WEEK-3-4-Bacteria PDF

BSEd (Sci) SESE 116: Microbiology & Parasitology Course Content (Lecture Notes) 2. Bacteria A. General Characteristics Sizes of Bacteria The size of most bacteria ranges from 1 to 3 μm. Mycoplasma, the smallest bacteria (and therefore the smalles...

BSEd (Sci) SESE 116: Microbiology & Parasitology Course Content (Lecture Notes) 2. Bacteria A. General Characteristics Sizes of Bacteria The size of most bacteria ranges from 1 to 3 μm. Mycoplasma, the smallest bacteria (and therefore the smallest cells), are 0.2 μm. Some bacteria, such as Borrelia, are as long as 10 μm; that is, they are longer than a human red blood cell, which is 7 μm in diameter. Structure of Bacteria The bacterium as a representative prokaryote has the following basic anatomical structures. , Plasmid 1 |Prepared by MMANALANG [email protected]  BSEd (Sci) SESE 116: Microbiology & Parasitology Course Content (Lecture Notes) Glycocalyx is differentiated as capsule or slime layer) Other Notable Chemical Substances & Structures in Bacterial Cells a. Endotoxin Found in the outer membrane of gram-negative bacteria in the form of lipopolysaccharide, LPS, the main inducer of septic shock. Endotoxin consists of lipid A, which causes the fever and hypotension seen in septic shock, and a polysaccharide called O antigen, which is useful in laboratory identification. b. β-lactamases It is located in the periplasmic space between the inner cell membrane and the outer membrane of gram-negative bacteria. This enzymes that degrade β-lactam antibiotics, such as penicillins and cephalosporins. c. Peptidoglycan It is found only in bacterial cells. It is a network that covers the entire bacterium and gives the organism its shape. It is composed of a sugar backbone (glycan) and peptide side chains (peptido). Lysozymes (enzyme found in lysosome organelles) kill bacteria by cleaving the glycan backbone of peptidoglycan. d. Techoic acid Teichoic acids are found within the cell wall of most Gram-positive bacteria. Teichoic acid contributes to the overall rigidity of the cell wall, which is important for the maintenance of the cell shape, particularly in rod- shaped organisms. They appear to play a role in resistance to adverse conditions such as high temperatures and high salt concentrations, as well as to β-lactam antibiotics. 2 |Prepared by MMANALANG [email protected]  BSEd (Sci) SESE 116: Microbiology & Parasitology Course Content (Lecture Notes) e. Bacterial Spores Spores are medically important because they are highly heat resistant and are not killed by many disinfectants. Boiling will not kill spores. They are formed by certain gram-positive rods, especially Bacillus and Clostridium species. Spores have a thick, keratin-like coat that allows them to survive for many years, especially in the soil. Spores are formed when nutrients are in short supply, but when nutrients are restored, spores germinate to form bacteria that can cause disease. Spores are metabolically inactive but contain DNA, ribosomes, and other essential components. f. Transposons are small pieces of DNA that move frequently between chromosomal DNA and plasmid DNA. They carry antibiotic-resistant genes and pathogenicity genes. If one of these transposable elements "jumps" from the chromosome into a plasmid, the genes it carries can be easily passed to other bacteria by transformation or conjugation. That means the genes can spread quickly through the population. 3 |Prepared by MMANALANG [email protected]  BSEd (Sci) SESE 116: Microbiology & Parasitology Course Content (Lecture Notes) Summary: Bacterial Classification and Nomenclature The classification of bacteria is based on various criteria, such as the shape and arrangement, anatomical and physiological features, staining characteristics, habitat and pathogenicity. 1. Shape and arrangement Bacteria are classified by shape into three basic groups: cocci, bacilli, and spirochetes. (However, there are still other common shapes as found in Figure 2-1) cocci are round, bacilli are rods, and spirochetes are spiral-shaped. Some bacteria are variable in shape and are said to be pleomorphic (many- shaped). The shape of a bacterium is determined by its rigid cell wall. The microscopic appearance of a bacterium is one of the most important criteria used in its identification. In addition to their characteristic shapes, the arrangement of bacteria is important. For example: a. certain cocci occur in pairs (diplococci), b. some in chains (streptococci), and c. others in grapelike clusters (staphylococci). These arrangements are determined by the orientation and degree of attachment of the bacteria at the time of cell division. 