Microbiology Foundations: What Microbes Are and How We Study Them

1) Core definitions: mapping the microbial world

Microbe

A microbe is an organism or biological entity that is typically too small to be seen clearly with the unaided eye. In everyday microbiology, the term includes bacteria, archaea, many fungi (like yeasts), many protists, and viruses (even though viruses are not cellular). “Microbe” is a size-and-study category, not a single branch on the tree of life.

Size scale (rough guide):

• Bacteria/archaea: often ~0.5–5 micrometers (µm) in at least one dimension.
• Viruses: often ~20–300 nanometers (nm) (0.02–0.3 µm), though some are larger.
• Human hair diameter: ~70 µm (for comparison).

Practical way to think about scale: if a typical bacterium were the size of a soccer ball, many viruses would be the size of a marble or smaller.

Prokaryote

A prokaryote is a cellular organism whose genetic material is not enclosed in a nucleus. Prokaryotes include bacteria and archaea. They are cells, so they have a cell membrane, cytoplasm, ribosomes, and DNA, but their internal organization differs from cells with nuclei.

Examples:

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• Bacterium: Escherichia coli (common gut bacterium).
• Archaeon: Halobacterium species (salt-loving archaea found in very salty environments).

Virus

A virus is an acellular infectious agent made of genetic material (DNA or RNA) packaged in a protein coat (and sometimes a lipid envelope). Viruses do not have ribosomes and do not carry out metabolism on their own; they replicate only by using a host cell’s machinery.

Examples:

• Influenza virus: an enveloped RNA virus that infects respiratory cells.
• Bacteriophage (phage): a virus that infects bacteria.

Microbiome

A microbiome refers to the community of microbes in a particular environment (such as the gut, skin, soil, or ocean) and often also includes their collective genes and interactions. A microbiome is not a single organism; it is an ecosystem.

Examples:

• Gut microbiome: a diverse community of bacteria and archaea (and sometimes viruses) living in the digestive tract.
• Soil microbiome: microbes that drive nutrient cycling, including bacteria and archaea involved in nitrogen transformations.

Where bacteria, archaea, and viruses fit (organization)

• Bacteria: cellular, prokaryotic; typically have a cell wall (composition varies), ribosomes, and a single circular chromosome (often with plasmids).
• Archaea: cellular, prokaryotic; cell wall and membrane chemistry differ from bacteria; many are found in diverse environments (not only extremes).
• Viruses: acellular; require a host cell to replicate; can infect bacteria, archaea, plants, animals, and other microbes.

Knowledge check: classify by description

• A: “A 1 µm cell with ribosomes and a circular chromosome; divides into two cells.” → Bacterium or archaeon
• B: “A 100 nm particle with RNA inside a protein shell; makes copies only inside host cells.” → Virus
• C: “A 2 µm cell from a high-salt lake; prokaryotic organization.” → Archaeon (most likely, based on habitat clue)

2) Cellular microbes vs acellular viruses (feature comparison)

One of the most important foundations in microbiology is distinguishing living cellular microbes (bacteria and archaea) from acellular viruses. The key differences show up in structure, metabolism, and how replication happens.

Practical interpretation: if you can observe an entity forming a colony on a nutrient surface without host cells present, you are likely dealing with a cellular microbe (bacterium/archaeon). If replication requires living host cells, you may be dealing with a virus (or another obligate intracellular agent).

Knowledge check: living cell or virus?

• D: “Has ribosomes and makes ATP from chemicals in its environment.” → Cellular microbe (bacterium/archaeon)
• E: “Genome is RNA; no ribosomes; new particles assemble inside host cells.” → Virus

3) Observation and measurement: how we see and quantify microbes

Microscopy basics: what you can and cannot see

Because microbes span micrometers to nanometers, the tool you choose determines what details are visible. The key concept is resolution: the ability to distinguish two close points as separate.

• Light microscopy: uses visible light and glass lenses. Typical resolution limit is about ~200 nm. This is enough to see most bacteria and archaea (shape, arrangement), but not most viruses as distinct particles.
• Electron microscopy (EM): uses electrons with much shorter wavelengths, enabling much higher resolution (down to the nanometer scale). EM can visualize many viruses and fine cellular structures.

