Microbiome lec 1

Course Introduction: ORBG 8021 Microbiome

• Instructor: Dr. Sumant Puri, MSc, PhD.

• Program: Post-Baccalaureate Program.

• Course Title: Microbiome (ORBG 8021).

• Lecture 1 Topic: Introduction to the Course: Microorganisms.

Course Schedule and Outline

Basic Microbiology and Interaction of Microbes with the Human Host

• May 27: Lecture 1 - Introduction to the Course: Microorganisms (SP).

• June 1: Lecture 2 - Bacteria 1 (SP).

• June 3: Lecture 3 - Bacteria 2 and Viruses (SP).

• June 8: 4th session - 5-minute presentations (Students 1-20) - SP.

• June 10: Quiz covering Lectures 1-3.

• June 15: Lecture 5 - Innate immunity (NA).

• June 17: Lecture 6 - Acquired immunity (NA).

• June 22: Lecture 7 - Host-microbe interactions and infection (NA).

• June 24: 8th session - 5-minutes presentations (Students 21-40) - NA.

• June 29: Mid-term exam.

Oral Cavity and Microbiome

• July 1: 9th session - 5-minutes presentations (Students 41-60) – SP.

• July 6: Lecture 10 - The oral cavity as a microbial habitat – dental biofilm (SP).

• July 8: Lecture 11 - Introduction to microbiome - oral microbiome in health (NA).

• July 13: Lecture 12 - Oral microbiome in disease (NA).

• July 15: 13th session - 5-minutes presentations (Students 61-80) - NA.

• July 20: Quiz covering Lectures 10-12.

• July 22: Lecture 14 - Saliva and oral yeast (SP).

• July 27: Lecture 15 - Modulation of microbiome – microbiome-based therapeutics (SP).

• July 29: Lecture 16 - Infection control in dentistry (NA).

• Aug 3: 17th session - 5-minutes presentations (Students 81-100) - NA.

• Aug 5: 18th session - 5-minutes presentations (Students 101-120) - SP.

• Aug 10: Final exam.

Defining Microbiology

• Core Definition: The study of organisms and acellular entities too small to be clearly seen by the unaided eye. Some members may be macroscopic.

• Construction: These organisms are relatively simple in construction, notably lacking highly differentiated cells and distinct tissues.

• Significance of Study:     * They constitute the most populous and diverse group of organisms.     * Ubiquity: Found everywhere on the planet.     * Essential Recycling: Play a major role in recycling essential biological elements.     * Nutrient Sources: Serve as a source of nutrients; some perform photosynthesis.     * Societal Benefits: Production of food, beverages, antibiotics, and vitamins.     * Pathogenicity: Some cause disease in plants, animals, and humans.

Classification of Microorganisms and Biological Entities

Cellular Entities

• Fungi: Includes Yeasts (unicellular) and Molds (multicellular).

• Protists: Includes Algae, Protozoa, Slime molds, and Water molds (known for devastating plant diseases).

• Bacteria: Single-celled organisms, often with peptidoglycan in cell walls. Example: Escherichia coli.

• Archaea: Distinguished from bacteria by unique rRNA sequences and membership in extreme environments. Example: Methanogens.

Acellular Entities

• Viruses: Composed of protein and nucleic acids.

• Viroids: Composed purely of RNA.

• Virusoids: Composed purely of RNA.

• Prions: Infectious agents composed purely of Protein.

Types of Microbial Cells and Domain Systems

Cellular Types

• Prokaryotic Cells: Lack a true membrane-delimited nucleus.

• Eukaryotic Cells: Contain a membrane-enclosed nucleus, possess higher morphological complexity, and are generally larger than prokaryotic cells.

The Three Domain System

Based on comparisons of ribosomal RNA (rRNA), the biological world is divided into:

1. Bacteria (True Bacteria): Usually single-celled; majority have peptidoglycan cell walls; most lack a membrane-bound nucleus; ubiquitous.

