Chapter 1: Introduction to Microbiology Flashcards
Microbiology
the stud of microorganisms or microbes; which are often invisible to the naked eye; at least half of earths life is microbial; inhabit every region
Microbe encompasses…
cellular, living microorganisms (bacteria, archaea, fungi, protists, and helminths); nonliving/noncellular entities (viruses and prions (infectious proteins)); and microorganisms that are not microscopic (some fungi, helminths, and protists)
Bacteria
prokaryotic; unicellular, pathogenic and nonpathogenic
Archaea
prokaryotic; unicellular; nonpathogenic; most live in extreme environments
Protists
eukaryotic; unicellular and multicellular; pathogenic and non pathogenic; unicellular- amoebae; multicellular- algae
Fungi
Unicellular and multicellular; pathogenic and nonpathogenic
(unicellular example: yeast; multicellular example: mushrooms
Helminths
eukaryotic; Multicellular;* parasitic roundworms and flatworms
Viruses
not cells; nonliving ; Infect animal, plant, or bacterial cells; can have a D NA or RNA
genome; they are considered non-living because they can not live outside of a host and do not create their own energy (metabolism)
Prions
not cells; nonliving; infectious proteins; Not discovered until the 1980s; transmitted by transplant or
ingestion; some prion diseases are inherited
Prokaryotic Cells
evolved about 3.5 billion years ago; earliest life forms; include unicelluar bacteria and archaea; does not contain membrane bound organelles and a nucleus
Eukaryotic Cells
all multicellular organisms and a number of unicellular microorganisms (amebae, yeast); contain membrane bound organelles and a nucleus; endosymbiotic theory
Pathogens
microbes that cause disease; about 1400 are known to infect humans; < 1% of all microbes are pathogenic
Opportunistic Pathogens
cause disease only in a weakened host; like already having a disease and the opportunistic pathogen taking advantage of that
Golden Age of Microbiology
1850-1920; innovation of microscops; observations; new techniques to isolate and grow microbes
Edward Jenner
successfully vaccinates against small pox
Florence Nightingale
establishes formal aseptic practices in nursing
Joseph Lister
think listerine; publishes aseptic surgery techniques
Robert Koch
first to prove microbes cause disease
Julius Petri
makes first petri dish
Alexander Fleming
discovers penicillin
Robert Hooke
first to publish descriptions of cells (cork)
Antonie Van Leeuwenhoek
refined earlier versions of the microscope and developed a better lens to focus on specimen; first to see bacteria
Spontaneous Generation
abiogenesis; life comes from nonliving items; like how they believed maggots just spontaneously came to be on meat
Biogenesis
life emerges from existing life (reproduction); the maggots were not sponateous and instead came from the flies that laid their eggs
Francesco Redi
tested spontaneous generation by leaving meat in an uncovered jar which resulted in maggots and then a meat in a sealed jar which resulted in no maggots on meat
Louis Pasteur
showed biogenesis is responsible for the propagation of life; pasteurization killed off yeast and prevented stored wine from turning sour (vinegar); developed first vaccine against anthrax and rabies; developed germ theory
Germ Theory of Disease
states that microbes cause infectious diseases; specifically infectious because some disease can be genetic, autoimmune, or cancer none of which are infectious
Endosymbiotic Theory
eukaryotic cells evolved from prokaryotic cells in a sequential way
What famous experiment did Pastueur do to disprove spontaneous generation?
swan necked flask experiment
How did the S-Neck experiment leave no room for skeptics to say that it still could have been spontaneous generation?
the flask had an opening that allowed air into the container; this meant that “life force” was not blocked
Why did the shape of the s-necked flask matter so much?
it did not allow particles/microbes to enter to the broth; gravity, water, and air (or currents) are the only thing that can move microbes; the s-neck did not allow the microbes to move because they were stuck in the bottom part; there was no gravity to push them up, no air current or liquid
How do microbes move?
