Microbiology and Parasitology Lecture Chapter 1-5 PDF

Microbiology and Parasitology Lecture 3.​ Some microorganisms,especially bacteria and fungi, are important sources of antimicrobial agents....

Microbiology and Parasitology Lecture 3.​ Some microorganisms,especially bacteria and fungi, are important sources of antimicrobial agents. 4.​ Some microorganisms act as saprophytes decomposers of waste products and dead organisms, making them essential in ★​ Microbiology is derived from the Greek words maintaining a balanced ecosystem. mikros (“small”), bios (“life”), and logia or logos 5.​ The study of microorganisms has led to a better (“study of”). understanding of how microorganisms produce ★​ Microbiology is the study of organisms that are disease, paving the way to better disease too small to be seen with the naked eye. management and control. This was further ★​ Microbiology is further classified into different improved through the discovery of vaccines that fields of study, namely: helped prevent sickness from infectious ○​ Bacteriology - the study of bacteria diseases. ○​ Virology - the study of viruses 6.​ Certain diseases which were thought to have ○​ Mycology - the study of fungi been eradicated are now re emerging. Some ○​ Parasitology - the study of protozoa have the potential as biological warfare agents. and parasitic worms At the same time, there are now a number of ○​ Phycology - the study of algae pathogens that are developing resistance to ○​ Immunology - the study of the immune antibiotics.In this context, the study of system and the immune response microbiology is relevant for better understanding of the negative instances in which science can be used. ★​ Microorganisms or microbes are organisms that are microscopic and require a microscope to be observed, and microbiology is the ★​ In 3180 BC, an epidemic known as the “plague” scientific field dedicated to studying them. broke out in Egypt. ★​ These organisms are categorized into two: ★​ In 1122 BC, an outbreak of smallpox like disease ○​ Cellular, it may either be prokaryotes that originated in China spread worldwide. (bacteria, cyanobacteria, and archaeans) ★​ The exhumed mummified remains of Rameses or eukaryotes (fungi, protozoa, and V showed skin lesions resembling smallpox. algae). ★​ In the late 1800s and the first decade of the ○​ Acellular, which includes viruses. 1900s came to be known as the Golden Age of Microbiology. ★​ After World War II, antibiotics were introduced 1.​ Microbiology has an impact in the daily lives of to the medical world. humans. Microorganisms are everywhere—in ★​ The electron microscope was developed in the the air one breathes,in the environment, and 1930s. even in one’s body. a.​ Normal flora or indigenous flora produce Robert Hooke disease in persons with compromised ★​ First to use a microscope immune systems. ★​ With the use of a microscope he was able to 2.​ Some microorganisms are essential in discover the cell—the basic unit of living biotechnology and a wide range of industries organisms. which include food and beverage, ★​ His discovery heralded the cell theory that pharmaceuticals,mining, genetics, and many stated living organisms are made up of cells. more. Antoine Van Leeuwenhoek ★​ In the 1970s, a Dutch merchant, created a single-lens microscope that he used to observe ★​ Microorganisms are miniscule organisms that microorganisms which he then called cannot be seen with the naked eye. animalcules. ★​ The discovery of the microscope has led to their ★​ He became known as the “Father of close observation, allowing microbiologists and Microbiology” and was the one who first other scientists to study them further. provided accurate descriptions of bacteria, ★​ A microscope is an optical instrument that can protozoa, and fungi. magnify organisms a hundredfold or even a thousand fold. Louis Pasteur ★​ From the time of its initial discovery in the ★​ He performed countless experiments that led to 1600s, the microscope has undergone great his germ theory of disease. revolutionary changes. ★​ He postulated that microorganisms were in the environment and could cause infectious Compound Microscope diseases. ★​ A type of microscope that contains more than ★​ He also developed the process of one magnifying lens. pasteurization,which kills microorganisms in ★​ It can magnify objects approximately a different types of liquids, and which became the thousand times their original size. Visible light basis for aseptic techniques. is its main source of illumination. ★​ He also introduced the terms aerobes and ★​ As Such, it is also known as the compound light anaerobes and developed the fermentation microscope. process. ○​ The eyepiece (or ocular) contains what is called the ocular lens that has a Robert Koch magnifying power of 10x. ★​ He proved that microorganisms caused certain ○​ The second lens system is located in the diseases through a series of scientific steps objective that is positioned directly which led to his formulation of