2. Archaea: Lack peptidoglycan; have unique membrane lipids; unusual metabolic characteristics; many are extremophiles.

3. Eukarya (Eukaryotes): Includes protists and fungi.

Comparative Analysis of Three Domains (Table 2.2)

Genetic Material and Replication

• Bacteria:     * DNA is free in the cytoplasm; single chromosome.     * Contains histone-like proteins and extrachromosomal plasmids.     * Introns not found in mRNA.     * Reproduction: Binary fission (asexual only).     * Genetic exchange: Conjugation, transduction, transformation.

• Archaea:     * DNA free in cytoplasm; single chromosome.     * Associated with histone-like proteins; plasmids may be found.     * Introns not found in most genes.     * Reproduction: Asexual; no spores.     * Genetic exchange: Processes similar to bacterial conjugation.

• Eucarya:     * DNA contained within a membrane-bound nucleus with a nucleolus.     * Multiple chromosomes; often diploid ($2n$).     * DNA complexed with histone proteins; plasmids rare (found in yeast).     * Introns found in all genes.     * Reproduction: Mitosis and Meiosis.     * Genetic exchange: Sexual reproduction (fusion of haploid gametes).

Cellular Organization

• Bacteria:     * Cytoplasmic membrane contains hopanoids.     * Possess Lipopolysaccharides and teichoic acids.     * Energy metabolism and photosynthesis associated with cytoplasmic membrane/vesicles.     * Ribosomes: $70S$.     * Flagella: Composed of flagellin protein.

• Archaea:     * Membranes contain isoprenes; no lipopolysaccharides or teichoic acids.     * Cell walls lack peptidoglycan.     * Ribosomes: $70S$ (but behave more like Eucarya when exposed to inhibitors).     * Flagella derive energy from proton pumps.

• Eucarya:     * Membrane contains sterols; internal membranes (ER, Golgi) and vesicles (lysosomes, peroxisomes) present.     * Organelles: Mitochondria and chloroplasts (the latter in algae/plants).     * Cytoskeleton: Microtubules present.     * Ribosomes: $80S$ in cytoplasm (mitochondrial/chloroplast ribosomes are $70S$).     * The "S" (Svedbergs) measures the rate molecules settle in a centrifuge.     * Cell walls: Cellulose or chitin.     * Flagella: Complex $9+2$ microtubular arrangement.

Structural Differences: Prokaryote vs. Eukaryote Summary

• Prokaryotes:     * DNA: Naked, circular, usually no introns.     * Organelles: No nucleus, no membrane-bound organelles, $70S$ ribosomes.     * Reproduction: Binary fission, single chromosome (haploid).     * Average Size: Smaller ($∼ 1-5\,μm$).

• Eukaryotes:     * DNA: Bound to protein, linear, usually has introns.     * Organelles: Has nucleus and nucleolus, membrane-bound organelles, $80S$ ribosomes.     * Reproduction: Mitosis and meiosis, paired chromosomes (diploid or more).     * Average Size: Larger ($∼ 10-100\,μm$).

Acellular Infectious Agents and the Nature of Life

• Viruses: Smallest microbes; require host cell to replicate; cause diseases and some cancers.

• Viroids/Virusoids: Infectious agents made of RNA.

• Prions: Infectious proteins.

• Characteristics of Living Cells: Organization, energy use/metabolism, response to stimuli, regulation/homeostasis, growth/development, reproduction, and biological evolution.

• The Central Dogma of Molecular Biology: DNA (Transcription) → RNA (Translation) → Protein.

Historical Discovery of Microorganisms

• Antony van Leeuwenhoek (1632-1723): First person to accurately observe and describe microorganisms.

• Spontaneous Generation: The idea that living organisms develop from nonliving/decomposing matter.

• Francesco Redi (1626-1697): Discredited spontaneous generation by showing maggots on meat come from fly eggs.

• John Needham (1713-1781): Attempted to prove spontaneous generation; boiled broth, then sealed it. Microorganisms grew (likely due to insufficient boiling or contamination during sealing).

• Lazzaro Spallanzani (1729-1799): Sealed flasks first, then boiled; no growth occurred. This refuted Needham.

