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(1.) Intro to Microbiology: Microbes, Microbiome, Infection, and Basic Concepts

Visuals, Scales, and Sampling Highlights

  • Electron micrographs illustrate the smallest forms of life: a rod-shaped bacterium and an influenza virus. Viruses are too small to be seen with classroom light microscopes; electron microscopy is required to visualize them.
  • The influenza virus is used as a class topic to be discussed in a future session.
  • An environmental sample is taken on an agar plate (spelled here as "auger plate" in the transcript). This will be the focus of the next lab where students sample the environment with a swab and inoculate plates containing nutrients that microbes need to grow.
  • Sampling sites include common touchpoints and surroundings: toilet seat, doorknob, throat, tabletop, floor, stairs, etc. The goal is to map where microorganisms are found.
  • After inoculation, plates are incubated for about 24 to 48 hours to allow growth. When students return, colonies appear and are analyzed to distinguish bacteria from fungi.
  • Colony morphology as a diagnostic cue:
    • Bacterial colonies tend to be smooth and shiny.
    • Fungal colonies tend to be fuzzy (cotton-like).
  • The class will aggregate data from all samples to determine which parts of the environment harbor microorganisms.
  • Microbes are ubiquitous: touching a doorknob can transfer microbes from your skin to the surface and vice versa, illustrating the concept that microbes are everywhere.
  • A striking claim: there are more microorganisms in one teaspoon of soil than there are people on earth. This emphasizes microbial abundance and the challenge of visualizing microbial diversity with the naked eye.
  • Scale and size relationships to frame why we use microscopes:
    • In terms of metric units, there are 10 millimeters in 1 centimeter: 1\ \text{cm} = 10\ \text{mm}
    • Therefore, 1 millimeter equals 1000 micrometers: 1\ \text{mm} = 1000\ \mu\text{m}
    • And 1 micrometer equals 1000 nanometers: 1\ \mu\text{m} = 1000\ \text{nm}
  • Viruses require nanometer-scale measurements, which is why electron microscopes are used for visualization.
  • Under a standard classroom compound light microscope (e.g., up to around 100x magnification), you can observe the shape, size, and arrangement of bacterial cells, but not intracellular structures. The complete cellular architecture is visible only with higher resolution tools (e.g., electron microscopy for viruses).
  • The lecture reiterates the vast difference in size between bacteria (generally micrometers) and viruses (nanometers), to justify the different microscopy techniques.
  • The biology field covers diverse microbial groups beyond bacteria and viruses, including algae (green, brown, red) and microscopic photosynthetic organisms; algae types depend on pigments and photosynthesis to convert sunlight into chemical energy.

Microbiome, Microbes, and Key Definitions

  • Microbiome definition: a group of microbes that help maintain good health and prevent pathogenic microbes from growing.
  • Pathogens vs pathogenic: a pathogen is a disease-causing organism; the term pathogenic describes an agent capable of causing disease.
  • Pathogenics (the transcript uses this term informally): the study or concept of disease-causing organisms.
  • Normal microbiota vs microbiome:
    • The term microbiome can refer to the aggregate community of microbes in a particular environment (including the body) and their genetic material.
    • Normal microbiota (also called normal flora) are microbes that are normally present on or in the body and typically do not cause disease; they can come and go depending on conditions (e.g., after bathing, they may be replenished or displaced).
    • Transients are microbes that temporarily reside on or in the body but do not establish permanent colonization.
  • Microbiome’s role in immune education:
    • The microbiome helps the immune system discriminate between what belongs to the body and what does not belong to the body.
    • When the microbiome balance is disrupted, pathogenic microbes may gain an opportunity to cause harm.
  • Parasites:
    • An organism that lives off its host and causes damage.
    • Distinguish between parasitic microbes and transient, non-damaging microbiota.
  • Founder notes on terminology and study:
    • Medical Terminology is useful across anatomy, physiology, and microbiology.
    • Understanding terms like pathogen, pathogenic, microbiome, microbiota, and parasite aids exam performance and clinical reasoning.
  • Microbiome complexity: international and multi-disciplinary research has studied the microbiome’s effects on health and disease; ongoing work continues to reveal new insights.
  • Classroom planning note: a future graded assignment may involve writing a paper on the human microbiome with guidelines to be provided by the instructor.

The Microbiology Field: History, Infections, and Diseases

  • Emergence of the microbiology field: about 150 years ago, many subfields (immunology, parasitology, virology) did not exist as distinct disciplines.
  • Historical origin of influenza terminology: influenza is linked to the idea of influence of the stars.
  • Infection vs disease:
    • An infection is the presence and multiplication of microorganisms within a host.
    • A disease implies tissue damage or dysfunction caused by infection or other mechanisms. Infection may or may not progress to disease.
    • The two terms are related but not identical; infection can exist without tissue destruction, whereas disease generally involves tissue damage.
  • Example with Staphylococcus infection:
    • Infection begins when the microbe enters the host and multiplies, but disease arises when the pathogen damages tissues.
    • Tissue integrity is maintained by structures such as hyaluronic acid in connective tissues; certain pathogens may degrade these components, leading to tissue destruction and disease.
  • Sepsis as a progression from infection to systemic disease:
    • When infection spreads into the bloodstream, the condition can progress to sepsis, with systemic inflammatory responses, possible organ damage, toxins production, shock, coma, and potentially death.
    • The immune system’s ability to control the infection is a key determinant of progression to sepsis.
  • Individual variability in infection outcomes:
    • Immune status (age, underlying conditions like diabetes or cardiovascular issues, lung issues) affects the likelihood that an infection becomes a disease.
    • Some infections (e.g., common cold pathogens) may remain as infections without progressing to disease in healthy individuals.
  • COVID-19 example:
    • SARS-CoV-2 infection may begin as an infection and progress to tissue/organ damage; progression varies by host immune response and health status.
    • The course of infection and progression to disease are influenced by the immune system and other host factors; the discussion acknowledges variability and complexity.
  • Sexually transmitted infections (STIs) example:
    • Many STIs begin as infections; if not controlled, they can become diseases.
  • Epidemic, endemic, and pandemic concepts:
    • Endemic: a disease that is always present in a population or region.
    • Epidemic: a large number of people in a given area become infected in a short period.
    • Pandemic: spread of an infection across multiple countries or worldwide.
  • Historical examples mentioned:
    • H1N1 influenza outbreak in 2009 as an epidemic example in some regions.
    • COVID-19 pandemic as a modern pandemic example.
  • Mechanisms of spread and public health relevance:
    • Travel and globalization contribute to rapid spread across countries and continents during epidemics and pandemics.
  • Endemic vs sporadic vs epidemic visuals:
    • Endemic: constant presence in a population.
    • Sporadic outbreaks: occasional incidents in certain areas.
    • Epidemic: rapid, widespread increase in cases within a population.

