Micro-organisms
The two dozen that decide who lives where there is no doctor: what each does, how it spreads, what kills it and which step stops it.
Home: Hygiene and disease, Level 1 · Foothold, level 1 of 3 in its track. Serves 11 steps across 5 subjects.
Where there is no doctor, most deaths from infection come from four routes: water and food carrying faeces, wounds, the air, and insect bites. Each route has a small number of organisms that do most of the killing, and each one has a known weak point: a temperature, a time, a chemical dose, a filter size or a habit. This guide is the basic set, about two dozen organisms, each with the number that stops it. It is not a catalogue. The formal record of every named micro-organism is kept by the nomenclature registries listed under Further, and the diseases are covered in full by WHO and CDC.
Medical content on this site has not yet been reviewed by a qualified practitioner (CIV-054). Check anything you act on against the WHO and CDC pages linked below.
What kills them
Learn this table first: it is what the rest of the guide keeps pointing back to. The right column matters as much as the middle one, because each method has organisms it misses.
| Method | Dose that works | Kills | Does not kill |
|---|---|---|---|
| Rolling boil | 1 minute; 3 minutes above 2,000 m | Bacteria, viruses, Giardia, Cryptosporidium | Bacterial spores (tetanus, botulism); toxins already made in food by Staphylococcus or moulds |
| Chlorine (household bleach) | 2 drops of 5% bleach per litre, 30 minutes before drinking. WHO: at least 0.5 mg/L free chlorine left after 30 minutes | Most bacteria and viruses | Cryptosporidium: chlorine tablets do not kill it. Giardia needs longer contact. Spores |
| Filter | 1 µm absolute pore size or finer, or a ripened slow sand filter | Giardia and Cryptosporidium (4–6 µm), most bacteria | Viruses, which are far smaller: disinfect after filtering |
| Sunlight (SODIS) | Clear PET bottle, 3 litres or less, 6 hours in full sun | Most bacteria and viruses | Muddy water: sunlight cannot get through |
| Cooking | 70 °C or hotter all the way through | E. coli O157, Salmonella and other bacteria in food | Spores; Staphylococcus toxin; aflatoxin |
| Pressure canning | 116–121 °C | Botulism spores | Nothing in the jar survives: this is sterilisation |
| Acid | pH below 4.6 | Stops botulism growing | Does not sterilise: it only prevents growth |
| Drying | Grain below 13% moisture | Stops the moulds that make aflatoxin | Toxin already made stays |
| Soap and water | At least 20 seconds, then rinse | Removes most germs from hands, including norovirus | Germs on hands you then wipe on a dirty cloth |
Spread by water and food
All of these leave the body in faeces and enter by the mouth. They are stopped by the same three things: safe water, waste kept apart from water and hands washed with soap. Treat diarrhoea with oral rehydration whatever the cause: the fluid loss kills before the germ does.
| Organism | What it does | Sick after | What kills it | Stopped by |
|---|---|---|---|---|
| Vibrio cholerae (bacterium) | Cholera: sudden, massive watery diarrhoea. Untreated, it can kill within hours | 12 hours to 5 days | Boiling, chlorine | Safe water; oral rehydration saves most patients |
| Salmonella Typhi (bacterium) | Typhoid: fever rising over days, stomach pain. Some people carry it for years without symptoms | 6–30 days | Boiling, chlorine, cooking | Safe water; carriers kept out of food handling |
| Shigella (bacterium) | Dysentery: bloody diarrhoea. A very small dose infects | 1–2 days | Boiling, chlorine, soap | Handwashing with soap |
| E. coli O157 (bacterium) | Bloody diarrhoea; up to 10% develop kidney failure (haemolytic uraemic syndrome), mostly children | 3–8 days, usually 3–4 | Cooking to 70 °C | Cook minced meat through; do not drink raw milk |
| Hepatitis A (virus) | Liver infection: yellow skin and eyes, weeks of weakness | 14–28 days | Boiling, chlorine | Safe water, handwashing; a vaccine exists |
| Norovirus (virus) | Sudden vomiting and diarrhoea; spreads through a household in days | 12–48 hours | Boiling; soap and water | Handwashing; sick people kept out of cooking |
| Giardia (protozoan) | Weeks of greasy, foul diarrhoea and wind | 1–2 weeks | Boiling, 1 µm filter; resists chlorine | Safe water from lakes and streams |
| Cryptosporidium (protozoan) | Watery diarrhoea; dangerous in infants and the malnourished | 2–10 days, usually 7 | Boiling, 1 µm filter; not chlorine tablets | Boil or filter; keep livestock out of water sources |
Wounds and skin
The skin keeps these out until it is broken. What saves the wound is cleaning it at once and keeping everything that touches it clean: see wound care and germ theory and antisepsis. In 1847 Ignaz Semmelweis cut deaths from childbed fever in his Vienna maternity ward by making doctors wash their hands in chlorinated lime; the killer was Streptococcus pyogenes.
