General Microbiology and Immunology Lecture Notes PDF

General Microbiology and Immunology Dr/ Hend Zeitoun M.Sc.,Ph.D. Lecturer of Microbiology and Immunology Faculty of Pharmacy, Alexandria University What is Microbiology? Micro - too small to be seen with the naked eye, Bio – life, ology - study of. “The s...

General Microbiology and Immunology Dr/ Hend Zeitoun M.Sc.,Ph.D. Lecturer of Microbiology and Immunology Faculty of Pharmacy, Alexandria University What is Microbiology? Micro - too small to be seen with the naked eye, Bio – life, ology - study of. “The study of microbiology is the study of microorganisms, which are organisms that are invisible to the naked eye, usually less than 1mm in diameter” Why should I study Microbiology? Microorganisms exist everywhere! - Bacteria occur in almost every environment on Earth, from the bottom of the ocean floor, deep inside solid rock, on your skin, hair, oral cavity, and gastrointestinal tract. In our body, they outnumber our cells by more than 10:1! Yet, we’re barely aware that they exist. We become aware when we become sick or notice spoiled or damaged goods. Less than 0.01% of bacteria cause disease. Most are beneficial to man and other life forms. Why should I study Microbiology? 1. Impact on Human Health. 2. Balance of Nature - food source, play a role in decomposition, help other animals digest grass (cattle, sheep, termites). 3. Environmental – provide safe drinking water; development of biodegradable products; use bacteria to clean up oil spills, etc. – called bioremediation. 4. Industrial – foodstuffs (beer, wine, cheese, youghurt, bread), antibiotics, insulin, genetic engineering. 5. Agricultural - research has led to healthier livestock and disease-free crops. The overwhelming majority of microbes are beneficial to mankind! Microorganisms aid in: Environmental recycling and Bioremediation Mining Agriculture Human health Biotechnology Food/beverage industry Microbes and Human Disease Although many microorganisms are beneficial, many others are the cause of infectious diseases. Microbiota / Normal flora. Microbes normally present in and on the human body are called normal microbiota. Normal microbiota prevent growth of pathogens. Produce growth factors such as folic acid and vitamin K.  Beneficial Microorganisms 1. Microorganisms as decomposers. Microorganisms degrade dead plants and animals and recycle chemical elements to be used by living plants and animals. For examples, bacteria are used to decompose organic matter in sewage and microbes decompose food into simple molecules. 2. Microorganisms and the food industry Dairy Product (cheese, yogurt, yogurt drinks) Baked goods Alcoholic beverages & Vinegar Branches of Microbiology By Taxonomy Bacteriology: the study of bacteria. Virology: the study of viruses. Mycology: the study of fungi. Parasitology: the study of parasites. Not all parasites are microorganisms, but many are. Nematology: the study of nematodes (roundworms). Protozoology: the study of protozoa, single-celled organisms like amoebae. Immunology: the study of the immune system. It looks at the relationships between pathogens such as bacteria and viruses and their hosts. Phycology: the study of algae. By Type of Research Pharmaceutical microbiology: the study of microorganisms used in pharmaceutical products, such as vaccines and antibiotics. Medical microbiology: the study of microorganisms responsible for human disease. Microbial biotechnology: using microbes in industrial or consumer products. Food microbiology: the study of microorganisms that spoil food or cause foodborne illnesses. Can also study microorganisms used in food production. Agricultural microbiology: the study of microorganisms that interact with plants and soils.  Microbial Morphology: The detailed structure of microorganisms. Microbial Physiology: Microbial function (metabolism) at the cellular and molecular levels. Microbial Taxonomy: Classification, naming, and identification of microorganisms. Microbial Genetics (Molecular Biology): The function of genetic material and the biochemical reactions of cells involved in metabolism and growth. Microbial Ecology: Interrelationships between microbes and the environment; the roles of microorganisms in the nutrient cycles of soil, water, and other natural communities. Genetic engineering and recombinant DNA technology: Involve techniques that deliberately alter the genetic makeup of organisms.  Bioinformatics: is an interdisciplinary field that develops methods and software tools for understanding biological data. Bioremediation: The processing of industrial waste by genetically modified microorganisms to generate a less toxic end products. Genomics is an interdisciplinary field of biology focusing on the structure, function, evolution, mapping, and editing of genomes. Proteomics is the large-scale study of proteins Metabolomics is the scientific study of chemical processes involving metabolites, the small molecule substrates, intermediates and products of metabolism.  