Comprehensive Microbiology Notes (Slides 8-54)

What is microbiology and what are microbes?

• Microbiology is the study of microbes.
• Microbes include living microorganisms and certain non-living/non-cellular entities.
  • Living microorganisms: bacteria, archaea, fungi, protists, and helminths.
  • Non-living/non-cellular entities: viruses and prions.
• Many bacteria and archaea are microscopic; many protists, fungi, and helminths are macroscopic.
• Earth’s largest organism is a fungus (honey mushroom) that lives in Oregon. Image referenced: Honey mushroom (Earth’s largest organism).

Microbes: living vs non-living components

• Microbes can be classified as living organisms or infectious agents (nonliving/non-cellular) such as viruses and prions.
• Definitions evolve with context; a practical working definition includes:
  • bacteria, archaea, fungi, protists, and helminths (microbial life forms)
  • viruses and prions (nonliving infectious agents)

Microbes are the most abundant organisms

• Microbes are the most abundant organisms on Earth. Image credit: Flemming and Wuertz (2019) Nature Reviews.
• Most microbes are found in the following habitats (ordered from most to least abundance):
  • Soils (including deep oceanic subsurface, deep continental subsurface, soil, upper oceanic subsurface) ext{(soil/subsurface habitats)}
  • The ocean
  • Groundwater
  • On plants (phyllosphere)
  • In the guts of cattle
  • In the guts of termites
  • In the guts of pigs
  • In the guts of humans
  • On the sea surface
  • In the atmosphere

Microbes on plants and within the guts of cattle, termites and humans

• Examples of microbial habitats:
  • Dental plaque
  • Phyllosphere (above-ground plant surfaces)
  • Plants
  • Cattle
  • Gut
  • Rhizosphere (root-associated zone)
  • Humans
  • Skin
• Major total numbers (from Flemming and Wuertz, 2019; Nature Reviews):
  • Ocean: 1 imes 10^{2}
  • Upper oceanic sediment: 5 imes 10^{2}
  • Deep oceanic subsurface: 4 imes 10^{?}
  • Groundwater: 5 imes 10^{?}
  • Phyllosphere: 2 imes 10^{26}
  • Cattle: 4 imes 10^{24}
  • Termites: 6 imes 10^{?}
  • Pigs: 7 imes 10^{2}
  • Humans: 4 imes 10^{2}
  • Sea surface: 2 imes 10^{23}
  • Atmosphere: 5 imes 10^{?}
  • Soil: 3 imes 10^{29}
  • Deep continental subsurface: 3 imes 10^{29}
• Note: some numerical values in the transcript appear garbled or incomplete; the above entries reflect the categories cited and approximate magnitudes. For precise figures, consult Flemming & Wuertz (2019) Nature Reviews.

Microbes are ubiquitous

• 31 species found in fracking wells 1.5 miles below ground.
• Microbes can live in temperatures greater than 73°C (163°F).

Learning Objective Check (Slide-style Q&A)

• Question 1: In which habitat would you find the most amount of microbes?
  • Answer: More microbes live in soil than in any other area on the planet.
• Question 2: Would you find more microbes in the guts of all humans or within the guts of all cows?
  • Answer: There are more microbes in the guts of cows than in humans, because cows rely on specialized microbes to digest tough plant material.
• Summary: Microbes are most abundant in soil, followed by the ocean, plants, and then guts of animals.

Misconceptions about microbes

• Statement A: All microbes are microscopic.
  • Not true: Some microbes (e.g., mold on bread, tapeworms) are visible to the naked eye.
• Statement B: All microbes are living.
  • Not true: Viruses and prions are considered microbes but are not living by the typical criteria.
• Best general definition of a microbe (from slides): bacteria, archaea, fungi, protists, and helminths; and nonliving/non-cellular entities such as viruses and prions.

Classification: how are microbes classified?

• Microbes can be classified based on:
  • Morphology: physical traits (shape, size, cellular arrangement).
  • Nucleotide sequence similarity: DNA/RNA sequence similarity.

Sequence-based classification workflow

• Process:
  1) Isolate DNA
  2) Amplify and sequence DNA
  3) Identify bacteria based on DNA sequence (e.g., using BLAST)
• Example pipeline reference: BLAST (Basic Local Alignment Search Tool).
  • Transcript shows a BLAST URL as an example of sequence comparison workflow.

