Introduction to Microbiology

Microbe Size Comparison

• A period in an article is about 0.5mm in size.
• Human cells are about 0.01mm, meaning roughly 50 human cells could fit within the period.
• Fungal hyphal cells measure approximately 0.01mm in width.
• Bacterial cells are around 0.001mm, thus about 500 could fit in a period.
• Bacteriophages (viruses) are the smallest at 0.00005mm; 10,000 could fit in a period.

Brief History of Microbiology

• Pre-1600s: Dark Ages
• 1600-1850: Microbes were observed but their functions were not widely understood or considered important.
• 1850-1990: First Microbial Renaissance, also known as The Golden Age
• 1990-present: Second Microbial Renaissance, or the Molecular Era

The Dark Ages (pre-1600s)

• Fermentation processes were used to make bread, wine, beer, and cheese, though microbes' role was unknown.
• Yeast fermentation creates ethanol and CO2.
• Disease spread was recognized, but its cause was a mystery.
• People with leprosy were quarantined, as noted in the Bible.
• Some viewed sickness as a punishment for immoral actions.
• The Ancient Greeks and Romans thought that diseases were spread by "bad air" (miasma theory.)
• Ancient Romans created sewage systems to combat waterborne illnesses based on the miasma theory.
• The plague from 1347-1351 killed 25 million people and was used as a bioweapon by flinging infected corpses into enemy territory.

Key Figures

• Hippocrates, the “father of western medicine”, suggested diseases had natural causes, not supernatural ones.
• Thucydides advocated evidence-based reasoning and observed that plague survivors became immune.
• Marcus Terentius Varro proposed unseen entities caused disease.

Period 2 - Observation without Comprehension (1600-1850)

• Robert Hooke (England, 1600s) observed cells in cork using early microscopy.
• Hooke proposed the cell theory: all living things are composed of cells.
• Anton van Leeuwenhoek (Dutch, 1600s) constructed over 400 microscopes and was likely the first to view live microorganisms.
• Van Leeuwenhoek discovered movement in bacteria from rainwater, feces, and dental plaque.
• Van Leeuwenhoek called single-celled organisms "animalcules".

Spontaneous Generation Debate (1700s)

• Spontaneous generation is the belief that life can arise from nonliving matter.
• Francesco Redi (Italy, 1668) tried disproving spontaneous generation by using sealed and unsealed jars of meat, though there was no conclusion.
• John Needham (England, 1745) heated and sealed chicken broth, leading to bacterial growth that he wrongly attributed to spontaneous generation.
• Lazzaro Spallanzani (Italy, 1765) boiled broth in a sealed flask with no bacteria growth, concluding that microorganisms in the air could be killed by heat.

Other Figures

• Agostino Bassi (early 1800s) found that a silkworm disease was transferable, implying a living cause.
• Benjamin Jesty successfully used cowpox inoculation to protect his family from smallpox in 1774.
• Edward Jenner, unaware of Jesty's work, performed a similar experiment and published his findings, thus is credited with creating the first vaccine.
• Ferdinand Cohn (German, mid-1800s), with a background in botany, founded bacteriology.
• Cohn studied heat-resistant endospores.

Microbial Renaissance 1 - The Golden Age (1850-1990)

• Rudolf Virchow (Germany, 1858) proposed biogenesis, stating that all living cells come from other living cells but did not provide evidence.
• Louis Pasteur (France, 1822-1895) expanded on Spallanzani's work, proving that microbes in the air cause contamination.
• Pasteur discovered anaerobic life forms and determined the mechanism for fermentation.
• Pasteur developed sterilization techniques such as pasteurization to prevent spoilage.
• Pasteur helped identify the cause of silkworm disease, expanding Bassi’s work.
• Pasteur developed a cholera vaccine for fowl, which led to the germ theory of disease that states microorganisms cause disease.

Continued

• Joe Lister (England, 1860s) applied germ theory to surgical procedures and used phenol to treat surgical wounds.
• Robert Koch (Germany, 1843-1910) is regarded as the first medical microbiologist.
• Koch focused on culturing, isolating, and identifying microorganisms.
• Koch developed pure culture methods using potatoes and later agar with nutrients.
• Koch worked with Bacillus anthracis and defined criteria for determining the cause of disease.
• Koch created rules to define what organism is causing each disease, that one microbe causes one disease.
• Koch's postulates state that the same pathogen must be present in every case of the disease and absent from healthy individuals.
• The pathogen must be isolated from the diseased host and grown in pure culture.
• The pathogen from the pure culture must cause the disease, when it is inoculated into a healthy, susceptible laboratory animal.
• Koch's postulates require that the pathogen must be re-isolated from the inoculated animal and must be shown to be the original organism.
• Exceptions to Koch's postulates include situations when the same symptoms do not always relate to the same disease.
• Exceptions to Koch's postulates include situations when animal models do not show the same symptoms as humans.
• Some microbes cannot be cultured.
• Ethical considerations prevent infecting a healthy person with a disease.
• Julius Petri, assistant to Robert Koch, created the Petri dish.

