Microbiology: Exam 1 Review

• The slides are for an Exam 1 review.

Microbiome

• An adult human contains 30 trillion body cells and harbors 40 trillion bacterial cells.
• Most bacteria in the microbiome cannot be identified using culture methods, according to the Human Microbiome Project.
• The microbiome or microbiota consists of microbes living stably on/in the human body.
• It helps maintain good health by limiting pathogenic species growth.
• Synthesizes necessary vitamins, like vitamins B and K.
• Aids in training the immune system to identify threats.

Normal Microbiota

• Normal microbiota is the collection of acquired microorganisms on or in a healthy human.
• Normal microbiota starts to be acquired before birth
• Colonization can occur indefinitely, or fleetingly, making them transient microbiota, and they're typically not harmful in normal circumstances.
• Colonization needs nutrients and the right environment for microbes to flourish.

Naming and Classifying Microorganisms

• Carolus Linnaeus started the scientific nomenclature system in 1735.
• Each organism has two names: genus and species, with Escherichia coli (E. coli) as an example where the genus and species must be spelled out on first mention.
• Bacteria names describe cell arrangement, habitat, or honor a scientist.

Nomenclature in the 21st Century

• Candidatus Liberibacter asiaticus (CLas): uncultured bacteria
• Molecular tools such as genome sequencing allow scientists to name uncultured bacteria.

Bacteria

• Bacteria and archaea are prokaryotes.
• Prokaryotes' genetic material is not enclosed in a special nuclear membrane.
• Bacteria are single-celled (unicellular).
• Cell walls are mostly peptidoglycan.
• Bacteria reproduce by dividing into two equal cells, called binary fission.
• Get nutrition from chemicals or photosynthesis.
• Move by using moving appendages called flagella.

Archaea

• Archaea are prokaryotes without a nuclear membrane.
• Their genetic material is not enclosed in a special nuclear membrane
• They lack peptidoglycan cell walls, maybe no cell wall.
• They live in extreme environments.
• Archaea types include:
  • Methanogens: respiration waste product is methane.
  • Extreme halophiles: live in salty environments, Great Salt Lake and Dead Sea.
  • Extreme thermophiles: live in hot springs, Yellowstone National Park
• They are not known to cause disease in humans.

Fungi

• Fungi are eukaryotes with a distinct nucleus containing DNA within a nuclear membrane.
• Chitin is in the cell walls.
• Absorb organic chemicals for energy.
• Yeasts are unicellular.
• Molds and mushrooms are multicellular.
• Molds consist of mycelia masses and hyphae filaments.
• Fungi reproduce sexually or asexually.
• They obtain nutrients from the environment, in the soil, animal or plant host.

Protozoa

• Protozoa are unicellular eukaryotes.
• Absorb or ingest organic chemicals.
• They are motile via pseudopods, cilia, or flagella.
• Free-living or parasitic, deriving nutrients from a living host.
• Some Protozoa are photosynthetic
• Reproduce sexually or asexually.
• Malaria is caused by a protozoan parasite from the Plasmodium genus.

Algae

• Photosynthetic eukaryotes need light, water, and carbon dioxide.
• Algae produce oxygen and carbohydrates used by other organisms.
• Cell walls of many algae are cellulose.
• Found in freshwater, saltwater, and soil.
• Sexual and asexual reproduction is possible.

The Cell Wall and Glycocalyx

• Cell wall made of carbohydrates, is found in plants, algae, and fungi.
• Cellulose is in plants and algae.
• Chitin is in fungi.
• Glycocalyx contains carbohydrates bonded to protein and lipids in the plasma membrane.
• Glycocalyx is found in animal cells.
• Glycocalyx strengthens, helps attach cells.

Viruses

• They are acellular, not cells.
• Are structurally simple, consisting of DNA or RNA core.
• Have a protein coat surrounding core.
• The protein coat can be enclosed in a lipid envelope
• Replicated in a living host cell.
• Require host cell machinery to reproduce.
• Inert outside of a living host, so they can't reproduce or replicate on their own.

Multicellular Animal Parasites

• Eukaryotes are multicellular animal parasites.
• Multicellular parasites are not strictly microorganisms.
• Microscopic worms are helminths in some stages.
• Medical importance.

Louis Pasteur (1822-1895)

• Louis Pasteur disproved spontaneous generation due to the swan-necked flask experiment.
• The experiment showed that oxygen does not enable spontaneous generation and that liquid remains sterile until microorganisms are introduced.

Endosymbiosis

• About 3.5 to 4 billion years ago life arose on Earth as simple, prokaryotic organisms.
• About 2.5 billion years ago eukaryotic cells evolved from prokaryotic cells via endosymbiosis.
• Endosymbiosis: a relationship where one organism lives within another, living together.
• Larger bacteria engulfed smaller bacterial cells, according to theory.

