THE PROCESS IN MOTION

What really ferments?

Start the scene or choose a stage. The animation simplifies the mechanism; what follows gives the details and the available references.

▶ Play the process01The mucilage, not the bean02The parchment keeps the bean apart03Molecules diffuse, slowly04Mannitol signals a transfer

The mucilage, not the bean

The bean does not ferment: what ferments is what surrounds it. Mucilage is 84.2% water, with proteins, reducing sugars and pectates, the molecules that hold the flesh together like a jelly. Microorganisms attack it because that is where the sugar is.

Read the stages without animation

1. The mucilage, not the beanThe bean does not ferment: what ferments is what surrounds it. Mucilage is 84.2% water, with proteins, reducing sugars and pectates, the molecules that hold the flesh together like a jelly. Microorganisms attack it because that is where the sugar is.
2. The parchment keeps the bean apartThe bean is protected by a rigid envelope, the parchment, and by its own skin. It is not a medium in which microbes can settle and multiply. A recent work suggests that bacteria might live inside the seed: a possibility, not a measurement.
3. Molecules diffuse, slowlyWhat reaches the bean is dissolved molecules that diffuse inward. A coffee “fermented ninety hours” is a bath that was loaded for ninety hours, and what that bath finally managed to pass through two envelopes. The sugars of the mucilage disappear; acids, ethanol, glycerol and mannitol accumulate.
4. Mannitol signals a transferMannitol does not come from the fruit: it is produced by heterofermentative lactic acid bacteria, those that yield several products at once. Its presence in the bean therefore signals a real transfer. For the rest, we cannot yet sort what diffused, what the bean produced itself and what stayed on the surface.

To remember: The bean does not ferment: what ferments is the mucilage, and what reaches the bean is dissolved molecules that cross its envelopes.

Read the full article and its sources ↓

This point is the most important of the plate, and the one most often wrong in what is read. The bean does not ferment. What ferments is what surrounds it.

Mucilage is almost entirely water, about four fifths. The rest is sugar, proteins and pectins, molecules that hold the flesh together like a jelly. It is this jelly that the microorganisms attack, because that is where the sugar is and because they cannot go anywhere else.

The bean, for its part, is protected by a rigid envelope, the parchment, and by its own skin. It is not a medium in which microbes can settle and multiply. What reaches it is dissolved molecules that diffuse slowly inward, and that is something else entirely from a fermentation.

The consequence is practical. When a coffee is advertised as “fermented ninety hours,” it does not mean a bean worked on for ninety hours: it means a bath that was loaded for ninety hours, and what that bath finally managed to pass through two envelopes.

What exactly the mucilage contains, and how far what crosses it goes

The classic analyses give, by mass: water 84.2%, proteins 8.9%, reducing sugars 4.1%, pectates 0.91%, ash 0.7%. Pectic substances are strongly esterified by methyl groups and are about 60% galacturonic acids, which matters for what follows: a highly methylated network is little sensitive to enzymes that cut chains already demethylated, and is on the other hand sensitive to acidification, which destabilizes it without cutting it.

The question of transfer to the bean remains open, and it is the most interesting in the field. We know that compounds pass: the organic acid profiles of the green bean change with the process. We do not know well which ones pass by diffusion, which are produced by the bean itself in response to stress, and which are merely surface contamination removed by washing.

A study on extended fermentations followed these transfers and measured the disappearance of fructose and glucose from the mucilage, with accumulation of acetic acid, ethanol, glycerol, lactic acid and mannitol. Mannitol is a useful marker: it does not come from the fruit, it is produced by heterofermentative lactic acid bacteria, so its presence in the bean signals a real transfer.

Composition: classic values reproduced by Haile and Kang, The Role of Microbes in Coffee Fermentation and Their Impact on Coffee Quality, Journal of Food Quality 2019; transfers: Transformation of organic acids and sugars in the mucilage and coffee beans during prolonged fermentation, Journal of Food Composition and Analysis, 2024

The mucilage, named molecule by molecule

The previous block gives the mucilage a composition by mass: four fifths water, about nine percent proteins, four percent reducing sugars, a little under one percent pectates. These figures say how much there is of each thing. They do not say what the things are, and it is this second question that governs what the microorganisms will be able to do with it.