Microbes & You Normal microbiota (less commonly referred to as normal flora) The microorganisms that establish more or less permanent residence (colonize) but that do not produce disease under normal conditions are members of the body’s normal microbiota (10 times more bacterial cells than human cells). Bacteria make up most of it. After birth, E. coli and other bacteria acquired from foods begin to inhabit the large intestine. What is a pathogen? An organism capable of colonizing a host where the interaction results in disease. Opportunistic Pathogens (part-time bad guys) Strict Pathogens (full-time bad guys) Opportunistic pathogens - Most of infections are due to opportunistic pathogens. - Normal microbiota for causing disease. - No disease in normal setting but disease when introduced into unprotected sites (e.g. blood, tissues). - Immunocompromised patients are more susceptible. Staphylococcus aureus Escherichia coli Strict pathogens - A few infections Mycobacterium tuberculosis (tuberculosis) Neisseria gonorrhoeae (gonorrhea)  Types of symbiotic microbe-host relationships Mutualism * Commensalism * Parasitism What are the benefits of normal flora? Benefit to the bacteria: they have a place to survive and multiply. Benefits to the human: Bacteria may produce vitamins (such as B and K), and break down food that host can not normally digest. Normal flora protect host against infection by pathogenic organisms: - take up space, so pathogen has nowhere to occupy and multiply. - may out-compete the invader for available nutrients. - may produce anti-bacterial chemicals (bacteriocins). Types of symbiotic microbe-host relationships Mutualism * Commensalism * Parasitism - One partner in the relationship Pathogens harm their host. benefits. The other neither Cost to the host can vary from benefits nor is harmed. slight to fatal. External parasites (ectoparasite) cause infestation. Internal parasites (endoparasite) cause infection.  Nomenclature of Microorganisms “father” of modern taxonomy” Carolus Linnaeus established the system of scientific nomenclature in 1735. Each organism has two names Binomial nomenclature: Genus + species Italicized (or underlined), genus capitalized, “latinized”, used worldwide. The genus designation can be replaced with an initial if the complete genus name has been used recently. For example, the bacterium Staphylococcus aureus becomes S. aureus. All eukaryotes & prokaryotes are named this way. Viruses are not!  Nomenclature of Microorganisms S. aureus E. coli Staphylococcus aureus (S. aureus); Staphylo- describes the clustered arrangement of the cells; -coccus indicates that they are shaped like spheres, ‘aureus’ is Latin for golden the color of many colonies. Escherichia coli (E. coli); The genus is named for a scientist, Theodor Escherich, whereas its species ‘coli’ reminds us that E. coli live in the colon. Diversity of Microbes Diversity of Microbes The Microbial diversity is defined as the variability among microorganisms. Bacteria-single celled prokaryotes Archeae- primitive, adapted to extreme habitats and modes of nutrition. Protozoa- eukaryotic, single celled, colonial, many ways of nutrition. Fungi-single celled or filamentous. Viruses-acellular entities. Algae- Others- worms, insects. Microbes can be: Cellular -Cytoplasmic membrane is present -Divided into prokaryotes and eukaryotes Acellular -Lacking cytoplasmic membrane or any cellular organization (viruses, viroids and prions). -Cannot be seen by light microscope, but only using an electron microscope. Prokaryotes and Eukaryotes Excluding the viruses, there are two types of microorganisms: Prokaryotes, which are small and lack a nucleus and organelles, and Eukaryotes, which are larger and have both a nucleus and organelles Viruses are not cellular and are therefore called particles rather than organisms. They are included in microbiology because of their small size and close relationship with cells. Prokaryotes and Eukaryotes Prokaryotes and Eukaryotes Prokaryotic Cells Eukaryotic cells small cells (< 5 mm) larger cells (> 10 mm) always unicellular often multicellular Chromosome found in a cytoplasmic Chromosomes found in a membrane- region called the nucleoid bound nucleus and have other membrane-bound organelles Single circular chromosome Multiple linear chromosomes ribosomes are small (70S) ribosomes are large (80S) no cytoskeleton always has a cytoskeleton cell division is by binary fission cell division is by mitosis or meiosis reproduction is always asexual reproduction is asexual or sexual Evolutionary time line Classification of Microorganisms  No single classification system is completely accepted by all biologists, but one of the most widely accepted is the five-kingdom system. Five Kingdoms (1969) Prokaryotae (Monera) Protista Fungae Plantae Animalia Based on: Morphology Metabolism (Biochemical Activity) Molecular Techniques Fatty Acid Profiles Protein Differentiation DNA Finger Printing Classification of Microorganisms Comparing the sequences of nucleotides in ribosomal 16S rRNA from different kinds of cells shows that there are three distinctly different cell