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Microbiology & parasitology ❁ SEMESTER 1 PRELIMS | PCBIO105L | IARABANO...

Microbiology & parasitology ❁ SEMESTER 1 PRELIMS | PCBIO105L | IARABANO SY. 2024-2025 rr Between 1674-1723 he wrote series of papers M1: HISTORY AND SCOPE OF MICROBIOLOGY describing his observations of bacteria, algae, protozoa, and fungi (Animalcules) MICROBIOLOGY The study of living things too small to be seen ORIGIN OF LIFE without magnification The theory of Spontaneous Generation Microorganisms or microbes Living organisms develop from nonliving matter Commonly called “germs, viruses, agents” Early belief that some forms of life could arise from “vital forces” present in non living PARASITOLOGY abiogenesis. In other words, living organisms The scientific discipline concerned with the study can arise from non-living matter of the biology of parasites, parasitic diseases, According to Aristotle, it was: and the interaction between parasites and their Readily observable that aphids arise from the hosts dew which falls on plants, fleas from putrid matter, mice from dirty hay” L1: HISTORY OF MICROBIOLOGY This belief remained unchallenged for more that 2000 EARLY OBSERVATIONS ON INFECTIOUS years DISEASES - Challenged in the 17th and 18th centuries Punishment of God, witch curse, and bad air 17th - 18th century: Experiments on the abiogenesis 1546 - Girolamo Fracastoro theory Proposed the theory of contagious diseases Tiny, free-living organisms called “seeds of 1668 - Francesco Redi diseases existed in nature” One of the first to formally challenge the Proposed: Diseases-causing organisms could accepted belief of spontaneous generation be transmitted from person-to-person or fomite Disprove the idea that maggots spontaneously intermediaries = contagion generate on meat left out in the open air 💡 Although the existence of creatures too small to be seen with the naked eye had been suspected for Redi’s experiment - Question: where do maggots come from? centuries, their discovery has to await the invention of - Hypothesis: maggots come from flies the microscope. - Experiment: Redi put meat into three separate jars 1665 - Robert Hooke Invented the first microscope - Zacharias Jansen He concluded that maggots could only form Robert Hooke was among the first to make when flies were allowed to lay eggs in the meat, significant improvements to the basic design and that the maggots were the offspring of flies, - Discovered the cell (honeycomb-like not the product of spontaneous generation. structures) - Stated that life’s smallest structural units 1745 - John Needham were cells Briefly boiled broth infused with plant or animal matter, hoping to kill all preexisting microbes then sealed the flasks later on 💡 In his famous book Micrographia (1665), the first book devoted to microscopic observations, Hooke illustrated After a few days, Needham observed that the broth had become cloudy and a single drop the fruiting structures of molds. contained numerous microscopic creatures His conclusion: new microbes arisen 1674 - Anton van Leeuwenhoek spontaneously First to observe bacteria and protozoa or “little animals” using his newly developed microscope 1765 - Lazzaro Spallanzani First to observe living microbes Did not agree with Needham’s conclusions His single-lens magnified 50-300x magnification 1  Microbiology & parasitology ❁ SEMESTER 1 PRELIMS | PCBIO105L | IARABANO SY. 2024-2025 rr Experimented broth in sealed and unsealed jars theory of disease, and eventually, to his work on infused with plant and animal matter vaccinations. Findings: - Heated but sealed flasks - clear (no sign of spontaneous growth) unless flask id SPONTANEOUS GENERATION opened to the air Louis Pasteur Theory of biogenesis - Debate on spontaneous generation - French Academy of Sciences offered Needham: argued that life originates from a “life force” monetary prize in 1862 to provide that was destroyed during Spallanzani’s extended boiling definitive evidence to either prove or disprove the concept of spontaneous GOLDEN AGE OF MICROBIOLOGY generation Major advances in microbiology were made in the 19th century: Disproving the abiogenesis theory nineteenth century because of the interest in two major 1858 - Louis Pasteur questions - Discredited the “Theory of spontaneous 1. Does spontaneous generation occur? generation” 2. What is the nature of infectious disease - Conclusively settled the dispute about spontaneous generation: spontaneous Louis Pasteur generation theory was incorrect and French chemist biogenesis theory is correct Initial work of Pasteur was on fermentation - He did so by preventing “dust particles” Showed that fermentation and yeast from reaching the sterile broth multiplication occur in parallel - Showed microbes caused by Fermentation is a consequence of the yeast fermentation and spoilage multiplication and the yeast have to be alive for alcohol to be produced Pasteur’s other contribution 1856 - Problem of Pasteur’s student: Alcohol The phenomenon of laboratory attenuation of from beetroot fermentation was rather sour microorganisms and developing targeted - Contained substantial amount of lactic vaccines acid instead of alcohol 1879 - Pasteur observed that after serial - Container with lactic acid had much passage, the chicken cholera bacillus (now smaller cells than yeast Pasteurella spp.) lost the capacity to cause lethality when injected to chickens 💡 - Artificial attenuation Pasteur’s finding showed that there are two types of In 1881, developed vaccine against anthrax and fermentation: alcoholic and lactic acid. Alcoholic fermentation occurs by the action of yeast; lactic acid 1885 vaccine against rabies and TB fermentation, by the action of bacteria Joseph Lister 1867 Antiseptic Surgery (Carbolic acid- Phenol) Fermentation = forming alcohols from sugar Developed a system of surgery designed