Koch's postulates. above the organism to be viewed. Edward Jenner ★​ He discovered the vaccine for smallpox. Joseph Lister ★​ He applied the theory to medical procedures paving the way for the development of aseptic surgery. Paul Ehrlich ★​ He discovered the antibiotic Salvarsan for the treatment of syphilis. ★​ This drug heralded the “magic bullet” of chemotherapy, which is treatment of disease by using chemical substances. Alexander Fleming ★​ He discovered the antibiotic penicillin from the mold Penicillium notatum. Brightfield Microscope Differential Interference Contrast Microscope ★​ Made up of a series of lenses and utilizing ★​ It is similar to the phase-contrast microscope visible light as its source of illumination, the except that it utilizes two beams of light instead brightfield microscope can magnify an object of one and therefore has higher resolution. 1,000 to 1,500 times. ★​ The resulting contrasting colors of the ★​ This is used to visualize bacteria and fungi. specimen being studied are due to the prisms ★​ Objects less than or thinner than 0.2 μm cannot that split the light beam. be visualized by this type of microscope. ★​ It was developed by Georges Nomarski in 1952 as ★​ The term “brightfield” is derived from the fact an improvement to the phase contrast that the specimen appears dark against the microscope. surrounding bright viewer field of this ★​ It is useful in examining living specimens when microscope. normal biological processes might be inhibited ★​ However, it has very low contrast and most of by standard staining procedures. the cells need to be stained to be properly ★​ However, the three dimensional image of the viewed. specimen produced may not be accurate since the enhanced areas of light and shadow may Darkfield Microscope distort the appearance of the image. ★​ This microscope utilizes reflected light instead of transmitted light, with a special condenser that Fluorescence Microscope has an opaque disc that blocks the light, such ★​ It makes use of ultraviolet light and fluorescent that only the specimen is illuminated. dyes called fluorochromes. ★​ The specimen to be studied appears bright ★​ It appears to shine against a dark background. against a dark background. ★​ It is based on the principle that certain ★​ This type of microscope is ideal for studying materials emit energy that is detectable as specimens that are unstained or transparent and visible light when they are irradiated with the absorb little or no light. light of a given wavelength. ★​ It is also useful in examining the external ★​ It uses a higher intensity of light source and this details of the specimen such as its outline or in turn excites a fluorescent species. surface. ★​ The fluorescent species then emits a lower ★​ This type of microscope is used to view energy light of a longer wavelength which spirochetes. produces a magnified image instead of the original light source. Phase-contrast Microscope ★​ It can be used to visualize structural ★​ It is based on the principle that differences in components of small specimens such as cells refractive indices and light waves passing and to detect the viability of cell populations. through transparent objects assume different ★​ It may also be used to visualize the genetic phases. material of the cell (DNA and RNA). ★​ This type of microscopy was first introduced by Frits Zernike, a Dutch physicist,in 1934. Confocal Microscope ★​ The phase contrast microscope has a contrast ★​ Known as the confocal laser scanning microscope enhancing optical technique in order to produce (CLSM) or laser confocal scanning microscope high contrast images of specimens that are (LCSM). transparent which include thin tissue slices, ★​ It uses an optical imaging technique that living cells in culture, and subcellular increases optical resolution and contrast of the particles(such as nuclei and organelles). micrograph by using a spatial pin-hole to block out-of-focus light in image formation.  ★​ The specimen is stained with a fluorescent dye to ★​ It can also be used to determine the variations in make it emit or return light. temperature inside the cell as well as its ★​ This is used, together with computers, to chemical properties. produce a three-dimensional image. ★​ It is also useful in the study of cell physiology. ★​ Most microorganisms besides being very tiny Electron Microscope are also devoid of any color and are thus ★​ It utilizes a beam of electrons to create an image difficult to see, even with the use of the of the specimen. microscope. ★​ The electron beams serve as the source of ★​ To facilitate visualization,staining procedures illumination and magnets are used to focus the have been developed by various scientists. beam. ★​ These staining procedures are meant to give ★​ The first prototype of this microscope was built color to the organisms, making them easier to by the German Engineer Ernst Ruska in 1933, see under the microscope. which had a resolution power of up to 50 nm. ★​ Modern electron microscopes are capable of Simple Staining magnifying objects up to 2 million times. ★​ It uses a single dye which can be either aqueous ★​ It is used to visualize viruses and subcellular (water-based) or alcohol-based. structures of the cell. ★​ This method of staining is a quick and easy way ★​ There are two types of electron microscopes: to visualize cell shape, size, and arrangement of ○​ Transmission Electron Microscope bacteria. (TEM) - the original form of the ★​ It uses basic dyes such as safranin, methylene electron microscope which produces blue, or crystal violet. two-dimensional, black and white ★​ These stains give up or accept hydrogen ions, images, and magnifies objects up to leaving the stain positively charged. 