Chemical Control of Microbes

• Paul Ehrlich (Germany) developed the first chemotherapy to treat syphilis.
• Alexander Fleming (England) accidentally discovered penicillin.

Microbial Renaissance 2 - Molecular Era (1990-present)

• Emergence of molecular microbiology enables analysis of DNA, RNA, and proteins.
• Molecular microbiology has allowed for the identification and tracking of previously non-cultivable microbes.
• It allows greater understanding of phylogenetics and evolutionary analysis.
• This field seeks understanding about what makes a pathogen a pathogen.
• This era focuses on what microbes can do and understanding the importance of bacteria to the Earth and human health.
• Bacteriology is the study of bacteria.
• Virology studies viruses.
• Mycology is the study of fungi.
• Parasitology studies parasites such as protozoans and parasitic worms.
• Immunology focused on studying the human defense system.

Cell Membrane and Cell Wall

• The cell membrane or plasma membrane is the outer layer of the cell.
• The cell membrane defines cell borders and regulates interaction with the environment.
• Cells must control what enters, exits, and is excreted, also sharing information and self-identifying.
• The cytoplasmic membrane is the membrane in contact with the cytoplasm.

Cytoplasmic Membrane Major Features

• Phospholipids containing a negatively charged phosphate head.
• Phospholipids contain nonpolar fatty acid tails.
• Proteins are embedded in the membrane and help in transport.
• The cell membrane is selectively permeable.

Membrane Permeability

• The lipid bilayer has a hydrophilic polar head on the outside and hydrophobic nonpolar tails on the inside.
• Nonpolar molecules can pass through easily, while larger polar molecules have a harder time.
• Ions cannot pass through by themselves.
• Semipermeable means selective, allowing nonpolar molecules and small polar molecules to pass through easily, while the rest need protein assistance.
• Eukaryotes use sterols like cholesterol to affect fluidity, while prokaryotes use hopanoids.

Tonicity in Living Cells

• Bacteria aren't protected like humans, thus need a strong cell wall.
• Cell walls surround the cell membrane, protecting it from changes.
• Tonicity impacts bacteria because they live in environments where ion concentrations can vary and need a rigid cell wall to prevent bursting.
• Cell walls are essential to bacteria and unique when compared to eukaryotes, making them an important antibiotic target.

Gram Staining

• Gram positive cells have a thick peptidoglycan layer.
• Gram negative cells have an extra outer membrane.
• Mycoplasma are bacteria without cell walls and are therefore not susceptible to some antibiotics like penecillin.

Gram Positive Cell Wall

• Contains a thick peptidoglycan layer
• Teichoic acids provide rigidity by attracting cations and allow for specificity between strains of the same bacteria.
• The periplasm is smaller and less important compared to Gram negative bacteria.

Gram Negative Cell Wall

• Gram negative cells have an extra outer membrane
• They have a thin PG layer.
• LPS aids in virulence and allows for specificity between strains of the bacteria.
• Periplasm

Peptidoglycan

• Peptidoglycan is present in both Gram positive and Gram negative bacteria.
• It’s a tough and rigid layer of repeating subunits of sugars which is made of N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM).
• NAG and NAM are glucose derivatives.
• Rows of these sugars are linked by polypeptides.
• Specifically the NAMs are linked by these multi-amino acid bridges.

Gram Negative PG Sheet

• Contains 4 amino acids from each NAM.
• L vs D amino acids, which affect the stereo- configuration of the amino acid
• L-amino acids are used in cells and proteins for all forms of life – including bacteria
• Bacteria are the only organisms that use D-amino acids, and it is only in their peptidoglycan.

Gram Positive PG Sheet

• Gram positive PG sheets use 4 amino acids indirectly with another 5-amino acid bridge called PENTAglycine.