to Alcohol + contaminating bacteria = turns prevent microorganisms from entering fermentation sour wounds-phenol (carbolic acid) sprayed in air Killed certain living organisms “pasteurizing” around surgical incision substances Decreased number of post-operative infections - Pasteurization - heating liquids at high in patients his published findings (1867) temperatures for short amount of time transformed the practice of surgery killing harmful microbes - Sterilization - destruction of all bacteria Ferdinand Cohn Botanist 💡 This led to Pasteur’s thought that if germs were the cause of fermentation, they could also be the cause of Study of unicellular algae and bacteria Discovery of endospore contagious diseases. He began to develop his germ - Life cycle of endospore - Showed that they are resistant to boiling 2  Microbiology & parasitology ❁ SEMESTER 1 PRELIMS | PCBIO105L | IARABANO SY. 2024-2025 rr System of bacterial classification Other contributions of Robert Koch Use of cotton plug Developed pure culture methods, employed the use of oil immersion technique, developed IMPORTANT FINDINGS FROM THE INSTITUT staining techniques for bacterial identification PASTEUR Developed methods of cultivating bacteria in Charles Chamberland - Invented the autoclave; solid media developed Pasteurella vaccine Richard Petri, another Koch’s assistant, Alexandre Yersin - Co-discoverer of the plague developed the Petri dish bacillus Fannie Hesse, the wife of one of Koch’s Emile Roux - Discovered diphtheria toxin and assistants proposed using agar antitoxin - Not digested by most bacteria Jules Bordet - discovered whooping cough - Melts at 100ºC bacillus and complement system - Used today ~2% in solid media Ilya Metchnikoff - Discovered phagocytosis and Identified cause of tuberculosis (Mycobacterium provided the initial descriptions of innate tuberculosis) & cholera (Vibrio cholera) immunity - Basis of Koch’s postulate; set of criteria Albert Calmette - Discovered antivenin and to be satisfied to infer an etiological role developed the first effective tuberculosis for a specific bacterial disease vaccine; Bacille Clamette-Guerin (BCG) vaccine IMPORTANT FINDINGS FROM THE KOCH INSTITUTE THE GERM THEORY OF DISEASE 1. Paul Ehrlich - Co-discoverer of antibodies, antigens, and chemotherapy for infectious Microorganisms might cause disease diseases In 1876 Robert Koch proved the “germ theory of 2. Richard Pleiffer - Discovered bacterial disease” by showing that bacteria actually endotoxin, the phenomenon of bacteriolysis, and caused disease played a major role in the development of killed - Investigated the etiology of anthrax in typhoid vaccines sheep 3. Emil von Behring - Discoverer of serum - Identified anthrax bacilli in the blood of therapy for diphtheria and tetanus infected sheep and successfully 4. Shibasaburo Kitasato & Ssakahiro Hata - transmitted the injection into healthy Serum therapy and the discovery of salvarsan experimental animals for the treatment for syphilis, respectively - Discovered that Bacillus anthracis produces spores - Accurately describe the life cycle of OTHER IMPORTANT MILESTONES anthrax and process of endospore formation 1868 - Armauer Hansen demonstrated that Koch established a sequence of experimental certain rods represent the infectious origin of steps for directly relating a specific microbe to a leprosy specific disease called KOCH’S POSTULATES 1875 - Ferdinand Cohn published for the first time an early classification of bacteria using the KOCH’S POSTULATES genus name, Bacillus 1877 - John Tyndall published a method for 1. The causative (etiological) agent must be fractional sterilization and clarifies the role of present in all affected organisms but absent in heat resistant factors (spores) in putrefaction healthy individuals 1892 - Dmitri Ivanowski - The first evidence of 2. The agent must be capable of being isolated the filterability of a pathogenic agent, the virus of and cultured in pure form tobacco mosaic disease. Emergence of virology 3. When the cultured agent is introduced to a 1910 - Paul Ehrlich discovered the cure for healthy organism, the same disease must occur syphilis (salvarsan), the first specific 4. The same causative agent must be isolated chemotherapeutic agent for a disease caused by again from the affected host a bacterium. 3  Microbiology & parasitology ❁ SEMESTER 1 PRELIMS | PCBIO105L | IARABANO SY. 2024-2025 rr 1915 - William Twort - Discovered microorganisms (ii) the impact of in situ bacteriophage conditions on community structure or (iii) the 1917 - Felix d’Herelle - Discovered the effect of changes in microbial community or bacteriophage’s capacity to kill bacteria composition on ecosystem function 1928 - Frederick Griffith - Discovered bacterial d. Molecular Microbiology - Covers genetic transformation and this established the organization, expression, mutation, and repair in foundation of molecular genetics organisms with environmental or practical 1929 - Alexander Fleming published the effects significance of penicillin on Gram positive organisms Sub branches according on the basis of Integrative 1946 - the process of conjugation in bacteria characteristics was discovered - Microbial cytology 1993 - The process of Polymerase Chain - Microbial taxonomy Reaction by Kary Mullis - Cellular microbiology L2:SCOPE OF MICROBIOLOGY APPLIED MICROBIOLOGY Two major fields of Microbiology Sub branches according on the basis of application Pure - theoretical study of organisms as the Medical Microbiology subject itself Veterinary Microbiology Applied - Application of microorganisms as in Public Health Microbiology specific processes Industrial Microbiology Pharmaceutical Microbiology Agriculture Microbiology TWO MAJOR FIELDS OF MICROBIOLOGY - Plant Microbiology PURE MICROBIOLOGY - Soil Microbiology Sub branches according to taxonomic classification Food and Dairy