Quantitative and Dimensional Contexts

  • Scale conversions to frame sizes:
    • 1 cm equals 10 mm: 1\ \text{cm} = 10\ \text{mm}
    • 1 mm equals 1000 μm: 1\ \text{mm} = 1000\ \mu\text{m}
    • 1 μm equals 1000 nm: 1\ \mu\text{m} = 1000\ \text{nm}
  • Magnification context:
    • Classroom light microscopes often yield up to around 100x magnification for observing bacteria, revealing shape, size, and arrangement but not internal structures.
    • Electron microscopes provide the resolution necessary to visualize viruses at the nanometer scale.
  • Size differential summaries:
    • Bacteria: typically micrometer-scale dimensions (example ranges not explicitly stated in the transcript but are implied by the need for light vs electron microscopy).
    • Viruses: nanometer-scale dimensions, requiring electron microscopy for visualization.
  • Large biological populations:
    • The human body is described as an ecosystem comprising both human cells and bacteria:
    • N_{ ext{body cells}} = 3.0 \times 10^{13} (about 30 trillion body cells)
    • N_{ ext{bacterial cells}} = 4.0 \times 10^{13} (about 40 trillion bacterial cells)
    • Difference: N{ ext{bacterial}} - N{ ext{body}} = 1.0 \times 10^{13} (about 10 trillion more bacterial cells than human cells)
  • Conceptual takeaway:
    • The human body hosts a vast microbiome; the organism is an ecosystem, constantly interacting with microbial inhabitants that come and go depending on conditions (e.g., bathing, environmental contact). The microbiome contributes to health and disease dynamics.

Practical Lab Procedures and Implications

  • Lab activity plan (as described in the transcript):
    • Use swabs to sample various environments and inoculate agar plates that contain nutrients for microbial growth.
    • Incubate approximately 24 to 48 hours to allow colonies to form.
    • Examine colonies to classify organisms: smooth/shiny (likely bacteria) vs fuzzy (likely fungi).
    • Analyze data to determine which environments harbor different microbes and map their distribution.
  • Agar plate terminology:
    • The transcript refers to an "auger plate"; the intended term is likely "agar plate" (food for microbes).
  • The role of microbial presence on skin and objects:
    • Microbes are present on skin and surfaces; contact transfers microbes between hands, skin, and objects like doorknobs.
    • This supports the concept that microbial exposure is constant and that the microbiome is a shared ecosystem with the environment.

Algae, Photosynthesis, and Ecological Roles

  • Algae types described: green algae (pond scum on surface), brown and red algae (seaweeds in oceans).
  • Pigments in algae influence coloration and energy capture:
    • Pigments drive photosynthesis by converting sunlight into chemical energy that organisms use for growth and metabolism.
  • These photosynthetic microbes contribute to ecosystems and global energy cycles, linking microbiology to broader biology themes.

Immune System, Self, and Ethical/Practical Considerations

  • The microbiome’s essential role in immune function highlights ethical and practical implications:
    • Maintaining a balanced microbiome may be important for preventing disease and guiding immune responses.
    • Medical terminology and microbiology concepts support understanding of disease processes, which affects patient care and health decisions.
  • Practical implications for coursework and research:
    • A future assignment on the human microbiome may be given, with guidelines provided, indicating ongoing emphasis on microbiome literacy in the course.

Quick Summary and Takeaways

  • Microbes exist in every environment; some are visible only with advanced microscopy (electrons) while others form visible colonies on agar plates after incubation.
  • The microbiome is a complex, dynamic ecosystem that assists health and modulates immune responses; disruption can lead to disease or susceptibility to pathogens.
  • Infection and disease are related but distinct concepts; infection can exist without tissue damage, while disease involves tissue destruction and systemic effects (e.g., sepsis).
  • Endemic, epidemic, and pandemic are terms describing the frequency and geographic spread of disease; human movement and travel influence these patterns.
  • The human body hosts a massive microbial community, with roughly comparable or greater microbial cell numbers than human cells, illustrating that humans are ecosystems as well as organisms.
  • The next lab session will involve environment sampling, plating, and observation to connect theory with observable outcomes.

Key Terms to Remember

  • Microbiome, Microbiota, Normal microbiota
  • Pathogen, Pathogenic
  • Parasite
  • Infection, Disease
  • Sepsis
  • Endemic, Epidemic, Pandemic
  • Agar plate (spelled "auger plate" in the transcript)
  • Hyaluronic acid (tissue component involved in the discussion of tissue destruction)
  • Transients (temporary microbiota)
  • Photosynthesis (algae pigments and energy conversion)