MICROBIOLOGY INTRODUCTION NOTES.docx

**MICROBIOLOGY 1 APH 4102 NOTES** Introduction to Microbiology - **Microbiology**, the study of microscopic organisms, derived its name from three Greek words: mikros ("small"), bios ("life"), and logos ("science"). Taken together they mean the study of microorganisms (MOs) which ar...

**MICROBIOLOGY 1 APH 4102 NOTES** Introduction to Microbiology - **Microbiology**, the study of microscopic organisms, derived its name from three Greek words: mikros ("small"), bios ("life"), and logos ("science"). Taken together they mean the study of microorganisms (MOs) which are very small and cannot be seen by unaided eye. - They are generally 1 millimeter (mm) or less in diameter. - MOs are present in vast numbers everywhere on the bodies of animals and humans, on plant surfaces, in the air, food, water, dust, soil, and even inside the intestinal canal of all insects, birds, animals and human beings. - Microbiology is the study of living organisms of microscopic size which includes: 1. Bacteria 2. Fungi 3. Algae 4. Protozoa 5. Viruses - Microorganisms, due to their unique ability to adapt to extreme conditions imposed by oligotrophy (low nutrients), temperature, pH, pressure, and radiation, among others, have so far been found in every environment imaginable - The associated structures and metabolic capabilities of a microorganism determine where it can be found and the ecological influence it has on the surrounding environment. - Although microorganisms are found everywhere, recently developed detection techniques are demonstrating that human perturbations can influence the diversity and distribution of microorganisms The "Branches" of microbiology; **Bacteriologists** - study bacteria, there are medical, agricultural, biotechnological specializations. **Mycologists** - study fungi, there are medical, agricultural, biotechnological specializations. **Protozoologists,** study small "animal - like" single celled organisms such as amoeba, and various disease causing parasites. **Phycologists** study algae. The study of lichens can also be regarded as a sub discipline of microbiology **Parasitologists-** a term generally used to describe those who study small animals as agents of disease (like some microscopic worms for instance) but also used to describe those who study p **Immunology** the study of the immune system protozoan pathogens **Prokaryotes**: No nucleus and organelles **Eukaryotes:** Membrane bound nucleus and organelles **Acellular agents (Viruses):** Genomes contain either DNA or RNA; newer agent is proteinaceous Size of microorganisms Microorganisms vary in size ranging from 10 nm (nanometers) to 100 mu (micrometers): Viruses in nm = 10-9 m (meter) Bacteria in um = 10-6 m Helminths in mm = 10-3 m The term microbiology was introduced by a **french Chemist Louis Pasteur**, who demonstrated that fermentation was caused by the growth of bacteria and yeast. He is known as father of microbiology - **Richard Petri**¬ Designed a special plate to hold a solid culture. This plate has great significance in microbiology and is referred as petri plate. - **Joseph Lister** -- Introduced concept of sterile surgical field -- Use of antiseptics followed -- Developed limiting dilution technique -- He is known as father of antiseptic surgery - **Robert Koch** - German physician (and Pasteur's rival) Studied the disease anthrax Developed a method to identify the etiologic agent. First utilized to identify Bacillus anthracis as etiologic agent of anthrax (1877) Developed staining technique. Developed a set of postulates - **Paul Ehrlich** is known as father of chemotherapy. In 1930 he introduced drug Salvarsan for the treatment of syphilis. - **Sir Alexander Fleming** accidentally discovered a substance produced by penicillium notatum. He extracted from the fungus a compoundwhich he called penicillin that could destroy several pathogenic bacteria. - **S.A Waksman** discovered another antibiotic streptomycin. - **In 1546, Girolamo Fracastoro** proposed that epidemic diseases were caused by transferable seed-like entities that could transmit infection by direct or indirect contact or even without contact over long distances. - **Antonie van Leeuwenhoek (1632--1723)** was one of the first people to observe microorganisms, using a microscope of his own design, - **Lazzaro Spallanzani (1729--1799)** found that boiling broth would sterilize it and kill any microorganisms in it. He also found that new microorganisms could settle only in a broth if the broth was exposed to the air. - **Louis Pasteur (1822--1895)** (father of biotechnology) expanded upon Spallanzani's findings by exposing boiled broths to the air in vessels that contained a filter to prevent all particles from passing through to the growth medium. He also did this in vessels with no filter at all, with air being admitted via a curved tube (swan‐necked flasks) that prevented dust particles from coming in contact with the broth. By boiling the broth beforehand, Pasteur ensured that no microorganisms survived within the broths at the beginning of his experiment. Nothing grew in the broths in the course of Pasteur's experiment. This meant that the living organisms