Microbiology - Bacteriology Environmental Microbiology - Mycology - Water/Aquatic Microbiology - Phycology - Aero-microbiology - Virology Vaccinology - Protozoology - Immunology SCOPE OF MICROBIOLOGY Sub branches according on the basis of Integrative ECOLOGY AND ENVIRONMENT characteristics a. Microbial physiology - Addresses questions Environmental Microbiology - Focuses on about how organisms adapt to changes in their ecological relationships, such as interactions environment, including bioenergetics, stress, among organisms, their structure and functional starvation, metabolic challenges, and responses role in an ecosystem, and community-level to nutritional variation studies b. Microbial genetics - Is the study of the Bacteria are primary decomposers - Recycle mechanisms of heritable information in nutrients back into the environment microorganisms. Microbial genetics provides Insect Pest Control: Some bacteria are used as powerful tools for deciphering the regulation, as pesticides to control insect pests. Eg. Bacillus well as the functional and pathway organization thuringiensis of cellular processes A natural spore-forming bacterium;toxic to - Mainly involves engineered microbes to lepidopteran insects make hormones, vaccines, antibiotics, Bioremediation: Microbes are also used to clean and many other useful products for up pollutants and toxic wastes. Eg. human beings. Pseudomonas putida; used to remove petroleum c. Microbial ecology - Covers a wide range of spills. topics on the ecology of microorganisms, including culture-independent molecular assessments that provide new insights into (i) structure-function relationships of 4  Microbiology & parasitology ❁ SEMESTER 1 PRELIMS | PCBIO105L | IARABANO SY. 2024-2025 rr FOOD MICROBIOLOGY INDUSTRIAL MICROBIOLOGY Include microbial food pathogens, microbial Microbes are used in economic and industrial ecology of foods, predictive food microbiology, purposes food fermentations, food spoilage, probiotics, Biotechnology, fermentation technology, food and prebiotics and beverages etc are not established on a Microbes are used in various food and dairy large industrial scale for income. industries to produce various food products - Cheese, pickles, sauerkraut, green AGRICULTURE MICROBIOLOGY olives Genetic engineering is used for the production of - Yogurt, soy sauce, vinegar, bread transgenic plants and animals - beer , wine, alcohol Animal and plant improvement by biotechnology for better production, resistant to environmental MEDICINE: CLINICAL AND PHARMACEUTICAL fluctuation MICROBIOLOGY Molecular farming: transgenic animal or plant Disease Treatment: Microbes are used to are used as bioreactor for mass production produce antibiotics Example: Penicillium notatum (Penicillin); GEOCHEMICAL MICROBIOLOGY discovered by Alexander Fleming (1928) Bacteria also synthesize vitamins which are Emphasizes the role of microorganisms in needed for our body. geochemical processes in terrestrial or aquatic Example: E. coli ecosystems, including subsurface, aquifer, and Vitamin-B; needed for metabolism oceanic environments Vitamin-K; needed for blood clotting Bioleaching: recovery of minerals from low Gene therapy for treatment of genetic diseases grade ores Role of microorganism in geochemical cycle VACCINE AND IMMUNOLOGY EXO MICROBIOLOGY / ASTRO MICROBIOLOGY Vaccine activates immune response Edward Jenner inoculated people with cowpox Exploring for life in outer space to protect against smallpox Pasteur developed the rabies vaccine (1885) APPLICATION OF MICROBIOLOGY Von Behring and Kitasato (1890) produced Extremophile archaea - Capable of surviving extreme toxoid vaccine against diphtheria and tetanus environmental conditions such as extreme climates, Metchnikoff (1884) described role of phagocytic extreme temperature conditions, extreme pH, and even cell in defense under radiation Restriction enzymes (RE) - RE functions as DNA GENETIC ENGINEERING scissors which recognizes and cuts the DNA sequence Microorganisms are used in Recombinant DNA at specific recognition sites technology or Genetic Engineering to Taq polymerase - A valuable tool in performing manipulate their genes for the production of polymerase chain reaction, a process that results in the useful products such as enzymes, hormones, amplification of DNA interferons, etc. DNA ligase - It covalently links, or ligates, fragments of Microorganisms are used as model organism in DNA together molecular biology Corynebacteria - Ubiquitous and are used for their production of amino acids and other nutrients Corynebacterium glutamicum - Produce the amino acid BIOCHEMISTRY AND PHYSIOLOGY glutamic acid, which is an additive in the food industry. It Microorganisms are used as a model for study is more popularly known as monosodium glutamate and many biochemical and physiological (MSG) processes Xanthomonas - produce an acidic exopolysaccharide commonly marketed as xanthan gum, used as thickening and stabilizing agent in foods and in cosmetic ingredients to prevent separation 5  Microbiology & parasitology ❁ SEMESTER 1 PRELIMS | PCBIO105L | IARABANO SY. 2024-2025 rr Aspergillus - A genus of fungi used in the production of PHYLOGENETIC CLASSIFICATION alcoholic beverages and pharmaceutical development Also called phyletic classification systems Aspergillus niger - Commonly used to produce citric Phylogeny - Evolutionary development of a acid, which is used in numerous products ranging from species household cleaners, pharmaceuticals, foods, cosmetics, Usually based on direct comparison of genetic photography and construction material and gene products Woese and Fox proposed using small subunit M2: TAXONOMY AND DIVERSITY OF (SSU) rRNA nucleotide sequence to assess MICROORGANISMS evolutionary relatedness of organisms TAXONOMY The science of classification of living organisms GENOTYPIC CLASSIFICATION Consists of three