Model of the Origin of Eukaryotes

• Bacteria and archaea cells are engulfed by a proto-eukaryote leading to a eukaryote capable of endosymbiosis.

Evidence for Theory of Endosymbiosis

• Mitochondria and Chloroplasts resemble bacteria.
• Mitochondria and Chloroplasts have circular DNA.
• Mitochondria and Chloroplasts reproduce independently.
• Ribosomes resemble prokaryote ribosomes.
• Antibiotics that inhibit protein synthesis on bacterial ribosomes also inhibit protein synthesis on ribosomes in mitochondria and chloroplasts

Prokaryotic vs Eukaryotic Organelle Comparison

• Key differences exist in DNA structure, the presence of histones, the first amino acid in protein synthesis, ribosome type, and growth mechanisms between prokaryotic cells and eukaryotic organelles.

Classification of Eukaryotes

• Protista is a kingdom that includes mostly unicellular eukaryotes currently grouped into genetically related clades based on rRNA.
• Fungi can be unicellular or multicellular and have chitin cell walls.
• Plantae are multicellular with cellulose cell walls and undergo photosynthesis.
• Animalia is multicellular, no cell walls.

Classification of Prokaryotes

• A prokaryotic species is a population of cells with high genomic similarity.
• Culture: bacteria grown in laboratory media often from a clone
• Clone: population of cells derived from a single parent cell
• Strain: genetically different cells within a clone

Classification of Viruses

• Viruses are not under any domain.
• They aren't composed of cells.
• They require a host cell to reproduce.
• Viral species constitute viruses with similar characteristics and that can be distinguished from other species by multiple methods such morphology, genomes, enzymes, and ecological niche.
• Viruses are intracellular parasites.

Morphology Bacterial Shapes

• Typical bacterial size is 0.2-2.0 µm diameter x 2-8 µm length
• Most bacteria are monomorphic (single shape) with the exception of bacteria that are pleomorphic (many shapes)
• Bacterial shapes include:
  • Coccus: spherical.
  • Bacillus: rod-shaped.
  • Spiral: vibrio, spirillum, spirochete.
  • Star-shaped
  • Rectangular
• Staphyle is a cluster of grapes.
• A streptos is a chain.

Changes in Cell Shape

• Bacterial cells have high morphological plasticity.
• Pleomorphic: cells have multiple shapes.
• Changes during growth: Cells become smaller as they age.
• Nutrient limitation leads to increase of surface/volume ratio to maximize bacterial cell growth.
• Larger surface/volume ratio is better because enzymes are on the membrane surface where many biological functions occur.
• Response to environmental stresses: host immune responses, & harsh conditions can cause cells to change shape.

The Structure of a Prokaryotic Cell

• Typical bacteria's outer layer may include glycocalyx, cell wall, or plasma membrane, which may enclose cytoplasm, ribosomes (70S), DNA within the nucleoid in addition to inclusions, and may carry plasmids that encode antibiotic production.
• Prokaryotic cells usually lack membrane-enclosed organelles.
• All bacteria contain a cytoplasm, ribosomes, a plasma membrane, and a nucleoid.
• There also maybe pili, fimbriae, capsule, and a flagella
• Specific roles for some outer-surface, bacteria include:
  • Capsule (glycocalyx): increase bacterial virulence.
  • Cell wall + flagella: aid in bacterial identification.
• Plasmids carry information for resistance to antibiotics.
• Plasmids can be shared between bacteria.

Advantage of Motility

• Motility enables a bacterium to move toward a favorable or away from an adverse environment.
• Taxis: the movement of a bacterium toward or away from a particular stimulus.
• Chemotaxis: movement in response to the presence of a chemical.
• Phototaxis: movement in response to the presence of light.
• Receptors in motile bacteria pick up stimuli such as oxygen and glucose.
• Attractant: a positive chemotactic signal causes the bacteria to move via runs.
• Repellent: a negative chemotactic signal causes the bacteria to move via tumbles.

Flagella

• Filamentous appendages on cell surface that propel bacteria.
• Three basic parts: -Made of the protein flagellin, the filament is the outermost region -Hook attaches the filament. -Basal body anchors flagellum to the cell.
• Bacteria that lack flagella are referred to as atrichous (without projections).

Axial Filaments

• Axial filaments are found in spirochetes.
• Spirochetes cause Syphilis and Lyme Disease.
• Anchored at one end of a cell, filament rotation causes movement in outer sheath.
• The cell then moves like a corkscrew.

Flagella and Cilia

• Eukaryotic projections used for movement or to move substances along the cell surface composed of microtubules (9+2 array).
• Flagella: long, few.
• Cilia: short, numerous. Both consist of microtubules made of the protein tubulin.
• Flagella move in a wavelike manner.

