Microbiology 1st Week Introduction Lesson 1 PDF

MICROBIOLOGY Assist. Prof. İlhan TAHRALI Academic Calendar Explanation Start End FALL SEMESTER 30.09.2024 10.01.2025 (Beginning-Ending Course)...

MICROBIOLOGY Assist. Prof. İlhan TAHRALI Academic Calendar Explanation Start End FALL SEMESTER 30.09.2024 10.01.2025 (Beginning-Ending Course) Mid-term Exams 16.11.2024 24.11.2024 General Exams 13.01.2025 24.01.2025 Make-up Exams 03.02.2025 07.02.2025 14 lessons during this semester 70% attendance requirement for theoretical courses and 80% attendance requirement for laboratory  70% attendance for theoretical courses 80% attendance for laboratory practices Resources 1. Burton's Microbiology for the Health Sciences Paul G. Engelkirk 2. Microbiology (Lippincott's Illustrated Reviews Series), international edition, Richard A Harvey. I Contain Multitudes: The Microbes Within Us and a Grander View of Life Ed Yong « this book not only covers the diseases' histories but also addresses public health responses and societal upheavals.» What is happening inside us? This course includes: Introduction to microbiology Classification of microorganisms The morphology of bacteria and viruses The reproduction, genetics and metabolism of bacteria Bacterial infection agents Viral and parasitic infection agents Fungi and fungal infection agents This course includes: Immunity, Hypersensitivity and Immunodeficiency Vaccines and Immune Serums Microbiota Antimicrobial Chemotherapy Sterilization and Disinfection Microbial Contamination in Pharmaceutical Products Sterile Pharmaceutical Products INTRODUCTION TO MICROBIOLOGY Assist. Prof. İlhan TAHRALI 1st Week  Biology Microbiology micros bios logos (very small) (life) (study of …) Microbiology: Scientific study of very small, unicellular living organism seen only by a microscope microorganisms - microbes  What does microbiology study? Microbiology Understanding the nature and function of the microbial world deals with two fundamental To apply our knowledge of the microbial world for the benefit of issues: human and the earth  «Microorganisms» within the scope of microbiology consist of: ✓ bacteria ✓ archaea ✓ fungi ✓ algae ✓ protozoa ✓ viruses Microscopic, unicellular, and cell-cluster organisms  Microorganisms are living things that have survived for over 3.5 billion years Everywhere In all circumstances soil hot and cold waters the depths of the earth oceans air icy poles water deserts plants salt lakes animals acidic environments human body – skin, hair, intestines, mouth and mouth cavities in every item and environment we touch, wear and use Most of Life is Invisible Although microorganisms are the smallest life forms, they constitute the main part of the biomass in the world Microorganisms carry out many chemical reactions necessary for higher organisms They affect people's daily lives both positively and negatively in many areas Practical Applications of Microorganisms Microorganisms play a crucial role in various industries, significantly impacts our lives both positively and negatively Their practical applications span across numerous fields, including: Medicine Agriculture Food production Environmental management Biotechnology Microorganisms in Medical Applications Microbiology has been at the forefront of research in medicine and biology Microbes are part of the human environment and have a close association with humans They are in us, on us, and nearly everywhere around us The vast majority of microorganisms are directly or indirectly beneficial, not only to other organisms, but also to humans Less than 1% of the known microorganisms cause disease, however, some of these are fatal  In the medical field, microorganisms are essential for the production of antibiotics, vaccines, and other pharmaceuticals E.g. Penicillium (a fungi) is used to produce penicillin, one of the first and most widely used antibiotics Vaccines, such as those for influenza or hepatitis B, are often developed using weakened or inactivated forms of viruses or bacteria Some microorganisms in the human colon compete with pathogenic or opportunistic microorganisms, as well as synthesizing some vitamins and essential nutrients  Beneficial bacteria are used in probiotics to promote gut health, demonstrating the positive influence of microorganisms on human health Microorganisms are also involved in gene therapy Recombinant DNA technology, which utilizes bacteria like E. coli, allows for the mass production of human insulin, providing a critical treatment for diabetes  Microorganisms in Agricultural Applications In agriculture, microorganisms are utilized to enhance soil fertility and promote plant growth Nitrogen-fixing bacteria, such as Rhizobium species, form symbiotic relationships with leguminous plants, converting atmospheric nitrogen into a form that plants can absorb and use This process reduces the need for chemical