separate but interrelated areas: Comparison of genetic similarity between 1. Classification organisms - The arrangement of organisms into Individual genes or whole genomes can be taxonomic groups, known as taxa, on compared the basis of similarities or relationships 70% of homology belong to the same species - Main taxonomic ranks: Domain, Kingdom, Phylum, Class, Order, Family, POLYPHASIC TAXONOMY Genus, and Species 2. Nomenclature Used to determine the genus and species of a newly - The assignment of names to the various discovered prokaryote taxa according to international rules Incorporates information from genetic, phenotypic, and - International Code of Nomenclature of phylogenetic analysis Prokaryotes (ICNP) 3. Identification TAXONOMIC RANKS - The process of determining whether an Microbes are placed in hierarchical taxonomic levels with isolate belongs to one of the each level or rank sharing a common set of specific established, named taxa or represents a features previously identified species. Highest rank is domain NATURAL CLASSIFICATION Bacteria and Archaea - microbes only Arranges organisms into groups whose members share Eukarya - microbes and microorganisms many characteristics First such classification in 18th century develop Within Domain by Carolus Linnaeus Phylum, Class, Order, Family, Genus, Species Based on such anatomical characteristics epithet (some subspecies) This approach to classification does not necessarily provide information on evolutionary SPECIES relatedness Collection of strains that share many stable properties and differ significantly from other PHENETIC CLASSIFICATION groups of strains Groups organisms together based on mutual Collection of organisms that share the same similarity of phenotypes sequences in their core housekeeping genes Can reveal evolutionary relationships but not dependent on phylogenetic analysis (does not STRAINS weigh characters) Descended from a single, pure microbial Best systems: Compass many attributes as culture possible Vary from each other in many ways - Biovars - Differ biochemically and physiologically - Morphovar - Differ morphologically - Serovars - Differ in antigenic properties 6  Microbiology & parasitology ❁ SEMESTER 1 PRELIMS | PCBIO105L | IARABANO SY. 2024-2025 rr Type Strains TECHNIQUES FOR DETERMINING TAXONOMY - One of the first strains of a species AND PHYLOGENY studied Classical characteristics - Often fully characterized Morphological - Not necessarily most representative Physiological member of species Biochemical Ecological GENUS Genetic Well-defined group of one or more strains Clearly separate from other genera ECOLOGICAL CHARACTERISTICS Often disagreement among taxonomist about Life cycle patterns the assignment of a specific species to a genus Symbiotic patterns Ability to cause disease BINOMIAL SYSTEM OF NOMENCLATURE Habitat preferences Devised by Carol von Linne (Carolus Linneaus) Growth requirements Each organism has two names - Genus name - italicized and capitalized GROWTH CHARACTERISTICS (e.g. Escherichia) Nucleic acid and base composition - Species epithet - italicized but not Nucleic acid hybridization capitalized (e.g. coli) Nucleic acid sequencing Can be abbreviated after first use (e.g., E. coli) Genomic fingerprinting A new species cannot be recognized until it has Amino acid sequencing been published in the International Journal of Systematic and Evolutionary Microbiology TAXONOMY AND BACTERIA We use Bergey’s Manual: Based on 3 primary things TAXONOMY: MICROBIAL NOMENCLATURE Binomial system developed by Carolus Linnaeus 1. Cell Wall (or lack of cell wall) - Gram reaction (+) - First name: Genus or (-) - Second name: Specific epithet 2. Cell Morphology (shape) Bacillus, Coccus, - First + Second name = Species name Spirillum, Vibrio 3. Biochemical characteristics: Sugar they ferment, Example: enzymes like catalase and oxidase, Bacteria - Domain decarboxylase, etc. Monera - Kingdom Proteobacteria - Phylum More modern techniques used today to get very specific Gammaproteobacteria - Class “strains” Enterobacteriales - Order Serological groups (antigen - antibody reaction) Enterobacteriaceae - Family DNA hybridization studies Escherichia - Genus DNA fingerprinting Coli - Species Bacterial viruses (phage typings) In writing, standard method of expressing the FIRST MICROORGANISMS ON EARTH species name: - To express the genus, capitalize the first Earth is 4.6 billion years old letter of the word and underline or Microbial life first appeared between 3.8 and 3.9 italicize the whole word billion years ago - To express the specific epithet, - 80% of Earth’s history was exclusively lowercase and italicize microbial life Microbial life estimated on Earth: 2.5 x 10^30 cells 7  Microbiology & parasitology ❁ SEMESTER 1 PRELIMS | PCBIO105L | IARABANO SY. 2024-2025 rr It is generally thought that all cells came from a A single lipid membrane common ancestor cell termed the last universal - Membrane lipids contain branched chain common ancestor (LUCA) isoprenoid units in fatty chains linked to a Eventually evolved into three different cell types glycerol-1-phosphate head group via ether each representing a domain linkages Reproduce asexually by fission or budding and THREE DOMAIN CLASSIFICATION no species are known to produce spores Proposed by Woese and coworkers in 1977 An evolutionary model of phylogeny based on THREE DOMAIN CLASSIFICATION the differences in: Prokaryotic microorganisms that are members of - Sequences nucleotides in the cell’s the third branch (or domain) of life ribosomal RNAs (rRNA) Originally thought to predominate in extreme - Cell’s membrane lipid structure environments that are very salty, acidic, alkaline, - Sensitivity to antibiotics hot, cold, or anaerobic where they are Eukarya: Contain a membrane-bound nucleus (includes sometimes dominant plants, animals, protists, and fungi) - Molecular methods