| Organism | What it does | Sick after | What kills it | Stopped by |
|---|---|---|---|---|
| Clostridium tetani (bacterium) | Tetanus: jaw lock, then spasms of the whole body. Spores live in soil, dung, ash and on rusty tools | 3–21 days, most within 14 | Spores survive boiling; steam sterilisation at 121 °C kills them | Clean deep wounds at once and leave contaminated ones open; the tetanus vaccine |
| Staphylococcus aureus (bacterium) | Boils, infected wounds, blood poisoning. In food left warm, a toxin that causes vomiting | Food poisoning: within hours | Cooking kills the bacterium but not its toxin | Clean dressings; keep cooked food hot or cold, never warm for hours |
| Streptococcus pyogenes (bacterium) | Sore throat, spreading skin infection, childbed fever after birth | 2–5 days | Soap, chlorine, penicillin | Handwashing before touching a wound or a birth; antibiotics |
Poisons made in food
These do not need to infect you. They grow in stored food and leave a poison behind, so the rule is about how food is kept, not only how it is cooked. The numbers are the ones in preserving the harvest and the preservation guide.
| Organism | What it does | Sick after | How it grows | Stopped by |
|---|---|---|---|---|
| Clostridium botulinum (bacterium) | Botulism: double vision, drooping eyelids, then paralysis that stops breathing | 12–36 hours (4 hours to 8 days) | Without air, in food above pH 4.6: home-canned vegetables, meat, fish, garlic in oil | Acid below pH 4.6, or pressure canning at 116–121 °C; boiling for 5 minutes destroys the toxin |
| Aspergillus flavus (mould) | Aflatoxin: liver damage and liver cancer; large doses kill in weeks | Chronic, or days after a large dose | Warm, damp stored maize, groundnuts and other grain | Dry grain below 13% moisture; throw out mouldy grain; cooking does not help |
| Claviceps purpurea (fungus) | Ergotism: burning limbs, gangrene, convulsions | Days to weeks of eating it | Replaces grains of rye and other cereals with dark purple-black bodies | Clean seed; pick out and burn the dark bodies before milling |
Diseases to recognise
These cannot be stopped with a boil or a filter. They are recognised by their signs and slowed by the habits in the last column, and cured only at the antibiotics and vaccines tier. A health authority that counts cases is what shows an outbreak starting.
| Organism | What it does | Sick after | How it spreads | Slowed by |
|---|---|---|---|---|
| Mycobacterium tuberculosis (bacterium) | Tuberculosis: cough lasting weeks, sometimes with blood; fever, night sweats, weight loss. About a quarter of the world is infected | Months to years | Through the air when a sick person coughs | Ventilation and daylight; the sick kept apart; treatment is 4–6 months of daily medicine |
| Plasmodium (protozoan) | Malaria: fever, chills and sweats in cycles; P. falciparum can kill in days | 10–15 days after the bite | Bites of female Anopheles mosquitoes, at night | Nets over sleepers, screens, draining standing water; artemisinin combination therapy; quinine, from cinchona bark, before it |
| Measles (virus) | Fever, then a rash spreading from the face. Kills through pneumonia and blindness, above all in the malnourished | 7–14 days | Through the air; one case infects about 18 people who are not immune | Two doses of vaccine; for sick children under 5, two doses of vitamin A |
| Rabies (virus) | Fear of water, agitation, paralysis. Once symptoms show, 100% fatal | Usually 2–3 months (1 week to 1 year) | Bites and scratches of infected animals; dogs cause 99% of human cases | Wash any bite with soap and water for at least 15 minutes, at once; vaccine after the bite |
Microbes to put to work
The same knowledge runs the other way. Most food preservation, all brewing, the first antibiotics and the fertility of legume fields are microbes doing the work. See fermentation and distilling.
| Organism | What it makes | What it needs | Used in |
|---|---|---|---|
| Saccharomyces cerevisiae (yeast) | Alcohol and carbon dioxide from sugar: glucose → 2 ethanol + 2 CO₂ | Sugar, warmth, no air for alcohol | Bread, beer, wine; distilling for stronger spirit and disinfectant |
| Lactic acid bacteria (Lactobacillus, Leuconostoc) | Lactic acid, which drops the pH below 4 and preserves the food | 2–2.5% salt by weight, no air | Sauerkraut, pickles, yoghurt, silage: preserving |
| Acetobacter (bacterium) | Vinegar: acetic acid from alcohol | Air | Pickling needs vinegar of at least 5% acidity |
| Penicillium (mould) | Penicillin, found by Alexander Fleming in 1928 | Grown in deep tanks for yield | The first antibiotic |
| Rhizobium (bacterium) | Nitrogen from the air, fixed in legume root nodules | Legume roots: clover, beans, peas, vetch | A legume ley adds 50–200 kg of nitrogen per hectare: holding fertility |
| Methanogens (archaea) | Biogas, roughly 50–70% methane, from manure and sewage | No air, and warmth | Fuel from waste: see the sanitation guide |
Build the gear
Where to go next
This page covers what you are most likely to meet. It is not a field guide, and on identification that difference can kill you. These are the works that go further — chosen because they can be held offline.
Still to come
Illustrations carry a technique further than prose, but some things only move well. Recorded here rather than left implicit.
- Micrographs of Giardia cysts and Entamoeba as they appear in a stool sample under a simple microscope
- A Gram-stain procedure using dyes and reagents a tier-3 settlement can make