Intro to Microbiology.docx

MICROBIOLOGY ============ - Greek words: **Mikros**- small; **logos**- science/study - Study of microorganisms - A [specialized area of biology] that deals with living things ordinarily too [small to be seen without magnification] - **Microorganisms**-microscopic organisms - *...

MICROBIOLOGY ============ - Greek words: **Mikros**- small; **logos**- science/study - Study of microorganisms - A [specialized area of biology] that deals with living things ordinarily too [small to be seen without magnification] - **Microorganisms**-microscopic organisms - **Microbes or germs** (pathogens)- terms used for microorganisms in reference to their role in infection and disease - Public health significant that causes or associated with diseases - Microorganisms include a large and diverse group of microscopic organisms that exist as single cells or cell clusters, and the viruses, which are microscopic but not cellular. - **Major Division of Microorganisms**: a. Prokaryotes- Bacteria & Archaea b. Eukaryotes- Algae, Fungi & Protozoa - **Three Domains of Life**: 1. Domain Eucarya; 2. Domain Bacteria; 3. Domain Archaea - **Major Groups of Microorganisms:** a. Bacteria b. Fungi c. Algae d. Protozoa e. Viruses f. Helminths (parasitic worms)  Fields of Microbiology ====================== Microbe-centered (Basic Research) --------------------------------- - **Bacteriology**- study of bacteria - **Phycology**- study of algae (Algaeology) - **Mycology**- study of fungi and yeast - **Protozoology**- study of protozoa - **Parasitology**- special branch of protozoology w/c deals exclusively with the parasitic disease producing protozoa - **Virology** -study of virus - **Cytology** -study of structure and function of cells Medical Microbiology (Applied Microbiology) ------------------------------------------- - **Serology**- the study and use of immunological tests to diagnose and treat disease or identify antibodies or antigens. - **Immunology**- study of the humoral and cellular immune response to disease agents and allergens - **Epidemiology** - (Greek epi - upon; demos - people; logos - study) study of the causes of disease among a population - **Etiology**- the study of the causation of disease - ### Infection Control - ### Chemotherapy Applied Environmental Microbiology (Applied Microbiology) --------------------------------------------------------- - **Bioremediation**- is the use of microbes to degrade organic matter in sewage and detoxify pollutants such as oil spills. - **Food Microbiology** - comprehends the study of microorganisms that colonise, modify, and process, or contaminate and spoil food. - ### Public Health Microbiology - **Agricultural Microbiology**- use of microbes to increase crop and livestock yield and control of plant pests and animal diseases Applied Environmental Microbiology (Applied Microbiology) --------------------------------------------------------- - **Biotechnology,** the use of microbes as miniature biochemical factories to produce food and chemicals is centuries old. - **Genetic engineering** makes use of molecular biology and recombinant DNA techniques as new tools for biotechnology. - **Gene therapy** replaces missing or defective genes in human cells through genetic engineering. - **Genetically modified bacteria** are used to protect crops from pests and freezing. impact of microbes on earth =========================== - Live in most of the world's habitats and are indispensable for normal, balanced life on earth - Involved in nutrient production and energy flow - Essential to the maintenance of the air, soil, and water. - Other microbes are responsible for the breakdown and recycling of nutrients.  Human Use of Microorganisms/ Importance of Microorganism ======================================================== - Called upon to solve environmental, agricultural, and medical problems. - In ***bioremediation***, microbes are used to clean up pollutants and wastes in natural environments. - ***Biotechnology*** applies the power of microbes toward the manufacture of industrial products, foods, and drugs. - ***Photosynthetic Microbes*** are involved in photosynthesis and accounts for \>50% of earth\'s oxygen. Also involved in decomposition and nutrient recycling.  - ***Decomposers:*** Many microbes break down dead and decaying matter and recycle nutrients that can be used by other organisms. - ***Nitrogen Fixation:*** Some bacteria can take nitrogen from air and incorporate it into soil. - ***Digestion:*** Animals have microorganisms in their digestive tract, that are essential for digestion and vitamin synthesis. - ***Probiotic bacteria*** provide many health benefits, including for the brain.  +-----------------------------------+-----------------------------------+ | Table 1. Some common strains of | | | beneficial gastrointestinal | | | microflora in dogs | | +===================================+===================================+ | Lactobacilli spp. | Improves digestion and absorption | | | of nutrients. | | | | | | Stimulates immune function | | | | | | Prevents colonization of | | | pathogenic bacteria | +-----------------------------------+-----------------------------------+ | Bifidobacterium spp. | Stimulates immune function | +-----------------------------------+-----------------------------------+ | Enterococcus spp. | Inhibits growth of pathogenic | | | bacteria | +-----------------------------------+-----------------------------------+ | Bacteroides spp. | Vitamin synthesis | +-----------------------------------+-----------------------------------+ | Streptococci spp. | Stimulates immune function | +-----------------------------------+-----------------------------------+ | Fusobacteria spp. | Improves digestion and absorption | | | of nutrients | +-----------------------------------+-----------------------------------+ | Eubacterium spp. | Inhibits growth of pathogenic | | | bacteria | +-----------------------------------+-----------------------------------+ | Saccharomyces boulardii | Improves the intestinal barrier, | | | suppress inflammation | +-----------------------------------+-----------------------------------+ | (Rastall, 2004; Aktas et al, | | | 2007; Wynn, 2009) | | +-----------------------------------+-----------------------------------+ Beneficial Uses of Microbes --------------------------- - ***Microbial ore leaching (bioleaching)*** is the process of extracting metals from ores with the use of microorganisms. This method is used to recover many different precious metals like copper, lead, zinc, gold, silver, and nickel. - ***Medicine:*** Many antibiotics and other drugs are naturally synthesized by microbes. - Members of a biohazard team from the National Oceanic and Atmospheric Agency (NOAA) participate in the removal and detoxification of 63, 000 tons of crude oil released by a wrecked oil tanker on the coast of Spain. The bioremediation of this massive spill made use of naturally occurring soil and water microbes as well as commercially prepared oil- eating species of bacteria and fungi. Modern Use of Microbiology ========================== - **Microbiomes** - Group of microorganisms - Diversity of microorganism - Microbiomes Day: June 27 - **Biotechnology**, the use of microbes as miniature biochemical factories to produce food and chemicals is centuries old. - **Genetic engineering** makes use of molecular biology and recombinant DNA techniques as new tools for biotechnology. - **Gene therapy** replaces missing or defective genes in human cells through genetic engineering. - **Genetically modified bacteria** are used to protect crops from pests and freezing. Microbial Dimensions ==================== - ***Micron or micrometer (***[*μ*]{.math.inline}***)***- 1 millionth of a meter ([10^ − 6^]{.math.inline} meters) - ***Nanometer (n)***- 1 billionth of a meter ([10^ − 9^]{.math.inline} meters) - **Bacteria** are usually several micrometers in diameter. - **Fung**i are about 10+ micrometers in diameters - **Smallest viruses**- measure around 10 nm  Historical Foundations of Microbiology ====================================== - **Archaea and Cyanobacteria** were the first microbes on Earth - **Bacteria** appeared 3.5 billion years ago **Antoni van Leeuwenhoek (1632-1723)** - A Dutch tailor, merchant, and self-made microbiologist, who hand-fashioned the clever [single-lens microscope]. - [First person to observe microscopic organisms] using single-lensed microscopes of his own design. - First person to see live bacteria and protozoa - Reported his "animalcules" to the Royal Society of London - **"Spontaneous Generation"** was an early belief that living things can arise from vital forces present in nonliving and decaying matter. (Ex.: maggots from meat or mushrooms from rotting wood) - The alternative hypothesis that living organisms can arise only from preexisting life forms is called **"BIOGENESIS".