that grew in such broths came from outside, as spores on dust, rather than spontaneously generated within the broth. - **In the 1860's, an English surgeon, Joseph Lister** showed the role of MO in the wound contamination, and developed Lister system which came to be known as Antiseptic Surgery, which includes the heat sterilization of instruments and the application of phenol to wound by means of dressings. - **Ferdinand Julius Cohn (1828 --1898**) was a German biologist. His classification of bacteria into four groups based on shape (sphericals, short rods, threads, and spirals) is still in use today. - **In 1876, Robert Koch (1843--1910**) established that microbes can cause disease. He found that the blood of cattle who were infected with anthrax always had large numbers of Bacillus anthracis. Koch found that he could transmit anthrax from one animal to another by taking a small sample of blood from the infected animal and injecting it into a healthy one, and this caused the healthy animal to become sick. He also found that he could grow the bacteria in a nutrient broth, then inject it into a healthy animal, and cause illness. **Koch's postulates.** Based on these experiments, he devised criteria for establishing a causal link between a microbe and a disease and these are now known as Koch's postulates. they do retain historical importance to the development of scientific thought and are still being used today. Koch postulates: **1**. The suspected causative agent must be found in every case of disease. **2.** This MO must be isolated from the infected individual and grown in a culture with no other types of MO. **3.** When inoculation into normal healthy susceptible animal a pure culture of the agent must be producing the specific disease. **4.** The same MO must be isolated from the experimentally infected host **The steps of Koch\'s postulates** used to relate a specific microorganism to a specific disease. \(a) Microorganisms are observed in a sick animal and - **Paul Ehrlich (1909)** by him chemotherapy was introduced and the modern era of control treatment began with the use of chemicals that would kill or interfere with the growth of the disease agent without damaging the infected individual. - **In 1929, Alexander Fleming** isolated a mold produced substance that inhibited bacteria but was nontoxic to lab animal. He named this antibacterial material Penicillin. is one type of antibiotics. - In the late 1800s and for the first decade of the 1900s, scientists seized the opportunity to further develop the germ theory of disease as enunciated by Pasteur and proved by Koch. There emerged a Golden Age of Microbiology during which many agents of different infectious diseases were identified. Many of the etiologic agents of microbial disease were discovered. - 19th Century, widespread use of the compound microscope and the development of staining techniques in order to better visualize microorganisms. In addition, people began to realize that microorganisms could cause disease, and did experiments on immunity. - 20th Century, was a time of great advancement for all forms of science, including microbiology. The first vaccines and antibiotics were developed, and the first chemotherapeutic agents were used to treat bacterial diseases such as syphilis. Deoxyribonucleic acid (DNA) was discovered to be the genetic material of the cell, which opened up the field of genetics research and allowed more recently for sequencing the genomes of microorganisms. 1796 First scientific Small pox vaccination (Edward Jenner) 1850 Advocated washing hands to stop the spread of disease (Ignaz Semmelweis) 1861 Disproved spontaneous generation (Louis Pasteur) 1862 Supported Germ Theory of Disease (Louis Pasteur) 1867 Practiced antiseptic surgery (Joseph Lister) 1876 First proof of Germ Theory of Disease with B. anthracis discovery (Robert Koch) 1881 Growth of Bacteria on solid media (Robert Koch) 1882 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) 1899 Recognized viral dependence on cells for reproduction (Martinus 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) (TIGR - The branches of microbiology can be classified into pure and applied sciences microbiology **Pure microbiology includes:** - **Bacteriology** (study of bacteria) - **Mycology (**study of fungi) - **Protozoology** (study of protozoa) - **Algology** (study of algae) - **Parasitology** (study of parasites) - **Genetics** (study of heredity and variation) - **Immunology** - The study of the immune system (study of mechanism involved in the development of resistance by body to infectious diseases). - **Nematology:**The study of the nematodes. - **Virology**: The study of the viruses. **Applied science microbiology** includes Medical microbiology Pharmaceutical microbiology Industrial microbiology Food microbiology Soil microbiology Agriculture microbiology Aquatic microbiology Air microbiology Epidemiology - **Medical microbiology** It deals with the study of causative agents of infectious diseases in human beings. Medical microbiology has close links with other disciplines such as pathology, clinical medicine, pharmacology and therapeutics. - **Pharmaceutical microbiology** It deals with the study of microorganisms which are responsible for the production of antibiotics, enzymes, vaccines, vitamins and other pharmaceuticals substances. It also includes the method of sterilization and disinfection, microbiological testing of pharmaceuticals, sterile product preparation and diagnosis of disease and treatment. - **Industrial microbioilogy** It is the study of industrially useful microorganisms in the production of alcoholic beverages,vitamins, aminoacids, enzymes, antibiotics and other drugs. It also includes fermentation techniques for the production of different compounds**.