either passively (such as gravity) or actively (with a flagella, cilia, or amoeba motion); this means that they require a aqueous environemnt to do so in
Scenario 1 of Swan Neck Experiment
broth is heated and cooled in flask; nothing is done; microbes are trapped in the neck and the broth remains pure
Secanrio 2 of Swan Neck Experiment
broth heated and cooled; microbes are trapped in neck; but the flask is tilted to the liquid goes up the neck which allows the microbes to get in the liquid and the broth is contaminated
Scenario 3 of Swan Neck Experiment
broth heated and cooled; microbes stuck in flask; break the neck of the flask (take out the S part) and airborn microes enter thorugh gravity and the broth is contaminated
Turbid
growth of microbes in a broth; cloudy broth
How do bacteria reproduce?
binary fission
What did the swan neck lead to?
creation of the petri dish; it is the same concept; the cover of the petri dish is larger and when it sits on top creates the “swan neck” shape
Robert Koch
interested in what specific microbe causes a specific disease; developed staining techniques and media for the isolation and cultivation of bacteria; worked with anthrax and found it was caused by the bacteria bacillus anthracis; developed a technique to determine the specific etiological agent of an infectious disease
Koch’s Postulates of Disease
1) same organisms must be present in every case of the disease; 2) organism must be isolated from the diases host and grown as a pure culture (taking the microbe out of the host and cultivating it); 3) isolated organism should cause same disease when iinoculated into a susceptible host (the microbe is given to a healthy host and should present the same symptoms as the infected host); 4) organism must be re-isolated from the inoculated, diseased animal (must be able to pull that same microbe out and determine that it was what caused the disease)
Ignaz Semmelweis
developed first aseptic techniques in the hospital setting; recommended handwashing to decrease mortality rates from childbed fever; father of handwashing
Joseph Lister
investigated processes for aseptic surgery; proved sterilizing instruments and sanitizing wounds with carbolic acid prevented pus formation
Florence Nightingale
established aseptic techniques in nursing; founder of modern nursing
What do aseptic processes prevent?
healthcare-acquired infections (HAIs) aka nosocomial infections and limited the spread of disease; types include hand washing, wearing gloves, sterilizing instruments, and decontaminating surfaces
Scientific Method
starts with a question that can be investigated; a hypothesis (proposed answer) is proposed; researches collect and analyze observations (data) and use them to formulate a conclusion; conclusion states whether the data supports or contradicts the hypothesis
Observation
any data collected using our senses or instrumentation
Conclusion
interprets observations; take a collection of observations to draw accurate conclusions
Law
a precise statement (or mathematical formula) that predicts a specific occurrence; predicts what happens
Theory
a hypothesis that has been proven through many studies with consistent, supporting conclusions; explain why and how something occurs
Taxonomy
the study of how organisms can be grouped by shared features
Morphology
shape, size, arrangement and distinguishing physiological features; was used for early classification of bacteria
Carl Linnaeus
father of taxonomy; established criteria for classifying organisms
Taxonomic Hierarchy in Order
domain, kingdom, phylum, class, order, family, genus, species; delightful king philip came over for great spaghetti
3 Domains
domain is the broadest grouping of organisms; bacteria (unicellular, prokaryotic organisms; archaea (some live in extreme conditions, no known pathogens); Eukarya (unicellular and multicellular eukaryotic organisms)
Old 5 Kingdom Classification
included animalia, plantae, fungi, protista, monera; monera includes both archaea and bacteria; but they are now their own kingdoms
What are the 6 kingdoms?
archaea, bacteria, fungi, plantae, animalia, protists
Kingdom Protista
miscelllaneous kingdom for organisms not categorized as plants, animals, or fungi; genetics now show that protists can not logically be lumped into a single kingdom
Eukaryotic Species
group of similar organisms that can sexually reproduce together; interspecies hybrids are usually sterile
Prokaryotic Species
cells that share physical characteristics and have at least 70% DNA similarity; at least 97% identical 16S rRNA sequence similarity (the protein that does transcription); asexual reproduction via binary fission produces clones
Strain
smaller/below species; used to recognize genetic variants of the same species; mutations and gene transfer often lead to new strains; names typcially includes numbers/letters after the species name such as E. coli K-12
What is the cornerstone reference for classifying bacteria?