fertilizers, leading to more sustainable farming practices  Microorganisms found in the nodules of legumes convert atmospheric nitrogen (N2) into ammonia, which the plant uses for growth Thanks to nitrogen fixation, the need to use expensive nitrogen fertilizer is eliminated  Soybean plant root nodules Legumes, such as peanuts, cowpeas, contain bacteria that fix soybeans, and fava beans, are good nitrogen molecular nitrogen for the plant fixers and will fix all of their nitrogen needs to use other than that absorbed from the soil Microorganisms in Agricultural Applications Microorganisms also play a role in pest control Bacillus thuringiensis is a bacterium used as a biological pesticide It produces toxins that are harmful to specific insect pests but are safe for humans and other non-target organisms This kind of pest control is an environmentally friendly alternative to chemical pesticides Microorganisms in Food Industry Applications Microorganisms are Yeasts, such as Lactic acid bacteria, e.g. indispensable for the Saccharomyces Lactobacillus sp., are involved production of various cerevisiae, are used in in the fermentation of dairy fermented foods and the production of products like yogurt and beverages bread, beer, and wine cheese  These microorganisms not only contribute to the flavor and texture of foods but also improve their nutritional value and shelf life Furthermore, the role of microorganisms in food safety cannot be overlooked The use of beneficial microbes can inhibit the growth of harmful pathogens in food products, reducing the risk of foodborne illnesses Microorganisms and Foods However, microorganisms have important effects in the degradation of foods The main reason for food spoilage is microorganisms This situation, which causes great economic losses in the food industry, has resulted in the food industry taking various protective measures against microbial spoilage  Microorganisms in Environmental Applications Microorganisms also have This process involves the use E.g., certain bacteria significant environmental of microbes to clean up can degrade applications, particularly contaminated environments, hydrocarbons, making in the area of such as oil spills or polluted them useful in the bioremediation water bodies treatment of oil spills Bioremediation One of the important contributions of microorganisms to our planet is their use to clean up pollution In bioremedition, the removal of oil pollution, solvents, pesticides and other pollutants that are toxic to the environment is done by microorganisms Bioremediation of an oil contamination. Fertilizer spraying initiates the breakdown of oil by stimulating the growth of bacteria in the area This technique is the fastest and most economical method for oil pollution on beaches  Other microorganisms can break down toxic substances like heavy metals, reducing environmental pollution Another critical application is in wastewater treatment, where microorganisms are used to break down organic matter in sewage, resulting in cleaner water This process not only protects water resources but also supports sustainable environmental management practices  Microorganisms in Biotechnology Applications In biotechnology, E.g., Clostridium Microbial enzymes are also widely microorganisms are acetobutylicum is used used in industries such as textiles, harnessed for the production in the production of bio- paper, and detergents, where they of biofuels, enzymes, and butanol, a renewable facilitate various chemical reactions other valuable products biofuel under mild conditions, reducing the need for harsh chemicals  A group of Archaea called methanogens produce natural gas (methane, CH4) as a product of anaerobic metabolism Ethyl alcohol is produced by microbial fermentation from glucose obtained from raw materials such as sugar cane and corn Ethanol and methane are obtained by microbial activity from waste materials such as household waste, animal waste and cellulose  Microorganisms are also used in industry in the production of antibiotics, enzymes and various chemicals by biotechnological methods Genomics has made it possible to examine the microorganism genome for genes of potential commercial importance Thus it led to the significant development of industrial microbiology  Moreover, the field of synthetic biology, which involves the design and construction of new biological parts, devices, and systems, relies heavily on microorganisms Scientists are engineering bacteria and yeasts to produce a wide range of products, from pharmaceuticals to bio- based materials It demonstrates the potential of microorganisms in advancing technology  Microorganisms impact our daily lives in numerous ways, both beneficial and harmful Impact of Although pathogenic microorganisms pose significant threats Microorganisms to human health, the vast majority of microorganisms do not on