A portrait of one bacterial species: the soil organism named after a jar of wet hay, the endospore that lets it wait out anything, and the fermented foods built on it from Japan to Nigeria.
Leave a handful of dry hay in a jar of water and stand it somewhere warm. After a day or two a thin, wrinkled film gathers across the surface and the water turns cloudy. Microbiologists have been making that infusion since the nineteenth century, because it is one of the simplest ways to coax a particular soil organism out of hiding.
The organism is Bacillus subtilis. It was first described in 1835 by the German naturalist Christian Gottfried Ehrenberg, who filed it under a different genus altogether; Ferdinand Cohn moved it to Bacillus in 1872 and the name has stood ever since. In English it is still called the hay bacillus, after the jar it was pulled from.
What Bacillus subtilis is
A single bacterial species: a rod a few micrometres long and less than a micrometre wide, Gram-positive, happiest with oxygen although it can manage for a while without. It is also one of the most thoroughly studied bacteria in science. Its whole genome was mapped in the 1990s, and it has long served as the standard laboratory model for how a Gram-positive cell divides, moves and switches genes on and off.
Like most decomposers, it works by secretion. It releases enzymes into whatever it is sitting on — amylases that cut starch into sugars, proteases that cut proteins into peptides and amino acids — and then takes up the fragments. One of those proteases, subtilisin, is named after the species and is now manufactured industrially at enormous scale for laundry detergents. That is the organism's basic trade: breaking large molecules in its surroundings into smaller ones.
Where the hay bacillus lives in nature
Soil, mostly — the top few centimetres, where dead plant material is being taken apart. From there it travels: onto the surfaces of leaves and roots, into dust, into fresh water and sediment, onto grain, straw and dried herbs. It is not a fussy organism and it is genuinely common. If you have handled compost, hay or garden soil this week, you have handled it.
Straw matters for the rest of this story. Dry rice straw carries Bacillus subtilis spores in quantity, and that fact — noticed long before anyone knew what a bacterium was — sits at the origin of one of the world's better-known fermented foods.
What an endospore actually is
When conditions turn against it, and the food and water run out, a Bacillus subtilis cell does something unusual. It stops dividing and builds a single survival structure inside itself, then dissolves the rest of the cell away from around it. What remains is an endospore.
It is not a seed, and not a reproductive spore in the way a fungus makes them. One cell produces exactly one endospore, so nothing multiplies — this is purely a way of waiting. The structure is a dehydrated core holding one copy of the chromosome, the DNA wrapped in small acid-soluble proteins and most of the water replaced by calcium dipicolinate. Around that core sit a thick layer of modified cell wall and several tough protein coats.
The result tolerates boiling, drying, ultraviolet light, solvents and long stretches of nothing happening at all. When water and nutrients return, the spore germinates within minutes and an ordinary growing cell walks back out of it. In practical terms this is why Bacillus cultures are straightforward to bottle, move and keep, where organisms without a spore stage need much more careful handling.
Bacillus subtilis in traditional fermented foods
Most fermented foods in the European repertoire are acidic: lactic acid bacteria turn sugars into acid, the pH falls, and the sharpness is the point. Bacillus fermentations run the other way. Working mainly on protein, the organism releases ammonia and the pH climbs, often well past neutral. These are called alkaline fermentations, and they taste and smell nothing like sauerkraut — savoury, deep, frequently pungent, with a stickiness that comes from the polymer the bacteria spin around themselves.
They form a global family, built mostly on beans and seeds:
- Natto — Japan. Steamed soybeans; the best-documented Bacillus subtilis food and the one most people have heard of.
- Kinema — the eastern Himalaya, in Nepal and north-east India. Soybeans fermented in baskets lined with leaves.
- Thua nao — northern Thailand. Soybeans again, often dried and pounded into a paste or pressed into flat cakes.
- Cheonggukjang — Korea. A quick soybean ferment, usually finished in a couple of days and cooked into stew.
- Dawadawa, iru and soumbala — West Africa. Not soybeans but locust bean, Parkia biglobosa, fermented into a dark seasoning.
- Ugba — south-eastern Nigeria. Fermented African oil bean seed, sliced fine and served as a salad.
- Tungrymbai — Meghalaya, north-east India. Soybeans fermented warm in a covered basket.
Natto and the rice straw method
Natto is worth describing in full, because it shows the organism working. Soybeans are soaked and steamed until soft, inoculated, and held at around 40 °C for about a day. In the traditional method there is no separate inoculation at all: the hot beans are packed into bundles of rice straw, and the spores already living on the straw do the work. Steaming kills off competing organisms while the spores survive it. That is the whole trick, and it is the endospore doing the heavy lifting.
By the end the beans are coated in long sticky threads. Those are poly-gamma-glutamic acid, a polymer the bacteria produce; lift a spoonful and it strings out a long way. Modern producers use a defined Bacillus subtilis var. natto starter rather than straw, but the process is the same one.
How it behaves as a starter organism
A few things make it useful to whoever is running the ferment. It is aerobic, so it works at the surface and in air rather than sealed under liquid. It grows across a wide temperature band. It secretes its enzymes generously, so it acts on a substrate quickly. And because it sporulates, a culture can be handled and stored without the fragility of cultures that must be kept wet, cold and fed.
At ETRAFLORA it is one of the cultures behind the drinks. The ferments run in ionised, highly alkaline water at pH 9.2, under pressure, with the temperature held below 45 °C for the whole cycle — the full method is set out on the production page. The same species appears in the composition of the 36-ingredient Fermentum Concentrate, alongside the plant-based cultures.
The ETRAFLORA Bacillus subtilis culture
Sold on its own it is a plain thing: a live Bacillus subtilis culture at 30% concentration, in a 100 ml bottle, €12. The taste is neutral. It is a culture rather than a drink, and it carries no fruit or herbs of its own.
The instruction on the label is short:
25–30 drops per 1 litre of water. Drink throughout the day. Or use as a starter culture for your own home ferments.
Both uses appear on the bottle because the material is the same either way. If you want to work with it as a starter, it sits in the starter cultures section of the catalogue next to the Concentrate, and the home method is a subject in its own right.
How to store Bacillus subtilis culture
Store it between +5 °C and +25 °C. That range is wider than the one for the finished drinks, which travel and keep chilled, and the spore stage is the reason. Keep it out of reach of children and avoid contact with the eyes. Beyond that it asks for nothing — no freezing, no feeding, no schedule.
There is something pleasing in the route this organism has taken: named for the wet hay it was pulled from, used for centuries to ferment beans in Japan, Nepal, Thailand and Nigeria, and now arriving at a door in Europe in a 100 ml bottle. A very old organism, doing a very ordinary job.