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Questions and Answers
What structure is present in Gram-positive bacteria but absent in Gram-negative bacteria?
What structure is present in Gram-positive bacteria but absent in Gram-negative bacteria?
Which characteristic distinguishes fungi from bacteria?
Which characteristic distinguishes fungi from bacteria?
What is the primary component of fungal cell walls?
What is the primary component of fungal cell walls?
What is the function of porin channels in Gram-negative bacteria?
What is the function of porin channels in Gram-negative bacteria?
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Which type of reproduction is NOT commonly associated with fungi?
Which type of reproduction is NOT commonly associated with fungi?
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What is the initial process by which microorganisms enter the body?
What is the initial process by which microorganisms enter the body?
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Which factor is NOT associated with the spread of microorganisms?
Which factor is NOT associated with the spread of microorganisms?
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What is required for microorganisms to multiply effectively within a host?
What is required for microorganisms to multiply effectively within a host?
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What type of damage is not directly caused by pathogens?
What type of damage is not directly caused by pathogens?
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Which scenario describes lateral propagation of a pathogen?
Which scenario describes lateral propagation of a pathogen?
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Which of the following is least likely to cause direct tissue damage?
Which of the following is least likely to cause direct tissue damage?
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What is the incubation period in the lifecycle of an infectious agent?
What is the incubation period in the lifecycle of an infectious agent?
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Which of the following pathogens is associated with ingestion?
Which of the following pathogens is associated with ingestion?
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What can affect the multiplication of microorganisms within a host?
What can affect the multiplication of microorganisms within a host?
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What is a significant advantage of prokaryotic organisms compared to eukaryotic organisms?
What is a significant advantage of prokaryotic organisms compared to eukaryotic organisms?
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How do prokaryotes primarily survive in changing environments?
How do prokaryotes primarily survive in changing environments?
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Which statement best differentiates bacteria into gram-positive and gram-negative groups?
Which statement best differentiates bacteria into gram-positive and gram-negative groups?
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What structure is primarily present in fungi but absent in bacteria?
What structure is primarily present in fungi but absent in bacteria?
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What adaptation helps prokaryotes achieve high metabolic rates?
What adaptation helps prokaryotes achieve high metabolic rates?
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What is an example of a demand placed on free-living microbes?
What is an example of a demand placed on free-living microbes?
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Which of the following is NOT a characteristic of prokaryotes?
Which of the following is NOT a characteristic of prokaryotes?
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What key feature distinguishes Archaea from Bacteria?
What key feature distinguishes Archaea from Bacteria?
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How do fungi differ fundamentally from viruses?
How do fungi differ fundamentally from viruses?
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Which factor is NOT included in the RON model for free-living microbes?
Which factor is NOT included in the RON model for free-living microbes?
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What is tissue tropism?
What is tissue tropism?
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Which of the following factors can affect tissue tropism?
Which of the following factors can affect tissue tropism?
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What must pathogens do to successfully establish an infection?
What must pathogens do to successfully establish an infection?
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Which of the following is NOT a step in the establishment of infectious diseases?
Which of the following is NOT a step in the establishment of infectious diseases?
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How does fibronectin influence bacterial colonization?
How does fibronectin influence bacterial colonization?
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What is an example of an endogenously acquired disease?
What is an example of an endogenously acquired disease?
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What occurs during the 'Encounter' phase of infectious disease establishment?
What occurs during the 'Encounter' phase of infectious disease establishment?
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What is a key structural difference between prokaryotic and eukaryotic cells?
What is a key structural difference between prokaryotic and eukaryotic cells?
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Which ribosome size is characteristic of prokaryotic cells?
Which ribosome size is characteristic of prokaryotic cells?
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What process do prokaryotes use for reproduction?
What process do prokaryotes use for reproduction?
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Which type of bacteria is characterized by a thick peptidoglycan layer?
Which type of bacteria is characterized by a thick peptidoglycan layer?
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What is the role of Lipid A in Gram-negative bacteria?
What is the role of Lipid A in Gram-negative bacteria?
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Which of the following is NOT a mechanism of bacterial resistance?