Daily Life harm humans Moreover, they are beneficial and necessary for human health and the function of the planet  Impact of Microorganisms on Daily Life E.g., microorganisms living in the rumen of ruminant animals digest and ferment cellulose Without these symbiotic microorganisms, these animals cannot benefit from cellulose-rich foods Microorganisms in the human colon not only synthesize some vitamins and essential nutrients, but also compete with pathogenic microorganisms Understanding and harnessing the power of microorganisms are therefore essential for improving health outcomes, advancing technology, and ensuring environmental sustainability The History of Microbiology  The living things that constitute the subject of microbiology existed on earth long before developed other living things The History of In ancient times, even if unconsciously,human Microbiology beings have begun to deal with microorganisms with the transition to social life The first examples of this were seen in the making and preservation of various foods The History of Microbiology The fermentation of bread dough, the discovery of dairy products such as yoghurt, the production of beer and wine, acid or pickled foods such as vinegar and pickles, and the preservation of some foods by salting or drying Some of them benefit from microorganisms (bread, yoghurt, pickling, etc.), while the other part aims at preservation (salting, drying, canning, etc.) However, all these activities were carried out without microorganism awareness The History of Microbiology Hippocrates (460-377 BC) believed that diseases were caused by the bad air coming out of the soil and the effects of water, stars, winds and seasons This teaching is called «miasma theory» The theory was abandoned by scientists and physicians after 1880 and was replaced by the «microbe theory» The History of Microbiology In addition, remarkable opinion were expressed, especially about the causes of infectious diseases, in ancient civilizations The most important of these is Ibn Sina's view that «disease- causing elements exist in nature, but cannot be seen or determined by eyes» The History of Microbiology İbn-i Sina (Avicenna) (980-1038) He is considered one of the most important doctors, astronomers, thinkers, writers and scholars of the Golden Age of Islam El-Kanun fi't-Tıp (Canon of Medicine) It was taught as a textbook in Medieval Europe for 400 years The History of Microbiology Other Islamic scholars who put forward hypotheses about the existence of microorganisms include; Ibn Zuhr, who discovered scabies mites, and Er-Râzi, who made the earliest known description of smallpox in his book Al-Hāwi Ottoman Sultan II. Mehmed's teacher Akşemseddin said, «Diseases are transmitted from person to person or from soil to person through living seeds that cannot be seen with the naked eyes.» Discovery of microorganisms Although some predictions have been made about the existence of microorganisms, definitive proof of the existence of these invisible creatures is only possible by making them visible In 1676, Antonie van Leeuwenhoek observed bacteria and other microorganisms with the microscope he designed Leeuwenhoek is also known as the father of microbiology for his discovery of the use of the simple single-lens microscope  Antonie van Leeuwenhook (1632-1723) made it possible to see microorganisms with the simple microscope with a single lense he made Leeuwenhook identified the creatures he observed with the microscope he developed as small animals (animalcules)  https://youtu.be/po_bWD yfd0I?si=xmDlkXOoZcTMa cdj Invention of the first microscope by Antonie van Leeuwenhoek (video) https://youtu.be/PCguJ4S GmPg?feature=shared  Discovery of microorganisms However, the first record of the observation of microorganisms belongs to Robert Hooke, not Leeuwenhoek, contrary to popular belief In 1665, Robert Hooke described the fruit-like structures he saw in molds for the first time with his microscope and Robert Hooke (1635-1703) published it in his book Micrographia The history of microscobes https://youtu.be/4WWLYr71J5I?si=bEu790_FJI4hfSJz Discovery of microorganisms J. Turberville Needham (1713-1781) defended the theories of «spontaneous generation» (life from inorganic matter) He boiled (or not) broth-containing flasks before closing the lids Microorganisms spontaneously appeared after a while in lidded jars containing pre- heated and unheated broth However, this result was due to insufficient boiling, not spontaneous generation  Discovery of microorganisms Antonie Lavoisier (1743-1794), one of the founders of modern chemistry, determined the presence of oxygen in the air with his experiments in 1775 and claimed that oxygen is necessary for life and that the oxygen in the bottle is destroyed by boiling, so living things cannot live Antonie Lavoisier George Schröder and Theodor von Dusch (1854), were