Our bacterial beginnings

Fermentation gives us wine, beer, chocolate, cheese, coffee, sauerkraut, kimchi, yoghurt and much more. It is the process whereby microorganisms, such as bacteria and yeasts, break down glucose or other carbohydrates to produce energy for themselves and release other byproducts.

However, it is not only bacteria and yeasts that are capable of fermentation – all of the cells in our bodies derive at least some energy by fermenting glucose (our red blood cells derive all their energy from fermentation). This is because the first single cell bacteria in the oceans derived their energy by fermenting hydrocarbons and later glucose. We evolved from those bacteria, and so our cells have retained fermentation as a process for energy. As Sandor Katz puts it nicely, “…humans did not invent or create fermentation; it would be more accurate to state that fermentation created us.”


The earliest lifeforms we know of were bacteria and archaea (known collectively as prokaryotes). These lifeforms occupied different ecological niches and, while the archaea are of great interest, I won’t return to them.

It is the bacteria that were critical to the evolution of more complex life (including us). These consisted of an enclosed cell that could control its internal environment, separate from the surroundings. There were no internal structures, and floating inside was a simple form of DNA and some enzymes and other molecules for decoding the DNA and performing functions for the cell. It is suspected that this DNA came from viroids, which were free-floating strands of RNA (think DNA split in two). The viroids later evolved into viruses (and prions). It is notable that viruses are adept at entering cells, and we can assume viroids were too. Viroids are not considered part of life (neither are prions, but there is debate as to whether viruses are).

These first bacteria energised themselves by fermenting hydrocarbons that had formed in the ocean. The bacteria did this by splitting the hydrocarbons into smaller molecules, and the energy that was released by this process was ‘stored’ in a molecule abbreviated ATP. All of the cells in our bodies still do that (get energy from fermentating glucose and store it in ATP), as do the cells in all other members of the animal kingdom. This is what biologists call a ‘preserved trait’, and why we can confidently trace members of the animal kingdom back to early bacteria.

We now call the hydrocarbons that are part of life, and that we eat, carbohydrates. In time, glucose became the carbohydrate used in bacterial fermentation. One glucose molecule produces 2 ATP, and some byproducts. The fermentation did not require oxygen, it was anaerobic. The reason for this was simple, there was no free oxygen in the atmosphere, or in the oceans. The main atmospheric gasses were probably nitrogen gas, carbon dioxide, sulphur dioxide, sulphur gas, hydrogen gas, ammonia and methane.

Oxygen gas in the atmosphere

Without fuss, bacteria persistently evolved. Evolution may have its dead ends, but it only travels in one direction – complexity and cooperation.

At some point, a bacterium formed that didn’t need carbohydrate in its surrounding environment for energy – it made its own glucose with something abundant: Sunlight. It had evolved chlorophyl. Plentiful renewable energy.

This was an evolutionary eureka moment, and these bacteria thrived and multiplied. They used carbon dioxide, water and sunlight to produce glucose and release oxygen gas as a byproduct. Over a billion or so years, their numbers and activity steadily increased the level of oxygen in the atmosphere, and in the oceans. They evolved into green algae, and some descendants (cyanobacteria) are still active today, continuing their multi-billion year project of oxygenating the atmosphere and re-engineering the planet.

However, it also meant that another niche was created – bacteria could now evolve to use oxygen. Respiring bacteria made an appearance and they too thrived, because oxygen metabolism released far more ATP than fermentation could.


Bacterial DNA started to become increasingly intricate as further viroids were co-opted. This also meant that cellular machinery could become more sophisticated. In time (1-1.5 billion years), a sub-cellular sac, called the nucleus, began to form around the DNA to keep it together and manageable. This was the first eukaryote (‘true kernel’) because it contained a nucleus. Recall that the prokaryotes (‘proto-kernel’) bacteria had no such internal structure. The eukaryotes represented the next step towards complexity, because their DNA held more possibilities. In fact, the transition from prokaryotes to eukaryotes turned out to be one of great consequence – the cells of all members of the animal, plant and fungi kingdoms are eukaryotes.

A most improbable event

We now have the foundations for life as we see it now. Bacteria and eukaryotes had energy available from either fermentation, respiration or photosynthesis. But – not from a combination of these. That was the next step.

An anaerobic (fermenting) eukaryote engulfed an aerobic (respiring) bacterium, and they both survived. It is thought that this has only happened (and been successful) once. That’s once in 4 billion years…

This new arrangement turned out to be massively advantageous to both organisms. The reason it was successful is energy again. The fermenting step yields only 2 ATP per glucose molecule, but the respiring bacterium could use byproducts of that fermentation, in combination with oxygen, to produce many more ATP – more than it needed, so it had energy for the cell too. The cell in turn seeks out glucose and ferments it to provide fuel for the bacterium. Win-win.

The engulfed bacterium evolved into a more complex structure that over time became what we now know as the mitochondria – the principle energy source for virtually all cells in our body (and the rest of the animal kingdom and even some of the plant kingdom).

This is why the mitochondria contain their own DNA, distinct from our own DNA (in the cell’s nucleus), and why mitochondria divide and multiply independently of our cells in a similar way to bacteria.


The cells that came together to specialise and cooperate and make a human are eukaryotes that evolved from bacteria. Inside these cells are other entities (such as the mitochondria) that are also evolved bacteria. Our bacterial heritage is complemented by live bacteria that we host on our bodies, and that we are co-dependent upon. The implications of this, particularly for our health, but also for our concept of identity, is discussed here.

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Further reading:

Sandor Katz: The Art of Fermentation
Ed Long: I Contain Multitudes
The Cell: A molecular approach
University of Sydney: Microbiological concepts