Step-by-step decision guide (conceptual):

1. Estimate size: is the target likely micrometers (cells) or nanometers (viruses)?
2. Choose method: light microscopy for cell morphology; electron microscopy for viral particles or ultrastructure.
3. Define the question: “What shape is it?” (light may suffice) vs “What is the capsid structure?” (often needs EM).

Why staining matters: contrast and classification clues

Many cells are nearly transparent under a basic light microscope. Stains increase contrast so you can see boundaries and patterns. Staining can also highlight differences among microbes that relate to their cell envelope structure.

Main purposes of staining (conceptual):

• Contrast: make cells stand out from the background.
• Shape and arrangement: observe forms such as rods, spheres, spirals; and arrangements such as chains or clusters.
• Structural hints: some stains differentiate broad cell-envelope types, which can guide identification and further testing.

Common morphology terms you’ll see:

• Coccus: roughly spherical cell.
• Bacillus: rod-shaped cell.
• Spirillum/spirochete: spiral-shaped cell.

Culture and colonies: what a colony represents

Culturing means providing conditions that allow microbes to multiply. On a solid nutrient surface, growth often appears as a colony—a visible cluster of cells.

Key idea: a colony is usually interpreted as arising from a single starting cell (or a small clump of cells) that replicated many times. This is why colonies are used to estimate counts and to obtain a population that is more uniform.

Step-by-step concept for interpreting a plate (no procedural details):

1. Observe colony differences: size, color, edge shape, texture.
2. Infer diversity: multiple colony types suggest multiple organisms may be present.
3. Connect to questions: “Is this sample mixed?” “Is one type dominant?” “Do different conditions change which colonies appear?”

Important limitation: not all microbes grow under standard lab conditions; “no colonies” does not necessarily mean “no microbes.”

Knowledge check: matching tool to target

• F: “You want to see the overall shape of a 2 µm rod-shaped cell.” → Light microscopy
• G: “You want to visualize a 90 nm particle suspected to be a virus.” → Electron microscopy
• H: “You want to compare colony appearances from two environments.” → Culture on solid media (concept)

4) Safety and contamination: scientific principles behind reliable microbiology

Aseptic technique (rationale, not procedure)

Aseptic technique refers to practices designed to prevent unwanted microbes from entering your sample and to prevent your sample microbes from spreading into the environment. The scientific rationale is about controlling variables and reducing confounders.

• Why contamination matters scientifically: if an unintended microbe enters a culture, it can change growth patterns, alter measurements, or produce misleading results (for example, a contaminant might grow faster and “hide” the organism you intended to study).
• Why it matters for interpretation: a surprising colony type or unexpected microscopy finding may reflect contamination rather than a new discovery.

Conceptual checklist for thinking like a scientist:

1. Identify exposure points: when is the sample open to the environment?
2. Predict likely contaminants: skin-associated microbes, airborne spores, microbes from surfaces.
3. Use controls: include comparisons that reveal whether growth could be coming from materials or environment rather than the intended sample.

Biosafety levels (high-level overview)

Biosafety levels (BSL) are categories that match laboratory safety requirements to the risk posed by the organisms and procedures involved. They reflect factors such as how an agent spreads, how severe disease could be, and what containment is needed.

• BSL-1: low-risk microbes not known to cause disease in healthy adults; basic containment principles.
• BSL-2: moderate-risk agents associated with human disease; additional containment and training.
• BSL-3: agents that can cause serious disease and may spread through the air; higher containment and specialized controls.
• BSL-4: dangerous and exotic agents with high risk of life-threatening disease; maximum containment.

Scientific takeaway: biosafety is a structured way to manage risk while enabling reproducible research. The same organism can require different precautions depending on how it is handled and what is being done with it.

Knowledge check: contamination and safety reasoning

• I: “A plate shows two very different colony types when you expected one.” What is a plausible explanation? → Contamination or a mixed starting sample
• J: “You are studying an agent that requires host cells to replicate and is associated with human disease.” Which category is it most likely to fall under? → Virus; biosafety level depends on the specific agent and risk
• K: “A 1 µm prokaryotic cell from a hot spring; grows as colonies on a specialized medium.” → Archaeon (likely), though some bacteria also fit; classification needs additional evidence