reveal that they are Eubacteria: Lack a nucleus and consist of the traditional common in all environments or ‘true’ bacteria (e.g. most pathogenic forms, E.coli, S. Archaeal genomes: 0.5-5.75 Mbp circles aureus, etc.) - Include genes for information transfer Archaea: Lack a nucleus and consists of extremophiles machineries (DNA replication, or ‘ancient’ bacteria (e.g. methanogens, thermophiles, transcription, and translation) halophiles) - Are simplified versions of their eukaryote counterparts EVOLUTION OF THE THREE DOMAINS OF LIFE Hypothesized that when RNA became enclosed in a lipid ARCHAEA sphere, the first primitive life forms were generated Consists of: - Methanogens LAST UNIVERSAL COMMON ANCESTOR (LUCA) - Extreme archaeal halophiles - Hyperthermophiles The root of the tree of life, based on SSU rRNA, 7 major phyla shows the earliest region is on the bacterial 5 cultivate phyla or archaea branch - Crenarchaeota Thought that Archaea and Eukarya evolved - Euryarchaeota independently of bacteria - Korarchaeota - Thaumarchaeota ENDOSYMBIOTIC ORIGIN OF EUKARYOTES (a) The nucleated line diverged from the archaeal EURYARCHAEOTA line and later acquired by endosymbiosis the Includes classes Methanobacteria, bacterial ancestor of the mitochondrion and then Methanococci, and Methanomicrobia the cyanobacterial ancestor of the chloroplast, at Generally described as methanogens - Reduce which point the nucleated line diverged into the carbon dioxide in the presence of hydrogen, lineages giving rise to plants and animals producing methane (CH4) Live in the most extreme environments DIVERSITY OF MICROORGANISMS Can reproduce at temperatures varying from ARCHAEA below freezing to boiling Consisting of cells bounded by: Though to contribute to the formation of anoxic - Cell walls peptidoglycan, but some sediments by producing hydrogen sulfide, contain a structurally similar substance making “marsh gas” called pseudopeptidoglycan or Class: Halobacteria pseudomurein Includes halophilic (salt-loving) archaea Require a very high concentration of sodium chloride in their aquatic environment (close to 8  Microbiology & parasitology ❁ SEMESTER 1 PRELIMS | PCBIO105L | IARABANO SY. 2024-2025 rr saturation, at 36%) such environments include CELLS OF BACTERIA AND ARCHAEA the Dead Sea as well as some salty lakes in Antarctica and south-central Asia 💡 Methanogens are strict anaerobes found in freshwater, marine sediments, soils and the gut of many animals and humans PHYLUM CRENARCHAEOTA Aquatic Most if not all, are hyperthermophiles (grow up to 113ºC) Genus Sulfolobus - Thermophiles (70-30ºC) - Acidophiles (pH of 2-3) - Aerobic (heterotrophs) or anaerobic (oxidize sulfur to produce sulfuric acid, which is stored in granules) CRENARCHAEOTA Genus: Thermoproteus Rod-shaped hyperthermophiles that grow in mildly acidic conditions at temperatures up to 95ºC Optimal growth temperature of 85ºC Motile Cellular membrane in which lipids form a monolayer rather than a bilayer Reduce sulfur or molecular hydrogen and use carbon dioxide or carbon monoxide as a source of carbon to produce ATP The deepest-branching genus of Archaea SINGLE-CELLED EUKARYOTIC ORGANISM DOMAIN EUBACTERIA Can be sub-classified according to a number of diverse features, including: Shape: round (coccus) rod-shaped (bacillus) common-shaped (vibrio) or spiral (spirilla/spirochete) Cell wall composition: Gram positive (thick peptidoglycan layer) or Gram negative (lipopolysaccharide layer) Gaseous requirements: Anaerobic (obligate vs facultative) or aerobic DOMAIN EUKARYA Nutritional patterns: Autotrophic (photosynthetic Consists of four kingdoms: Protista, Plantae, vs chemosynthetic) or heterotrophic Fungi, Animalia Additional structures: Flagella, slime capsules, True nucleus hyphae, endospores 9  Microbiology & parasitology ❁ SEMESTER 1 PRELIMS | PCBIO105L | IARABANO SY. 2024-2025 rr KINGDOM FUNGI SLIME MOLDS Fungi - Ubiquitous and diverse group of Fungus-like protists, which include Myxomycota, and organisms Dictyosteliida All fungi lead a heterotrophic existence as Heterotrophic - obtain energy by decomposing VIRUSES organic material Not classified into the three domains of life because they a. Saprobes don’t possess any of their traits. Not even one gene is b. Symbionts shared by all the viruses. They are considered as non c. Commensals living cells d. Parasites Habitats - Ubiquitous in terrestrial and A non-cellular agent consisting of a protein coat freshwater (capsid) and genetic material Distribution - Cosmopolitan (all over the world) The following criteria are used to classify viruses: Ecology - Important ecological roles as 1. Morphology - structure of capsid; presence of saprotrophs, mutualistic symbionts, parasites absence of envelope Nutrition - Heterotrophic 2. Size of the virion Cell wall - glucans and chitin 3. Type of host/host structures the virus infected: CLASSIFICATION OF FUNGI - Bacteriophages: infect bacterial cells - Plant viruses infect plant cells - Animal viruses 4. Genome composition - DNA/RNA (double stranded or single stranded) Genetic material may be DNA (adenovirus) or RNA (retrovirus) and may be single-stranded or double-stranded Some viruses the protein coat may be exposed (naked capsid) or covered in a membranous bilayer (enveloped capsid) Retroviruses have a reverse transcriptase component to allow for production of viral DNA KINGDOM PROTISTA Any eukaryote that is not classified as a fungus, plant, or animal Three major groups: - Animal-like: unicellular heterotrophs - Plant-like: Autotrophic - Fungus-like: unicellular decomposers Either unicellular or multicellular Most are aquatic PROTOZOA Unicellular, animal-like, which include many different phyla: Sacromastigophora, Ciliophora, and Apicomplexa ALGAE Plant-like protists that are capable of photosynthesis, include Chlorophyta, Phaeophyta, Rhodophyta, Bacillariophyta, and