Which of the following is NOT a mechanism of bacterial resistance?
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What type of bacteria have an outer membrane that contains lipopolysaccharides?
What type of bacteria have an outer membrane that contains lipopolysaccharides?
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Which antibiotic class inhibits the synthesis of peptidoglycan?
Which antibiotic class inhibits the synthesis of peptidoglycan?
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What shape do bacilli bacteria typically have?
What shape do bacilli bacteria typically have?
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Which characteristic is true of eukaryotic cells compared to prokaryotic cells?
Which characteristic is true of eukaryotic cells compared to prokaryotic cells?
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Study Notes
Human Microbiome
- Estimated to have over 100 trillion bacteria.
- Outnumbering the number of human cells.
- Bacterial genes account for more than 100 times the human genome.
- Microbiome may weigh as much as 5 lbs.
- Helps digest food
- Regulates the immune system
- Protects against disease-causing bacteria
- Produces vitamins B12, thiamine, riboflavin, and vitamin K (involved in blood coagulation).
- Gut-brain axis.
- The human body is made up of 10 trillion human cells, and 100 trillion bacterial cells, with the bacteria weighing 3-4 pounds.
The Virome
- Contains ~10 quintillion virus particles on the planet.
- Outnumbers bacteria by 10 to 1.
Class Objectives
- Define vocabulary and use them accurately.
- Identify normal microbiota and where it colonizes.
- Define opportunistic vs. strict pathogens.
- List examples of the role of normal microbiota.
- Understand dysbiosis and its consequences.
- Compare & contrast prebiotics and probiotics.
- Define tissue tropism and what is required for it.
- Learn the 6 steps required for infectious disease establishment.
- Apply today's material to clinical settings.
Vocabulary Words
- Microbiota: Community of microbes in/on an individual. Can vary between different body sites.
- Normal Flora: Refers to the normal microbiota in health.
- Microbiome: Collection of microbial genomes in the microbiota. Defines community structure.
- Core Microbiome: Commonly shared microbes across different individuals.
- Secondary Microbiome: Unique microbial species at specific body sites.
- Functional Redundancy: Diverse members of microbiota fulfill required functions.
- Taxonomic Diversity: Wide variety of species in the microbiota.
- Proteomics: Study of the proteins produced by the microbiome population.
- Metabolomics: Study of the metabolic activities of the microbiome population.
- Prebiotic: Dietary ingredient supporting one or more components of the microbiota.
- Probiotic: Live microbe ingested to provide benefits to the host.
The Microbiota
- Core Microbiome- Species present in 95% or more individuals at a specific site.
- Secondary microbiome includes a smaller number of microbial species present.
- "Normal" flora depends on the pathogenicity, virulence and host response.
- The microbiome is usually in a mutualistic relationship with its host.
Normal Microbiota
- Common locations: Skin (moist areas), respiratory tract, digestive tract (mouth and large intestine), urinary tract, genital system (vagina).
- Less common locations: Rest of the respiratory and gastrointestinal tract, urinary bladder, and uterus.
- Important locations: Blood, cerebrospinal fluid (CSF), synovial fluid, deep tissues.
Role of Normal Flora
- Keeping out invaders.
- Role in metabolism and human nutrition (vitamin synthesis).
- Converting ingested compounds (good and bad).
- Impacts on ingested compounds. Cyclamate (a sweetener) converted to carcinogens.
- Regulates the immune system.
- Important for proper bodily functions like digestion, immune system, and more.
Role of Normal Microbiota
- Immune stimulation (stimulation of antibodies, like IgA).
- Common source of infection (if normal flora ends up in an unusual location it may cause illness).
Frequent Types of Normal Bacterial Microbiota
- Effect of antibiotics: Patients with antibiotic treatments are often studied to see if their microbiota changes.
What Happens When the Normal Microflora Is Disrupted?
- Dysbiosis (imbalance in normal flora) can be linked with many health conditions like anxiety, depression, schizophrenia, obesity, autoimmune disease, cancer, allergies, etc.
- Important for health and disease.
