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Chapter 1 Notes: Introduction to Microbiology

Chapter 1: Introduction to Microbiology

  • Define microbiology as the study of microbes and recognition that microbes include both living and non-living entities relevant to biology and health.

  • Microbes include:

    • Living organisms: bacteria, archaea, fungi, protists, and helminths.
    • Non-living/non-cellular entities: viruses and prions.

  • Most bacteria and archaea are microscopic; many protists, fungi, and helminths are macroscopic.

  • Earth’s largest organism example: the honey mushroom (a fungus) in Oregon. This highlights microbial scale and ecological significance.

  • Microbes are the most abundant organisms on Earth and occupy diverse habitats.

  • Major habitats and sites where microbes are most abundant (ordered roughly from highest abundance to lower):

    • Soils (including deep oceanic and continental subsurface soils, upper oceanic subsurface)
    • The ocean
    • Groundwater
    • Phyllosphere (surface of plants)
    • Gut environments: cattle, termites, pigs, humans
    • Sea surface
    • Atmosphere

  • Examples of microbial habitats show global distribution and ecological importance in nutrient cycles, digestion, and health.

  • How microbes are studied and described: classification is based on morphology and genetic sequence similarity; sequencing increasingly drives taxonomy.

  • Human microbiome and host interaction overview:

    • The human body harbors a complex microbiota across skin, digestive, genital-urinary, and respiratory systems.
    • Microbes are not evenly distributed; densities are highest in the gut, mouth, skin, nose, and vagina.
    • Some familiar members include Staphylococcus aureus on about half the population and Lactobacillus as a major component of the vaginal microbiome.

  • Definitions essential for chapter concepts:

    • Symbiosis: a relationship between two or more organisms living in close association.
    • Mutualism: both partners benefit.
    • Commensalism: one partner benefits, the other is unaffected.
    • Parasitism: the parasite benefits at the host’s expense.
    • Biofilm: a sticky community of microbes that can include single or multiple species, embedded in a matrix.

  • Microbes in health and disease:

    • Normal microbiota provide benefits such as training the immune system, producing vitamins, aiding digestion, and crowding out pathogens.
    • Dysbiosis refers to disruptions in the normal microbiota, which can contribute to disease.
    • Pathogens can be true pathogens (disease-causing in healthy hosts) or opportunistic pathogens (cause disease when host defenses are weakened or conditions favor infection).

  • How microbes can cause disease (overview):

    • Host factors (genetics, immune status, age, etc.) influence susceptibility.
    • Microbe location matters: a microbe’s location within the body can determine pathogenicity.
    • Dysbiosis, host factors, and xenial factors (microbe location) interact to influence disease risk.

  • Biofilms in clinical contexts:

    • Biofilms are implicated in 60–80% of infectious diseases.
    • They are highly tolerant to antibiotics, sometimes up to ~1000x higher doses than required to kill planktonic cells.
    • Dental plaque is a classic example of a biofilm.

  • Planktonic vs biofilm forms:

    • Planktonic: free-floating single cells.
    • Biofilms: communities living in a protective matrix, with altered metabolism and increased resistance to antimicrobials.

  • Hand hygiene and aseptic technique:

    • Aseptic technique reduces contaminating microbes and infection risk in clinical settings.
    • Handwashing by healthcare workers reduces healthcare-associated infections (HAIs).
    • In lab settings, aseptic technique enables safe study of microbes and maintenance of pure cultures.

  • Course logistics and learning supports (from Week 1 information):

    • Tutoring: Tierza Dunn is the embedded tutor; attending at least 4 tutoring sessions can significantly improve performance; extra credit tutoring available (see Canvas section 1.3).
    • Week 1 reminders:
    • Week 1: Engagement survey due Thursday by 11:59 PM.
    • Chapter 1 reading quiz due by Sunday 11:59 PM.
    • Course and syllabus quiz due by Sunday 11:59 PM.
    • Cerego set C01 due this week.
    • Complete Chapter 1 section of Unit Study Guide.
    • Drop-in tutoring hours (via Zoom):
    • Mondays 10:30 am – 1:00 pm
    • Tuesdays 12:00 – 2:30 pm
    • Thursdays 4:15 – 5:15 pm

  • Course grading components and totals (as outlined):