** ### Theory of Abiogenesis/Theory of Spontaneous Generation (Growth) - The idea that life can arise from spontaneously from non-living material - Ex: maggots from meat or mushrooms from rotting wood ### Theory of Biogenesis - The idea that life arise from \"pre-existing life\" - First proposed by a German scientist Rudolf Virchow in 1858. - Francesco Redi (1668)- opposed the prevailing theory of Spontaneous Generation, maggots in meat. - He used covered jars to show that maggots came from flies-strong evidence against spontaneous generation  Louis Pasteur ------------- - Showed microbes caused fermentation - Studied spoilage and introduced \"Pasteurization" to prevent it - Used cotton plugs in his cultures to prevent airborne contamination, devised [Aseptic Technique]. - A key proponent of the **Germ Theory of Disease**. [(Microbes are the culprit of diseases)] - He coined the term \'microbiology\', \'aerobic\', and \'anaerobic\'. - He demonstrated that **Anthrax** (Bacillus anthracis) was caused by bacteria and also produced the vaccine for this disease. - Developed the earliest effective vaccine against rabies that was first used to treat a human victim in July 1885 (Medical Dilemma) - Joseph Meister - Rabies= Fatality - Louis Pasteur put an end to Abiogenesis debate with his Goose Neck Flask Experiment - French chemist discovered pasteurization (used to kill pathogens in many liquids) - Developed vaccines for chicken cholera, anthrax, swine erysipelas and rabies Robert Koch ----------- - Robert Koch (1843-1910) - German physician who made numerous contributions to microbiology - Made significant contributions to the **Germ Theory of Disease** - Discovered that *Bacillus anthracis* produced spores - Developed methods of fixing and staining bacteria, developed methods to cultivate bacteria - German physician who [discovered bacteria that causes TB (Tuberculin Skin Test), Cholera]. He proved that B. anthracis is the cause of Anthrax. He provided proof that a bacterium causes anthrax using experimental steps now called the Koch\'s Postulates - He was the first to use agar as solid culture medium in bacteriology. ### Koch\'s Postulates 1. A particular microbe must be found in all cases of the disease and must not be present in healthy animals or humans 2. The microbes must be isolated from the diseased animal or human and grown in pure culture in the laboratory. 3. The same disease must be produced when microbes from the pure culture are inoculated into healthy susceptible laboratory animals 4. The same microbe must be recovered from the experimentally infected animals and grown again in pure culture **Germ Theory of Disease:** - Belief that microbes cause diseases. - Koch\'s and Pasteur\'s work helped establish the "Germ Theory of Disease\"- that microorganisms cause disease (in people, animals, and even plants) Golden Age of Microbiology -------------------------- - **How can we Prevent Infection and Diseases?** - Ignaz Semmelweis advocated handwashing - Joseph Lister\'s antiseptic technique (surgery) - John Snow -infection control and epidemiology - Edward Jenner\'s vaccine- field of immunology - Paul Ehrlich\'s \"magic bullets\"- field of chemotherapy Microorganism Classification ============================ **Taxonomy** (Gr. *taxis*, arrangement, and *nomos*, name) - The science of classification of living organisms - The formal system for organizing, classifying, and naming living things. - Originated more than 250 years ago when Carl von Linné (Carl Linnaeus 1701-1778), a Swedish botanist, laid down the basic rules for taxonomic categories, or **taxa.** - Father of Modern Taxonomy **Taxonomy consists of three (3) separate but interrelated areas (PRIMARY CONCERNS):** - ***Classification*** -the orderly arrangement of organisms into groups, preferably in a format that shows [evolutionary relationships.] - ***Nomenclature*** (Latin: *nomen*- name and *clare* - to call)- the process of assigning names to the various taxonomic rankings of each microbial species. - Binomial System of Nomenclature - Genus & Species - Microbial nomenclature: naming microorganism - ***Identification*** - the process of discovering and recording the traits of the organisms so that they may be placed in an overall taxonomic scheme ### Levels of classification - ***Domain***- giant, all-inclusive category based on a unique cell type (Super Kingdom) - #### Kingdom - ***Phylum*** (Gr. phylon, race/ tribe) for protozoa, animals and bacteria or Division for algae, plants and fungi - #### Class - #### Order - #### Family - ***Genus*** (L. birth, kind) - ***Species***- the smallest and most specific taxon **NOTE**: Just remember the mnemonics: **Did King Philip Come Over For Good Spaghetti?