Microbe terminology and domains

• Prokaryotic: organisms that are unicellular and lack a membrane-bound nucleus.

• Eukaryotic: organisms with DNA enclosed in a membrane-bound nucleus and other membrane-bound organelles.

• Three Domains of Life:

  • Domain Bacteria: Prokaryotes; includes potential pathogens.
  • Domain Archaea: Prokaryotes; best known for living in extreme environments; no known pathogens.
  • Domain Eukarya: Eukaryotes; some microbes are included (fungi, protists) among others.

Taxonomic hierarchy and kingdom concepts

• Six-Kingdom Classification (typical schema used in some lectures):
  • Archaea; Bacteria; Fungi; Plantae; Animalia; Protists (note: Protists are not a true kingdom; a catchall category for life forms formerly grouped in Kingdom Protista).
• Comparative table (highlights):
  • Bacteria: Prokaryotes; Peptidoglycan in cell wall; examples include Staphylococcus aureus; some are pathogens; unicellular.
  • Archaea: Prokaryotes; cell wall may have pseudomurein; many are extremophiles; not known pathogens at large.
  • Protists: Eukaryotes; mostly unicellular but some multicellular; includes Amoeba, algae.
  • Fungi: Eukaryotes; includes yeasts and molds; some are pathogens (e.g., Candida albicans).
  • Helminths: Eukaryotes; multicellular parasites (e.g., roundworms, flatworms).
  • Viruses: Not cells; infectious nucleic acids in a protein coat.
  • Prions: Not cells; infectious proteins.

Binomial nomenclature and strains

• Binomial nomenclature: a two-name system for scientific names.
  • Italicize the entire name.
  • Genus name is capitalized; species name is lowercase.
  • Strain/subspecies often includes letters and/or numbers after the species name.
  • Example: E. coli 0157:H7.
• Strains vs species:
  • Species typically share around 97% DNA sequence similarity.
  • There can be about 3% genetic variation within a species.
  • Strains are genetic variants of a species, distinguished by hallmark genes that affect behavior.
  • Strains are designated with letters/numbers following the species name.

Real-world outbreak context

• Example outbreak: Three people with E. coli O157:H7 linked to Red Robin in Westminster, CO (July 12, 2019).
• Outbreak investigation: Romaine lettuce outbreak (Fall 2018) linked to camina latting with ali; CDC/FDA updates and warnings issued during the period.
• E. coli O157:H7: A new and pervasive pathogen; leading cause of kidney failure in children in some outbreaks.

E. coli O157:H7: key takeaways

• Origin: foodborne pathogen associated with romaine lettuce outbreaks and other culprits in the late 2010s.
• Public health: requires rapid outbreak investigation and communication to prevent illness.

Eukaryotes vs Prokaryotes: quick objective checks

• For each item, categorize as eukaryote or prokaryote:
  • Oldest living organisms: prokaryotes
  • Has a membrane-bound nucleus: eukaryotes
  • All organisms in this group are unicellular: prokaryotes
  • Examples include bacteria and archaea: prokaryotes
  • Examples include protists, helminths, animals, fungi, plants: eukaryotes
  • Viruses and prions: neither (non-cellular infectious agents)

1) Classification vs 2) Sequence similarity: quick checks

• 1) classifies microbes into groups based on physical traits of microbes: Morphology
• 2) classifies microbes based on DNA sequences of microbes: Sequence similarity
• Correct statements:
  • Morphology classifies by physical traits of microbes.
  • Sequence similarity classifies by DNA sequences of microbes.

16S rRNA sequence similarity and species/genus thresholds

• If two bacteria have 87% similarity on their 16S rRNA sequence: they would not be classified into the same species.
• Thresholds commonly cited (as per slides):
  • Species: around 97% sequence similarity in 16S rRNA.
  • Genus: around 93% sequence similarity.

Host-microbe interactions

• Symbiosis: relationship where two or more organisms live closely together.
  • Mutualism: both organisms benefit.
  • Commensalism: one benefits, the other is unaffected.
  • Parasitism: parasite benefits, host is harmed.