    • Syllabus quiz: 5 points
    • Reading quizzes: 5 points × 9 = 45 points (lowest 2 grades dropped; 11 assignments total)
    • Unit quizzes: 20 points × 4 = 80 points
    • Cerego checks: 4 checks totaling 70 points
    • In-class assignments: 10 points × 5 highest = 50 points
    • Study Guide assignments: 20 points × 4 = 80 points
    • Unit Exams plus Final Exam: 100 points × 4 (5 exams with lowest dropped) = 400 points
    • CLO assessment quiz: 20 points
    • Total: 750 points

  • Learning objectives and foundational concepts (highlights you should be able to recall):

    • Define microbiology and microorganisms; give examples of microbes.
    • Explain how microbes are classified and define binomial nomenclature.
    • Outline basic aspects of the scientific method and scientific theory.
    • Describe the role of microbes in shaping Earth and ecosystems.
    • Define and differentiate pathogen and opportunistic pathogen.
    • Name at least two ways microbes interact with a host (mutualism, commensalism, parasitism).
    • Define biofilm and explain why biofilms are a concern to healthcare professionals.
    • Explain how microbes can cause disease via dysbiosis, host factors, and microbe location differences.
    • Define normal microbiota and explain their benefits.

  • Binomial nomenclature and strains (core terms):

    • Binomial nomenclature is a two-name system for scientific names:
    • The entire name is italicized.
    • Genus name is capitalized.
    • Species name is lowercase.
    • Strain or subspecies often includes letters and/or numbers after the species name (e.g., Escherichia coli 0157:H7).
    • Strains are genetic variants within a species; typical sequence similarity within a species is about 97 ext{-}98 ext{ ext{%}}; differences at the 3% level can define distinct strains.
    • Strains arise via mutation and horizontal gene transfer; designation often includes alphanumeric markers.
    • For species and genus assignment, approximate sequence similarity thresholds are used (e.g., 97–98% for species, around 93% for genus).

  • Taxonomy and the tree of life (concepts to know):

    • Three Domains of Life:
    • Domain Bacteria (prokaryotes)
    • Domain Archaea (prokaryotes; many extreme environments; no known pathogens in the material)
    • Domain Eukarya (eukaryotes; includes microbes among others)
    • Six-Kingdom classification (as presented in the transcript): Archaea, Bacteria, Fungi, Plantae, Animalia, Protists (note: Protists is described as a catchall and not a true kingdom)
    • Taxonomic hierarchy examples (illustrative): Domain > Kingdom > Phylum > Class > Order > Family > Genus > Species.
    • Some slides illustrate specific examples (e.g., Clostridium tetani as a species within Bacteria; segregation into broader categories like Firmicutes, Clostridia, Clostridiales, Clostridiaceae).

  • How a microbe is identified using sequence-based methods:

    • Isolate DNA → Amplify and sequence the DNA → Identify bacteria based on DNA sequence using databases (e.g., BLAST).
    • Conceptual workflow: sequence similarity is used to place organisms into taxonomic groups; this approach underpins modern microbiology beyond morphology alone.
    • A representative example of sequence-based thinking is the use of 16S rRNA gene sequences for bacterial identification and classification.

  • Practical examples and case contexts cited in the material:

    • Outbreak case: E. coli O157:H7 associated with restaurant exposure (Red Robin, Westminster, CO, July 2019). Illustrates outbreak investigation processes and public health response.
    • Real-world pathogen example: E. coli O157:H7 linked to romaine lettuce outbreaks (various reports around 2018). Emphasizes foodborne disease risk and public health communication.

  • Normal microbiota and host benefits (more detail):

    • Train the immune system
    • Produce vitamins for the host
    • Help digest foods
    • Crowd out potential pathogens (colonization resistance)
    • Microbiomes are highly individual; each person harbors a unique microbial community

  • Sterile sites and microbe-free tissues (from the human body):

    • Heart and circulatory system; liver; kidneys; bladder; brain and spinal cord; ovaries and testes; bones and muscles; glands and sinuses; middle and inner ear; internal eye
    • Sterile sites include blood, bone and bone marrow, cerebrospinal fluid (CSF), internal body sites (brain, heart, liver, kidney, etc.), joint fluid, pericardial fluid, pleural fluid, peritoneal fluid, and other listed fluids.