** ### Nomenclature (Assigning Specific Names) - ***Binomial System of Nomenclature:*** the method of assigning the scientific or specific name. - **Linnaeus** introduces the binomial system of scientific nomenclature - Each organism has two names: the genus and the species epithet - Italicized or underlined - Genus name is capitalized and species in lower case. ##### Scientific Names: - Example: ***Staphylococcus aureus*** - Describes clustered arrangement of cells and golden yellow color of colonies. - ***Escherichia coli*:** Honors the discoverer, Theodor Escherich and describes its habitat, the colon - After the first use, scientific names may be abbreviated with the first letter of the genus and full species epithet. (Ex: E. coli) ##### Special notations: - sp. - is used to designate single species - spp. - is used to designate more than one species - ssp. - is used to designate subspecific epithet **Phylogeny** (Gr. phylon, race/tribe, and geneia, manner of origin, production or development) - The natural relatedness between groups of living things. ### Phylogenetic relationships - Used by biologists to create a system of taxonomy. - First phylogenetic trees of life → plants and animals - Recognition of 3rd kingdom →protists - 4th kingdom → bacteria - 5th kingdom →fungi Systems of presenting a universal tree of life: ----------------------------------------------- ### Traditional Whittaker System - **Robert Whittaker** added a 5th kingdom for fungi during the period 1959-1969.  #### 5 kingdoms - **Monerans** (Prokaryotae)- Bacteria and Archaea - **Fungi** - **Protists**- Algae and Protozoa - **Plants** - **Animals** #### 2 cell types - **Prokaryotic**- no true nucleus - **Eukaryotic**- true nucleus ### Woese-Fox 3 Domain System - Divides cellular life forms into [archaea, bacteria, and eukaryote domains (3 Super Kingdoms)]. The key difference from earlier classification is the splitting of archaea from bacteria. - A system proposed by **Carl Woese** and **George Fox** that assigns all organisms to one of three domains, each described bya different type of cell. - ***3 Domains***- Bacteria, Archaea, Eukarya - ***2 Cell types*** - Procaryotic (Bacteria and Archaea) and Eucaryotic (Eukarya) - It is believed that the 3 super kingdoms arose from an ancestor most like archaea. - Woese\'s 3-Domain System of Classification is based on the sequence of nucleotides bases in their ribosomal RNA molecules Physiological Diversity of Microorganisms =========================================  Based on Source of Carbon ------------------------- - **Heterotrophs**- Organisms that derive their nutrients from other organisms; require one or more [organic compounds] as their carbon source. - **Autotrophs**- Organisms that utilize [inorganic source] of carbon (CO2). - Also called **primary producers** Based on Source of Energy ------------------------- - **Chemotrophs**- organisms that obtain energy from organic and inorganic [chemical compounds]. - **Phototrophs** - contain pigments that allow them to use [light] as an energy source. Based on Required Electrons --------------------------- - **Organotrophs** - organisms that acquire electrons from the [same organic molecules] that provide them carbon and energy. - **Lithotrophs**- organisms that acquire [electrons from inorganic sources] (H~2~, H~2~S) - **Chemoorganotrophs** -organisms that obtain energy from organic compounds. - ***Aerobes*** - microorganisms that can extract energy from the compound only in the presence of oxygen. - ***Anaerobes*** - microorganisms that can extract energy from the compound only in the absence of oxygen. - **Chemolithotrophs**-organisms that can tap the energy available from inorganic compounds. - This form of energy-yielding mechanism is found only in prokaryotes. - **Extremophiles**- organisms inhabiting extreme environments. - A remarkable group of prokaryotes that collectively define the physiochemical limits of life. - Abound in such harsh environments as boiling hot springs, on or within the ice covering lakes, glaciers or the polar seas, in extremely salty bodies of water, and in soils and waters with pH lower than 0 or as high as 12. - Example: TARDIGRADE - ***Capnophiles*** - grow best in environments rich in CO~2~ (usually 5-10%) - ***Microaerophiles***- grow in the presence of minute quantities of molecular oxygen (around 5% oxygen) - ***Acidophiles*** - extremely acidic (pH 2-5) - ***Alkaliphiles***-extremely alkaline (pH \> 8.5) - ***Thermophiles/ Sternothermophiles***-extremely hot - ***Psychrophiles/ Cryophiles***-extremely cold - ***Piezophiles/ Barophiles***-extremely high pressure - ***Halophiles***- extremely salty - ***Haloduric*** - organism that do not prefer to live in salty environments but are capable of surviving there (Staphyococcus aureus) - ***Radiophiles-** can survive harmful radiation* - ***Xerophiles-*** live in extreme dry condition Methods for Studying Microorganisms =================================== **Specimen collection**- Nearly any object can serve as a source of microbes. Common ones are body fluids and tissues, foods, water and soil. Specimens are removed by some form of sampling device: a swab, syringe or a special transport system that holds, maintains, and preserves the microbes in the sample. Methods for Culturing Microorganisms ------------------------------------ **The Five "I" s**- how the sample is processed and profiled ***Inoculation***- [producing a culture by introducing a tiny sample **(inoculum)** into a container of nutrient medium]. The sample is placed into a container of sterile medium containing appropriate nutrients to sustain growth. Inoculation involves spreading the sample on the surface of a solid medium or introducing the sample into a flask or tube. Selection of media with specialized functions can improve later steps of isolation and identification. Some microbes may require a live organism (animal, egg) as the growth medium.  ***Incubation***-using an incubator that creates and maintain appropriate growth temperature and other conditions. This promotes multiplication of the microbes over a period of hours, days, and even weeks. Incubation produces a culture - the visible growth of the microbe in or on the medium. ***Isolation***- [separating one species from another]. One result of inoculation and incubation is isolation of the microbe. Isolated microbes may take the form of separated colonies (discrete mounds of cells) on solid media, or turbidity (free floating cells) in broths. Further isolation by sub culturing involves taking a bit of growth from an isolated colony and inoculating a separate medium. This is one way to make a pure culture that contains only a single species of microbe.  ##### Isolation Technique Stages in the formation of an isolated colony, showing the microscopic events and the macroscopic result. Separation techniques such as streaking can be used to isolate single cells. After numerous cell divisions, a macroscopic mound of cells or a colony, will be formed. ##### Methods for Isolating Bacteria a. Steps in a quadrant streak plate b. Resulting isolated colonies of bacteria c. Steps in the loop dilution (or pour plate) method and d. The appearance of plate 3 e. Spread plate and f. Its results ***Inspection***- The colonies or broth cultures are observed macroscopically for growth characteristics (color, texture, size) that could be useful in analyzing the specimen contents. Slides are made to assess microscopic details such as cell shape, size, and motility. Staining techniques may be used to gather specific information on microscopic morphology.  ***Identification***- Information used in identification can include relevant data already taken during initial inspection and additional tests that further describe and differentiate the microbes. Specialized test includes biochemical tests to determine metabolic activities specific to the microbe, immunologic tests, and genetic analysis. CELL TYPES  Prokaryotic Cells Eukaryotic Cells -------------------------------------------------------------------- ------------------------------------------------------------------ Small cells (\5 [*μ*]{.math.inline}m) Always unicellular Often multicellular No nucleus or any membrane- bound organelles, such as mitochondria Always have nucleus and other membrane- bound organelles DNA is circular, without proteins DNA is linear an associated with proteins to form chromatin Ribosomes are small (70S) Ribosomes are large (80S) No cytoskeleton Always has a cytoskeleton Motility by rigid rotating flagellum (made of flagellin) Motility by flexible waving cilia or flagellae (made of tubulin) Cell division is by binary fission Cell division is by mitosis or meiosis Reproduction is always asexual Reproduction is asexual or sexual Huge variety of metabolic pathways Common metabolic pathways SUMMARY: Bacteria -------- - Prokaryotes - Peptidoglycan cell walls - Binary fission - Ex: Escherichia coli Archaea ------- - Prokaryotes - Lack peptidoglycan - Live in extreme environments (extremophiles) - **Include:** - Methanogens - Extreme halophiles - Extreme thermophiles Fungi ----- - Eukaryotes - Chitin cell walls - Molds and mushrooms are multicellular - Yeasts are unicellular Protozoa -------- - Eukaryotes - Mostly saprobes and commensals - May be motile by means of pseudopod, cilia or flagella Algae ----- - Eukaryotes - Cellulose cell walls - Photosynthetic - Produce molecular oxygen and organic compounds - Part of food chain Helminths --------- - Eukaryotes - Multicellular animals - Parasitic flatworms and roundworms called helminths - Microscopic stages in life cycles Viruses ------- - Acellular - Obligate intracellular parasites - Genome consist of DNA or RNA called Core - Core surrounded by protein coat called Capsid - Virion may be enclosed in lipid envelope Prions ------ - Proteinaceous infectious agents - Causes Bovine Spongiform Encephalopathy (BSE) - Also causes Creutzfeldt-Jacob Disease (CJD) - An Emerging Infectious Disease (EID)