Gram Positive vs. Gram Negative Cell Walls

• Gram positive cells contain a thick layer of PG; gram negative cells contain a thin layer.
• Gram positive cells use teichoic acids.
• Both cell walls have NAG and NAM sugars.

Gram Positive Cell Wall

• Amino acids indirectly link sugars with 4 amino acid bridges from NAMs that are linked by a pentaglycine bridge.

Gram Negative Cell Wall

• Amino acids link the sugars directly using 4 amino acid bridges from NAMs that are directly connected.

PG Sheets - Connected

• Gram + cells can have up to 50 peptidoglycan sheets.
• Gram + cell walls contain teichoic acid, linking the peptidoglycan sheets.

Outer Membrane (OM): Gram Negative Only

• The OM is a phospholipid bilayer, like the cell membrane.
• Has more porin channel proteins.
• Has lipopolysaccharide (LPS) which is made of 3 parts:
• Lipid A - unique phospholipid to anchor it in the OM
• Core polysaccharide - similar with genera of bacteria
• O polysaccharide - varies within species to give strain-specificity
• LPS is mainly a carbohydrate bacteria uses to identify each other - like an ID badge.
• Its lipid A component is an endotoxin that causes fever and inflammation as a systemic system response.

Periplasmic Space/Periplasm

• The periplasmic space is located between the cell membrane and an outer layer (OM or PG).
• The periplasmic space is used to break down enzymes.
• Present in both gram-neg and gram-pos cells. Has a more important enzymatic function in gram negative bacteria, and can change the pH.

External Layers

• Glycocalyx = polysaccharide outer layer
• Capsule
• Slime layer
• Capsule is structured and organized glycocalyx.
• Capsules Help in attaching and is a physical barrier.
• Capsules prevent dessiccation
• Capsules also evade the immune system.

Slime Layer

• A slime layer is Loose, unstructured, and thin layer
• Primarily made up of secreted polysaccharides.
• Help bacteria slide around and prevents dehydration.
• Slime layers can provide some protection but less so than capsules.

Endospores

• They are a special form bacteria can take (in gram positives)
• Endospores are a response to lack of nutrients.
• Endospores are basically a dehydrated cell covered by protective case.
• Ideal for dispersal via wind, water, or gut. Examples: Clostridium and Bacillus.
• Dipicolinic acid makes up 10% of spore weight and aids in heat resistance by dehydrating and stabilizing.
• Small acid-soluble proteins (SASPs) tightly bind and condense the DNA.
• SASPs provide protection from UV and DNA-damaging chemicals.

Prokaryotic Form and Features

• Prokaryotic cell diameter = ~1.0um typically
• Prokaryotic cell length = 2 to 8um typically
• These diameters can range from 0.2um to 700um
• Bacteria have better surface area to volume ratio and are very efficient.
• Bacteria replicate every 30 minutes
• Humans replicate every ~4 hours
• The smaller a cell is, the higher its SA:Vol ratio.

Prokaryotic Cell Shapes

• Cocci
• Bacilli
• Spirillum
• Vibrio
• Spirochete
• Modern day cell shapes

Cocci: Cell Arrangement

• Diplo = pair/two
• Strepto = chains
• Tetrad = set of 4
• Staphylo = clusters

Other Bacterial Arrangements

• Bacilli can only replicate on one plane.
• Coccobacillus exist as rounded rods and replicate on only one plane.

Bacterial Motility

• Bacteria are the fastest organism in relation to size.
• Flagella act as bacterial arms and legs.

Flagella Arrangments

• Atrichous = no flagella
• Polar = flagella at one or both ends, but nowhere else
• Montotrichous = single flagella
• Lophotrichous = 2+ flagella at one end
• Amphitrichous = flagella at both ends
• Petrichous = many flagella around perimeter of cell

Structure and Movement

• the Basal body is embedded in cell wall and acts as the motor.
• A hook connects the basal body to filament.
• The filament which extends outside of cell
• Runs and tumbles help bacteria movement depending on the rotation of flagella which consumes a large amount of energy.
• Taxis is used for the direct movement for bacteria which includes: Chemotaxis, Phototaxis and Magnetotaxis.

Motility: Taxis

• Taxis describes movement in response to the environment.
• Chemotaxis describes movement in response to a chemical.
• Phototaxis is movement in response to light.
• Magnetotaxis is movement in response to a magnetic field.

Fimbrae & Pili

• Fimbrae is used for attachment
• Pili is used for attachment, motility, and DNA transfer.
• All pili are hollow.

