causative relationship

Microbiology and Parasitology between a microbe and a

Notes disease. He also identified
the causative agents of
Module 1: Introduction to tuberculosis, cholera, and
Microbiology anthrax.
Week 1-2: Basics of Microbiology
Classification of
History and Scope of Microbiology
Microorganisms
● Definition: Microbiology is the
Microorganisms are a diverse group of
scientific study of
organisms that are too small to be seen
microorganisms, which are
with the naked eye. They play crucial
unicellular, multicellular, or
roles in various ecological and
acellular microscopic organisms.
physiological processes.
These include bacteria, archaea,
Microorganisms are classified into
viruses, fungi, protozoa, and
several categories based on their
algae. Microbiology encompasses
cellular structure, genetic makeup, and
several sub-disciplines including
biochemical properties.
bacteriology, virology, mycology,
and parasitology. 1. Bacteria
● Key Historical Figures:
○ Antonie van Leeuwenhoek: Characteristics:
Known as the father of
● Prokaryotic: Lack a true nucleus
microbiology, he was the
and membrane-bound organelles.
first to observe and
● Unicellular: Consist of a single
describe microorganisms
cell.
using a single-lens
● Cell Wall Composition: Typically
microscope he developed.
composed of peptidoglycan.
○ Louis Pasteur: Disproved
the theory of spontaneous Examples:
generation through his
swan-neck flask ● Escherichia coli (E. coli): A
experiments, developed the common inhabitant of the human
process of pasteurization to gut, some strains can cause food
kill pathogens in food and poisoning.
beverages, and created the ● Staphylococcus aureus: Found
first vaccines for rabies and on the skin and respiratory tract;
anthrax. can cause infections like boils,
○ Robert Koch: Formulated pneumonia, and sepsis.
Koch's postulates, which are
Importance:
criteria to establish a
 ● Ecological Roles: Decomposers, ● Diverse: Includes both unicellular
nitrogen fixers, and symbionts. and multicellular organisms.
● Industrial Uses: Fermentation,
a. Fungi
biotechnology, antibiotics
production. Characteristics:

2. Archaea ● Eukaryotic: True nucleus and

organelles.
Characteristics: ● Cell Wall Composition: Contains
chitin.
● Prokaryotic: Similar to bacteria
● Modes of Nutrition: Saprophytic,
but with distinct genetic and
parasitic, or symbiotic.
biochemical features.
● Extremophiles: Many archaea Examples:
live in extreme environments such
as high salinity, temperature, or ● Candida albicans: A yeast that
acidity. can cause opportunistic
● Cell Wall Composition: Lack infections in humans.
peptidoglycan; have unique ● Aspergillus: A genus of mold
membrane lipids. known for its role in
decomposition and production of
Examples: aflatoxins.

● Methanogens: Produce methane; Importance:

found in anaerobic environments
like wetlands and the guts of ● Ecological Roles: Decomposers,
ruminants. symbionts in mycorrhizae.
● Halophiles: Thrive in high-salt ● Industrial Uses: Fermentation
environments such as salt lakes. (e.g., yeast in baking and
brewing), antibiotic production.
Importance:
b. Protozoa
● Ecological Roles: Key players in
Characteristics:
biogeochemical cycles like
methane production. ● Eukaryotic: Single-celled
● Biotechnological Uses: Enzymes organisms.
from extremophiles are used in ● Modes of Movement: Cilia,
industrial processes. flagella, or pseudopodia.
● Nutrition: Heterotrophic.
3. Eukaryota
Examples:
Characteristics:
● Plasmodium: Causes malaria,
● Eukaryotic: Have a true nucleus
transmitted by Anopheles
and membrane-bound organelles.
mosquitoes.
 ● Entamoeba histolytica: Causes ● Eukaryotic: Multicellular parasitic
amoebiasis, a type of worms.
gastrointestinal infection. ● Complex Life Cycles: Often
involve multiple hosts.
Importance:
Examples:
● Medical Significance: Many
protozoa are pathogens causing ● Ascaris lumbricoides: A large
diseases in humans and animals. intestinal roundworm causing
● Ecological Roles: Part of the ascariasis.
aquatic food web, nutrient ● Schistosoma: A genus of
recycling. flatworms causing
schistosomiasis.
c. Algae
Importance:
Characteristics:

● Eukaryotic: Photosynthetic ● Medical Significance: Cause

organisms. various diseases in humans and
● Unicellular or Multicellular: Can animals.
form colonies or complex ● Ecological Roles: Part of the food
multicellular structures. web, can impact host populations.
● Chlorophyll and Other
4. Viruses
Pigments: Used for
photosynthesis. Characteristics:

Examples: ● Acellular: Not composed of cells,

lack cellular structures.
● Chlamydomonas: A unicellular
● Obligate Intracellular Parasites:
green alga used in research.
Require a host cell for replication.
● Spirogyra: A filamentous green
● Genetic Material: Can be DNA or
alga found in freshwater
RNA.
environments.
Examples:
Importance:
● Influenza Virus: Causes the flu,
● Ecological Roles: Primary
characterized by seasonal
producers in aquatic ecosystems.
outbreaks.
● Industrial Uses: Biofuel
● Human Immunodeficiency Virus
production, food supplements
(HIV): Causes AIDS, affecting the
(e.g., spirulina).
immune system.
d. Helminths
Importance:
Characteristics:
 ● Medical Significance: Cause categories: prokaryotic and eukaryotic
numerous diseases in humans, cells. Each type has distinct structural
animals, and plants. features and functions.
● Biotechnological Uses: Gene
therapy, vaccines, molecular Prokaryotic Cells
biology research.
Prokaryotic cells are simpler and
smaller than eukaryotic cells. They lack
5. Prions
a true nucleus and membrane-bound
Characteristics: organelles. Prokaryotic cells are
typically found in the domains Bacteria
● Acellular: Infectious proteins
and Archaea.
without nucleic acids.
● Misfolded Proteins: Induce Structure
abnormal folding of normal
1. No Nucleus:
cellular proteins.
● Nucleoid Region: The DNA is
Examples: located in an irregularly shaped
● Creutzfeldt-Jakob Disease region called the nucleoid. This
(CJD): A fatal neurodegenerative area is not surrounded by a
disorder in humans. membrane.
● Kuru: A neurodegenerative 2. Single Circular Chromosome:
disorder historically found in the
Fore people of Papua New ● Genetic Material: The genetic
Guinea. material of prokaryotes is
typically a single circular DNA
Importance: molecule that contains all the
● Medical Significance: Cause necessary genetic information for
fatal and transmissible the cell's functions.
neurodegenerative diseases. 3. Cell Wall:
● Research Significance: Provide
insights into protein folding and ● Composition: In bacteria, the cell
misfolding diseases. wall is primarily composed of
peptidoglycan, a polymer
Structure and consisting of sugars and amino
acids. Archaea have cell walls
Function of
made of different substances,
Prokaryotic and such as pseudopeptidoglycan.
Eukaryotic Cells ● Function: The cell wall provides
structural support, maintains the
Cells are the basic units of life, and they shape of the cell, and protects
can be broadly classified into two
 against mechanical stress and 8. Plasmids:
osmotic lysis.
● Structure: Small, circular,
4. Plasma Membrane: double-stranded DNA molecules
separate from the chromosomal
● Structure: The plasma membrane
DNA.
is a phospholipid bilayer with
● Function: Plasmids often carry
embedded proteins.
genes that confer advantages
● Function: It controls the passage
such as antibiotic resistance.
of substances into and out of the
cell, maintaining the internal Function
environment and facilitating
Prokaryotic cells perform all essential
communication and transport.
life processes, including metabolism,
5. Ribosomes: growth, and reproduction. They
reproduce asexually through binary
