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• Study notes for Microbiology and Parasitology

Microbiology

• Study of microscopic organisms
• Microbiology is derived from Greek words: mikros (small), bios (life), and logia (study)

Microorganisms

• Microbes too small to be seen without aid
• Germ refers to a rapidly growing cell

Microbes in Our Lives

• Some microbes are pathogenic, meaning they cause disease
• Microbes decompose organic waste
• Crucial producers in ecosystems via photosynthesis
• Involved in producing industrial chemicals like ethanol and acetone
• Utilized in producing fermented foods like vinegar, cheese, and bread
• Used in the manufacturing and treatment of diseases

Knowledge of Microorganisms

• Allows humans to prevent food spoilage
• Helps prevent disease occurrence
• Leads to aseptic techniques which prevent contamination in medicine and labs

Naming Microorganisms

• Linnaeus established scientific nomenclature
• Each organism has two names: genus and specific epithet
• Names are italicized or underlined
• Genus is capitalized and the specific epithet is lowercase

Scientific Names

• Latinized and used universally
• Names may be descriptive or honor a scientist
• Scientific names can be abbreviated after first use by using the first letter of the genus and the specific epithet;
  • Escherichia coli and Staphylococcus aureus are located in the human body
    • E. coli is found in the large intestine, while S. aureus is on the skin

Types of Microorganisms

• Bacteria
• Archaea
• Fungi
• Protozoa
• Algae
• Viruses
• Multicellular animal parasites

Classification of Microorganisms

• Three domains: Bacteria, Archaea, and Eukarya
  • Eukarya includes: protists, fungi, and plants

Germ Theory of Disease

• Agostino Bassi (1835) demonstrated that a silkworm disease was caused by a fungus
• Pasteur (1865) proposed that another silkworm disease was caused by a protozoan
• Ignaz Semmelweis (1840s) advocated for handwashing to prevent puerperal fever transmission
• Joseph Lister (1860s) used chemical disinfectant to prevent surgical wound infections, applying Pasteur's work
• Robert Koch (1876) proved a bacterium causes anthrax using Koch's postulates to show a specific microbe causes a specific disease

Anthrax

• Serious infectious disease
• It is caused by gram-positive, rod-shaped bacteria known as Bacillus anthracis

Vaccination

• Edward Jenner (1796) inoculated a person with the cowpox virus, protecting them from smallpox
• Vaccination derives from vacca (cow)
• The protection is called immunity

Chemotherapy

• Treatment via chemicals
• Chemotherapeutic agents: synthetic drugs or antibiotics used for infectious diseases
• Antibiotics are chemicals produced by bacteria and fungi to kill microbes
• Paul Ehrlich contributed to Chemotherapy
• Synthetic drugs created man-made chemicals

First Synthetic Drugs

• Quinine from tree bark to treat malaria
• Ehrlich's "magic bullet" concept could destroy pathogens without harming the host
• Ehrlich (1910) developed salvarsan to treat syphilis
• Sulfonamides were synthesized in the 1930s

Antibiotics

• Syphilis is a bacterial infection usually spread by sexual contact.
• Alexander Fleming discovered the first antibiotic in 1928
• Penicillium fungus made penicillin that killed S. aureus

Penicillin

• Penicillin was tested and mass produced clinically in the 1940s

Bacteriology

• Study of bacteria

Mycology

• Study of fungi

Virology

• Study of viruses

Parasitology

• Study of protozoa and parasitic worms

Immunology

• Study of immunity
  • Vaccines and interferons are investigated to prevent and cure viral diseases
• Rebecca Lancefield (1933) proposed using immunology to identify some bacteria according to serotypes

Interferons

• Proteins part of the body's natural defenses

Serotype

• Distinct variation within a bacteria/virus species or immune cells

Recombinant DNA Technology

• Microbial genetics studies how microbes inherit traits
• Molecular biology studies how DNA directs protein synthesis
• Genomics studies an organism's genes, providing new tools for classifying MCO
• Recombinant DNA from two sources
• Paul Berg (1960s) inserted animal DNA into bacterial DNA, prompting the bacteria to produce an animal protein
• George Beadle and Edward Tatum (1941) showed that genes encode a cell’s enzymes
• Oswald Avery, Colin MacLeod, and Maclyn McCarty (1944) showed that DNA is the hereditary material
• Francois Jacob and Jacques Monod (1961) discovered mRNA’s role in protein synthesis

Microbial Ecology

• Bacteria recycle carbon, nutrients, sulfur, and phosphorous for plants and animals

Bioremediation

• Bacteria degrade organic matter in sewage
• Bacteria degrade or detoxify pollutants like oil and mercury

