1, 2, and 3: Human Microbiome, Basic Characteristics of Pathogens, & Host-Pathogen Interactions Pt. 1

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).

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.