Microorganisms

Awareness level only. Do not try to grow microorganisms at home. In a lab, cultures and patient samples are handled at the biosafety level set by your institution, after training and under supervision.

Why it matters

Microbiology labs identify the organism behind an infection so the right treatment can be chosen. Biotech labs grow bacteria and yeast to make insulin, enzymes and vaccines. Every lab protects its work from contamination. All of this starts with telling three big groups apart: bacteria, viruses and fungi.

Bacteria

• Prokaryotic cells: no nucleus, a circular chromosome and often plasmids, ribosomes, a cell membrane and usually a cell wall made of peptidoglycan.
• Size about 1–5 µm: visible with a light microscope.
• Shapes: cocci (spheres), bacilli (rods), spirilla (spirals).
• Reproduce by binary fission: one cell splits into two. Under good conditions some, like E. coli, can double about every 20 minutes.
• Most are harmless or helpful (gut bacteria, soil bacteria, bacteria used in yoghurt). A minority cause disease, such as Streptococcus pyogenes (strep throat) and Mycobacterium tuberculosis.

The Gram stain is one of the first tests on a bacterial sample. It sorts bacteria by cell wall:

• Gram-positive bacteria have a thick peptidoglycan wall that holds the purple crystal violet dye: they stain purple.
• Gram-negative bacteria have a thin wall plus an outer membrane, lose the purple dye and take up the red counterstain: they stain pink/red.

A report such as "Gram-positive cocci in clusters" (often Staphylococcus) gives the clinician an early clue hours or days before culture results.

Treatment: antibiotics target bacterial structures humans do not have, such as the peptidoglycan wall (penicillins) or bacterial ribosomes (tetracyclines).

Viruses

• Not cells. A virus is genetic material (DNA or RNA) inside a protein coat called a capsid, sometimes wrapped in a lipid envelope taken from the host cell.
• Size about 20–300 nm: too small for a light microscope; seen with an electron microscope.
• They have no ribosomes or metabolism, so they can reproduce only inside a host cell, by hijacking its machinery. Each virus infects particular cell types.
• Examples: influenza, SARS-CoV-2, HIV, hepatitis B.

Treatment: antibiotics do not work on viruses. Antiviral drugs target specific viral steps (for example, blocking a viral enzyme), and vaccines prepare the immune system in advance.

Detection: because viruses cannot be grown on plates, labs detect their genetic material with PCR or RT-PCR, or detect viral proteins (antigens) or the patient's antibodies against them (lesson 3).

Fungi

• Eukaryotic cells: a nucleus and organelles, and a cell wall made of chitin (not peptidoglycan or cellulose).
• Two forms: single-celled yeasts (such as Candida and baker's yeast, Saccharomyces) and multicellular moulds made of threads called hyphae (such as Aspergillus and Penicillium).
• Reproduce by budding (yeasts) or by spores (moulds). Airborne mould spores are a common lab contaminant.
• Fungi gave us penicillin, are used in baking and brewing, and cause infections from athlete's foot to serious infections in people with weak immune systems.

Treatment: antifungal drugs, which often target ergosterol, the fungal version of cholesterol in their membranes.

Side by side

Worked example: reading a scenario

A patient has a sore throat. A rapid test detects a viral antigen. Should they get an antibiotic? No: antibiotics do not act on viruses, and unnecessary use drives antibiotic resistance. If instead the throat swab grows Gram-positive cocci in chains identified as Streptococcus pyogenes, an antibiotic such as penicillin is appropriate. The lab result changes the treatment.

Common mistakes

• Calling viruses bacteria or "germs" interchangeably. They are fundamentally different, and treatment differs.
• Expecting antibiotics to treat colds or flu.
• Forgetting fungi are eukaryotes. That is why antifungal drugs can have more side effects: fungal cells resemble ours.
• Assuming all microbes are harmful. Most bacteria and fungi are harmless or useful.

Quick recap

• Bacteria: prokaryotic cells, 1–5 µm, peptidoglycan wall, binary fission, antibiotics.
• Viruses: not cells, nanometre-sized, reproduce only in host cells, antivirals and vaccines.
• Fungi: eukaryotic, chitin wall, yeasts and moulds, antifungals.
• The Gram stain sorts bacteria into purple (Gram-positive) and pink (Gram-negative).