Probiotic vs. Prebiotic
- Prebiotic: Dietary ingredient supporting growth of microorganisms in the microbiota.
- Probiotic: Live organism that provides benefit to the host when ingested (e.g. yogurt, kombucha).
Test Your Knowledge #1
- Role of normal microbiota- keeping out invaders, important for metabolism/nutrition, conversion of compounds, immune stimulation, and a source of infection.
Tissue Tropism of Infectious Agents
- Tissue preferences of pathogens.
- Site of entry (e.g. Gonococcus, Pharyngeal gonnorrhea, Opthalmia, Gonococcal arthritis).
- Affinity for receptors (e.g. ACE2).
- Temperature differences in organ.
Bacterial Colonization
- Must resist host defenses and successfully compete with other species.
- Taking advantage of host characteristics like fibronectin on epithelial cells (Gram+).
- Poor health/hospitalization can increase Gram- infections.
Bacterial Colonization
Establishment of Infectious Diseases
- Encounter: Organism meets the host.
- Entry: Organism enters the host.
- Spread: Organism spreads from the entry site.
- Multiplication: Organism multiplies within the host.
- Damage: Organism, host response, or both cause tissue damage.
- Outcome: Organism or host wins, or co-existence happens.
Encounter
- Fetus is mostly sterile (except for some pathogens that can cross the placenta).
- First encounter: typically at parturition (birth).
- Antibodies and colostrum are involved to prepare the newborn.
- Exogenous vs. Endogenous exposure. Endogenous means the infectious agent is already in or on the body. Exogenous agents are found in the outside environment.
Entry
- Ingress of microorganisms- into body cavities from outside environment.
- Inhalation (e.g., Cholera, whooping cough).
- Ingestion (e.g., Cholera, traveler's diarrhea).
- Penetration of microorganisms into deeper tissue after crossing epithelial barriers (e.g., insect bites, etc.).
Spread
- Lateral propagation- travel to contiguous tissues.
- Dissemination- spread to distant sites.
- Anatomical factors—affect spread (e.g., bacterial abscess in the lungs).
- Fluid dynamics—affect spread (e.g., blood, CSF).
Multiplication
- Incubation period- time for infectious agents to overcome early host defenses.
- Environmental factors (e.g., temperature, pH, osmotic pressure) affect rate.
- Must evade host defenses (constitutive and induced).
- Constitutive defenses include complement and phagocytosis.
- Induced defenses include cellular and humoral immunity.
Damage
- Type and intensity vary depending on tissues/organs affected.
- Direct damage by toxins or cell death.
- Damage from the host immune response.
- Endotoxin (LPS)- dependence on amount affecting damage
Outcome
- Depends on stages of infection; factors like endogenous encounter, entry, tissue spread, multiplication, damage, and immune response outcome.
Test Your Knowledge #2
- Six things needed for viral infection establishment: Encounter, Entry, Spread, Multiplication, Damage, Outcome.
Stages in Viral Pathogenesis
- Entry - Virus enters the body
- Primary Replication - Virus replicates in the initial location in the body.
- Spread - Virus spreads from it's primary location in the body to other sites
- Secondary Replication - Virus replicates in secondary location.
- Secondary Viremia - Replication of the virus in the bloodstream.
- Reach Target Organs -Virus reaches target organs where it causes disease and symptoms, or where it perpetuates the infection.
Test Your Knowledge #3
- Stage in the establishment of infectious disease where the patient is - Endogenous encounter, Entry
Also a Scientist
- Individuals with significant contributions to scientific knowledge in the field of study.
- Individuals are mentioned.
Basic Characteristics of Pathogens
- Number of antibiotic-resistant infections each year, and deaths related to these infections.
- Antibiotic-resistant bacteria list, posing risk to the US.
Class Objectives
- Comparing prokaryotes vs eukaryotes
- Finding differences in bacteria
- Defining fungi, viruses, and parasites
- Classifying viruses.
Phylogenetic Tree of Life
- Bacteria, Archaea, and Eukaryota.
- Relationships between these branches of life.
