant DNA technology which modifies an organisms DNA to achieve a desired outcome --> better taste, better shelf life, etc. This has lead to gene therapy Gene therapy: inserting a missing gene or replacing a defective one in human cells  This technique uses harmless virus to carry the missing or new gene into certain host cells, where the gene is picked up and inserted into the appropriate chromosome  Allows for treatment of numerous disease Biological insecticides  Microbes that are pathogenic to insects are alternatives to chemical pesticides  Prevent damage to crops by killing many insects, but are harmless to humans 1.1.19 Normal Microbiota: microbes inside and on our bodies and in our every day, normal environments that do us no harm, and even benefit us. Some normal microbiota can cause disease or infect people we contact, for instance, when normal microbiota leave their habitat. 

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Whether our bodies overcome offensive tactics of a microbe depends on our resistance--the ability to ward off diseases.  Resistance provided by skin barrier, mucous membranes, cilia, stomach acid, and antimicrobial chemicals such as interferons. Microbes can be destroyed by white blood cells, inflammatory response, fever and specific responses of our immune system, Biofilms: a complex aggregation of microbes  Ex: slime covering lake, or film on your teeth  Can be beneficial --> protecting mucous membranes or providing food for aquatic organisms  Can be harmful --> clogs pipes, can cause inflammation of heart  Bacteria in biofilms are often resistant to antibiotics because the biofilm offers a protective barrier Infectious disease: a disease in which pathogens invade a susceptible host, such as a human or animal  Pathogen carries out part of its life cycle in the process within the host Emerging infectious diseases (EIDs): new diseases that are cropping up in recent years  Have potential to increase in incidence in the near future  Propagated by evolutionary changes in existing organisms, the spread of known diseases to new geographic regions by modern transport, and increased human exposure to unusual infections from places undergoing ecological changes such as deforestation.  Ex: Middle east respiratory syndrome  Ex: severe acute respiratory syndrome (SARS)  H1N1 influenza (flu)/aka swine flu: caused by new type of influenza virus  Avian influenza A (H5N1)/bird flu  Subtypes of influenza A usually seen in one species, but sometimes can travel from one to another. Antibiotic resistant bacteria also a problem --> able to propagate due to advantage over other bacteria in presence of antibiotic  Methicillin-resistant S. Aureus (MRSA) West Nile encephalitis is the inflammation of the brain caused by west Nile virus Bovine spongiform encephalopathy AKA mad cow disease  Lead to boycott of UK beef  °°Part of handful of infectious diseases caused by an infectious protein called a prion  Creutzfeldt-Jakob disease also caused by a prion Escherichia coli is a normal inhabitant of large intestine or vertebrates and its presence is beneficial because it helps produce certain vitamins and breaks down otherwise indigestible foodstuffs. However, the

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strain E. Coli O157:H7 causes bloody diarrhea when it grows in the intestines Infectious disease can transmit itself very quickly  Ebola hemorrhagic fever  Marburg virus --> another hemorrhagic virus  Cryptosporidiosis AIDS (acquired immunodeficiency syndrome): severe weakening of the immune system which can lead to death  Caused by human immunodeficiency virus (HIV) which destroys CD4 T cell, one type of white blood cell important to immune system defenses. Sickness and death cased by MO or cancerous cells that otherwise would have been defeated by bodies natural defenses...