MICROBIO 1.1

Human Microbiome

• Estimated to have over 100 trillion bacteria
• Outnumbering human cells
• Bacterial genes outweigh human genes by more than 100x
• Microbiome can weigh as much as 5 lbs
• Aids in digestion
• Regulates the immune system
• Protects against disease-causing bacteria
• Produces vitamins B12, thiamine, riboflavin, and vitamin K (blood coagulation)
• The human gut-brain axis is associated with this

Virus Particles

• Over 10 quintillion virus particles on Earth
• Outnumber bacteria 10-1 across most ecosystems
• Many viruses are unknown but many are known

Class Objectives

• Define vocabulary words and use them properly
• Identify normal microbiota & where it colonizes
• Define opportunistic and strict pathogens (DITKI)
• List examples of normal microbiota's ("flora") role
• Understand dysbiosis and its consequences
• Compare and contrast probiotics & prebiotics
• Define tissue tropism and identify its requirements
• Learn the 6 steps required for infectious disease establishment
• Apply today's material to clinical settings

Vocabulary Words

• Microbiota: Community of microbes residing on and in an individual, varying between individuals depending on environmental sites and host niches
• Normal flora: Microbiota
• Microbiome: Collection of microbes and their genomes in a specific area
• Core microbiome: Shared microbial species in individuals at specific body sites; comprises the largest population
• Secondary microbiome: Additional microbial species that contribute to diversity; generally present in smaller numbers
• Functional redundancy: Required functions (e.g. metabolism) from diverse members
• Taxonomic diversity: Number of species within the microbiome
• Proteomics: Study of protein products of microbiome
• Metabolomics: Examination of metabolic activity of the microbiome
• Prebiotic: Food component that promotes growth of microbes
• Probiotic: Live organisms that benefit the host upon ingestion

The Microbiota

• Core microbiome: present in 95% or more of individuals
• Secondary microbiome: fewer individuals share the species present
• Normal flora impacted by pathogenicity and virulence of the host response
• Usually a mutualistic relationship

Normal Microbiota Locations

• Common locations: Skin (especially moist areas), respiratory tract, digestive tract, urinary tract, and genital system
• Less common locations: Rest of respiratory and digestive tracts, urinary bladder, and uterus
• Diagnostically significant locations: Blood, cerebrospinal fluid (CSF), synovial fluid, and deep tissues

Role of Normal Flora

• Defence against invaders (bacteriocins)
• Essential role in human nutrition and metabolism (synthesis of vitamins K & B)
• Conversion between good and bad compounds
• Important function of maintaining ingested compound toxicity
• Important regulatory function in maintaining metabolism

Role of Normal Microbiota

• Immune stimulation (stimulates antibodies = IgA)
• Contributing to host immunity (nude mice and bacteriodes)
• Potential source of infections (e.g. E. coli causing UTIs)

Frequent Types of Normal Bacterial Microbiota

• Effect of antibiotics on gut microbiota (using fecal samples from 4 patients)
• Total microbiota (16S rRNA gene analysis)
• Metabolically active microbiota (16S rRNA transcripts)

What happens when the normal flora is disrupted?

• Dysbiosis correlates with a variety of conditions
• Conditions include (but are not limited to): anxiety, depression, schizophrenia, obesity, cancer, allergy, liver disease, atherosclerosis, type-1 diabetes, metabolic syndrome, aging, hypertension, multiple sclerosis, and Alzheimer's disease

Bristol Stool Chart

• Visual representation of bowel movements types (from type 1-7)

Probiotic VS Prebiotic

• Probiotics: Live organisms (e.g., bacteria, yeasts) beneficial to the host on ingestion
• Prebiotics: Food components that stimulate growth of beneficial microorganisms in the gut

Test Your Knowledge #1

• Roles of normal microbiota: Keeping invaders out, human nutrition & metabolism, conversion of ingested compounds (good and bad), immune stimulation, and source of infection

Tissue Tropism of Infectious Agents

• Tissue tropism: site preferences
• Hepatitis viruses prefer liver; cholera bacillus prefers small intestine
• HIV can infect any site; Staphylococcus can infect any site
• Factors affecting tropism include site of entry, affinity for host receptors, and organ temperature.

Bacterial Colonization

• Resistance to host defenses
• Competition with other microbial species
• Advantageous for host features (e.g., fibronectin)
• Increased Gram- negative infection rates in poor health or hospitalization conditions due to decrease in fibronectin.

Bacterial Colonization (Adhesion to host cells/ECM)

• Gram-negative strains: Pili (e.g., P pili, Type 1 pili, Curli pili)
• Gram-positive strains: Pili (e.g., Type IV pili), Spa, GAS M1
• Non-pilus surface adhesins (e.g., MSCRAMMs)
• Biofilm formation: adhering bacterial cells to each other and host structures

Establishment of Infectious Diseases

• Encounter
• Entry
• Spread
• Multiplication
• Damage
• Outcome (agent or host wins out, or they co-exist; breach in host defenses required for each stage)

Encounter

• Fetus is mostly sterile in the early stages
• Initial encounter occurs at birth (parturition)
• Mothers antibodies may be passed to the baby via the colostrum

Entry

• Microorganisms can enter the body via body cavities (e.g., nose, mouth, respiratory tract)
• Passing through the epithelial barrier (e.g., ingestion, inhalation, insect bites)
• Factors impacting entry include size, number of invading organisms

Spread

• Lateral (contiguous tissue)
• Dissemination (distant sites)
• Spread affected by anatomical factors (e.g., lungs, ruptures), fluid dynamics or body fluids (e.g., blood, CSF, lymph)

Multiplication

• Threshold of microorganisms needed
• Overcome early host defenses
• Environmental factors impacting multiplication (temperature, pH, osmotic pressure)
• Evasion of host defenses (constitutive, induced defenses, complement, phagocytosis, humoral immunity, cellular immunity)

Damage

• Affected tissues and organs determine the type and severity of damage
• Damage can be directly due to pathogen or a consequence of host immune response (cytokine storm)
• Toxins and cell death are examples of direct tissue damage

Outcome

• Outcomes depend on all above stages in disease evolution
• Determine whether the host or pathogen wins or if they co-exist
• Encompasses endogenous and exogenous factors of disease

Test Your Knowledge #2

• Six stages of a viral infection
• 1. Encounter, 2. Entry, 3. Spread, 4. Multiplication, 5. Damage, 6. Outcome

Stages in Viral Pathogenesis

• Key viral-host interactions, virus entry, spread, secondary replication, reaches target organs, cell damage, potential persistence, host defenses, factors related to viral pathogenesis (morphology and tropism, if it is cytopathic, etc.), and cytopathic effects are included in this stage

Test Your Knowledge #3

• Focus is on the stage of infection and possible stage of disease (encounter, etc).

Also a Scientist (Elisabeth Bik)

• Details about her background, research, and recognitions.
• Contributions include research on developing vaccines for Vibrio cholerae, examining the differences between gut and oral microbiota of humans, studying dolphin microbiomes, a blog on microbiome research, and identifying over 400 papers with manipulated data.