Biological Insecticides

• Microbes pathogenic to insects are alternatives to chemical pesticides
• Bacillus thuringiensis infections are fatal to insects but harmless to other animals, including humans and plants

Biotechnology

• Centuries-old use of microbes to produce foods and chemicals
• Recombinant DNA technology enables bacteria and fungi to produce proteins like vaccines and enzymes
• Missing or defective genes in human cells can be replaced via gene therapy
• Genetically modified bacteria are used to protect crops from insects and from freezing

Biofilms

• Microbes attach to solid surfaces and grow into masses
• Microbes grow on rocks, pipes, teeth, and medical implants

Normal Microbiota

• Bacteria were classified as plants, leading to the term flora for microbes
• Term "flora" replaced by microbiota
• Normal microbiota are microbes present in and on the human body
• Prevents growth of pathogens
• Produces growth factors like folic acid and vitamin K
• Resistance is the body's ability to ward off disease

Resistance Factors

• Include skin, stomach acid, and antimicrobial chemicals

Infectious Diseases

• Disease results when a pathogen overcomes the host’s resistance
• Emerging infectious diseases (EIDs) are new or increasing diseases

Drug Resistance

• New Threat in Microbiology: Methicillin-resistant Staphylococcus aureus (MRSA)
  • 1950s: Penicillin resistance
  • 1980s: Methicillin resistance
  • 1990s: Vancomycin resistance reported
    • VISA stands for vancomycin-intermediate-resistant S. aureus
    • VRSA stands for vancomycin-resistant S. aureus
• Methicillin-resistant Staphylococcus aureus (MRSA) is a difficult-to-treat staph infection due to antibiotic resistance

Methicillin

• An antibiotic previously used for Staphylococcus infections
• It is a semisynthetic derivative of penicillin

Bacteria Definition

• Unicellular organisms lacking organelles and a true nucleus
  • Peptidoglycan cell walls
  • Reproduce via binary fission
  • Obtain energy from organic, inorganic chemicals, or photosynthesis

Bacteria

• Single-celled microorganisms classified as prokaryotic
• They lack a nucleus and other cell organelles
• Versatile and able to survive in harsh conditions

Extremophiles

• Versatile organisms, surviving in extremely inhospitable conditions
  • Thermophiles: survive high temperatures
  • Acidophiles: thrive under highly acidic conditions (pH 2.0 or below)
  • Alkaliphiles: grow at pH values above 9.0, showing little to no growth at near neutral pH values
  • Osmophiles: adapted to high osmotic pressures, such as high sugar concentrations, halophiles (salt-loving organisms)
  • Barophiles: An organism that lives and thrives under high barometric pressure
  • Cryophiles: an organism that is able to survive and thrive in areas that have very low temperatures.

Bacteria's Protective Cell Wall

• Made of peptidoglycan, found only in bacterial cell walls

Structures of Bacteria

• Capsules are the outer protection layer
  • Either Flagella or pili which functions as a locomotory organ is attached. Pili can also help certain bacteria to attach themselves to the host's cells. They do not contain any cell organelle as in animal or plant cell except for ribosomes. Ribosomes are protein synthesis sites that have an extra-circular DNA called plasmid which make some strains of bacteria resistant to antibiotics

Bacteria can be classified based on features such as

• Shape (bacillus, spirilla, coccus, vibrio)
• Cell wall composition
• Respiration Mode
• Nutrition Mode

Bacteria: Cell Wall

• Gram-positive bacteria have thick peptidoglycan layers
• Whereas gram-negative bacteria have thin peptidoglycan layers
• Gram-postive retains the purple stain during the gram staining procedure

Bacteria: Exotoxins vs Endotoxins

• Gram-positive bacteria produce exotoxins
• Gram-negative bacteria produce endotoxins
• Gram-negative bacteria cause many human infections

Bacteria: Reproduction

• Reproduce asexually via binary fission
• Replication starts with replication of DNA. Then elongation of cells lead to 2 daughter cells
• Reproduction depends on temperature and nutrient availability

Bacterial Reproduction

• Rapid; E. coli produces about 2 million bacteria every 7 hours
• Primarily asexual, but can undergo sexual reproduction rarely
• Genetic recombination potential via conjugation, transformation, or transduction, leading to antibiotic resistance

Beneficial Bacteria

• Many are useful to humans
  • Convert milk to curd
  • Ferment food products
  • Aid digestion and boost immunity