200,000 times. ○​ Scanning Electron Microscope (SEM) - Differential Stains it relies on interactions at the surface ★​ It is used to differentiate one group of bacteria rather than transmission; it can from another. magnify bulk samples with greater ★​ There are two types of differential staining depth view which produces procedures commonly used, namely: three-dimensional structure of the ○​ Gram Stain - distinguishes sample, but the image is still only black gram-positive bacteria from and white, and magnifies objects up to gram-negative bacteria. 10,000 times. ​ Gram-positive bacteria stain blue or purple. Scanning Probe Microscope ​ All cocci except ★​ It was developed in the 1980s by the Swiss Neisseria, Veillonella, scientists Dr. Gerd Binnig and Dr. Heinrich and Branhamella. Rohrer. ​ Gram-negative bacteria stain ★​ It is used to study the molecular and atomic red or pink. shapes of organisms on a nanoscale. ​ All bacilli except ★​ A physical probe is used to scan back and forth Corynebacterium, over the surface of a sample. Clostridium, Bacillus, ★​ A computer then gathers data that are used to and Mycobacterium. generate an image of the surface. ○​ Acid-fast Stain - used for bacteria with high lipid content in their cell wall,  hence cannot be stained using gram According to Physical State stain. ★​ Liquid media - commonly called broths, milk, ​ Ziehl-Neelsen Stain - known as or infusions, these are water-based solutions that the “hot method” because it do not solidify at temperatures above the requires steam-bathing the freezing point. prepared smear after addition ○​ It does not contain gelling agents such of the primary dye which is as gelatin or agar. aqueous (water-based). ○​ It is suited for the propagation of a ​ It will appear red on a large number of organisms, blue background. fermentation studies, and other tests. ​ Kinyoun Stain - known as the ★​ Semi-solid media - it exhibits a clot-like “cold method” as it does not consistency at ordinary room temperature and utilize heat after addition of the contains agar at concentrations of 0.05% or less primary stain which is that allows thickening of the media without oil-based. producing a firm substance. ​ It will appear red on a ○​ They have a soft consistency. green background. ○​ It is suited for culture of microaerophilic bacteria or for the study of bacterial motility. ★​ Solid media - It contains a solidifying agent such as 1.5% - 2% agar, giving them a firm surface on which cells can form discrete colonies. ○​ It is used for isolation of bacteria and fungi or for determining the colony Special Stains characteristics of the organism. ★​ It is used to demonstrate specific structures in a ○​ It comes in two forms: bacterial cell. ​ Liquefiable (or reversible) solid ​ Metachromatic granules can be media visualized using Loeffler's ​ Non-liquefiable (or Alkaline Methylene Blue (LAMB). non-reversible) solid media ​ Hiss stain (capsule or slime layer) ​ Dyer stain (cell wall) According to Chemical Composition ​ Fischer-Conn stain (flagella) ★​ Synthetic media - it contains chemically-defined ​ Dorner and Schaeffer-Fulton substances which are pure organic and/or stain (spores) inorganic compounds. ​ India ink or nigrosine (capsule ★​ Non-synthetic media - it is the complex media of the fungus Cryptococcus that contains at least one ingredient that is not neoformans) chemically defined, which means that it is neither a simple or pure compound. ○​ It can support the growth of more ★​ Media (sing. medium) are used to grow fastidious organisms. microorganisms. ★​ A culture medium is basically an aqueous According to Functional Type solution to which all the necessary nutrients ★​ General purpose media - it is designed for essential for the growth of organisms are primary isolation of a broad spectrum of added. microbes and contains a mixture of nutrients  that support the growth of pathogenic and ○​ These are usually agar-based solid media non-pathogenic organisms. that allow isolation of individual ○​ Peptone water, nutrient broth, and bacterial colonies. nutrient agar ​ Thayer-Martin agar - contains ★​ Enrichment media - it contains complex organic the antibiotic trimethoprim, substances such as blood, serum, or special nystatin, vancomycin, and