Prokaryotes vs Eukaryotes
- Prokaryotes don't have a nucleus, DNA is circular, small, reproduce by binary fission, have 70S ribosomes, haploid.
- Eukaryotes have a nucleus, DNA is linear, large, reproduce by mitosis or meiosis, have 80S ribosomes, diploid.
Pros of Being Prokaryotic
- Fast reproduction rate and smaller size.
- Coupled transcription and translation are faster.
Did You Know?
- High bacterial concentration compared to the small human population in the large intestine.
Cons of Being Free Living
- Resistance (survival against damaging agents).
- Occupancy (habitability of the environment).
- Nutrition (intermittent availability of food).
Current Objective: Survive
- Microbes' fundamental goal is to survive in different environments.
Test Your Knowledge #1
- Three differences between prokaryotes and eukaryotes: Nucleus, circular DNA, reproduction methods, organelle size and types.
Resistance
- Pathogens' ways to avoid host detection and develop, as well as resistance to environmental threats.
Mechanisms of Survival
- Cell walls and outer membranes provide protection for bacteria.
- Different bacterial species protect their cytoplasmic membranes (e.g. Gram-positive bacteria, Gram-negative bacteria, acid fast).
Gram Positive vs Gram Negative
- Ability to retain purple dye & iodine after an alcohol challenge.
- Gram- positive bacteria can retain the dye, while Gram-negative bacteria cannot.
Peptidoglycan
- Component of the bacterial cell wall.
- Structure determines bacterial shape; important for survival against osmotic pressure.
- Some antibiotics (penicillins, cephalosporins, and carbapenems) inhibit its synthesis.
Outer Membrane & Lipopolysaccharide
- Component of Gram-negative cell walls.
- Endotoxin (LPS) anchoring the outer membrane and causing fever in hosts.
- Hydrophillic compounds enter through porin channels.
Periplasmic Space
- Space between two bacterial membranes.
- Enzymes and molecules required for sustenance and transport.
Acid-Fast
- Differentiate Acid-Fast bacteria.
Occupancy
- Microbes must find suitable environments to survive.
- Development of mechanisms to avoid the typical behaviors of their environments.
- Example of Biofilm.
Occupancy & Movement: Capsules, Flagella, & Pili
- Capsule: Protective outer layer preventing phagocytosis.
- Flagella: Motility, chemotaxis (towards attractant or away from repellant).
- Pili (Fimbriae): Attachment to surfaces.
Nutrition
- Availability of nutrients for bacteria, including the process of nutrient movement to bacteria, and the result of nutrient depletion.
Cytoplasmic Membrane & Transport
- Permeases facilitate entry of metabolites.
- Facilitated diffusion (down concentration gradient).
- Active transport.
- Group translocation.
Test Your Knowledge #2
- Gram+ have teichoic acid and thick peptidoglycan layers and retain dye.
- Gram- have LPS and retain counterstain.
What are Fungi & how do they differ from bacteria?
- Kingdom of eukaryotic organisms—heterotrophs.
- Reproduce sexually or asexually; play a role in nutrient cycling.
Basics of Fungi
- Eukaryotic cells (nucleus, mitochondria, and more).
- Fungal cell walls are made of chitin and glucans.
- Cell membranes have sterols (ergosterol).
- Can be unicellular ("yeast") or multicellular ("mold").
- Can alternate between yeast and mold forms.
- Reproduction methods dependent on environmental factors.
Parasites
- Organisms that live on or in a host to get nutrients.
- Two major groups: Protozoa (e.g. Amoebozoa, flagellates, ciliates).
- Animalia parasites (e.g. Helminths, Ectoparasites)
But what about Viruses?
- Viruses are neither prokaryotic nor eukaryotic.
- They are not considered living things (lacking the cellular functions of metabolism and independent reproduction).
- Categorized based on morphology and replication.
Virus Classification
- Morphology and replication-based classification of viruses.
Also a Scientist
- Syra Madad: Biodefense, Biosecurity, Global health-related roles and research (various degrees).
- Brigitte Askonas: Immunology Researcher (PhD in Biochemistry).