Soil Bacteria

• Produce antibiotics
• Used to treat and prevent infections

Harmful Bacteria

• Cause illnesses like pneumonia, tuberculosis, diphtheria, syphilis, tooth decay
• Effects can be rectified via antibiotics
• Eliminating disease-causing bacteria by sterilizing or disinfecting items or surfaces via heat, disinfectants, UV radiation, pasteurization, boiling, etc

Archaea

• Domain Archaea: single-celled prokaryotic organisms - The cells lack a defined nucleus that has distinct molecular features that separate them from bacteria, as well as from eukaryotes
  • Derives from the Greek word “archaios” (ancient/primitive)
    • Includes “Pyrolobus fumarii”, which holds the upper temperature limit for life at (113 °C/235 ° F), located in hydrothermal vents;
    • Species of Picrophilus were isolated from acidic soils in Japan and are the most acid-tolerant organisms known capable of growth at; and methanogens, which create methane gas

Archaea Features

• Prokaryotic
• Lack peptidoglycan
• Live in extreme environments
  • Methanogens
  • Extreme halophiles
  • Extreme thermophiles

Eukaryote

• An organism of the Eucaryotae, whose cell have a true nucleus, consists of chromosomes and divides by mitosis
  • Eukaryotic cells contain organelles such as mitochondria, chloroplasts, lysosomes, and the Golgi apparatus
• Include: plants, animals, protozoa, fungi, and algae
  • EXCEPT blue-green algae.

A cell is characterized by;

• containing a chromosome of DNA and proteins, having a mitosis cell division
• a present mitochondria
• plastids are found in photosynthetic species, undulipodia which are composed of microtubules and various proteins

Superkingdom Eukaryotae

• Eukaryote cell type characterizes four kingdoms above the Monera or prokaryote level of complexity
• Protoctista, Fungi, Plantae, and Animalia combined

Fungus

• Any member of eukaryotic organisms
• The group entails yeasts, molds, and mushrooms
• Fungi are free-living in soil or water and the others form relations with plants and animals

Fungi (Eukaryotic Organisms)

• Fungi are free-living in soil or water; others form parasitic or symbiotic relationships with plants or animals
• The cells contain organelles and included in the plant kingdom
• Fungi are distinguished by unique structural and physiological features
• Fungi: chitin cell walls, use organic chemicals for energy, molds and mushrooms are multicellular, consisting of masses of mycelia and yeast

Plant vs Fungi

• Clearly distinguished from all other organisms, including animals, by the vegetative growth and nutrient intake principal modes
• Fungi grow from hyphae (filaments that make up mycelia) and digest nutrient and organic matter/material
• From the Latin word means mushroom fungus
• While mushrooms and toadstools means the numerous that are most recognized, the study of fungi is known as mycology (from the Greek word for mushroom- mykēs)

Protozoa (definition & characteristics)

• Phylum of the kingdom Protistia
• Includes unicellular, animal-like microorganisms
• Many protozoa are saprophytes that live on dead matter in water and soil
• Many parasitic protozoa infect humans
• Infections are spread through contaminated foods
• Protozoa: unicellular, animal-like organism, resides a dead matter
• Absorb/ingest organic chemicals
• Motile via pseudopods, cilia, and flagella

Protozoa

• Are classified as living on a dead matter, they infect person that have low immune system, absorb chemicals, and motile.

Common Protozoan infections

• Malaria, gastroenteritis, leishmaniasis, sleeping sickness, and vaginal infections
• Cryptosporidium parvum and toxoplasma gondii are seen in patients who are immunosuppressed

Protozoa: Motility

• Cilia: tiny hair like structures that cover the outside of the microbe
• Flagella: long thread-like structures that extend from the cell surface
• Amoeboid movement: organism moves by protrusions that fill with cytoplasm from the body

Algae definition & characteristics

• Are grouped aquatic that of kingdoms protista
• Many types of life cycles and range
• Their pigments are more varied vs. plants
• They function to provide source, oil
• The taxonomy is constantly changing

Algae Characteristics

- Are eukaryotes, cellular, autotrophs and produce oxygen compounds

Viruses (Definition & Characteristics)

• Infectious agent with both living and nonliving organisms depends on a host call for replication, which has DNA or RNA
• Made of Acellular, consists of DNA or RNA with protein coat as enveloped
• They affect the body when living in a host cell

Virus Definition & Criteria

• Infectious agent with living and nonliving characteristics totally dependent on a host cell for replication
• Contain DNA or RNA
• Viral genome directs the synthesis of what will occur

Virus Replication

Bacteria and Prokaryotic

• Undergo mitosis or cellular reproduction

Multicellular Animal Parasites Characteristics

• Eukaryotes
• Multicellular Animals
• Parasitic flatworms and roundworms called helminths
• Microscopic stages in life cycles