  • Mechanisms of disease and interaction types (revisited):

    • Pathogens can cause disease through parasitism (pathogen benefits, host harmed).
    • Human microbiota can contribute to disease via three main concepts:
    • Dysbiosis: disruption of the normal microbiota
    • Host factors: patient-specific factors influencing susceptibility
    • Difference in microbe location: same microbe can be harmless in one site but pathogenic in another

  • Conceptual framework for studying microbiota and disease (relevant checks and checks-and-balance ideas from the slides):

    • Many objective-style checks differentiate between: dysbiosis, host factors, and microbe location; and between mutualism/commensalism/pathogenic relationships.
    • Example exercise prompts provided in the slides emphasize the ability to classify relationships and scenarios based on these definitions.

  • Biofilms in depth (clinical relevance and biology):

    • Definition: biofilms are sticky communities of microbes embedded in a matrix, sometimes consisting of multiple species.
    • Clinical impact: responsible for 60–80% of infectious diseases; extremely tolerant to antibiotics; biofilm-associated microbes can survive antibiotic doses up to about 1000× higher than what kills planktonic bacteria.
    • Common example: dental plaque is a biofilm.
    • Attachment–Growth–Maturation–Detachment cycle:
    • Attachment: microbes adhere to a surface.
    • Growth: cells divide and produce extracellular matrix.
    • Detachment: cells disperse to colonize new niches.
    • Why biofilms are hard to eradicate:
    • The matrix acts as a barrier to antibiotics.
    • Cells in the deeper layers experience reduced oxygen and slower metabolism, making many antibiotics less effective.
    • Biofilms are often multi-species, requiring combination or different strategies to eradicate all members.
    • Implications for human disease: chronic infections, device-associated infections (e.g., catheters, implants), and persistent colonization.
    • Distinction from planktonic cells: biofilm communities exhibit altered gene expression, increased resistance, and complex microenvironments versus free-floating cells.

  • Illustrative comparisons and summaries (quick reference):

    • Planktonic vs Biofilm:
    • Planktonic: free-floating single cells that are typically more susceptible to antibiotics.
    • Biofilm: attached, matrix-embedded communities with protective advantages and altered physiology.
    • Biofilms contribute to a large fraction of infectious disease burden and require targeted strategies for management and prevention.

  • Learning objectives and self-check prompts (practice relevance):

    • For each characteristic, identify whether it describes a eukaryote or a prokaryote (e.g., nucleus presence, habitat breadth, examples).
    • Distinguish organisms and features in the three domains (Bacteria, Archaea, Eukarya) and recognize that viruses and prions are non-cellular infectious agents.
    • Explain why some statements about microbes may be misleading (e.g., not all microbes are microscopic; not all microbes are living) and provide accurate definitions that reflect the current understanding.

  • Additional context and real-world relevance:

    • The study of microbes informs ecology, medicine, public health, and industry (e.g., fermentation, bioremediation).
    • Understanding biofilms is critical to address antimicrobial resistance challenges and to design better infection control strategies in hospitals and clinics.

  • Quick reference to key sequence and taxonomy thresholds (for exam preparation):

    • Species-level similarity threshold (16S rRNA gene or equivalent): ext{similarity}
      ightarrow ext{approximately }97 ext{ ext{-}98}
    • Genus-level similarity threshold: around 93 ext{ ext{%}}
    • 16S rRNA sequence-based identification workflow: isolate DNA → amplify and sequence → compare to reference databases (e.g., BLAST) to determine taxonomic placement.

  • Notable figures and facts mentioned (for recall):

    • The honey mushroom represents a real-world example of a fungus that constitutes a single, genetically connected organism spanning a vast underground network.
    • The Earth hosts a diverse and abundant microbial biosphere across oceans, soils, atmospheres, and animal/plant hosts.
    • Biofilms contribute to the majority of persistent infections due to their resilience to antimicrobial treatments.

  • Summary of essential terms to memorize:

    • Microbiology, microorganisms, bacteria, archaea, fungi, protists, helminths, viruses, prions
    • Symbiosis, mutualism, commensalism, parasitism
    • Biofilm, planktonic, dysbiosis, normal microbiota, pathogen, opportunistic pathogen
    • Binomial nomenclature (Genus species; italics; capitalization rules)
    • 16S rRNA sequencing, sequence similarity thresholds (≈97 ext{-}98 ext{ ext{ extpercent}} for species, ≈93 ext{ extpercent}}$$ for genus)
    • Sterile sites, human microbiome, colonization resistance

  • End of Chapter 1 overview: You should be able to explain what microbiology encompasses, how microbes are classified, the importance of binomial nomenclature and strains, the role of the microbiome in health, how microbes interact with hosts, and why biofilms pose challenges for treatment and infection control.