Netflix's "Pandemic"
- Syra Madad's video on YouTube (relevant video about pandemic preparedness).
Host Pathogen Interactions Pt I
Why Do We Care? Host-Pathogen Interactions II
- Normal microbiota, dysbiosis, establishment of infectious disease.
- Immune system basics.
Class Objectives
- Innate immune system and adaptive immunity.
- Immune cells, their function and involvement.
- Major processes and functions of the immune system.
Big Picture
- Innate and adaptive immunity are important components of a broader immune response.
Innate Immune System
- Early, generalized, and first-line of defense.
- Recognize microbes (PAMPs). Receptors include TLRs. Innate immune system initiates adaptive immune responses.
- Prevent infection by eliminating microbes or allowing them to exist harmlessly on body surfaces
Components of the Innate Immune System: Cellular
- Skin, mucous membranes, mechanical defenses (coughing, sneezing), phagocytes, pro-inflammatory cells (macrophages, mast cells, eosinophils, etc.), antigen presenting cells (APCs), and natural killer cells (NK cells).
- Neutrophils are key players in these cellular defenses.
Cells of the Innate Immune System
- Different types of cells in the innate immune system.
Components of the Innate Immune System: Humoral
- Humoral factors important in preventing invasion.
- Antimicrobial peptides (e.g. bile, mucus, tears, etc).
- Complement- enhances phagocytosis, opsonization, and induces inflammation as well as killing some microorganisms.
- Cytokines- small proteins that signal and trigger immune processes.
- Chemokines- involved in the movement of immune cells.
Complement
- Complements antibodies by making invading microorganisms susceptible to phagocytosis
- Triggers the inflammatory response
- Produces substances chemotactic for white blood cells.
- Lyses some organisms directly & by forming MAC.
- LPS can block MAC.
Consequences of Recognizing Antigen: Induced Innate Immunity
- Increased Antimicrobial peptide production.
- Secretion of inflammation mediators.
- Activation of complement system.
- Chemotactic attraction of phagocytes and lymphocytes to the infection site.
- Acute phase response- increased production of many defense proteins.
- Inflammation
Inflammation
- Characterized by redness, heat, swelling, and pain
- Loss of function.
Adaptive Immune Response
- Specific defenses targeting specific pathogens.
- Enhanced, rapid response to known pathogens (immunological memory)
- Adaptive and innate systems are interconnected and activate one another.
Lymphocytes
- Cellular components of adaptive immunity.
- Types of cells include CD8 (cytotoxic T cell), CD4 (helper T cells), B cells (plasma cells), and regulatory T cells.
Lymphocyte Development, Activation, & Antigen Presentation
- T and B cells go through stages to distinguish "self" from "non-self".
- Activation occurs upon antigen presentation; cells proliferate and differentiate.
- Helper T cells, cytotoxic T cells, and B cells.
Immunoglobulins
- Antibody-based components that bind to microbial epitopes.
- The different classes of Immunoglobulins (IgA, IgD, IgE, IgG, and IgM).
- Roles of the different antibodies.
Initiation of Adaptive Immune Responses by Innate Immunity (Antigen Presentation)
- Microbial antigen triggers pattern recognition responses.
- Dendritic cells take up antigen, migrate to lymph nodes and mature to antigen presenting cells.
- Presentation of antigen to lymphocytes for activation.
Major Histocompatibility Complex (MHC)
- Glycoproteins for antigen recognition.
- MHC class I presents endogenous antigens to cytotoxic T cells.
- MHC class II presents exogenous antigens to helper T cells.
Immunological Memory
- Adaptive immune system's ability to recognize and respond more efficiently in future exposures to the same pathogens.
- Differences in primary and secondary responses.
Test Your Knowledge #3
- Differences between MHC class I and II.
Also a Scientist
- Brigitte Askonas (immunologist).
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Description
Test your knowledge on the differences between Gram-positive and Gram-negative bacteria, as well as characteristics that distinguish fungi from bacteria. This quiz covers various aspects of microbial life, including reproduction, pathogenicity, and the life cycles of infectious agents.