bergeys manual of determinative bacteriology
Binomial Nomenclature System
two name sys; genus is the first name; genus is always capitalized; species is the second name; species is always lowercased; scientific names are italicized (or under lined if hand written);
Symbiotic Relationship
exists when two or more organisms are closely connected
Parasitism
hurts the host
Mutualism
helps the host
Commensalism
no perceived benefit or cost to the host; but it can become parasitic if (for example) it was an opportunistic pathogen that was commensalist until the host got sick and then it became a pathogen
Pathogens have a…
parasitic relationship with their host; the term parasite is commonly used to describe helminths (worms) and protozoans
Human Microbiome Project
HMP; aims ot characterize all of the microbes in and on our bodies
Human Microbiome
many parts of the human body teem with microbial life; there are at least as many microbial cells in and on us as there are human cells; our skin, nose, mouth, gut and genital/urinary tract harbor the most microbes
Normal Microbiota
aka normal flora; includes bacteria, archaea, and eukaryotic microbes; functions- assist immune system, produce vitamins for us, help us digest foods, may even impact moods and brain function
Where are the most and least amounts of microbes found in the body?
most- intestines (over 40,000 species ); least- stomach (25 species)
What makes microbiota “normal”?
more so the location of the microbe instead of the actual species; our normal microbiota includes pathogens (but depending on the location they may not be harming); majority is harmless and helps “crowd out” pathogens
How are normal microbiotas established?
babies are colonized by microbes during delivery and early interactions with their environment and caregivers; influenced by delivery (c section or vaginal_ and feeding (breast or formula); normal microbiota expands, develops and evolves throughout the early weeks of life to adulthood
What is a disruption to normal microbiota?
when normal flora is disturbed we are put at risk for infection; can be disrupted with antibiotic therapy; kills resident bacteria and the pathogen; reduction of normal flora allows opportunistic pathogens to establish infections
Transient Microbiota
temporary passengers that do not persist as stable residents of our bodies; picked up through a handshake or contact with environmental surfaces; can be removed through hygiene
Biofilms
sticky communities made up of single or diverse microbial species; cells that seed a biofilm made adhesion factors to help them attach to a target surface; multiple layers; microbes are released as free growing planktonic cells; can develop on teeth, contact lenses, water filtering units, cutting boards, catheters
Planktonic
single, free floating bacteria
Most infectious diseases in humans are due to…
biofilm creating microbes; internal biofilms are not easily managed, more resistant to antibiotics, protected from immune system
Bioremediation
harnesses the power of microbes to help clean up toxic waste; certain microbes can metabolize toxic substances into harmless intermediates; ex) hundreds of species can degrade petroleum oil spills into co2
Growth Media
aka culture media; mixtures of nutrients that support growth in an artificial setting; agar added to solidify; can be a both, plate, slant, or deep
Pure Culture
isolation of a single type of microbe from a diverse sample of specimen
What are some aseptic culture techniques?
sterile media, sterile instruments, decontaminating surfaces, gloves and other protective clothing, use of heat source (bunsen burner/electruc sterilizer)
Biological Safety Cabinet
an enclosed cabinet that minimizes the chances of contaminating the culture and protects the researchers; uses HEPA filtration
Streak Plate Technique
helps to isolate colonies of a specific microbe to study; produces isolated pure colony forming units
Colony
grouping of cells (clones) that developed from a single parent cellM
Mixed Cultures
have more than one characterisically different colonies
Stains
aka dyes; increase contrast so the sample is easier to see
What do most staining techniques involve?