Dinophyta 1 0  Microbiology & parasitology ❁ SEMESTER 1 PRELIMS | PCBIO105L | IARABANO SY. 2024-2025 rr M4: BACTERIAL GROWTH AND NUTRITION Fermentation - Yield = 2 ATP MICROBIAL METABOLISM - End products: Lactic acid/Alcohol The collected of controlled biochemical reactions that - Final electron receptor is organic takes place within the cells of an organism molecule Anaerobic respiration Metabolic processes are guided by the following eight - Yield > 2 elementary statements: - Absence of oxygen, other electron 1. Every cell acquires nutrients, which are the acceptor than O2 chemicals necessary for metabolism 2. Metabolism requires energy from light or from AEROBIC RESPIRATION the catabolism of acquired nutrients 3. Energy is stored in the chemical bonds of Most efficient way to extract energy to glucose adenosine triphosphate (ATP) Process: Glycolysis, Kreb’s Cycle, Electron 4. Using enzyme, cells catabolize nutrient transport chain molecules to form elementary building blocks Glycolysis: Several glycolytic pathways called precursor metabolites The most common one: glucose – pyruvic acid + 5. Using these precursor metabolites, energy 2 NADH + 2ATP from ATP, and other enzymes, cells construct larger building blocks in anabolic reactions ANAEROBIC RESPIRATION 6. Cells use enzyme and additional energy from Final electron acceptors: never O2 ATP to anabolically link building blocks Sulfate reducer: final electron acceptor is together to form macromolecules in sodium sulfate (Na2SO4) polymerization reactions Methane reducer: Final electron acceptor is 7. Cells grow by assembling macromolecules sodium nitrate (NaNO3) into cellular structures such as ribosomes, O2/H2O coupling is the most oxidizing, more membranes and cell walls. energy in aerobic respiration 8. Cell typically reproduce once they have Therefore, anaerobic is less energy efficient doubled in size FERMENTATION METABOLISM Fermentation pathways 1. Catabolism: Break down a substrate and a. Homolactic acid Fermentation capture energy Pyruvic acid — Lactic Acid 2. Anabolism: Synthesis of more complex E.g. Streptococci, Lactobacilli compounds and use of energy b. Alcoholic Fermentation Pyruvic acid — Ethyl alcohol ENERGY GENERATING PROCESS E.g. Yeast Sugars formed or obtained - broken down to release energy MICROBIAL GROWTH - Aerobic respiration Microbial population is measured by increase in - Anaerobic respiration population - Fermentation Increase in number of cells, not cell size Microbes that use aerobic respiration, detoxify One cell becomes colony of millions of cells generated waste: The prokaryotes reproduce by various ways such as by: - Catalase: H2O2 → H2O and O2 Binary fission - Superoxide dismutase: Oxygen radical Budding → H2O and O2 Intracellular offspring Aerobic respiration - Complete breakdown of glucose to CO2 & H2O - Final electron acceptor = O2 - Yield = 38 ATP 1 1  Microbiology & parasitology ❁ SEMESTER 1 PRELIMS | PCBIO105L | IARABANO SY. 2024-2025 rr BACTERIAL GROWTH - Rate of cell growth = rate of cell death - Cannibalize and reuse resources released from Binary Fission dying cells. - The cell copies its genetic material (DNA) and 4. Death phase segregates these copies to opposite ends of the - Cells are dying at an exponential rate cell - Nutrient limitation and toxic waste accumulation - Protein monomers of FtsZ and other components of the division apparatus assemble into a ring-like structure at the center of a cell, MEASURING MICROBIAL GROWTH the division site. Direct methods - count individual cells - The cytoplasm is cleaved in two without Indirect methods - measure effects of bacterial damaging the DNA and in many bacteria new growth cell wall is synthesized PLATE COUNT METHOD Determine the number of cells in a sample capable of forming colonies in a suitable agar medium METABOLIC ACTIVITY Research has found that there is a direct relationship between the bacterial population and acid or gas production due to consumption of nutrients. Hence measuring acid or any other metabolic product could be GENERATION TIME used indirectly to find the bacterial population The amount of time it takes for the population to double in number FACTORS AFFECTING BACTERIAL GROWTH Average for bacteria is 1-3 hours CHEMICAL REQUIREMENTS OF E.coli generation time = 20 min MICROORGANISMS 1. Carbon PHASES OF BACTERIAL GROWTH About 50% of the dry weight of a bacterial cell is Microbes are grown in batch culture, which describes the carbon growth of microbes in a fixed volume of liquid enclosed All cells require carbon and most prokaryotes within a container such as a test tube or a flask. The require organic (carbon-containing) compounds nutrients in such a culture flask are finite and cannot as their source of carbon support growth indefinitely. Hence, in batch culture Some microorganisms are autotrophic and these microbes typically exhibit a growth cycle called the organisms build their cellular structures from microbial growth curve. CO2 Carbon is obtained from amino acids, fatty Microbial growth curve - A graph that plots the number acids, organic acids, sugars, nitrogen bases, of organisms in a growing population over time aromatic compounds, and countless other organic compounds 1. Lag phase It is the structural backbone of living matter’ it is - Period of apparent inactivity needed for all the organic compounds that make - Associated with physiological adaptation up a living cell. - Synthesizing new components 2. Nitrogen - Increase in size but do not divide Makes up about 13% of the dry weight of 2. Log (exponential) phase microbial cells - Growing at the maximal possible Acquire nitrogen from organic and inorganic 3. Stationary phase nutrients - Population growth decrease - Growth curve becomes horizontal 1 2  Microbiology & parasitology ❁ SEMESTER 1 PRELIMS | PCBIO105L | IARABANO SY. 2024-2025 rr Most photosynthetic organisms can reduce