4 |Prepared by MMANALANG [email protected]  BSEd (Sci) SESE 116: Microbiology & Parasitology Course Content (Lecture Notes) 5 |Prepared by MMANALANG [email protected]  BSEd (Sci) SESE 116: Microbiology & Parasitology Course Content (Lecture Notes) 6 |Prepared by MMANALANG [email protected]  BSEd (Sci) SESE 116: Microbiology & Parasitology Course Content (Lecture Notes) 2. Anatomical & Physiological Features a. Presence or absence of capsule Capsulate (with capsule) e.g. Streprococcus pneumoniae Non-capsulate (without capsule) e.g.Viridans streptococci b. Presence or absence of flagella Flagellate (with one flagellum or more flagella) e.g. Vibrio cholerae Aflagellate (without flagellum) e.g. Shigella spp. c. Spore-forming or not Spore-forming (forms spore) e.g. Bacillus spp. Non-spore forming (does not form spore) e.g. Escherichia coli d. Ability to grow in the presence or absence of oxygen Aerobic (requires oxygen for survival) e.g. Pseudomonas aeruginosa Anaerobic (do not live or grow when oxygen is present) e.g. clostridium botulinum e. Nutrition Autotroph (able to synthesize their own food from light or chemical reactions) e.g. Chlorobiaceae (green sulfur bacteria) Heterotroph (live by consumption of biomass or nonliving organic matter) e.g. Pseudomonas, Salmonella, Escherichia, Rhizobium 3. Habitat/Living Environment Mesophiles (Grow in moderate or regular environmental conditions) e.g. Staphylococcus aureus Extremophiles (tolerant to environmental extremes and that has evolved to grow optimally under one or more of these extreme conditions. Includes acidophiles, methanogens, thermophiles, halophiles) e.g. Alicyclobacillus tolerans. 7 |Prepared by MMANALANG [email protected]  BSEd (Sci) SESE 116: Microbiology & Parasitology Course Content (Lecture Notes) 4. Staining characteristics a. Gram stain Gram positive, e.g. Staphylococcus aureus Gram negative, e.g. Escherichia coli b. Acid fast stain Acid fast positive Acid fast negative ACID FAST BACTERIA NON ACID FAST BACTERIA Resist decolorizing by acid after Readily decolorized bay acid staining after staining Final color is pink or red Final color is blue Consist of mycolic acid in their Does not consist of mycolic acid cell wall in their cell wall 8 |Prepared by MMANALANG [email protected]  BSEd (Sci) SESE 116: Microbiology & Parasitology Course Content (Lecture Notes) 5. Pathogenicity a. Pathogenic (causes and spreads diseases) e.g. Vibrio cholerae b. Nonpathogenic (does not cause or spread disease) e.g. Lactobacillus acidophilus **NOTE: The criterion currently used now is the base sequence of the genome DNA. Several bacteria have been reclassified on the basis of this information. Using these criteria, along with various biochemical reactions, many bacteria can be readily classified into separate genus and species. However, there have been several examples of these criteria placing bacteria into the same genus when DNA sequencing of their genome reveals they are significantly different and should be classified in a new or different genus. For example, an organism formerly known as Pseudomonas cepacia has been reclassified as Burkholderia cepacia because the base sequence of its DNA was found to be significantly different from the DNA of the members of the genus Pseudomonas. Bacterial Reproduction Bacteria have only one copy of their genome DNA (i.e., they are haploid). In contrast, eukaryotic cells have two copies of their genome DNA (i.e., they are diploid). Bacterial DNA is circular; human nuclear DNA is linear. Bacteria reproduce by binary fission. It is a type of asexual reproduction by a separation of the body into two new bodies. In the process of binary fission, an organism duplicates its genetic material, or deoxyribonucleic acid (DNA), and then divides into two parts (cytokinesis), with each new organism receiving one copy of DNA. Bacteria are among the fastest reproducing organisms in the world, doubling every 4 to 20 minutes. Bacterial Growth Cycle The bacterial growth cycle consists of four phases: a. the lag phase, during which nutrients are incorporated; b. the log phase, during which rapid cell division occurs; c. the stationary phase, during which as many cells are dying as are being formed; and d. the death phase, during which most of the cells are dying because nutrients have been exhausted. 9 |Prepared by MMANALANG [email protected]  BSEd (Sci) SESE 116: Microbiology & Parasitology Course Content (Lecture Notes) Genetic Variation in Bacteria Bacteria reproduce by splitting in two via binary fission. Binary fission makes clones, or genetically identical copies, of the parent bacterium. Since the "child" bacteria are genetically identical to the parent, binary fission does not provide an opportunity for genetic recombination or genetic diversity (aside from the occasional random mutation). This contrasts with sexual reproduction. Still, genetic variation is key to the survival of a species, allowing groups to adapt to changes in their environment by natural selection. That is true for bacteria as well as plants and animals. So it is not too surprising that prokaryotes can share genes by three other mechanisms: conjugation, transformation, and transduction. a. Transformation In transformation, a bacterium takes in DNA from its environment, often DNA that is been shed by other bacteria. In a laboratory, the DNA may be introduced by scientists. If the DNA is in the form of a circular DNA called a plasmid, it can be copied in the receiving cell and passed on to its descendants. Image modified from "Conjugation," by Adenosine (CC BY-SA 3.0). 