growth factors, and are designed to increase the colistin. It is used for the number of desired microorganisms without isolation of Neisseria. stimulating the rest of the bacterial population. ​ Mannitol Salt agar – contains ○​ It is used to grow fastidious or 10% NaCl and is used for the nutritionally exacting bacteria. isolation of Staphylococcus ​ Blood agar - it contains general aureus. nutrients with 5% - 10% blood ​ MacConkey’s agar – promotes added to a blood agar base. the growth of gram negative Certain gram positive bacteria bacteria, primarily those produce exotoxins that cause belonging to the family hemolysis of red blood cells Enterobacteriaceae,and inhibits contained in the blood agar. the growth of gram positive Their hemolytic reaction is bacteria through the addition of categorized into three, which is bile salts. It is both selective useful in the classification of and differential. these bacteria. The hemolytic ​ Löwenstein Jensen Medium – a patterns are: selective medium used to ​ Beta hemolysis - shows recover Mycobacterium complete lysis of red tuberculosis.It is made selective blood cells resulting in by the incorporation of complete clearing malachite green. around the colonies. ​ Saboraud’s dextrose agar – ​ Alpha hemolysis - used for the isolation of fungi. shows incomplete lysis ★​ Differential media - it allows the growth of of red blood cells, several types of microorganisms. These are producing a greenish designed to show visible differences among discoloration of the blood certain groups of microorganisms. agar around the ○​ It allows the growth of more than one colonies. target microorganisms that ​ Gamma hemolysis - demonstrate morphological variations shows no hemolysis, in colony morphology. resulting in no change in ​ MacConkey’s agar the medium. ​ Triple Sugar Iron agar ★​ Selective media - it contains one or more ★​ Transport media - it is used for clinical substances that encourage the growth of only a specimens that need to be transported to the specific target microorganism and inhibit the laboratory immediately after collection. growth of others. ○​ It prevents the drying of specimens and ○​ It is designed to prevent the growth of inhibits the overgrowth of commensals unwanted contaminating bacteria or and contaminating organisms. commensals so only the target bacteria ​ Cary Blair transport medium - will grow. it is used for the transport of  feces of suspected cholera patients. ​ Pike’s medium - it is used to transport throat specimens of patients with streptococcal infection. ★​ Anaerobic media - it is used specifically for organisms that cannot survive in the presence of oxygen and require reduced oxidation-reduction potential and other nutrients. ○​ These are supplemented with nutrients such as vitamin K and hemin. ○​ It undergoes boiling to remove dissolved oxygen. ○​ To reduce the oxidation reduction potential, substances such as 1% glucose, 0.1% ascorbic acid, 0.1% thioglycolate,or 0.05% cysteine are added. ○​ Methylene blue or resazurin is added as an indicator of the oxidation reduction potential. ​ Chopped cooked meat ​ Thioglycolate broth  Microbiology and Parasitology Lecture ★​ There are organisms that are considered medically important that have the potential or ★​ Living cells can be classified into two general the ability to produce significant clinical disease categories: prokaryotes and eukaryotes. in humans. ★​ Prokaryotes are organisms that do not possess a ★​ They may be part of the normal flora of the true nucleus and membrane bound organelles body or are true pathogenic organisms. (e.g., bacteria). ★​ These may be categorized into bacteria, viruses, ★​ Eukaryotic organisms are those that possess a fungi, algae, and parasites (protozoa and true nucleus and membrane bound organelles. helminths). They are usually multicellular organisms and include plants, animals,fungi, parasites,and Viruses algae. ★​ Acellular organisms. ★​ Viruses are acellular organisms that possess only ★​ The outer surface is called capsid, which is DNA or RNA. composed of repeating subunits called capsomeres. ★​ It only possesses a single nucleic acid, either DNA or RNA, but never both. ★​ It also lacks the genes and enzymes that are necessary for energy production; and necessary cellular parts that can allow them to replicate independent of the host cell. ★​ It relies on the cellular machinery of the host cell for protein and energy production. ★​ Viruses are considered obligate intracellular parasites. ★​ Viruses are classified based on the following: ○​ Type of nucleic acid ○​ Shape of the capsid ○​ Number of capsomeres ○​ Size of the capsid ○​ Presence or absence of an envelope ○​ Type of host they infect ○​ Type of disease they produce ○​ Target cell or tropism ○​ Immunologic or antigenic properties  ★​ It exists in two morphological forms: (1) cysts, Bacteriophages the infective stage; and (2) trophozoites, the ★​ A special type of viruses that primarily infect pathogenic