Functions of a Cell Wall

• Structure
• Permeability barrier
• Metabolite uptake
• Energy production
• Motility
• Mating
• Host interaction
• Adhesion to host cells
• Immune recognition by host
• Escape from host immune system
• The cell wall is Medical relevant as it acts as both antibiotic targets and aids antibiotic resistance.

Cell Wall Damage

• Damage differs between gram positive and gram negative cell walls due to structural differences which can be caused via:
• Digestive enzymes, such as Lysozymes
• The use of Antibiotics.
• Penicillin which is a β-lactams, interfers with the new linkage creation of amino acids during new peptidoglycan production.

Archaea

• Archaea is a Prokaryote (single-celled, no membrane bound organelles)
• Is similar to bacteria in structure and function, but differ in their chemical makeup
• Are highly recognized as different from bacteria in their genetics in the 1980's after sequencing studies.
• Is as diverse, if not more than bacteria
• Most famously known for their abilility to live in extreme temperature conditions
• Contains pigmented extremophiles which help with the extreme environments
• Archaea have a larger genome from living in such extreme environments

####### Major Groups

• Divided by functions or environments where they originate which includes:
• Methanogen - anaerobes that produce methane from CO2 and H2
• Halophiles - high salt concentration environments
• Hyperthermophiles - grow in very hot environments
• Possess a larger genome bc they require extra proteins/genes to survive in extreme conditions.
• Some Archaea has be found in human gut microbiome.
• Archaea is associated with infectious diseases for humans, animals or plants
• Important in sewage treatment plants

Cell membranes and Cell Walls

• Same basic structure - phospholipids, and proteins but is structured differently than bacteria structure.
• No OM
• Different bond connects the tail to the phosphate head
• Composed of a monolayer instead of a bilayer.
• Nonlinear (branched) chains.
• Ether linkage (stronger bond), not ester (old lady, weak) linkage

Cell Wall

• Contains no peptidoglycan, rather pseudomurein.
• Utilizes NAG and N-acetyltalosaminiuronic acid (NAT) with the amino acid bridges only using L amino acids.
• The S-Layer Is another type of layer in cell wall, and the outer layer of the wall is a surface-layer of proteins.

Archea Flagella

• Shorter and thiner than it's bacterial counterpart and may render it slower.
• It contains more flagellin types in comparison to Bacteria's one exclusive flagealla.

Differences Between Fungi and Bacteria

• Fungi are Eukaryotes.
• Fungi do not have Chloropasts.
• Fungi can be Macroscopic (mushrooms) AND microscopic (unicellular yeast).
• Not many are human pathogens.
• Important to the food chain because they can decompose dead things.

Forms of Fungi

• Mold - multicellular fungi
• Yeast - unicellular fungi
• Dimorphic - can be both mold and yeast
• Spores - form for reproduction

Characteristics

• Made of a mycelium network which is made from filaments called hyphae.
• Reproduce by replicating by budding.
• Can be pathogenic and are temperature-dependant.
• At body temperature (~37 C) are more yeast-like
• At room temperature (~25 C) are more mold-like

Reproduction

• Can be reproduced asexually or sexually
• Division of cells causes the creation on two identical cells (asexual)
• Combining two cells with different sexes causes a mixed genetic individual (sexual)
• asexual: cell elongates and splits in two.
• Budding: uneven dividing
• fragmentation: hyphae breaking into pieces.
• Sexual spores consist of clones that go germinate and grow into new fungi.

Structure

• Conidiospore - unicellular or multicellular spore that is not enclosed in a sac.
• Sporangiospore - formed within a sac (sporangium) at the end of a hypha.

Fungal Cell Structure and Life Cycle

• Plasmogamy
• Karogamy
• Meiosis
• Help identify various levels of taxonomy

Cell Membrane and Cell Walls

• Uses ergosterol on the cell membrane for fluidity
• Uses a thick chitin layer that forms the insects and crustaceans exoskelton Glucan is in abundance for the middle layer
• Mannoproteins contain outmost protection due to glucan attachments
• Chemoheterotrophs
• Thrives at lower pHs compared bacteria.
• They use all molds for aerobics, and yeasts for survivial.
• They thrive with high sugar and salt concentration environments.
• Needs less moisture an nitrogen.
• They metabolize higher carbohydrates compared to their bacteria counterpart

This lesson covers the basics of microbiology, including the characteristics, functions, and historical context of microorganisms. It explores cell structures, sizes, and the timeline of significant discoveries in the field.