making a smear of the specimen; fixing the specimen by exposing it to heat (or chemical reagent); staining of the specimenq
Basic Dyes
most commonly used; positively charged; attracted to the negatively charged cell surface; result: cell appears the color of the dye;, ex) methylene blue, crystal violet, safranin, malachite green
Acidic Dyes
used in negative staining; negatively charged; repelled from negatively chraged cell surface; results in the stain of the background; ex) nigrosin, india ink
Mordants
chemicals that may be required in certain staining procedures to interact witha dye making it less soluble this will “trap” it on or inside a treated specimen; ex) iodine, alum, tannic acid
Simple Stains
use one dye; used to determine size, shape, cellular arrangment
Flagella Staining
structural staining; mordants are added to coat the thin flagella and then a basic dye is applied
Capsule Staining
structural stain; both basic dye (stains the cell) and acidic dye (stains the background) are used; capsule appears as a clear halo
Bacterial Endospore Staining
specimen is heated to drive the dye (malachite green) into the spores; nonsporulating cells are stained with safranin
Differential Staining
highlights differences in bacterial cell walls in order to discriminate between classes of cells; ex) gram stain and acid fast stain
Gram Stain
classifies bacteria as either gram positive or gram negative
Grame Positive Cells
will appear purple; contain a thick layer of peptidoglycan; no outer membrane
Gram Negative Cells
will appear pink; contain a thin layer of peptidoglycan; contain an outer membrane rich in lipids
Gram Stain Technique
crystal violet (primary stain) is added to a heat fixed bacterial smear; iodine (mordant) is added forming an insoluble crystal violet - iodine complex ; acetone-alcohol (decolorizing step) is used to rinse the sample ; safranin (counterstain) is added to the sample
Results of Acetone-alcohol treatment on Gram Negative
dissolves the outer membrane; damaes the thin peptidoglycan layer (makes it porous); CV-I washes out
Results of the Acetone-Alcohol treatment on gram postive
slightly dmamges the thick peptidoglycan; dehydration makes it less permeable (matrix collapses); CV-I retained
Acid Fast Stain
distinguishes between cells with and without waxy cell walls
Acid Fast Bacteria
contain waxy cell walls rich in mycolic acid; retain red-colored primary dye after exposure to an acid wash
Non-Acid Fast Cells
red primary stain is washed away after exposure to an acid wash
Ziehl Neelsen Method
acid fast staining method; carbol-fuchsin (primary dye) is added to a heat fixed smear; sample is steamed for several minutes to drive the red dye into the bacteria; acid-alcohol (decolorizing agent) is used to rinse the sample; methylene blue (counterstain) is added to the sample
What does acid fast staining detect?
mycobacterium species and nocardia species
Light Microscopy
uses visible light to illuminate the specimen; photons in a light wave interact with the specimen and are then channeled up to the viewers eyes thourgh a series of lenses; the compound light microscope is the most common type of optical microscope
How is final magnification determined?
multiplying th emagnification of the ocular and objective lenses
Condenser Lenses
sharpen light into a precise cone to illuminate the specimen
Iris Diaphragm
controls amount of light aimed at the specimen to improve contrast
Resolution
the ability to distinguish two distinct points as separate
Oil Immersion
air has a lower refractive index than glass; light passes thorugh a slide then into the air above the slide where it scatters; light is not channeled through the objective lens; immersion oil focuses the light and keeps it from scattering; oil immersion has the same feractive index as glass
Bright Field
darjer contrasting image on a bright background; compound light microscope; illuminates sample with solid cone of light; image formed based on how light is absorved; sample must be stain or have natural coloration
Dark Field
Negative image, where the sample appears light on a darker
background; Modified condenser in a compoundl ight microscope
;Illuminates sample with hollow cone of light; image formed
based on how light is scattered as opposed to how light is absorbed, so staining is not necessary;
negative image made by dark field microscopy should not be confused with negative staining; visualizes unstained specimens (live or dead) and stained specimens
Phase Contrast
negative image; where the sample apears light on a darker background; odified condesner in a compound light microscope; illuminates sample with hollow cone of light; a device in the microscope (i.e., a phase plate) interacts with light that
passes through the viewed sample— thereby enhancing image brightness, shading, and contrast; visualizes unstained specimens (live or dead) and stained specimens
Electron Microscope
uses an electron beam; large; expensice; complex sample preparation; only black and white images; can magnify over 500,000; specimens are all dead; stains must be an electron dense substances like smium or gold
Transmission Electron Microscopy
most common form of electron microscopy; 1 million times magnification and 1000 times better resolution; samples must be extensively pretreated; specimens cannot be thicker than 1/285th of a human hair; electron beam passes through specimen; hits a detector; generates 2D images of internal structures
Scanning Electron Microscopy
electron beam scans over the specimen; detectors sense how the electrons interact with the surface of the specimen; generates a 3D image of the surface
Fluorescence
occurs when a substnace absorbs energy (ultraviolet UV light) and then emits that energy as visible light
Flurorochromes
flourescent dyes that can be used to stian samples so they will flouresce when illuminated by UV light microscoe
Immunofluorescence
uses flourescent dyes linked ot antibodies that can recognize a specific target; can be used for identification of bacteria in blood cultues, virus identification in patient samples, and screening for bacteria in food processing plants
