What's the Difference Between Fermentation and Rotting?
― It's the Same Process, Just Named by Us
We prize yogurt, natto and miso as "fermented foods." Yet food that gives off a foul smell at the back of the fridge is called "rotten" and thrown out at once. In both cases, invisible microbes are changing the food. So what actually separates fermentation from rotting?
Open a pack of natto and a strong, distinctive smell hits you. It's hardly a "pleasant fragrance," but we take it as a sign of fermentation and happily eat it.
Now suppose meat or fish you forgot to refrigerate gives off a similar smell, or an even stronger one. You'd throw it out without a second thought.
Both are the result of microbes changing food. Yet one ends up on the dinner table and the other goes straight into the bin. Where does the difference come from?
In both fermentation and rotting, invisible microbes break down substances in the food to get energy. As a process, they are exactly the same.
If the resulting substances seem useful, safe and tasty to us, we call it "fermentation." If they seem harmful or unpleasant, we call it "rotting."
There is no strict scientific line between fermentation and rotting. Let's see why.
Fermentation and rotting are both just microbes "eating and breaking down"
Microbes such as bacteria, moulds and yeasts break down the organic matter around them (sugars, proteins and so on) to live and get energy. The act of breaking down is not, in itself, either "good" or "bad."
The lactic acid bacteria that make yogurt break down the sugar in milk (lactose) into lactic acid. The yeast that makes bread rise breaks down sugar into carbon dioxide and alcohol. Bacteria that attack neglected meat break down protein into ammonia and hydrogen sulfide.
Chemically, these are all the same kind of job: microbes breaking down organic matter and turning it into other substances.
So what differs? Our judgement of the products
The difference comes from the combination of which microbes, breaking down what, and making what.
The lactic acid made by lactic acid bacteria and the alcohol and carbon dioxide made by yeast are substances that are safe for us, enrich flavour and help food keep longer. Much as in how freezing-point depression works, an acid like lactic acid lowers the food's pH and makes it harder for other, harmful microbes to grow.
By contrast, the ammonia, hydrogen sulfide and amines made by bacteria attacking neglected meat or fish not only smell bad but, in large enough amounts, can make you ill.
What separates "fermentation" from "rotting" is less a difference in the chemical reaction itself than our judgement of whether the finished substances are useful or harmful to us.
They are the same "microbial breakdown," named according to the outcome.
The line is blurry ― natto's smell is the proof
Natto's distinctive smell is said to include compounds similar to ammonia. These are substances produced as natto bacteria break down protein, and chemically they are quite close to those made during rotting.
Even so, natto counts as a "fermented food," not "rotten," because a specific microbe, the natto bacterium, is used under safe conditions, and long experience of eating it has confirmed its safety. The same kind of breakdown is judged differently depending on who does it and in what environment.
Why can microbes be controlled?
In making fermented foods, people adjust salt concentration, the presence of oxygen, temperature, and the use of a starter culture (the desired microbes, prepared in advance). This creates an environment where the target microbes grow easily and others struggle.
In miso and soy sauce, for example, a high salt concentration holds back many harmful microbes while helping salt-tolerant koji mould and lactic acid bacteria do their work. Creating a "managed environment" is what makes fermentation fermentation, and not rotting.
Food left out at room temperature for a long time becomes an "unmanaged environment" where all kinds of microbes, not just the desired ones, can grow freely. In such conditions, unwanted microbes can take over and produce substances that may cause stomach trouble. Don't be overconfident that "I can tell by the smell"; the basic precaution is to refrigerate or freeze perishable food promptly.
How fast do microbes multiply if left alone?
In both fermentation and rotting, how fast the microbe numbers grow has a big effect on the result. In good conditions, microbe numbers grow not "in proportion to time" but "by doubling again and again." In the fold-out below, we check how fast that is using numbers.
Things you can check yourself
- Gather the packaging of fermented foods you have at home, such as yogurt, natto, miso and bread
- Read the ingredient list and look for the microbe names, such as "lactic acid bacteria," "yeast," "natto bacteria" or "koji mould"
- Think about how each food keeps unwanted microbes out, through salt, heat, sealing and so on (for example, salt in miso, baking for bread, cold storage for yogurt)
You should notice that even with the same "microbial action," each food manages its environment in a different way.
Summary
Fermentation and rotting are the same kind of process: microbes breaking down organic matter. What creates the difference is only the combination of which microbes, in what environment, make what, together with our judgement of the result. Grow only the target microbes in a managed environment and you tend to get fermentation; let all kinds of microbes grow freely in an unmanaged one and you tend to get rotting.
What separates fermentation from rotting is not a law of chemistry.
It is our own yardstick: "what is convenient for us."
This way microbes draw energy from food is closely related to how our own bodies "slowly burn" food. What a food's calories actually measure is explained in this article.
For those who want more ― terms, numbers and links to textbooksFrom middle-school science to current research, with each level clearly labelled
- Middle schoolCovered in middle-school science
- High schoolCovered in high-school Basic Biology
- High school+High-school Biology, or advanced material and side columns in textbooks
- UniversityUniversity-level specialist content (food microbiology), not taught in high school
- ResearchTopics researchers are investigating now, not yet taught even at university as settled fact
Middle schoolTerms: words around fermentation and rotting
- Microbe: a living thing so small it can't be seen, such as bacteria, moulds and yeasts.
- Organic matter: substances built on a carbon backbone, such as sugars, proteins and fats, which make up living things and food.
- Breakdown: a substance splitting into simpler substances.