● Structure: Prokaryotic ribosomes fission, where the cell divides into two
are smaller (70S) than eukaryotic identical daughter cells.
ribosomes (80S) and consist of
two subunits (30S and 50S). Eukaryotic Cells
● Function: They are the sites of
Eukaryotic cells are more complex and
protein synthesis, translating
larger than prokaryotic cells. They have
genetic information into proteins.
a true nucleus and membrane-bound
6. Flagella: organelles. Eukaryotic cells are found in
the domains Eukarya, which includes
● Structure: Flagella are long, animals, plants, fungi, and protists.
whip-like appendages made of
the protein flagellin. Structure
● Function: They are used for 1. Nucleus:
motility, allowing the cell to move
toward favorable environments or ● Structure: The nucleus is a
away from unfavorable membrane-bound organelle that
conditions through a process contains the cell's DNA organized
called chemotaxis. into multiple linear chromosomes.
It is surrounded by a double
7. Pili and Fimbriae: membrane called the nuclear
envelope, which has nuclear
● Structure: Hair-like structures on
pores for the exchange of
the surface of the cell.
materials.
● Function: Pili (or pilus) are
● Function: It acts as the control
involved in DNA transfer during
center of the cell, regulating gene
conjugation, while fimbriae help
expression and mediating the
the cell adhere to surfaces and
other cells.
 replication of DNA during the cell ○ Structure: A series of
cycle. flattened, membrane-bound
sacs.
2. Cell Membrane:
○ Function: It modifies, sorts,
● Structure: The cell membrane is a and packages proteins and
phospholipid bilayer with lipids for transport to
embedded proteins, cholesterol, different destinations within
and carbohydrates. or outside the cell.
● Function: It regulates the ● Lysosomes:
passage of substances into and ○ Structure:
out of the cell, provides Membrane-bound
protection, and facilitates organelles containing
communication and signal hydrolytic enzymes.
transduction. ○ Function: They digest and
recycle cellular waste,
3. Organelles: pathogens, and
macromolecules.
● Mitochondria:
● Peroxisomes:
○ Structure:
○ Structure: Small,
Double-membrane-bound
membrane-bound
organelles with their own
organelles containing
DNA and ribosomes.
oxidative enzymes.
○ Function: They are the
○ Function: They detoxify
powerhouses of the cell,
harmful substances and
generating ATP through
break down fatty acids.
cellular respiration.
● Cytoskeleton:
● Endoplasmic Reticulum (ER):
○ Structure: A network of
○ Structure: A network of
protein filaments
membranous tubules and
(microfilaments,
sacs. It has two types:
intermediate filaments, and
rough ER (studded with
microtubules).
ribosomes) and smooth ER
○ Function: Provides
(lacks ribosomes).
structural support,
○ Function: Rough ER is
maintains cell shape, and
involved in protein synthesis
facilitates cell movement
and processing, while
and intracellular transport.
smooth ER is involved in
● Chloroplasts (in plant cells):
lipid synthesis,
○ Structure:
detoxification, and calcium
Double-membrane-bound
storage.
organelles with their own
● Golgi Apparatus:
DNA and ribosomes,
containing chlorophyll.
 ○ Function: They perform many physiological processes and
photosynthesis, converting plays a critical role in maintaining
light energy into chemical health.
energy stored in glucose.
● Vacuoles: Functions of the Human
○ Structure: Large, Microbiome
membrane-bound sacs. 1. Digestive Health
○ Function: In plant cells,
vacuoles store nutrients, Role in Digestion:

waste products, and help ● Breakdown of Complex

maintain turgor pressure. In Carbohydrates: Microbes in the gut
animal cells, vacuoles are produce enzymes that human
smaller and involved in cells cannot, allowing the
storage and transport. digestion of complex
Function carbohydrates (e.g., cellulose,
hemicellulose) into simpler sugars
Eukaryotic cells perform complex that can be absorbed.
functions necessary for life, such as ● Production of Short-Chain Fatty
energy production, protein synthesis, Acids (SCFAs): Fermentation of
waste elimination, and cellular dietary fibers by gut bacteria
communication. They reproduce produces SCFAs (e.g., acetate,
through mitosis (for somatic cells) and propionate, butyrate), which
meiosis (for gametes), allowing for serve as an energy source for
growth, development, and reproduction colonocytes and have various
in multicellular organisms. health benefits.

Nutrient Absorption:
Human Microbiome and
Its Role in Health and ● Synthesis of Vitamins: Gut
bacteria synthesize essential
Disease
vitamins such as vitamin K,
Definition biotin, and folate, which are
absorbed by the host.
The human microbiome refers to the ● Mineral Absorption: The
collective genomes of the microbiome aids in the
microorganisms (including bacteria, absorption of minerals like
viruses, fungi, and archaea) that live in calcium, magnesium, and iron by
and on the human body. These modifying the gut environment.
microorganisms inhabit various
environments, such as the gut, skin, Regulation of Gut Motility:
mouth, and respiratory tract. The
● Neurotransmitter Production:
human microbiome is essential for
Gut microbes produce
 neurotransmitters (e.g., serotonin) 3. Protection Against Pathogens
that influence gut motility and
Competitive Exclusion:
peristalsis, ensuring efficient
transit of food through the ● Nutrient Competition: Commensal
digestive tract. microbes compete with
pathogenic organisms for
2. Immune System Modulation
nutrients and resources, limiting
Development of the Immune System: the growth and colonization of
pathogens.
● Immune Education: The
● Space Occupation: Beneficial
microbiome plays a critical role in
microbes occupy niches on
the development and maturation
mucosal surfaces, preventing
of the immune system,
pathogens from adhering and
particularly during infancy.
establishing infections.
Exposure to diverse microbial
antigens helps train the immune Production of Antimicrobial
system to distinguish between Compounds:
harmful and harmless agents.
● Bacteriocins: Some commensal
● Tolerance Induction: The gut
bacteria produce bacteriocins,
microbiota promotes immune
which are antimicrobial peptides
tolerance to dietary antigens and
that inhibit the growth of closely
commensal bacteria, preventing
related bacterial species.
unnecessary immune responses
● Acid Production: Fermentation
that could lead to inflammation
by gut bacteria lowers the pH of
or allergies.
the gut environment, creating an
Regulation of Immune Responses: inhospitable environment for
many pathogens.
● Anti-Inflammatory Effects:
Certain gut bacteria produce Stimulation of Mucosal Immunity:
metabolites that have
● Immune Activation: The
anti-inflammatory effects, such
presence of commensal bacteria
as SCFAs, which modulate the
stimulates the production of
activity of regulatory T cells
mucins, antimicrobial peptides,
(Tregs) and other immune cells.
and secretory IgA (sIgA) in
● Stimulation of Immune Cells:
mucosal surfaces, enhancing the
The microbiome stimulates the
barrier function and immune
production and activity of various
defense.
immune cells, including
macrophages, dendritic cells, and
Diseases Associated with
natural killer (NK) cells,
Microbiome Imbalance
enhancing the body's ability to
fight infections.
A balanced microbiome is crucial for excessive fat accumulation that
health. Dysbiosis, or an imbalance in poses a risk to health.
the microbial community, can lead to ● Microbial Influence: Obese
various diseases and health conditions. individuals often have a distinct
gut microbiota composition
1. Inflammatory Bowel Disease (IBD)
compared to lean individuals,
Characteristics: with differences in the relative
abundance of certain bacterial
● Chronic Inflammation: IBD,
phyla (e.g., Firmicutes,
including Crohn's disease and
Bacteroidetes).
ulcerative colitis, is characterized
by chronic inflammation of the Mechanisms:
gastrointestinal tract.
● Dysbiosis: Patients with IBD ● Energy Harvesting: Certain gut
often have reduced microbial microbes are more efficient at
diversity and an imbalance in the extracting energy from the diet,
gut microbiota, with a decrease in contributing to increased calorie
beneficial bacteria (e.g., absorption and fat accumulation.
Bifidobacterium, ● Metabolic Regulation: The
Faecalibacterium prausnitzii) and microbiome influences host
an increase in pathogenic metabolism through the
bacteria (e.g., Escherichia coli). production of metabolites that
regulate fat storage, insulin
Mechanisms: sensitivity, and inflammation.

● Immune Dysregulation: 3. Type 2 Diabetes

Dysbiosis in IBD contributes to an
Characteristics:
abnormal immune response,
leading to persistent ● Insulin Resistance: Type 2 diabetes
inflammation and tissue damage. is characterized by insulin
● Barrier Dysfunction: Altered gut resistance and high blood sugar
microbiota can disrupt the levels.
intestinal barrier, allowing ● Dysbiosis: Individuals with type 2
bacterial translocation and diabetes often exhibit dysbiosis,
further stimulating the immune with alterations in gut microbiota
response. composition and reduced
microbial diversity.
2. Obesity
Mechanisms:
Characteristics:

● Excessive Fat Accumulation: Obesity ● Inflammation: Dysbiosis can

is a condition characterized by promote systemic inflammation
through the production of
 pro-inflammatory molecules, ● Electron Microscope: Uses
contributing to insulin resistance. electron beams for higher
● Gut Barrier Dysfunction: A magnification and resolution.
compromised gut barrier can ○ Transmission Electron
allow the translocation of
Microscope (TEM):
endotoxins (e.g.,
Provides detailed images
lipopolysaccharides), triggering
of internal structures by
inflammatory responses and
transmitting electrons
metabolic disturbances.
through the specimen.
Week 3: Microscopy and Staining ○ Scanning Electron
Techniques Microscope (SEM):
Provides
Types of Microscopes
three-dimensional images
● Light Microscope: Uses visible of surfaces by scanning
light to magnify specimens up to the specimen with a
1000x. Includes bright-field, focused beam of
dark-field, phase-contrast, and
electrons.
fluorescence microscopes.
● Electron Microscope: Uses Gram Staining and Other
electron beams for higher Differential Stains
magnification and resolution.
○ Transmission Electron ● Gram Staining:
Microscope (TEM): Provides ○ Steps: Involves four steps
detailed images of internal - application of crystal
structures. violet (primary stain),
○ Scanning Electron iodine (mordant), alcohol
Microscope (SEM): Provides (decolorizer), and safranin
three-dimensional images (counterstain).
of surfaces.
○ Outcome: Differentiates
Week 3: Microscopy and Staining bacteria into
Techniques Gram-positive (purple)
with thick peptidoglycan
Types of Microscopes
walls and Gram-negative
● Light Microscope: Uses visible (pink) with thin
light to magnify specimens up peptidoglycan walls and
to 1000x. Includes bright-field, an outer membrane.
dark-field, phase-contrast, and ● Other Differential Stains:
fluorescence microscopes. ○ Acid-Fast Stain:
Identifies Mycobacterium
 species by staining blocks for macromolecules and
mycolic acids in their cell cellular structures.
walls. Example:
1. Carbon (C):
Ziehl-Neelsen stain.
○ Endospore Stain: ● Role: Major component of all
Highlights endospores in organic molecules, including
bacteria like Bacillus and carbohydrates, proteins, lipids,
Clostridium using and nucleic acids.
malachite green and ● Sources: Organic compounds
safranin. (e.g., glucose) or carbon
dioxide (CO2) for autotrophic
Module 2: Bacterial bacteria.
Physiology and
2. Nitrogen (N):
Genetics
● Role: Essential for the synthesis
Week 4-5: Bacterial Growth of amino acids, nucleotides,
and Metabolism and other nitrogen-containing
Bacterial growth and metabolism compounds.
are fundamental aspects of ● Sources: Ammonium (NH4+),
bacterial physiology that involve the nitrate (NO3-), or nitrogen gas
acquisition and utilization of (N2) for nitrogen-fixing
nutrients, environmental bacteria.
adaptations, and the regulation of 3. Hydrogen (H):
cellular processes. Understanding
these concepts is essential for ● Role: Integral part of all
studying bacterial behavior, organic molecules and involved
pathogenicity, and the development in redox reactions and energy
of antimicrobial strategies. transfer.
● Sources: Water (H2O), organic
Nutritional Requirements and compounds, or hydrogen gas
Growth Conditions (H2).
Macronutrients
4. Oxygen (O):
Macronutrients are elements
● Role: Component of many
required in large amounts for
organic molecules and a key
bacterial growth and cellular
element in cellular respiration
function. They are the building
and energy production.
 ● Sources: Water (H2O), oxygen including temperature, pH, and
gas (O2) for aerobes, and oxygen levels.
organic compounds.
1. Temperature:
Micronutrients
Bacteria have varying temperature
Micronutrients are trace elements ranges for optimal growth, classified
required in small amounts, often into three main categories:
serving as cofactors for enzymes
and other biochemical functions. ● Psychrophiles:
○ Optimal Range: -5°C to
1. Iron (Fe): 15°C.
○ Habitats: Arctic and
● Role: Critical for electron
Antarctic regions, deep
transport and enzyme function.
ocean waters.
● Sources: Ferric (Fe3+) and
● Mesophiles:
ferrous (Fe2+) iron, often
○ Optimal Range: 20°C to
complexed with siderophores
45°C.
to enhance uptake.
○ Habitats: Human body,
2. Zinc (Zn): soil, water, and food.
● Thermophiles:
● Role: Cofactor for numerous
○ Optimal Range: 45°C to
enzymes involved in DNA
80°C.
synthesis, protein metabolism,
○ Habitats: Hot springs,
and regulation of gene
compost piles,
expression.
geothermal areas.
● Sources: Zinc ions (Zn2+).
2. pH:
3. Manganese (Mn):
Most bacteria prefer neutral pH
● Role: Involved in oxidative
environments, but some can thrive in
stress protection, enzyme
acidic or alkaline conditions.
activation, and photosynthesis
in some bacteria. ● Neutrophiles:
● Sources: Manganese ions ○ Optimal Range: pH 6.5 to
(Mn2+). 7.5.
○ Habitats: Huma
Growth Conditions
Full Lecture Notes at 50+ pages
Bacterial growth is influenced by
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