stage. bacteria. ★​ They play a role in the acquisition of virulence Algae factors of certain bacteria, as well as in the ★​ An eukaryotic organism whose outer surface transfer of genetic material from one bacterium consists primarily of cellulose. to another (as in transduction). ★​ It is described as plant-like organisms because most of them have chlorophyll and are thus Bacteria capable of photosynthesis but unlike plants, they ★​ A prokaryotic cell with majority having an outer do not have true roots, stems, or leaves. covering called the cell wall that is composed ○​ Diatoms mainly of peptidoglycan. ​ It is an unicellular algae that ★​ It possesses both DNA and RNA. inhabit both fresh and saltwater. ★​ Bacteria possess a nucleoid instead of a true ​ Their cell wall contains silicone nucleus, smaller ribosomes, and lack dioxide that may be utilized in mitochondria. filtration systems, insulation, and as abrasives. Fungi ○​ Dinoflagellates ★​ A eukaryotic cell with an outer surface mainly of ​ It is also an unicellular algae chitin. that are important members of ★​ Their cell membrane is made up mostly of the phytoplankton group. ergosterol. ​ They contribute greatly to the ★​ It possesses both DNA and RNA. oxygen in the atmosphere. ★​ Fungi possess a true nucleus that is enclosed by ​ They are also responsible for a nuclear membrane and mitochondria that what is known as “red tide”. function for ATP production. ​ These small organisms produce ★​ Fungal ribosomes are also larger than bacterial a powerful neurotoxin which, ribosomes (80 Svedberg units). when ingested, is responsible for the potentially fatal disease called paralytic shellfish poisoning. Protozoa ★​ Representatives for parasites. ★​ It is also an eukaryotic cell that has an outer surface called a pellicle. ★​ These are unicellular organisms that usually divide through binary fission, similar to bacteria.  Microbiology and Parasitology Lecture ★​ It is called a capsule if it is strongly attached to the cell wall. ○​ Indicative of the virulence of an organism ★​ In terms of morphology, bacteria may be ○​ It can stimulate an antibody response classified into three basic shapes: coccus (pl. from the immune system cocci), bacillus (pl. bacilli), and spiral-shaped or ○​ Serves to protect the organism from curved. dehydration ★​ It is also called a slime layer if it is loosely Coccus (pl. cocci) attached. ★​ It can be described as spherical or round-shaped organisms. Cell Wall ○​ Ex: Staphylococcus, Streptococcus ★​ It is sometimes called the murein sacculus. ★​ They may be arranged singly, in pairs ★​ Its principal component is peptidoglycan, which (diplococci), in chains (streptococci), in clusters is also called murein or mucopeptide. (staphylococcus), in groups of four (tetrad), or ★​ It is multi-layered in gram-positive bacteria and in groups of eight (octad). single-layered in gram-negative bacteria. ★​ It provides rigid support and gives shape to the Bacillus (pl. bacilli) bacteria. ★​ It can be described as rod-shaped organisms. ★​ It protects the bacteria from osmotic damage ○​ Ex: Escherichiacoli, Salmonella and plays an important role in cell division. ★​ Some may be very short, resembling elongated cocci called coccobacilli. Teichoic acids Curved or spiral-shaped ★​ Compromise major surface antigens of ★​ It may show variations in their morphology gram-positive organisms and can elicit antibody ○​ Vibrio cholerae, the organism causing response. cholera, is described as comma shaped. ★​ These also provide tensile strength to ○​ The causative agent of syphilis, gram-positive bacterial cell walls. Treponemapallidum, is spiral in shape. ○​ The causative agent of diphtheria, Polysaccharides Corynebacteriumdiphtheriae, is club ★​ It includes neutral sugars such as mannose, shaped. arabinose, rhamnose, and glucosamine. ★​ It also includes some acidic sugars such as glucuronic acid and mannuronic acid. ★​ Prokaryotic cells are surrounded by a complex envelope that may vary in composition. Outer Membrane ★​ The envelope serves to protect the bacteria ★​ It is a bilayered structure. from harsh environmental conditions. ★​ The inner leaflet is composed of a lipopolysaccharide (LPS). Glycocalyx ○​ It has a complex glycolipid called Lipid ★​ The outermost covering of some bacteria. A, responsible for its endotoxin activity. ★​ A gelatinous substance that is located external to ★​ The porins allow the passage of substances like the cell wall, composed of polysaccharide or sugars and amino acids. polypeptide, or both. ★​ The inner core is a polysaccharide made up of repeat units, also called the O antigen.  ★​ It also functions for motility. Lipoprotein ★​ They function for adherence to cell surface ★​ It functions to anchor the outer membrane to the (common pili) or attachment to another peptidoglycan layer and stabilizes the outer bacterium during a form of bacterial gene membrane. exchange called conjugation (sex pili). Periplasmic Space Axial Filaments ★​ A fluid-filled space between the outer ★​ It is also called endoflagella found in spirochetes membrane and the inner plasma membrane. (e.g., Treponema pallidum causing syphilis). ★​ It contains enzymes for the breakdown of large ★​ It is composed of bundles of fibrils. non-transferable molecules into transportable ★​ The filaments rotate producing movement of ones and enzymes that serve to detoxify and the outer sheath of the spirochetes propelling inactive antibiotics. them forward. ★​ Mycobacterium tuberculosis possesses an outer layer that is lipid-rich. ★​ Also called cell membrane or plasma membrane ★​ It is composed of large amounts of waxes that located beneath the cell wall. are known as mycolic acids. ★​ It is sometimes called the cell sac as it encloses ★​ Hydrophobic the cytoplasm of the cell. ★​ It cannot be stained using the reagents used in ★​ It allows for transport of selected solutes. gram staining. ★​ In aerobic organisms, it is the site of the ★​ Its hydrophobic nature protects them from electron transport chain and serves as the site harsh chemicals such as strong acids and of ATP production. detergents. Nucleoid Flagella ★​ Bacteria have no true nucleus that is surrounded ★​ A thread-like structure made up entirely of the by a nuclear membrane. protein subunit flagellin. ★​ Its genetic material is packaged in a structure ★​ They project from the capsule and are organs called nucleoid. for motility. ★​ Bacteria possess a single, circular, ★​ Bacteria without flagella are called atrichous. double-stranded DNA. ○​ Monotrichous: single polar flagellum ○​ Lophotrichous: a tuft of flagella at one Mesosomes end of the bacterium ★​ It functions for cell division. ○​ Amphitrichous: flagella at both ends of ★​ It is also involved in the secretion of substances the bacterium produced by bacteria. ○​ Peritrichous: flagella all around the bacterium Ribosomes ★​ It functions for protein synthesis. Pili or Fimbriae ★​ Bacterial ribosome is smaller (70S). ★​ A rigid surface appendages found on many gram-negative bacteria. Granules or Inclusion Bodies ★​ They are fine and short. ★​ Found in certain bacteria and serve for storage ★​ Their structural protein subunits are called of food and energy. pilins. Endospores ★​ Structures produced by many bacteria when they are placed in a hostile environment. ★​ It is composed of dipicolinic acid and calcium which confers resistance to heat, drying, chemical agents, and radiation; making it very difficult to destroy. ○​ Sporulation: the process of spore production, and this occurs when the environmental conditions are detrimental to the bacteria. ○​ Germination: a process where endospores revert to their vegetative state when their environmental conditions become favorable.  Microbiology and Parasitology Lecture ○​ Potassium is required for the normal functioning and integrity of ribosomes and participates in certain enzymatic activities of the cell. ○​ Calcium is an important component of ★​ Growth as defined in medical dictionaries gram positive bacterial cell wall and involves an orderly and organized increase in contributes to the resistance of the sum of all components of the organisms. bacterial endospores against adverse ★​ The process entails the replication of all cellular environmental conditions. structure, organelles, and components. ○​ Iron is a component of cytochrome,a ★​ Microbial growth is concerned with the component of the electron transport increase in the number of cells and not an chain, and functions as a cofactor for increase in the size of the organism. enzymatic activities. ★​ Bacterial colonies are composed of thousands of ○​ Trace elements are components of cells; hence, colonies in culture are actually enzymes and function as cofactors. composed of billions of cells. Some are necessary for the maintenance of protein structure. Carbon Growth Factors ★​ It makes up the structural backbone or skeleton ★​ It promotes the growth and development of the of all organic molecules. bacterial cell. ○​ Autotrophs (lithotrophs): utilize ★​ It includes vitamin B complex and amino acids. inorganic compounds and inorganic salts as their sole carbon source. ○​ Heterotrophs (Organotrophs): Moisture/Water organisms that make use of organic ★​ The bacterial cell is composed mainly of water. substances like sugars or glucose as ★​ It serves as the medium from which bacteria their carbon source. acquire their nutrients. Nitrogen, Sulfur, Phosphorus Oxygen ★​ Nitrogen and sulfur are required for the ★​ It is used by aerobic bacteria for cellular synthesis of proteins. respiration and serves as the final electron ★​ Nitrogen and phosphorus are essential for the acceptor. synthesis of nucleic acids and ATP. ★​ It is classified as either aerobes or anaerobes ★​ Approximately14% of the dry weight of a based on their oxygen requirements. bacterial cell is nitrogen and about 4% is sulfur ○​ Aerobes: strictly utilize molecular and phosphorus. oxygen for energy production. ○​ Obligate Anaerobes: microbes that Inorganic Ion cannot survive in the presence of ★​ These include magnesium,potassium, calcium, oxygen and do not have the enzymes iron, and trace elements (e.g., manganese, zinc, that break down free radicals produced copper, cobalt). in the body. ○​ Magnesium stabilizes ribosomes, cell ○​ Facultative organisms: organisms that membranes, and nucleic acids. It also can grow and survive under both serves as a cofactor in the activity of aerobic and anaerobic conditions; most many enzymes. medically important bacteria.  ○​ Microaerophiles: organisms that are Lag Phase able to grow at low oxygen tension but ★​ The period of adjustment for the bacteria in the their rate of growth is diminished. new environment. ○​ Capnophiles: organisms that may ★​ The organisms will show increased metabolic require the addition of carbon dioxide activity in order to synthesize DNA as well as to enhance their growth. secrete enzymes which might not be present in their new environment but which are needed by Temperature the organism. ★​ Thermophiles: grow best at temperatures ★​ Bacteria attain their maximum size toward the higher that 40C (pasteurization - 62.8C) end of the lag phase. ★​ Mesophiles: require an optimal temperature of ★​ This phase may last for 1 to 4 hours. 20 - 40C (human body - 37C) ★​ Psychrophile: require an optimum temperature Log/Logarithmic/Exponential Phase of 10 - 20C (refrigerator - 4C) ★​ Rapid cell division = an increase in the number of bacteria pH ★​ It exhibits high metabolic activity ★​ The extent of acidity or alkalinity of the ★​ The period when the generation time or doubling environment. time of the organism is determined ○​ Alkalophiles: grow best in 8.4 - 9.0 pH ★​ A generation time of 10 minutes means that the ○​ Neutrophiles: grow best in 6.5 - 7.5 pH bacteria will double in number every 10 ○​ Acidophiles: grow best at less than 6.0 minutes showing exponential growth pH ★​ The average duration of this phase is about 8 hours Osmotic Conditions ★​ Most organisms grow best under ideal Stationary Phase conditions of osmotic pressure, which is ★​ The period of equilibrium determined by the salt concentration. ★​ The rate of growth slows down, nutrients start ○​ Normal microbial cytoplasmic salt to deplete, and toxic wastes begin to concentration: approximately 1% accumulate ○​ Optimum Condition: same salt ★​ Some bacterial cells may die but there is still concentration cell division ★​ If the extracellular salt concentration is ★​ Living bacteria = Dead bacteria increased, the water will flow out of and the ★​ Sporulation occurs towards the end of this organism will shrink and die phase ★​ If the external environment does not contain salt, water will flow into the bacterial cell Death or Decline Phase causing the organism to swell and rupture ★​ The period of rapid cell death where the number ○​ Halophiles: require high salt of dead cells is greater than the living cells due concentrations for growth to continuous depletion of nutrients and ○​ Osmophiles: require high osmotic accumulation of waste materials. pressure for optimal growth ★​ The duration of this phase may vary from a few hours to a few days. ★​ It illustrates the phases in the growth of the population of bacteria when they are grown in a culture of fixed volume.  Microbiology and Parasitology Lecture ○​ It’s easy to prevent this with a vitamin K shot. The injection is given at the anterior lateral thigh within 6 hours of birth. ★​ Microbial ecology is the study of relationships between microorganisms and their environment. ★​ The skin is the part of the human body that is in ★​ Normal flora consists of the group of constant contact with the environment, making it organisms that inhibit the body of a normal the most exposed to microorganisms. healthy individual in the community. ★​ There are certain factors that eliminate non ★​ These may be non-pathogenic or pathogenic and resident flora from the skin, namely: may at times behave as opportunistic pathogens. ○​ Lysozyme in the skin ○​ Resident flora: organisms that are ○​ Acidic pH of the skin due to sweat relatively of fixed types and are ○​ Free fatty acids in sebaceous secretions; regularly found in a given area of the and body at a given age. ○​ Constant sloughing off of the skin ○​ Transient flora: inhabit the skin and ★​ The normal flora of the skin consists mainly of mucous membrane temporarily for bacteria and fungi. hours, days, or weeks and are derived ★​ Most microorganisms in the skin are found in from the environment. its superficial layer (stratum corneum) and hair follicles. ★​ The skin may be divided into three regions: ★​ Inhibit growth of pathogenic organisms by ○​ Axilla, perineum, and toe webs: have priming the immune system of newborns. higher moisture levels, higher body ★​ Protects the body's organs and systems that are temperature, and higher levels of in direct contact with the external environment surface lipids prone to attack by invasive organisms. ○​ Hand, face, and trunk: dry sites due