ON THE BASIS OF ENERGY SOURCE nitrate to ammonium which can then be used for Organisms can be categorized according to whether biosynthesis they use chemicals or light as source of energy All cells recycle nitrogen from their amino acids and nucleotides 1. Phototrophs Contained in many organic compounds, - The organisms which can utilize light as an including the amine group of amino acids and as energy source are known as phototrophs. These part of nucleotide bases bacteria gain energy from light Protein synthesis requires considerable amounts 2. Chemotrophs of nitrogen as well as sulfur. The syntheses of - These bacteria gain energy from chemical DNA and RNA also require nitrogen compounds (breaking chemical bonds) they 3. Oxygen cannot carry out photosynthesis Essential for obligate aerobes because it serves - Redox reactions: aerobic respiration, anaerobic as the final electron acceptor of electron respiration, or fermentation transport chains, which produce most of the ATP in these organisms ON THE BASIS OF ELECTRON SOURCE By contrast, oxygen is a deadly poison for obligate anaerobes (TRANSFER OF ELECTRON) Source: contact with air The transfer of electrons between molecules via Use of oxygen: for aerobic respiration, oxygen oxidation and reduction is important because most of serves as the final electron acceptor. the energy stored in atoms is in the form of Neither atmospheric or covalently bound oxygen high-energy electrons; it is this energy that is used to in compounds such as carbohydrates and water fuel cellular functions - cellular respiration, production of is poisonous ATP, breaking down of food Toxic forms of oxygen are those that are highly reactive 1. Lithotrophs Oxygen is a strong electron acceptor because of Some organisms can use reduced inorganic its high degree of electronegativity compounds as an electron donors and are They are toxic for the same reasons that oxygen termed as Lithotrophs is the final electron acceptor for aerobes: they Photo-litotrophs: These bacteria gain energy are excellent oxidizing agents, so they steal from light and use reduced inorganic electrons from other compounds, which in turn compounds such as H2S as a source of steal electrons from still other compounds electrons eg: Chromatium okeinii The resulting chain of vigorous oxidations Chemo-lithotrophs: These bacteria gain causes irreparable damage to cells by oxidizing energy from reduced inorganic compounds important compounds, including proteins and such as NH3 as a source of electron eg: lipids. Nitrosomonas 4. Other chemical requirements 2. Organotrophs Phosphorus - Component of Some organisms can use organic compounds phospholipid membranes, DNA, RNA, as electron donors and are termed as ATP organotrophs Sulfur - A component of Some can be Chemoorganotrophs and sulfur-containing amino acids, which Photo-organotrophs bind to one another via disulfide bonds Chemo-organotrophs: These bacteria gain that are critical to the tertiary structure of energy from organic compounds such as protein and in vitamins such as thiamine glucose and amino acids as a source of B1 and biotin electrons eg; Pseudomonas pseudoflora Potassium, magnesium, and calcium Photo-organotrophs: These bacteria gain - Cofactors for enzymes energy from light and use organic compounds such as Succinate as a source of electrons eg; Rhodospirillum 1 3  Microbiology & parasitology ❁ SEMESTER 1 PRELIMS | PCBIO105L | IARABANO SY. 2024-2025 rr ON THE BASIS OF CARBON SOURCE HYDROMONAS All organisms require carbon in some form for Convert hydrogen into water use in synthesizing cell components However, some can use CO2 as their major or FERROMONAS even sole source of carbon; such organisms Inhabit water and obtain energy by oxidation of ferrous are termed as Autotrophs (Autotrophic compounds into ferric forms bacteria) Other require organic compounds as their carbon source and are known as Heterotrophs METHANOMONAS (Heterotrophic bacteria) Oxidation of methane into water and carbon dioxide Organic compounds: are derived from or produced by living organisms and have carbon-hydrogen covalent NITROSOMONAS bonds Oxidation of ammonia and nitrogen compounds into Inorganic compounds: are derived from nonliving nitrates components and generally have ionic bonds, lack carbon-hydrogen bonds, and rarely, if ever, contain any CARBON BACTERIA carbon atoms Oxidizes CO into CO2 AUTOTROPHIC BACTERIA HETEROTROPHIC BACTERIA These bacteria synthesize all their food from inorganic substances (H2O, CO2, H2S salts) The autotrophic Obtain their-ready made food from organic bacteria are two types: substances, living or dead Two types: a. Photoheterotrophs PHOTOAUTOTROPHS - Can utilize light energy but cannot use These bacteria capture the energy of sunlight CO2 as their sole source of carbon and transform it into chemical energy. b. Chemoheterotrophs In this process, CO2 is reduced to - Obtain both carbon and energy from carbohydrates. Photosynthesis organic compounds such as Photoautotrophs has Chlorophyll pigment in the carbohydrates, lipids and proteins cell and its main function is to capture sunlight e.g., Cyanobacteria SAPROPHYTIC BACTERIA Some photoautotrophic bacteria are anaerobes and have bacteriochlorophyll and bacterioviridin Dead and organic decaying matter pigments respectively PARASITIC BACTERIA PURPLE SULFUR BACTERIA Tissues of the hosts These bacteria have the pigment bacteriochlorophyll located on the intracytoplasmic membrane i.e., SYMBIOTIC BACTERIA thylakoids. These bacteria obtain energy from sulfur Live in close association with other organisms compounds Beneficial to the organisms E.g Chomatiiun. Theopedia rosea, Thiospirilium PHYSICAL/ENVIRONMENT FACTORS GREEN SULFUR BACTERIA REQUIREMENTS Use hydrogen sulfide (H2S) as hydrogen donor FOUR ENVIRONMENTAL FACTORS AFFECTING GROWTH SULPHOMONAS Temperature Obtain energy by oxidation of elemental