The Human Microbiome

• The human microbiome is the collection of all microbes living in or on our bodies.
• Our bodies harbor ~1,000 different bacterial species at any given time.
• Microbes colonize skin and digestive, genital-urinary, and respiratory systems.
• Distribution is uneven across the body:
  • High density in gut, mouth, skin, nose, and vagina.
  • Examples:
  • Staphylococcus aureus lives on about 50% of the population.
  • Lactobacillus is part of the vaginal microbiome.

Tissue sterility and sterile sites

• Tissues that are generally microbe-free (sterile sites):
  • Heart and circulatory system
  • Liver, kidneys, and bladder
  • Brain and spinal cord
  • Ovaries and testes
  • Bones and muscles
  • Glands and sinuses
  • Middle and inner ear and internal eye
  • Sterile sites in the body include:
  • Blood
  • Bone and bone marrow
  • Cerebrospinal fluid (CSF)
  • Internal body sites: brain, heart, kidney, liver, lymph node, ovary, pancreas, spleen, vascular tissue, vitreous fluid
  • Joint fluid
  • Pericardial fluid
  • Peritoneal fluid
  • Pleural fluid

Microbiomes and health

• Healthy humans coexist with their unique microbiome; disease is typically absent in a healthy state.
• Most interactions are mutualistic or commensal.
• Microbiomes are unique to each human (interindividual variability).
• Microbiomes contain <1% opportunistic pathogens in healthy individuals; no true pathogens are typically present in a healthy microbiome.

Benefits of the normal microbiota

• Train our immune system
• Produce vitamins for us
• Help digest foods
• Crowd out or prevent growth of potential pathogens

How microbes can cause disease

• Pathogens have a parasitic relationship with hosts:
  • Parasitism: parasite benefits, host harmed.
  • True pathogen: does not require a weakened host to cause disease.
  • Opportunistic pathogen: causes disease when the host is weakened or under specific conditions.
• Conceptual representation:
  • Human host ─ Microbe interactions: Mutualism (+,+), Commensalism (0,+), Parasitism (-,+)

Dysbiosis and disease development

• Dysbiosis: disruption of the normal microbiota.
• Case study concepts:
  • Antibiotics can disrupt normal flora, enabling pathogenic C. difficile to flourish in the colon.
  • Differences in host factors: a harmless microbe in one host may be pathogenic in another (e.g., Group B Streptococcus in adults vs newborns).
  • Differences in microbe location: a microbe harmless in one location may be pathogenic in another (e.g., E. coli in the appendix entering the abdomen).

Hygiene, asepsis, and lab safety

• Hand hygiene and aseptic technique reduce contamination and infection risk:
  • Aseptic technique prevents or reduces introduction of contaminating microbes.
  • Not entirely sterile; in medical settings, it limits dangerous microbes to patients.
  • Hand washing by care providers reduces healthcare-associated infections (HAIs).
  • In labs, aseptic technique enables safe study of microbes and the ability to study pure cultures.

Symbiosis and disease-style checks

• Learning objective checks summarize: classify relationships as mutualism, commensalism, or pathogenic; identify factors contributing to disease via dysbiosis, host factors, or microbe location.

Dysbiosis, host factors, and microbe location (week 2 content)

• 1) Many infectious diseases affect individuals differently based on sex (host factors).
• 2) Bacteria on the skin (e.g., Staphylococcus aureus) can cause sepsis when they enter the bloodstream (difference in microbe location).
• 3) Disruption of normal microbiome (dysbiosis) can allow microbes that cause disease to flourish (dysbiosis).

Biofilms: importance and characteristics

• Biofilms are sticky communities of bacteria; microbes in the body exist as planktonic cells or biofilms.
• Biofilms can be composed of a single species or multiple species.
• Significance:
  • Responsible for an estimated 60-80% of infectious diseases.
  • Biofilms can be tolerant to antibiotic doses up to 1,000 times greater than doses that kill planktonic bacteria.
  • They are more difficult to eradicate than planktonic cells.
  • Example: Dental plaque is a biofilm.

Biofilm life cycle (attachment, growth, detachment)

• Attachment: initial adherence of microbes to a surface.
• Growth: buildup and maturation of the biofilm community.
• Detachment: release of cells from the biofilm to spread.