the first to introduce the idea of using cotton plugs for plugging microbial culture tubes. They passed the air through cotton and gave it to the broth. As a result of the experiment, they reported that no living things were formed in the tubes Theodor von Dusch  Discovery of microorganisms Italian scientist Lazzaro Spallanzani (1729-1799) did not agree with the theory of spontaneous generation In 1799, to prove that microorganisms come from outside, he boiled nutrient-containing infusions for at least 1 hour He closed the mouth of the tubes containing boiled infusions A few days later, the infusion in the tubes was still clear, demonstrating that microbes do not occur in bottles spontaneously  However, his findings were not accepted because it was thought that bacteria died due to the lack of oxygen Pasteur demolished the oxygen theory and proved Spallanzani's theory, establishing a mechanism where bacteria could not enter from the outside, but air could  Discovery of microorganisms John Tyndall (1820-1893) suggested two forms of microorganisms: thermolabile and thermostable Tyndall suggested that sterilization should be done gradually, and found the tyndalization method: Substances are heated between 56-100 °C for 45-60 minutes for 3 consecutive days After each heating, the substances are kept at 37 °C for 24 hours, thus, bacteria in spore form become vegetative and are killed during the next heating ❖ Tyndalization is a method used to sterilize substances such as vaccines and serum that may deteriorate at high temperatures  Louis Pasteur The term «microbiology» was first introduced by the French microbiologist Louis Pasteur (1822-1895) Pasteur is considered one of the founders of modern microbiology and made groundbreaking discoveries in the science of microbiology His demonstration that fermentation was caused by the growth of bacteria and yeasts provided a main impetus for the development of the science  L. Pasteur boiled nutrient solutions in a swan-necked flask and purified them from microorganisms When the bottles were left to cool, contamination was prevented since the swan-shaped neck of the bottle allows air to enter the bottle and prevents the entry of microorganisms  Pasteur’s suggestion that microorganisms cause disease in humans, founded the discipline of microbiology In addition to working with factors such as anthrax, gas gangrene, blood poisoning, puerperal fever, he also successfully applied the rabies vaccine The rabies vaccine was first discovered in 1885 by Louis Pasteur  After finding the vaccine, Pasteur wrote a letter to the heads of state and requested help for the institute he would establish Ottoman Sultan II. Abdülhamid formed a delegation and sent it to France, a year after the discovery of the vaccine The Institute Pasteur in Paris  Sultan II. Abdülhamid aimed to bring innovations in the field of bacteriology to the country and supported Pasteur to establish the Pasteur Institute Abdulhamid also presented 10 thousand gold coins and the Mecidiye Medal of the first degree for Pasteur and his Institute Sultan II. Abdülhamid (1842-1918) Document dated 29 May 1886 and its Latin version regarding the 10 thousand Francs aid given by Sultan Abdülhamid to Pasteur and the 1st Degree Mecidiye Medal he wore Document dated June 16, 1896, documenting the aid sent by Sultan Abdülhamid to Pasteur  After returning to Istanbul, the delegation began to work at the "Dârü'l-Kelb Treatment Center" (Rabies Hospital), which Abdülhamid had established They applied what they saw at the Pasteur Institute in the Ottoman lands Only 3 years after its discovery, the vaccine began to be produced in Istanbul The warm relations between Abdülhamid Khan and Pasteur continued and developed further due to the "cholera epidemic" that broke out in Istanbul in 1892 The delegation that went to France Pasteurization Pasteur also made a very important contribution to the dairy industry by defining «pasteurization» Pasteurization, heat-treatment process that destroys pathogenic microorganisms in certain foods and beverages Pasteur demonstrated that abnormal fermentation of wine and beer could be prevented by heating the beverages to about 57 °C (135 °F) for a few minutes Pasteurization Pasteurization of milk, requires temperatures of about 63°C (145 °F) maintained for 30 minutes or, alternatively, heating to a higher temperature, 72°C (162 °F), and holding for 15 seconds (higher temperatures for shorter periods of time) The times and temperatures are those determined to be necessary to destroy heat-resistant, non-spore-forming, disease-causing microorganisms found in milk The treatment also destroys most of the microorganisms that cause spoilage and so prolongs the storage time of food  Discovery of microorganisms British surgeon Joseph Lister (1827-1912) influenced by Pasteur's work, applied his principles in surgery Lister