** - **Food microbiology** It deals with the interaction of microorganisms and foodin the relation to food processing, food spoilage, food borne diseases, their prevention and includes preparation and preservation of food products. It is the study of soil microbes and interaction amongs the soil microorganisms. - **Agricultural microbiology** It is the study of relationships of microorganisms and crops with on emphesis on the control of the plant diseases and improvement of yield. - **Aquatic microbiology** Aquatic microbiology is the study of microorganisms and their activity in the freash and marine water including lakes, rivers, bays, estuaries and seas. It also includes water purification, microbiological examination and biological degradation of waste. - **Air microbiology** It deals with the role of aerospora in contamination and spoilage of food. It also deals with the spreading of plant and animal diseases through air - **Epidemiology** It is concerned with the monitoring, control and spread of diseases in communities. **Integrative arrangement in microbiology** 1\. Microbial cytology: The study of microscopic and submicroscopic details of microorganisms. 2\. Microbial physiology: The study of how the microbial cell functions biochemically. Includes the study of microbial growth, microbial metabolism and microbial cell structure. 3\. Microbial ecology: The relationship between microorganisms and their environment. 4\. Microbial genetics: The study of how genes are organized and regulated in microbes in relation to their cellular functions. Closely related to the field of molecular biology. 5\. Cellular microbiology: A discipline bridging microbiology and cell biology. 6\. Evolutionary microbiology: The study of the evolution of microbes. This field can be subdivided into: o Microbial taxonomy: The naming and classification of microorganisms. o Microbial systematics: The study of the diversity and genetic relationship of microorganisms. 7\. Generation microbiology: The study of those microorganisms that have the same characters as their parents. 8. Systems microbiology: A discipline bridging systems biology and microbiology. 9. Molecular microbiology: The study of the molecular principles of the physiological processes in microorganisms **Criteria Useful in the Identification and/or Classification of Microorganisms** They also relates to microbial growth and the culture of microorganisms; however, since it also relates to identification and classification, it will be presented here. **1. Morphology** --Many different types of bacteria form colonies and cells with similar morphology even when subjected to various stain techniques. **2. Mode of Reproduction** -- Variation in reproductive structures/methods is of primary consideration in the classification of plants, animals and fungi; but somewhat less useful in the classification of single-celled organisms. Most single-celled eukaryotes, bacteria and archaea reproduce by means of fission, i.e., one cell divides itself into two daughter cells. **3. Nutrition and Metabolism** -- All living organisms can be categorized on the basis of their nutritional requirements and type of metabolism. A. Nutritional categories are based on energy source and carbon source. - Organisms can obtain the energy they require either from light or from chemicals. - Those using light energy are called **phototrophs (photo = light)** and - those using chemical energy are called **chemotrophs (Chemo = chemical).** - **troph** refers to activity and organisms can be activated either by light or by chemicals. - Organisms can obtain the carbon they need either from inorganic or organic carbon compounds. - Organisms using inorganic compounds as carbon sources are called **autotrophs (auto = self)** while - those using pre-formed organic compounds as their source of carbon are called **heterotrophs (hetero = different**). - The term troph refers to feeding, so organisms are either feeding themselves or feeding on a variety of different organic materials. - By combining energy source and carbon source, we obtain four nutritional categories: - **Photoautotrophs** = Organisms using light energy and inorganic compounds for carbon. - **Photoheterotroph**s = Organisms using light energy and organic compounds for carbon. - **Chemoautotroph**s = Organisms using chemical energy and inorganic compounds for carbon. - **Chemoheterotrophs** = Organisms using organic compounds for both energy and carbon. - Plants, algae and some bacteria are photoautotrophs, but only prokaryotic cells function as **photoheterotrophs or chemoautotrophs.