• Louis Pasteur (1822-1895): Used swan-neck flasks. Solutions remained sterile even when exposed to air because dust was trapped in the neck. No growth occurred until the neck was broken.

• John Tyndall (1820-1893): Demonstrated that dust carries microbes. Provided evidence for heat-resistant bacteria.

• Ferdinand Cohn (1828-1898): Discovered that heat-resistant bacteria could produce endospores.

The Role of Microbes in Disease

• Early Views: Believed to be caused by supernatural forces.

• Agostini Bassi (1773-1856): Silkworm disease caused by a fungus.

• M. J. Berkeley (ca. 1845): Potato Blight of Ireland caused by a water mold.

• Heinrich de Bary (1853): Smut and rust fungi caused cereal crop diseases.

• Louis Pasteur: Demonstrated fermentations were microbial; developed pasteurization; showed pébrine disease in silkworms was protozoan.

• Ignaz Philipp Semmelweiss (1818-1865): Hungarian doctor who advocated hand washing to prevent childbed fever spread by doctors.

• Joseph Lister (1827-1912): Used antiseptic chemicals to clean surgical instruments.

• William Stewart Halsted (1852-1922): Introduced the use of rubber gloves during surgery to prevent the spread of microbes.

Koch’s Postulates and the Germ Theory of Disease

Robert Koch (1843-1910) established the relationship between Bacillus anthracis and anthrax using criteria from Jacob Henle.

The Four Original Postulates

1. The organism must be isolated from every patient with the disease; its distribution must correspond to observed lesions.

2. The organism must be isolated and grown in pure culture (in vitro).

3. The pure organism must cause the disease when injected into healthy, susceptible animals.

4. The organism must be recovered from the experimentally infected animal.

The Fifth Postulate

• The antibody to the organism should be detected in the patient’s serum.

Limitations of Koch’s Postulates

• Some organisms cannot be grown in pure culture (Unculturables are now studied via genomics).

• Causative organisms may be present in healthy hosts without causing disease (depends on "microbial load" and host immune system).

• Ethical constraints forbid using humans for the postulates; animal models are used instead.

Legacy of Koch’s Work

Led to the development of agar, the petri dish, nutrient broth/agar, and isolation methods.

Advancements in Virology and Immunology

• Charles Chamberland (1851-1908): Developed porcelain bacterial filters. Used by Ivanoski and Beijerinck to show tobacco mosaic disease was caused by agents smaller than bacteria (later identified as viruses).

• Pasteur and Roux: Discovered attenuation (long incubation intervals cause pathogens to lose virulence).

• Vaccines: Pasteur developed vaccines for chicken cholera, anthrax, and rabies.

• Edward Jenner: Developed smallpox vaccination procedure before the role of microbes was fully understood.

Host-Microbe Relationships and Symbiosis

Symbiotic Types

• Mutualism: Both individuals benefit.

• Commensalism: One organism benefits without affecting the other.

• Parasitism: One species is harmed while the other benefits.

Benefits of Normal Flora

• To Bacteria: Food, survival, and a place to multiply.

• To Humans: Production of vitamins (B and K), breakdown of indigestible food, and protection against pathogens.

• Protective Mechanisms: Occupying space (niche exclusion), nutrient competition, and production of bacteriocins (anti-bacterial chemicals).

Nosocomial Infections (Healthcare-Associated Infections - HAI)

• Primary types: UTIs, surgical site infections, bloodstream infections, and pneumonia.

• 2011 Statistics:     * $1$ in $25$ hospital patients had at least one HAI.     * Estimated $722,000$ HAIs in US acute care hospitals.     * Approximately $75,000$ deaths during hospitalization related to HAIs.

Microbial Landscape and Emerging Diseases

Key emerging or drug-resistant threats mentioned include:

• Vancomycin-resistant S. aureus (VRSA).

• Multidrug-resistant tuberculosis.

• SARS, Ebola, Marburg, HIV, West Nile virus, and H5N1 influenza.

• E. coli O157:H7.

• Bioterrorism agents like Anthrax.

• Relevance to Dentistry: Application of Koch's logic to dental caries and infection control (including COVID-19).