sulphur or H2S pH Osmolarity Oxygen 1 4  Microbiology & parasitology ❁ SEMESTER 1 PRELIMS | PCBIO105L | IARABANO SY. 2024-2025 rr HOW DOES TEMPERATURE AFFECT M5: MICROBIAL GENETICS MICROBIAL GROWTH GENES AND GENOMES As temperature rise, the rate of enzymatic reactions Genetics increases and growth becomes faster - Study of heredity in general and of genes in Above a certain temperature, proteins or other cell particular components may be denatured or otherwise irreversibly - Study of inherited traits, rooted in DNA, and their damaged variations and transmission Heredity CARDINAL TEMPERATURES - Transmission of inherited traits from generation For every microorganism there is to generation Genes A minimum temperature below which growth is not - A section of a DNA molecule whose sequence possible of building blocks instructs a cell to produce a particular protein An optimum temperature at which growth is most rapid Genomes - The complete set of genetic instructions in the A maximum temperature above which growth is not cells of a type of organism possible Genomics - The field that analyzes and compares genomes TEMPERATURE CLASSES OF MICROORGANISMS MICROBIAL GENETICS Microorganisms can grow over a wide range of The study of the mechanisms of heritable information in temperatures. These are four broad classes of microorganisms microorganisms based on their growth temperature optima GENETIC INFORMATION OF MICROBES Psychrophiles - with low temperature optima Circular DNA molecule Mesophiles - with midrange temperature optima Supercoiled and localized within the nucleoid of the cell Thermophiles - with high temperature optima 500,00 base pairs to 5 million Hyperthermophiles - with very high Bacteria have a cell cycle with a duration on the temperature optima order of tens of minutes Genome folding and transcription are intimately coupled with genome replication pH A typical bacteria genome has approximately Neutrophiles - organisms that grow optimally at a pH 4,400 genes (humans 25,000) value in the range termed circumneutral (pH 5.5 to 7.9) The genome of bacteria encodes are called neutrophiles - Biochemical functions necessary for Acidophiles - grow best below pH 5.5. survival Alkaliphiles - pH optima 8 or higher - Virulence factors for pathogenic bacteria - Noncoding regions OSMOLARITY/OSMOTIC PRESSURE Halotolerant - prefer NaCl concentrations of around 3% OPERON - BACTERIAL GENE ORGANIZATION Halophile - prefer NaCl concentrations of 5-10% or A set of functionally related structural genes higher Extreme halophile - prefer NaCl concentrations of PLASMID 15%-30% Xerophiles - organisms able to live in very dry Extrachromosomal DNA environments Exist and replicate independently of Osmophiles - able to grow in high sugar environments chromosome Contain few genes that are non-essential Used in genetic engineering 1 5  Microbiology & parasitology ❁ SEMESTER 1 PRELIMS | PCBIO105L | IARABANO SY. 2024-2025 rr GENETIC INFORMATION OF MICROBES KINDS OF TRANSPOSITION Bacterial DNA (Deoxyribonucleic acid) 1. Replicative Transposition Circular chromosome + plasmid Copy and Paste Mechanism Creates a copy of itself at a new genomic STAGES OF DNA REPLICATION location Leaving the original element intact at its original 1. Initiation site 2. Elongation 2. Non-replicative or Conservative 3. Termination Transposition (Cut-and-paste) The transposable element is physically moved In an mRNA, the instructions for building a polypeptide from one location to another without creating a are RNA nucleotides (AUGC) read in group of three = copy Codons 3. Transformation Acquired directly from the environment EXCHANGE OF GENETIC INFORMATION Gene transfer refers to the transfer of DNA containing HOW DOES BACTERIAL TRANSFORMATION functional genes between any two organisms WORK IN THE LABORATORY 1. Restriction enzymes - cleaves DNA sequences WAYS THAT GENES CAN BE TRANSFERRED at sequence-specific sites 1. Reproduction - binary fission 2. Ligase - a DNA-joining enzyme - Vertical gene transfer - transfer of genetic material from parental organism to progeny TRANSDUCTION Transfer of genes from a donor to a recipient by GENETIC VARIABILITY a bacteriophage 2. Horizontal Gene Transfer - transfer of genetic Does not require physical contact between the material environment cell donating the DNA and the cell receiving the - Transformation: bacteria take up DNA DNA from their environment Two types: generalized, specialized - Conjugation: Bacteria directly transfer genes to another cell BACTERIOPHAGE - Transduction: Bacteriophages Viruses that infect bacteria, may have a lytic (bacterial viruses) move gene from one cycle or a lysogenic cycle cell to another LYTIC CONJUGATION Phage which multiply on bacteria and kill the cell A donor bacterium transfers a copy of a plasmid by lysis at the end of the life cycle to a recipient bacterium, through a pilus via direct cell to cell contact Donor cell - f+ conjugative plasmid LYSOGENIC Recipient cell - f- does not contain conjugative Quiescent state in cell plasmid TRANSPOSABLE SPECIALIZED TRANSDUCTION Can insert into plasmids which can be Pick up only specific portions of the host’s DNA transferred to recipient cells by conjugation Designed to move from one location to another within a DNA molecule by a process known as transposition 1 6  Microbiology & parasitology ❁ SEMESTER 1 PRELIMS | PCBIO105L | IARABANO SY. 2024-2025 rr TYPES OF RECOMBINATION Homologous - Involves the exchange of genetic material between two similar or identical DNA sequences Site-specific - DNA strand exchange takes place between dna segments that possess at least a certain degree of sequence MOLECULAR RECOMBINATION In each of the cases of Horizontal Gene Transfer, the process is only successful if the genes can be expressed by the altered cell For genes to be expressed, the DNA must be recombined with the recipient’s chromosome 1 7