10 |Prepared by MMANALANG [email protected]  BSEd (Sci) SESE 116: Microbiology & Parasitology Course Content (Lecture Notes) Why would this be important? Imagine that a harmless bacterium takes up DNA for a toxin gene from a pathogenic (disease-causing) species of bacterium. If the receiving cell incorporates the new DNA into its own chromosome (which can happen by a process called homologous recombination), it too may become pathogenic. b. Transduction In transduction, viruses that infect bacteria move short pieces of chromosomal DNA from one bacterium to another "by accident." Even bacteria can get a virus. The viruses that infect bacteria are called bacteriophages. Bacteriophages, like other viruses, are the pirates of the biological world. They take over a cell's resources and use them to make more bacteriophages. Sometimes, chunks of host cell DNA get caught inside the new bacteriophage as they are made. When one of these "defective" bacteriophages infects a cell, it transfers the DNA. Some bacteriophages chop the DNA of their host cell into pieces, making this transfer process more likely11start superscript, 1, end superscript. Image modified from "Conjugation," by Adenosine (CC BY-SA 3.0). The modified image is licensed under a CC BY-SA 3.0 Virus infects cell by injecting its DNA. Bacterial DNA is fragmented and viral DNA is replicated. New viral particles are made and exit the cell. One contains host DNA instead of viral DNA. When this virus infects a new host, it injects the bacterial DNA, which can recombine with the chromosome of the new host. Archaea, the other group of prokaryotes besides bacteria, are not infected by bacteriophages but have their own viruses that move genetic material from one individual to another. c. Conjugation In conjugation, DNA is transferred from one bacterium to another. After the donor cell pulls itself close to the recipient using a structure called a pilus, DNA is transferred between cells. In most cases, this DNA is in the form of a plasmid. 11 |Prepared by MMANALANG [email protected]  BSEd (Sci) SESE 116: Microbiology & Parasitology Course Content (Lecture Notes) Image modified from "Conjugation," by Adenosine (CC BY-SA 3.0). The modified image is licensed under a CC BY-SA 3.0 Donor cells typically act as donors because they have a chunk of DNA called the fertility factor (or F factor). This chunk of DNA codes for the proteins that make up the sex pilus. SUMMARY: B. Pathogenicity Pathogenicity is an organism’s potential ability to produce disease. A bacterium can cause disease by: a. destroying tissue (invasiveness) 12 |Prepared by MMANALANG [email protected]  BSEd (Sci) SESE 116: Microbiology & Parasitology Course Content (Lecture Notes) b. producing toxins (toxigenicity) c. stimulating overwhelming host immune response (e.g. increase in white blood cells, inflammation, fever) Here are some examples of pathogenic bacteria. Disease Description Bacterial Pathogen Disease Transmission Anthrax Fever, severe Bacillus anthracis Inhalation of spores difficulty in breathing Bubonic plague Fever, bleeding, Yersinia pestis Bite of an infected swelling lymph flea nodes, often fatal Cholera Severe diarrhea, Vibrio cholerae Drinking vomiting, fatal if contaminated not treated water Dental caries Destruction of Streptococcus Dense collections of tooth minerals mutans oral bacteria Lyme disease Rash, pain, Borrelia burgdorferi Bite of an infected swelling of joints tick Tuberculosis Fever, difficulty Mycobacterium inhalation breathing Typhus Headache, fever Rickettsia Bite of infected flea or louse 13 |Prepared by MMANALANG [email protected]  BSEd (Sci) SESE 116: Microbiology & Parasitology Course Content (Lecture Notes) C. Source and Mode of Transmission Sources of Bacteria Bacteria can be found just about every surface including the human body. In humans, normal flora are those microorganisms that are the permanent residents of the body that everyone has. Some people can be colonized, either transiently or for long periods, with certain organisms, but those are not considered members of the normal flora. Carriers (also called chronic carriers) are those individuals in whom pathogenic organisms are present in significant numbers and therefore are a source of infection for others. Normal flora organisms inhabit the body surfaces exposed to the environment, such as the skin, oropharynx, intestinal tract, and vagina. Members of the normal flora differ in number and kind at various anatomic sites. Members of the normal flora are low-virulence organisms. In their usual anatomic site, they are nonpathogenic. However, if they leave their usual anatomic site, especially in an immunocompromised individual, they can cause disease. Members of the Human Normal Bacterial Flora 1. Skin. The predominant member of the normal flora of the skin is S. epidermidis. It is an important cause of infections of prosthetic heart valves and prosthetic joints. S. aureus is also present on the skin, but its main site is in the nose. It causes abscesses in the skin and in many other organs. 