1.1 What counts as a microbe #
1.1.1 A working definition #
A microbe, here, is an organism studied as a single cell, a filament, or a non-cellular infectious particle, usually below the size one can resolve by eye. The word is not a clade. Bacteria and archaea are separate prokaryotic domains. Fungi, protozoa, and algae are eukaryotes in different parts of the tree. Viruses are not cells. Prions and viroids are narrower: a misfolded host protein, and a small circular RNA. They share a subject because the same questions of structure, growth, and control apply, and because they interact.
A typical bacterium is about 1–5 µm long. A typical virion is about 20–300 nm, at or below the light microscope’s resolution of about 0.2 µm. A yeast is often about 5–10 µm. Thiomargarita can be seen unaided, and kelps are metres long without being land plants. Helminths are animals and are outside these notes. So is the organelle-by-organelle account of a eukaryotic cell: a fungal mitochondrion is cell biology.
1.1.2 Boundaries with the other subjects #
The cell-biology notes own eukaryotic organelles, the fluid mosaic, the cytoskeleton, and image formation. These notes add the microbial consequence: wall chemistry, why a spore survives boiling, and why a bacterial flagellum is not a cilium.
Biochemistry owns the pathways. These notes ask only where the machinery sits without a mitochondrion, which acceptor is used, and which products leave. Genetics and molecular biology own mapping, replication, and operators. A plasmid appears here as an object; a cross does not. Immunology owns antibodies, complement, and vaccines. The barrier, and the microbial answer to it, are as far as these notes go.
1.2 Hooke, Leeuwenhoek, and the germ theory #
1.2.1 The first microscopes #
Robert Hooke, in Micrographia (1665), named the empty compartments in cork cells. He was looking at walls of dead plant tissue, not at bacteria. Antonie van Leeuwenhoek, in the 1670s and 1680s, ground fine single lenses and described living “animalcules” to the Royal Society: rainwater, infusions, and scrapings from his teeth. Bacteria and protozoa were among them. He had no theory of contagion.
Seeing an organism and knowing what it does to a host were two centuries apart. Until the mid-nineteenth century, fermentation was often treated as a chemical decay, with yeast as a by-product if it was noticed at all, and disease was blamed on miasma as readily as on a specific microbe.
1.2.2 Pasteur against spontaneous generation #
The claim that mattered in the 1850s was that microbes arise de novo in nutrient broth once air is present. John Needham boiled meat broth, stoppered it, and later found it cloudy. Lazzaro Spallanzani boiled longer, sealed the vessels, and saw no growth. Critics said he had spoiled the air or excluded a vital principle. An experiment that excludes air cannot decide whether air generates life or only delivers organisms.
Penicillin Spheroplast Generation
Louis Pasteur’s swan-neck flasks, in his 1861 memoir, separated the two. Infusion was boiled in a flask whose neck bent down and up, open to the air. Air passed. Dust settled in the bend. The liquid stayed clear. Tipped so that liquid washed the dust and ran back, it grew. The nutrient had not lost the capacity to support life. Air as gas was not the source. Airborne organisms were. The same idea explains fermentation: specific microbes cause specific chemical changes, and the spoilage of wine is contamination. Heating enough to kill those contaminants, without ruining the product, is the origin of pasteurisation (Chapter 7). The flasks do not speak to the origin of life on a lifeless early Earth. They also do not say every microbe can be grown in broth.
Control sometimes preceded a pure culture. John Snow in 1854 tied cholera to the Broad Street pump. Ignaz Semmelweis cut childbed fever by making physicians wash between the autopsy room and the ward. Joseph Lister’s phenol on instruments and wounds is the surgical version. Phenol’s chemistry is in Chapter 7.
1.3 Koch’s postulates #
1.3.1 The four criteria and the pure culture #
Robert Koch turned the germ theory into criteria that can fail. From anthrax in the 1870s and tuberculosis in the early 1880s, and in the familiar wording around 1890, the chain is: the organism is present in every case; it is grown in pure culture; that culture reproduces the disease in a susceptible host; the same organism is re-isolated. Jakob Henle had sketched the logic; Friedrich Loeffler’s diphtheria work helped fix the textbook form.
A pure culture descends from one cell, or one colony-forming unit, so its properties belong to one kind of organism. On a solid surface those descendants form a colony. Agar, a red-algal polysaccharide most bacteria cannot digest, stays solid where gelatin would melt. The Hesses introduced it; Petri’s dish kept the surface clear. That is how the idea became practicable. It is not a medium to mix. A colony is only an argument for purity. Stuck cells, an invading neighbour, or an organism that cannot grow on the medium all break it.
1.3.2 Modern limits #
Carriage breaks the first statement. Vibrio cholerae, Salmonella enterica serovar Typhi, and Neisseria meningitidis live in people who are not ill. Failure to grow on lifeless media breaks the second. Mycobacterium leprae has not been grown that way. Chlamydia, and every virus, replicates only inside host cells, so a “pure culture” of a virus is a pure infection of a host system, not a colony. Preformed toxin separates damage from colonisation: foodborne botulism and staphylococcal food poisoning are caused by toxin made before the food is eaten. Other limits are polymicrobial disease, human-only pathogens for which no ethical animal test exists, and opportunists that are present in health. When the difference between strains is a gene, Stanley Falkow’s molecular postulates (Chapter 8) are the right grain.
Winogradsky and Beijerinck added the other view: microbes as physiological types selected by habitat chemistry. A nitrogen-free condition reveals fixers; an inorganic electron donor reveals lithotrophs. A Winogradsky column shows the result. Oxygen enters from the top, sulfide accumulates below, and each guild occupies the band its metabolism fits. The column demonstrates sorting. It is not a way to enrich a pathogen. Most microbes are not human pathogens. Koch’s postulates describe the minority that cause a specific disease.
1.4 Key terms, summary, and self-check #
Key terms. Microbe; germ theory; swan-neck flask; pure culture; colony; Koch’s postulates; carriage; unculturable organism; preformed toxin.
Summary. The subject covers bacteria, archaea, eukaryotic microbes, and non-cellular infectious agents, and leaves organelles, pathways, mapping, and adaptive immunity to their own notes. Hooke named cells in cork; Leeuwenhoek saw living microbes. Pasteur showed that airborne organisms, not air, start growth in sterile broth. Koch’s postulates tie one pure culture to one disease. Carriage, failure to grow on lifeless media, and preformed toxin are where the chain breaks. A pure culture is a population argument, not a recipe.
Self-check.
1. Why did Spallanzani’s sealed flasks fail to settle spontaneous generation, and what did the bend in Pasteur’s neck add?
2. State the four postulates. Which one fails in carriage, which in an unculturable bacterium, and which when disease is preformed toxin?
3. Why is a colony only an argument for purity?
4. Why are viruses in this subject if the cell theory excludes them?
5. What can Winogradsky’s approach answer that Koch’s postulates cannot?