groups: the eukaryotes and two different types of prokaryotes—the bacteria and the archaea. In 1990, Carl R. Woese proposed elevating the three cell types to a level above kingdom, called domain. He believed that the archaea and the bacteria, although similar in appearance, should form their own separate domains on the evolutionary tree. In addition to differences in rRNA, the three domains differ in membrane lipid structure, transfer RNA molecules, and sensitivity to antibiotics. Classification of Microorganisms  Woese-Fox Classification The three-domain system, which classifies life on the planet into three different domains - Archaea, Bacteria and Eukaryote, was put forth by American microbiologist and physicist Carl Woese in 1990. It is based on the differences in their 16S rRNA genes. The domain Eukarya contains all those kingdoms of eukaryotic organism (animals, plants, fungi, and protists). The traditional kingdom Monera has been divided into 2 domains: the domain Eubacteria (true bacteria ) and the domain Archaeabacteria. The bacteria of interest in pharmacy and medicine belong to the group known as the eubacteria (true bacteria). The other subdivision of prokaryotes, the archaea, have little or no pharmaceutical importance and largely comprise organisms capable of living in extreme environments. Woese-Fox Classification “The Archaea exhibit many differences from the Bacteria: ¨ Different cell membrane structure¨ Cell wall present, but not composed of peptidoglycan¨ First amino acid in proteins not methionine like in other bacteria and eukaryotes¨ DNA Contains histone-like proteins similar to eukaryotes (true bacteria have no histone proteins)¨ Live in only extreme environments (groups include extreme halophiles, extreme thermoacidophiles, and methanogens). 1. Microscopic morphology 2. Macroscopic morphology – colony appearance 3. Physiological / biochemical characteristics 4. Chemical analysis 5. Serological analysis 6. Genetic and molecular analysis G + C base composition DNA analysis using genetic probes Nucleic acid sequencing and rRNA analysis Classification of Bacteria *Kingdom Phylum Kingdom: Bacteria Class Phylum: Firmicutes Order Class: Cocci Family Order: Bacillales *Genus ( 1st name) Family: Staphylococcaceae *Species ( 2nd name identifier) Genus: Staphylococcus Species: S. aureus Remember: King Philip Came Over For Good Spaghetti The Staphylococcus genus includes at least 40 species, some of these can have two or three subspecies.  Species –a collection of bacterial cells which share an overall similar pattern of traits in contrast to other bacteria whose pattern differs significantly Strain or variety – a culture derived from a single parent that differs in structure or metabolism from other cultures of that species (biovars, morphovars) Type – a subspecies that can show differences in antigenic makeup (serotype or serovar), susceptibility to bacterial viruses (phage type) and in pathogenicity (pathotype) Classification of Bacteria Domain Bacteria – (main phyla…) Phylum Proteobacteria – Gram-negative cell walls Phylum Firmicutes – mainly Gram-positive with low G + C content Phylum Actinobacteria – Gram-positive with high G + C content. Phylum Spirochetes Phylum Cyanobacteria – Photosynthetic bacteria Phylum Chlamydiae 35 Eubacteria Diversity Chlamydias Spirochetes Actinobacteria Photosynthetic Bacteria Proteobacteria Gram-Positive Bacteria Classification of Microorganisms  1- Protozoa The Protozoa: These are unicellular eukaryotic organisms, larger than bacteria. The most important groups of medical protozoa are: A- Amoeba: Entamoeba species. Amebic dysentery B- Mastigophora: Gastrointestinal flagellates: Giardia intestinalis Urogenital flagellates: Trichomonas vaginalis C- Ciliophora: D- Sporozoa: intracellular infection. Example: Plasmodium that cause Malaria.  2- Fungi These are saprophytic or parasitic Eukaryotic organisms possessing relatively rigid cell walls. (Chitin) Medical fungi can be divided into: 1- Mold: Branching filaments; hyphae, mycelium. Example: Aspergillus. 2- True Yeasts: Ovoid or spherical cells that reproduce asexually by budding and sexually with formation of spores. Example : Cryptococcus spp. 3- Dimorphic fungi: Produce a vegetative mycelium in artificial media, but are yeast like in infected lesions. Example: Histoplasma. 4- Yeast- like fungi: Example: Candida (Pseudomycelium).  Algae are unicellular or multicellular eukaryotes that obtain nourishment by photosynthesis. Cellulose cell walls Algae produce oxygen and carbohydrates that are used by other organisms.  4- Viruses Viruses consist of DNA or RNA enclosed in a simple protein shell known as a capsid. General properties of viruses They are very small in size, from 20-300 m. Viruses consist of a nucleic acid core (RNA or DNA) surrounded by a protein coat (Capsid) An envelope may surround the coat. They are obligate intracellular parasites. They are only seen by electron microscope. Depend on the parasitized cell for survival and multiplication Illnesses caused by viruses; Colds, Influenza, Hepatitis, Warts.