** - Animals (including humans), fungi, protozoa and many prokaryotes function as **chemoheterotrophs**, so this category is often subdivided. - **Saprotroph**s = Chemoheterotrophs using dead or decaying organic materials for nutrients. These are sometimes called saprophytes or decomposers. - P**arasites** = Chemoheterotrophs using living organisms as their source of nutrients (some living inside their host and others living outside). - **Hypotrophs** = Obligate intracellular parasites, i.e., organisms able to grow and reproduce only when inside a living cell. Viruses, some protozoa and some bacteria are hypotrophs. - **Carnivores** = Chemoheterotrophs obtaining nutrients from meat. - **Herbivores** = Chemoheterotrophs obtaining nutrients from plant material. - **Omnivores** = Chemoheterotrophs able to obtain nutrients from both meat and plant material. B. Metabolism -- Metabolism includes all the chemical reactions occurring within living organisms (anabolism and catabolism), and can be categorized as either fermentative or respiratory (oxidative). Fermentative organisms use organic compounds (usually pyruvic acid) as the final electron acceptors in their metabolic processes. Respiratory (oxidative) organisms use inorganic compounds (usually molecular oxygen) as the final electron acceptors in their metabolic processes. **4. Gas Requirements** -- The gas requirements of organisms (based on oxygen utilization) can be useful in their classification including: - **Obligately aerobic organisms** (obligate aerobes) = Organisms requiring molecular oxygen for growth and reproduction (metabolic processes). - **Obligately anaerobic organisms** (obligate anaerobes) = Organisms unable to tolerate exposure to molecular oxygen; oxygen is often toxic to these and they cannot grow in its presence. - **Facultatively anaerobic/aerobic organisms** (facultative anaerobes/aerobes) = Organisms able to grow and reproduce with or without oxygen available to them. - **Microaerophiles** = Organisms able to grow best in environments with limited oxygen, as might occur in the mud at the bottom of a pond, lake, sea, etc., or within the gastrointestinal tract. - **obligately aerobic organisms** have a respiratory or oxidative metabolism and require oxygen as a final electron acceptor. - **obligately anaerobic** organisms are fermentative. - Many types of bacteria can use inorganic compounds other than molecular oxygen as final electron acceptors for their respiratory metabolic processes. - **Psychrophiles** are cold-loving organisms (psychro = cold, phil = love). These organisms grow best at cold temperatures (between --5 and 20 degrees C). - **Mesophiles** are moderate-loving organisms (meso = medium or intermediate) and grow best at moderate temperatures (between 20 and 45 degrees C). - **Thermophiles** are warm-loving organisms (thermo = warm) and grow best at warm temperatures (between 45 and 60 degrees C). - **Hyperthermophiles** are hot-loving organisms and grow best at hot temperatures, e.g., above 60 degrees C. - **Hyperthermophiles** living in hot springs grow at temperatures above 90 degrees C. - Organisms can also be described relative to their temperature tolerance, i.e., ability to survive or tolerate exposure to temperature extremes. - Organisms that can tolerate exposure to extreme cold are said to be **psychroduric.** They cannot grow at these temperatures, but do not die either. Most bacteria are psychroduric and can be maintained in a viable state at --70 degrees C. - Organisms that can tolerate exposure to heat are said to be **thermoduric.** They cannot necessarily grow in hot environments, but are not killed by exposure to them. - Endospores are thermoduric. **6. Acidity Vs Alkalinity or pH Requirements** -- Although most organisms grow best in neutral environments (pH between 6.5 and 7.5), some prefer acidic environments, and others prefer alkaline. - Many types of culture media contain buffers (substances that resist pH change) to help stabilize the pH or pH indicators (substances that change color in response to changes in pH) to indicate the presence of acidic or alkaline metabolic end products. - Organisms that grow best in acidic environments are called **acidophiles,** but are relatively rare. - Highly acidic or alkaline environments tend to inhibit microbial growth because cellular enzymes fail to function under these conditions. **7. Osmotic Pressure Requirements** -- - The effective osmotic pressure (tonicity) of an environment is influenced by the solute concentration present, and can significantly impact microbial growth. - **Isotonic environments** (iso = same) contain solute levels similar to protoplasm (cell), so cells placed into them will experience neither a net gain nor net loss of water. - **Hypotonic environments** (hypo = under, beneath, less than or too little) contain lower levels of solute than protoplasm (cell) and will cause cells placed into them to gain water. - Microorganisms equipped with cell walls (e.g., algae, fungi, bacteria and archaea) or contractile vacuoles (many types of fresh water protozoa) can live comfortably in hypotonic environments. - Organisms lacking these protective structures