2. Oropharynx. The main members of the normal flora of the mouth and throat are the viridans streptococci, such as S. sanguinis and S. mutans. Viridans streptococci are the most common cause of subacute endocarditis. 3. Gastrointestinal tract. The stomach contains very few organisms because of the low pH. The colon contains the largest number of normal flora and the most diverse species, including both anaerobic and facultative bacteria. There are both gram-positive and gram-negative rods and cocci. The members of the colonic normal flora are an important cause of disease outside of the colon. The two most common members of the colonic flora that cause disease are the anaerobe B. fragilis and the facultative E. coli. E. faecalis, a facultative, is also a common pathogen. 4. Vagina. Lactobacilli are the predominant normal flora organisms in the vagina. They keep the pH of the vagina low, which inhibits the growth of organisms such as C. albicans, a cause of vaginitis. 5. Urethra. The outer third of the urethra contains a mixture of bacteria, primarily S. epidermidis. The female urethra can become colonized with fecal flora such as E. coli, which predisposes to urinary tract infections. 14 |Prepared by MMANALANG [email protected]  BSEd (Sci) SESE 116: Microbiology & Parasitology Course Content (Lecture Notes) Bacterial Transmission Most bacterial infections are communicable (i.e., capable of spreading from person to person), but some are not (e.g., botulism and Legionella pneumonia). Modes of Transmission 1. Human-to-human Human-to-human transmission can occur either by direct contact or indirectly via a vector such as an insect, notably ticks or mosquitoes. 2. Nonhuman-to-human Nonhuman sources include animals, soil, water, and food. Animal-to- human transmission can also occur either by direct contact with the animal 15 |Prepared by MMANALANG [email protected]  BSEd (Sci) SESE 116: Microbiology & Parasitology Course Content (Lecture Notes) or indirectly via a vector. The main “portals of entry” into the body are the respiratory tract, gastrointestinal tract, skin, and genital tract. Human diseases for which animals are the reservoir are called zoonosis. Bacteria are transmitted because of their ability to: 1. Adhere to cell surfaces Pili are the main mechanism by which bacteria adhere to human cells. They are fibers that extend from the surface of bacteria that mediate attachment to specific receptors on cells. Glycocalyx is a polysaccharide “slime layer” secreted by some strains of bacteria that mediates strong adherence to certain structures such as heart valves, prosthetic implants, and catheters. 2. Secrete enzymes Bacterial enzymes degrade barriers in the subcutaneous tissue and mucous membranes, allowing the organism to spread rapidly. 3. Intracellular survival This is a process by which bacteria can evade the host defenses (i.e., bacteria that can live within cells are protected from attack by macrophages and neutrophils). Note that many of these bacteria (e.g., M. tuberculosis) are not obligate intracellular parasites (which can grow only within cells), but rather have the ability to enter and survive inside cells. Summary: D. Impact and Applications of Bacteria to Human Health and the Environment In bacteria, reproduction can be very fast, with a generation taking little more than a few minutes for some species. This short generation time, together with random mutations and the mechanisms of genetic recombination allow bacteria (and other prokaryotes) to evolve very quickly. Is that a good thing? It depends on your perspective. Rapid evolution means that bacteria can adapt to environmental changes, such as the introduction of an antibiotic, very quickly. That is good for them—but bad for other organism in instances where they are considered to be pathogenic. 16 |Prepared by MMANALANG [email protected]  BSEd (Sci) SESE 116: Microbiology & Parasitology Course Content (Lecture Notes) Negative Impacts: 1. They cause of disease or even death in humans, animals and crop plants. 2. They are agents of spoilage and decomposition of foods, textiles and dwellings. Positive Impacts: 1. CO2 Fixation. Photosynthetic organisms which take up CO2 in the atmosphere and convert it to organic (cellular) material. Unicellular organisms like cyanobacteria, which float in the ocean are the "grass of the sea", and they are the source of carbon from which marine life is derived. 