Hackler and Särchen give the identities. Mucilage is a hydrogel, that is, a network of molecules that holds water like a sponge without dissolving. This network carries a wide range of sugars, arabinose, galactose, xylose, rhamnose and other polysaccharides, lipids and fatty acids, linoleic, palmitic and oleic, organic acids, caffeic, quinic and oxalic, and proteins.

Three of these mentions change the reading of the rest of the plate.

• Arabinose and xyloseThese are pentoses, sugars built on five carbon atoms and not six. This difference is not decorative: it denies lactic acid bacteria their simplest pathway and forces them onto another, which produces acetic acid. The block devoted to this constraint, further down the plate, draws a direct consequence from it for closed tanks.
• Caffeic acid and quinic acidThese are the two pieces whose assembly forms chlorogenic acid, the most abundant family of acids in green coffee. Finding them free in the mucilage sheds light on the sheet's discussion of wet hulled about the hydrolysis of these acids during storage: the building blocks are present on both sides of the parchment, so the question of which way the reaction goes arises as early as the tank.
• Lipids and proteinsMucilage is not just a bath of sugar. These two families are the substrates of entirely different pathways, that of the lipases that cut up fats and take part in forming aroma compounds, and that of the alkaline fermentation that starts from proteins and makes the pH rise instead of fall.

The methodological lesson is worth writing down. A composition by mass makes it possible to size a tank; it does not make it possible to predict what it will smell like. Two mucilages assaying the same four percent of reducing sugars but one rich in hexoses and the other in pentoses will not give the same balance of acids, with the same flora and the same duration. Yet none of the sources consulted publishes the split between six-carbon and five-carbon sugars for a coffee mucilage, nor says whether it varies with variety, maturity or altitude. This is a precise gap, and it can be filled: a chromatography of sugars on a few contrasting lots would do.

Hackler and Särchen, chapter 2, p. 9. Masses: classic values already carried by the plate, after Haile and Kang, Journal of Food Quality, 2019.

Bacteria even inside the seed? The possibility of endophytes

The section is categorical, and that is its interest: the bean is not a medium in which microbes can settle and multiply, what reaches it is dissolved molecules that diffuse. A recent work writes the opposite, and it must be said, because it is the only place in the plate where a claim of impossibility is contested in the literature.

Hackler and Särchen write that there is the possibility that bacteria live inside the cherry and as far as the seed, and that even if the pulp and mucilage are removed, a fermentation could still take place inside the bean. They rely on the work of Vega and his colleagues, published in 2005, who described endophytes in the coffee plant.

An endophyte is a microorganism that lives inside the tissues of a plant without making it ill, lodging between the cells or in the vessels, and its presence in many cultivated species is well documented.

The mood of the verbs must be noted. The authors write that a fermentation could take place. They put forward a possibility, they do not report a measurement: no population counted in a bean protected by its parchment, no kinetics, no metabolite attributed to an internal organism. The contradiction is therefore real, but it is not of the same nature on both sides. The site asserts an impossibility, the work puts forward an undemonstrated possibility, and neither of these formulations is of the level of proof that the rest of the plate demands of itself.

Two remarks make it possible to place the gap without closing it. The first is that the presence of an organism and its fermentative activity are two distinct things: endophytes can reside in a tissue without having there the free sugar, the available water and the anoxia that fermenting would require. The second is that the bean, between picking and drying, is not an inert object: it respires, its own enzymes work, and it produces stress metabolites. A metabolite found inside the bean after fermentation therefore does not prove that a microbe made it there.

What would settle the matter is an identifiable experiment, and it apparently has not been done on coffee being processed. One would have to sterilely dissect beans still in parchment, sampled at several moments of the same fermentation, decontaminate their surface in a controlled way with a control that checks the effectiveness of this decontamination, then culture and sequence the internal tissue. Only two results would be conclusive: an internal population that increases during the fermentation, which would vindicate the hypothesis of active endophytes, or a stable and low population, which would vindicate the plate.

As long as this measurement is missing, the honest formulation is that nothing establishes that a fermentation takes place in the bean, and that nothing establishes either that it is impossible.

Hackler and Särchen, chapter 4, p. 42, after Vega and colleagues, 2005. Position of the site: plate XX, section “What ferments, and what does not.”