hypothesized that airborne microorganisms caused wound infection He demonstrated the importance of antiseptics in surgery by preventing infection with dressings dipped in a disinfectant Since there was no distinction between pathogenic microorganisms and harmless ones at the time, Lister strongly believed that the air in medical environments should be disinfected  Lister argued that infections could be prevented in the postoperative setting by placing an antiseptic shield between the wound and the surrounding air Since filtration and heat exposure were not suitable for treating human skin, Lister suggested a chemical agent In 1865, carbolic acid, commonly known as creosote, was used to disinfect fractures Lister soaked a pad in a solution of carbolic acid and then applying it to the wound of a child Four days later, he found that no infection had appeared, and the child's bones began to boil without any signs of inflammation Robert Koch Robert Koch (1843-1910) succeeded in obtaining pure cultures from mixed cultures with the solid media he developed He was able to observe the tuberculosis agent: Mycobacterium tuberculosis by isolating and staining it He also obtained extracellular culture of Anthrax bacteria He introduced some criteria called Koch's postulate  Koch’s Postulate Koch's postulates are four criteria designed to establish a causal relationship between a microbe and a disease The postulates were formulated by Robert Koch and Friedrich Loeffler in 1884, based on earlier concepts described by Jakob Henle The statements were refined and published by Koch in 1890 Koch’s Postulate The organism considered to be pathogenic should be present in all cases of the disease and not in healthy individuals The agent must be isolated and grown as pure cultures The pure cultured organism should be capable of causing disease when administered to susceptible healthy animals The organism must be able to be reproduced in pure cultures and demonstrated to be identical to the original organism  Discovery of microorganisms Frederick W. Tword found "bacteriophages" in England in 1915 and Felix H. d'Herelle in France in 1917 Frederick W. Tword Felix H. d’Herelle The image of a bacteriophage under electron microscope and their schematized version Alexander Fleming and his discovery of penicillin  Penicillin was introduced for treatment after being used in clinical trials by Howard Florey and Ernst Chain in 1940 Howard Florey Ernst Chain With his discovery, Gerhard Domagk led to the production of a series of sulfa drugs, the first type of antibiotics in 1932 Gerhard Domagk  Selman Abraham Waksman (1888-1973) discovered actinomycin and streptomycin He named these substances, obtained from molds or bacteria and cause the death of other microorganisms, as antibiotics He received the Nobel Prize in 1952 for the discovery of streptomycin as the first antibiotic against tuberculosis  Alfred Hershey (1908-1997) and Martha Chase (1927-2003) used bacterial viruses in their studies They were able to demonstrate that DNA was transferred from bacteriophages to bacteria They laid the foundations of molecular biology, by stating that the genetic material is DNA Microbiology Today Microbiologists have learned more about microorganisms over time The application of this information has significantly increased human health and well-being The science of microbiology has made significant progress in understanding the role of microorganisms both as disease agents and in food and agriculture  Microbiology Today At the beginning of the 20th century, the main causes of human deaths were bacterial and viral pathogens. Especially the elderly and children were greatly affected by microbial diseases Today, infectious diseases have less lethal effects in developed countries The most important factors in the formation of this situation are: increase in our knowledge of disease processes, advanced hygienic and public health practices, active vaccination campaigns and widespread use of antimicrobial substances such as antibiotics Mortality rates of leading causes of death in the United States: 1900 and today  Microbiology Today However, many infectious diseases in developing countries can still be a major threat E.g, diseases such as malaria, tuberculosis, cholera, measles, pneumonia, other respiratory diseases and severe diarrheal syndromes are still prevalent in developing countries All people in the world are threatened by diseases that are primarily animal diseases such as bird flu, swine flu or Ebola, which can be transmitted to humans and spread rapidly in the population Microbiology Today As a result, pathogenic microorganisms continue to pose serious health threats to humans worldwide When the problem of antibiotic resistance is added to this situation, the issue of treatment of microbial diseases is still of great importance today E-mail: [email protected]