to ★​ Secrete vitamin K. their exposure to the environment ○​ It can prevent pathogenic organisms ○​ Upper arms and legs: dry sites due to from attaching to and penetrating the their exposure to the environment skin and other tissues by producing mucin. Staphylococcus Epidermidis ○​ Normal flora in the intestines aid in the ★​ Major skin inhabitant, comprising digestion of food by producing enzymes approximately 90% of resident aerobic flora such as cellulase, galactosidase, and glucosidase. Staphylococcus Aureus ○​ It also helps in the metabolism of ★​ Most commonly found in nose and perineum steroids. ★​ In the nose, number varies with age (greater in newborns that in adults) ★​ Once born, the newborn normal flora is derived Micrococci (Micrococcus Luteus) from the mother’s genital tract during delivery, ★​ Accounts for 20 - 80% of micrococci in the skin from the skin and respiratory tract. ★​ Newborns have very little vitamin K in their Diphtheroids (Coryneforms) bodies at birth. This puts them at risk for ★​ Lipophilic: common in axilla bleeding. ★​ Non-lipophilic: common in hairless or glabrous skin such as palms of hands  ★​ Anaerobic diphtheroids (Propionibacterium ★​ Most of the bacteria cultured include acnes): common in areas rich in sebaceous streptococci, lactobacilli, and Bacteroides which glands are all transient. Gram-negative Bacilli (Enterobacter, Klebsiella, Large Intestines Escherichia coli, and Proteus spp.) ★​ It has more bacteria than small intestine ★​ Seen in moist intertriginous areas such as toe ★​ The colon is inhabited predominantly by webs and axilla anaerobes (95 - 99%) ○​ Bacteroides fragilis (most common) Nail Flora ○​ Bifidobacterium/Lactobacillus Bifidum ★​ Similar to that of the skin (predominant in breast fed infants) ★​ Fungi may also be present (Aspergillus, ○​ Eubacterium Penicillium, Cladosporium, Mucor) ○​ Peptostreptococcus ○​ Clostridium. ★​ In bottle fed infants, the predominant intestinal ★​ The normal flora in the conjunctivae are very flora is Lactobacillus acidophilus. scanty/sparse because they are held in check by ★​ About 1 - 4% of the flora of the colon are the flow of tears that contain lysozyme. facultative aerobes. ○​ The lysozyme may interfere with the ○​ Escherichia coli cell wall synthesis. ○​ Enterobacteriaceae ★​ Some bacteria may transiently colonize the conjunctiva including Neisseria, Moraxella, and Corynebacterium. ★​ Synthesis of vitamin B complex and vitamin K ★​ Conversion of bile into bile acids ★​ Competition with transient flora for nutrients Esophagus ★​ Prevention of colonization of the intestines by ★​ It contains transient mouth flora. transient flora ★​ Production of potentially pathogenic Stomach end-products of metabolism that are toxic to ★​ Minimal bacteria may be found due to hostile transient flora environments. ★​ Most bacteria found here may be swallowed with the food or those that are dislodged from the mouth. ★​ It has an acidic environment because of the release of gastric acid. ○​ Helicobacter pylori: most common cause of duodenal ulcer; it produces urease that causes alkalinization of gastric acid which enables colonization of the stomach. Small Intestine ★​ Scanty flora may be found due to constant peristaltic movement.  ​ Young girls are more prone to gonococcal ★​ The urinary tract is sterile above the distal 1 cm infection compared to of the urethra. adult women because the normal acidic pH of Anterior Urethra the vagina as well as the ★​ The predominant flora isolated are S. normal vaginal flora are epidermidis, enterococci, and diphtheroids. not yet fully developed. ○​ After menopause: the vaginal pH Both male and female increases once more due to the ★​ Mycobacterium smegmatis may be found as lessened production of glycogen. normal commensals in their secretions. ​ Normal flora during this period are similar to those of Penile Urethra pre-puberty. ★​ Gardnella vaginalis, bacteroides, and alpha ​ Most of these flora are derived streptococci may be found. from the skin and colon. ​ Fungi such as Torulopsis and Female Urethra Candida may also be found (10 - ★​ Either sterile or contains Staphylococcus 30%). epidermidis. ​ Some conditions may allow overgrowth of Vaginal Flora these fungi (intake of ★​ It varies depending on the age, hormonal levels, antibiotics) can lead to and vaginal pH of the host. vaginal infections such ○​ Female infants: the predominant as vaginitis. vaginal flora is Lactobacillus spp. ○​ From 1 month of age until puberty: there is cessation of glycogen secretion making the vaginal pH higher (around 7.0). ​ S. epidermidis, streptococci, diphtheroids, and Escherichia coli. ○​ Onset of puberty: there is resumption of glycogen secretion making the vaginal pH acidic. ​ Predominant flora include Lactobacillus acidophilus, corynebacteria, peptostreptococci, streptococci, Bacteriodes, and staphylococci. ​ Lactobacillus: plays a role in preventing gonococcal infection by producing lactic acid that adds to the acidity of the vagina.