Fimbriae and Pili

• Fimbriae:
  • allow for attachment.
  • are involved in the formation of biofilms.
  • enable some bacteria to adhere to body surfaces.
  • E. coli O157 causes severe diarrhea as it adheres to the lining of the intestine.
  • In the absence of fimbriae, colonization and disease do not occur.
• Pili:
  • involved in motility via gliding and twitching motility. -pilus extends via added subunits of pilin, which makes surface contact.
  • DNA transfer between cells vis conjugation (sex) pili -transfers antibiotic resistance.

Mycoplasmas - Atypical Cell Walls

• Smallest known bacteria that can grow and reproduce outside a living host cell and pass through bacteria filters.
• Unique plasma membranes among bacteria: they have lipids called sterols.
• Significant human pathogen Mycoplasma pneumoniae (pneumonia).

Atypical Cell Walls

• Acid-fast cell walls
  • Contain peptidoglycan
  • Waxy lipid (mycolic acid) that prevents the uptake of dyes.
  • Arabinogalactan: polysaccharides that hold together mycolic acid and peptidoglycan.
  • Acid-fast genera include mycobacterium and nocardia.

Active Transport: Group Translocation

• Substrates enter the cells by facilitated diffusion through specific transporter proteins.
• Substrates are modified during the transportation process, such as glucose turning into glucose 6 phosphate
• Uses energy from phosphoenolpyruvate (PEP), which attaches a phosphate to specific sugars.

Types of Microscopy

• Types of Light Microscopy: uses visible light to observe specimens. -Bright-field (light) microscopy. -Darkfield microscopy. -Phase-contrast microscopy. -Fluorescence microscopy. -Confocal microscopy.
• Types of Electron Microscopy: microscope used with electron beams. -Transmission electron microscope (TEM). -Scanning electron microscope (SEM).

Fluorescence Microscopy

• A light microscope that uses blue or ultraviolet light to illuminate.
• Very useful for the rapid detection of pathogenic microorganisms in clinical samples due to their florescence.
• Fluorescence: the substances ability to glow with a particular color when exposed to light of another color.
• Organisms fluoresce naturally under UV light or can be stained with fluorochromes like auramine O, which glows yellow under UV and absorbed by Mycobacterium tuberculosis.
• Fluorescent antibodies are from chemically combined fluorochrome and antibody, which helps detect unknown bacterium.

Bacterial Oxygen Preferences

• Bacterial oxygen preferences rank from high oxygen to "no" oxygen needed for:
  • Obligate aerobes, like M. tuberculosis.
  • Facultative anaerobes like E. Coli.
  • Aerotolerant anaerobes like C. acnes.
  • Microaerophiles like H. Pylori.
  • Obligate anaerobes such as C. perfringens.

Explanation for Bacterial Growth Patterns in Oxygen

• Reactive oxygen species cause water + oxygen via Superoxide Dismutase and Catalase/Peroxidase.
• Growth patterns depend on whether they contain needed enzymes.
• Bacteria growth ranks: Aerobes/Anaerobes/Facultative Anaerobes/Aerotoleant Anaerobes/Microaerophiles

Selective and Differential Media

• Selective media suppresses unwanted microbes and encourages desired microbes by way of Bismuth sulfite agar: for Salmonella Typhi and that inhibits gram-positive microorganisms.
• Differential media uses blood agar to help to distinguishes colonies on the same plate to find Streptococcus pyogenes, which lyses red blood cells

Selective and Differential Media: Mannitol Salt Agar

• Staphylococcus aureus tolerates the high salt concentration
• Uses mannitol for energy generation which causes acid as byproduct.
• S. epidermidis is not going to ferment mannitol

Generation Time

• Cell number doubles after each binary fission.
• Time to double the number of cells is called the generation time or doubling time(ta).
• Most bacterial doubling times are 1-3 hours, some make take over 24 hours; Ta varies with growth.
• Initial number of cells * 2number of generations = Number of cells

Direct Measurement: Viable Plate Count

• Serial dilutions from a liquid culture sample are placed upon a plate, then counts the number of colonies to reflect the original, reproducing (viable) cells after incubation.
• Count only accurately count 30-300 colonies/ per plate.

Terminology of Microbial Control: Sterilization

• Sterilization is the destruction of all microorganisms, including endospores.
• Heating is commonly used as a sterilant
• Commercial sterilization is used to limit he heat treatment of destroying endospores for canned goods in Clostridium botulinum bacteria.

Terminology of Microbial Control: Disinfection and Antisepsis

• Disinfection controls microbes on inanimate objects (vegetative pathogens) using UV, steam, or chemicals.
• Antisepsis eliminates harmful microorganisms from living tissue.
• Disinfectant used in antisepsis are called antiseptics.
• Sepsis refers to a pathogenic organism or toxin presence in blood and tissue that results disease. Many chemical disinfectants may be too hard to use as antiseptics