will tend to take on water (via osmosis) until they explode. - **Hypertonic environments** (hyper = over, above, too much or excessive) contain higher levels of solute than protoplasm (cell) and will cause cells placed into them to lose water. - Hypertonic environments containing high levels of salt or sugar are often used to preserve foods, i.e., inhibit microbial growth within those foods. - **Halophiles** Organisms capable of growing and reproducing in environments containing high levels of salt are called halophiles. - These may be categorized as extreme halophiles/obligate halophiles (those requiring high levels of salt for growth) or facultative halophiles (those capable of growing with or without salt). **Symbiosis** -- Symbiosis is a condition or circumstance existing when two or more different types of organisms are living together in a close association.. **Pathogen Vs Host** -- Pathogens growing within a host benefit from host resources, but the host is harmed, and sometimes killed. - Microorganisms capable of causing infection and disease in humans, domestic animals and plants.. **Parasite Vs Host** -- Parasites also benefit from their hosts without giving in return. - Organisms capable of parasitizing humans and other animals some cause disease and others serve as vectors involved in the transmission of disease-causing agents. - **Mutualistic relationships** (mutualism), i.e., those involving organisms in mutually beneficial arrangements are the most common form of symbiotic relationships. pathogens and parasites. - they help prevent population overgrowth and maintain balance within ecosystems, a concept foreign/repugnant to most humans **Biochemical Analysis** -- Biochemical analysis allows for a more technical evaluation of the relationships existing between organisms and has become the method of choice for the classification of bacteria and archaea. Various subcategories exist as follows: a\. **Enzymatic Testing** -- The types of enzymes organisms produce can be determined by testing their ability to catabolize various materials and/or to form specific end products.. **b. Chromatography** -- Various applications of chromatography can be used to identify specific chemical constituents of cells, e.g., cell wall lipid or amino acid content, membrane protein content, or the presence of specific pigments. **c. Serology** -- Serology is the science or study of antibody and antigen interactions in vitro, and has multiple applications in the detection, identification and classification of microorganisms. - Microorganisms are antigenic, i.e., are perceived by the body as foreign agents (antigens), and stimulate the production of immune proteins called antibodies. Because the interactions between antigens and antibodies are quite specific, and because antibodies can bind with antigens, it is possible to use known types of antibodies to detect or identify specific types of antigens. **D. Phage Typing** -- Phage typing (bacteriophage typing) involves the use of viruses called bacteriophages. - They will recognize and bind with specific types of bacteria, they cause infection resulting in cell death. - Because these viruses are host-specific, known types of virus particles can be used to identify unknown types of bacteria.. **E. Nucleic Acid Analysis** -- The analysis of nucleic acids, DNA and RNA, can provide considerable information useful in the identification and classification of microorganisms. Techniques commonly used in nucleic acid analysis include: **1. Percent base composition** (G + C or A + T) -- Organisms with identical percentages in base composition may or may not be closely related, but organisms with very different percentages in base composition are not related. **2. Nucleic Acid Hybridization** -- Hybridization, the ability of two nucleic acid strands to form hydrogen bonds with one another, has multiple applications including PCR and DNA chip technology. **3. Polymerase Chain Reaction (PCR**) -- The polymerase chain reaction involves hybridization and can be used to amplify DNA or RNA in vitro. **4. Gel Electrophoresis** -- Gel electrophoresis can be used to separate DNA or RNA fragments on the basis of size by exposing them to an electric field. **5. DNA Fingerprinting or RFLP analysis** -- Fragments of DNA generated by restriction endonuclease digestion will form patterns when subjected to electrophoresis. These patterns are called DNA fingerprints or RFLP patterns. **6. Nucleotide sequencing** -- Determining the sequence of nucleotides in a strand of DNA or RNA can yield information highly significant to identification and classification. **F. Protein analysis** -- The analysis of proteins other than antibodies can also be useful in the identification and classification of microorganisms. Some methods involved include: **1. Gel electrophoresis** -- Similar to methods used with nucleic acids. **2. Amino acid sequencing** -- Determining the sequence of amino acids present in a protein can be useful in determining protein function and sometimes protein origin. For example, the origin of prions (infectious protein particles) was determined using amino acid sequencing in conjunction with nucleic acid analysis.