2. Decomposition or biodegradation. Bacteria can help in the breakdown of complex organic materials to forms of carbon that can be used by other organisms. 3. Nitrogen fixation. This is a process found only in some bacteria (Rhizobium) which removes N2 from the atmosphere and converts it to ammonia (NH3), for use by plants and animals. Nitrogen fixation also results in replenishment of soil nitrogen removed by agricultural processes. Some bacteria fix nitrogen in symbiotic associations in plants. Other Nitrogen-fixing bacteria are free-living in soil and aquatic habitats. 4. Production of Oxygen. Photosynthesis occurs not only in plants, but in microorganisms like algae and cyanobacteria. Photosynthesis results in the production of O2 in the atmosphere. At least 50 percent of the O2 on earth is produced by photosynthetic microorganisms (algae and cyanobacteria like Synechococcus), and for at least a billion years before plants evolved, microbes were the only organisms producing O2 on earth. 5. Symbiosis with Animals and Plants. The microbes that normally live in associations with humans on the various surfaces of the body (called the normal flora), such as Lactobacillus and Bifidobacterium, are known to protect their hosts from infections, and otherwise promote nutrition and health. Microbes in the rumen (forestomach) of cows, sheep and other ruminant animals are responsible for the initial digestion of nutrients (primarily cellulose), and they provide not only a source of carbon for their host, but also a source of protein and vitamins. Lactobacillus acidophilus and a vaginal squamous epithelial cell. CDC. L. acidophilus (informally known as Doderlein's bacillus) colonizes the vagina during child-bearing years. As a lactic acid bacterium, the organism creates a low pH (acidic environment) on the tissues which prevents colonization by potentially harmful yeast and other bacteria. 6. Production of Foods and Fuels. In the home and in industry, microbes are used in the production of fermented foods. Yeasts are used in the manufacture of beer and wine and for the leavening of breads, while lactic acid bacteria are used to make yogurt, cheese, sour cream, buttermilk and other fermented milk products. Vinegars are produced by bacterial acetic acid fermentation. The main species responsible for the production of vinegar 17 |Prepared by MMANALANG [email protected]  BSEd (Sci) SESE 116: Microbiology & Parasitology Course Content (Lecture Notes) belong to the genera Acetobacter, Gluconacetobacter, Gluconobacter and Komagataeibacter. 7. Medical, Pharmaceutical and Biotechnological Applications In human and veterinary medicine, for the treatment and prevention of infectious diseases, microbes are a source of antibiotics and vaccines. Antibiotics are substances produced by microorganisms that kill or inhibit other microbes which are used in the treatment of infectious disease. Antibiotics are produced in nature by molds such as Penicillium and bacteria such as Streptomyces and Bacillus. Vaccines are substances derived from microorganisms used to immunize against disease. The microbes that are the cause of infectious disease are usually the ultimate source of vaccines. Thus, a version of the diphtheria toxin (called toxoid) is used to immunize against diphtheria, and parts of Bordetella pertussis cells are used to vaccinate against pertussis (whooping cough). Microbiology makes an important contribution to biotechnology, an area of science that applies microbial genetics to biological processes for the production of useful substances. Microorganisms play a central role in recombinant DNA technology and genetic engineering. Important tools of biotechnology are microbial cells, microbial genes and microbial enzymes. The genetic information for many biological products and biological processes can be introduced into microbes in order to genetically engineer them to produce a substance or conduct a process. The genes can come from any biological source: human, animal, plant or microbial. This opens the possibility for microbial production of foods, fuels, enzymes, hormones, diagnostic agents, medicines, antibiotics, vaccines, antibodies, natural insecticides and fertilizers, and all sorts of substances useful in our civilization and society. 8. Bioremediation. This involves the use of microorganisms like bacteria to degrade pollutants. Microbial decomposition of petroleum products by hydrocarbon-oxidizing bacteria and fungi is of considerable ecological importance. The microbial decomposition of petroleum is an aerobic process, which is prevented if the oil settles to the layer of anaerobic sediment at the bottom (natural oil deposits in anaerobic environments are millions of years old). Hydrocarbon-oxidizing bacteria attach to floating oil droplets on the water surface, where their action eventually decomposes the oil to carbon dioxide. 2 Worksheets/Laboratory or Learning Activities 1 SUMMATIVE TEST 18 |Prepared by MMANALANG [email protected]