- Lactic acid bacteria, yeast, natto bacteria, koji mould: typical microbes used to make fermented foods.
High schoolChecking with a formula: how fast do microbes multiply?
When conditions are favourable, the number of microbes is said to double at regular intervals. Let's work out just how sharp this "doubling again and again" is.
The number of microbes doubles at regular intervals
| In symbols | N ＝ N₀ × 2^( t ÷ T ) |
| In words | number at a given time = starting number × 2 to the power of (elapsed time ÷ doubling time) |
| Where the formula comes from | One division doubles the number. That happens (elapsed time ÷ doubling time) times, so we multiply 2 by itself that many times. |
| N, N₀ | the number of microbes at a given time, and the starting number (cells) |
| t, T | elapsed time, and doubling time (minutes) |
| Doubling time | the time it takes for the number of microbes to double |
| Rough doubling time | With favourable conditions (temperature, nutrients and so on), about 20 minutes |
This rests on the simple idea that one microbe divides into two. Each time they multiply, the number that will multiply next grows too, so growth is not "in proportion to time" but "doubling again and again."
Suppose we start with 100 microbes. With a doubling time of 20 minutes, let's stack up the doublings over 2 hours (120 minutes).
| After 20 min | 100 × 2 ＝ 200 |
| After 40 min | 200 × 2 ＝ 400 |
| After 60 min | 400 × 2 ＝ 800 |
| After 80 min | 800 × 2 ＝ 1600 |
| After 100 min | 1600 × 2 ＝ 3200 |
| After 120 min | 3200 × 2 ＝ 6400 |
By this calculation, in just 2 hours, 100 microbes grow to 6400, a 64-fold increase.
| Growth factor in 2 hours | 6400 ÷ 100 ＝ 64 |
| Same answer by formula: number of divisions | 120 ÷ 20 ＝ 6 |
| Multiplying 2 by itself 6 times | 2^6 ＝ 64 |
This is why food can change a great deal even if it's "just left out at room temperature for a while." Careful control of temperature and salt in fermented food-making is thought to be a way of steering this rapid growth to favour only the target microbes.
* Doubling time varies widely with the kind of microbe and the conditions; 20 minutes is only a rough figure for good conditions. In real foods it can be faster or slower.
High school+There are several kinds of fermentation
Fermentation comes in several types, depending on what is broken down and what is made. Typical examples are lactic acid fermentation, which breaks down sugar into lactic acid; alcoholic fermentation, which breaks down sugar into alcohol and carbon dioxide; and acetic acid fermentation, which breaks alcohol down further into acetic acid. All of them share one feature: they draw out energy using little oxygen (a relative of respiration that uses almost no oxygen).
UniversityThe view of microbes as competitors
Inside food, several kinds of microbes are thought to compete for limited nutrients and space. Conditions such as salt, temperature, oxygen and acidity (pH) favour some microbes over others and decide which one comes out on top. Making fermented food can be described as a technique for manipulating these conditions so the target microbe wins.
A standard mathematical tool for this competition is the Lotka–Volterra competition equations. They take the "doubling again and again" formula above and add a slowdown in growth when nutrients or space run short, and a drop in your own growth caused by the presence of the rival species. With them you can work out, condition by condition, which microbe ends up dominant.
📖 Derivations and further reading: Exponential growth (differential-equation form) ／ Lotka–Volterra competition equations
ResearchWhat is still unclear
- Many traditional fermented foods are said to be made not by a single microbe but by a "wild" community of several species mixed together. Research that examines the whole picture of such communities at the gene level (metagenomic analysis and the like) is still developing.
- How far eating fermented foods benefits the gut microbes and health is still under study, and there is much about the size of the effect and the mechanism on which no clear conclusion has yet been reached.
- "Microbial community ecology," which asks why and how a group of microbes comes to dominate in a particular environment, is an important research area that also bears on predicting fermentation and rotting, but it has not yet untangled all of the complex interactions.
Humans have used fermentation for thousands of years, but the relationships among microbes behind it are still a complex world under active study.
Links to textbooks (by level)
| Level | Subject / unit | Where in this article |
|---|---|---|
| Middle school | Science: the work of microbes | Basic terms: microbes, organic matter, breakdown |
| High school | Basic Biology: population growth | Estimating microbial growth from doubling time |
| High school+ | Biology: respiration and fermentation | Differences among lactic acid, alcoholic and acetic acid fermentation |
| University | Food microbiology | Competition among microbes, control by environmental conditions |
| Research | Microbial ecology (ongoing research) | Metagenomic analysis of fermented foods, links to the gut environment |
- Ministry of Agriculture, Forestry and Fisheries (農林水産省), explanatory material on "fermented foods."
- Explanations of the definitions and classification of fermentation and rotting in food microbiology textbooks.
- Japan Society for Bioscience, Biotechnology, and Agrochemistry (日本農芸化学会) and other explanatory articles on fermentation science (on the metabolic pathways of lactic acid, alcoholic and acetic acid fermentation).
- Ministry of Health, Labour and Welfare (厚生労働省), general-audience explanatory material on "food poisoning prevention" (on microbial growth and temperature control).
- Marco, M. L. et al., Health benefits of fermented foods, Current Opinion in Biotechnology, 2017 (a research review on fermented foods and health).
* Figures such as doubling time are typical rough values under good conditions, and vary with the kind of microbe and the state of the food.
* This article is a general-audience science explainer. For food storage and safe handling, always check each product's packaging and information from public bodies such as the Ministry of Health, Labour and Welfare. Do not judge safety by appearance or smell alone.