- A 2024 model indicates gut microbes lessened brain energy needs by 25% in early humans.
- Early hominins consumed diets with lots of fiber, which are good for gut bacteria fermentation.
- SCFAs from gut microbes aided in providing energy to help growing brain size.
- Microbial development followed human development and diet changes closely.
- Modern gut health still affects mood, thinking, and brain health.
For many years, we have given credit for higher intelligence to tools, working together socially, and fire. However, now, researchers are looking at something much smaller — the trillions of microbes that live inside our gut. New modeling studies propose that these very small organisms may have quietly powered the significant increase in human brain size during development by changing food into energy that supported thinking. This idea could change how we understand our brains, our diets, and our past development.
The Human Brain’s Significant Growth
The human brain is one of the organs in our bodies that uses the most energy. Even though it only makes up about 2% of our body mass, it uses around 20% of our energy needs when resting — a figure that is not in proportion when compared to our closest animal relatives. For example, in chimpanzees, the brain only uses about 9% of resting metabolic energy (Pontzer et al., 2022).
Over a relatively short period in developmental terms, about 2 million years, hominin brain size had a significant threefold increase. This quick growth moved humanity into a new cognitive level, helping our ability for complex language, abstract thought, social structures, and long-term planning. But providing energy for such a large organ presented a major developmental challenge. Unlike muscles, which only use energy when active, the brain needs constant energy, even when resting.
Scientists have wondered for a long time how early humans met this metabolic need. Traditional explanations point to the role of cooked foods (by making calories easier to get), meat consumption (high calorie density), and cooperation (sharing resources). While these factors certainly played roles, new research now considers if the gut microbiome assisted in bridging this energy gap, making brain development possible without too much cost.
Gut Microbiome Introduction
The gut microbiome is the ecological group of trillions of microorganisms — including bacteria, fungi, protists, archaea, and viruses — that live mainly in the human intestinal tract. These microbes are not just passive riders, they do important jobs: digesting complex carbohydrates, making vitamins, starting immune responses, controlling inflammation, and even affecting brain function.
But could this microbial system have played a deeper developmental role? Recent ideas suggest that our gut microbiome may have been not just a co-pilot on our path through development but a builder shaping the direction of human brain size. The theory is based on a simple idea: that microbes increased our body’s ability to get energy from diets that would otherwise be low in calories, allowing more energy to be sent to growing and keeping the brain working.
The Gut-Brain Energy Connection
One of the main ways microbes help host metabolism is through fermentation. When we eat plant-based foods with lots of insoluble fibers — such as tubers, root vegetables, leaves, and bark — our own digestive enzymes can’t fully break them down. That’s where gut microbes are useful.
Microbial fermentation mainly happens in the colon, where bacteria such as Bacteroides and Firmicutes digest these fibers and make short-chain fatty acids (SCFAs) like butyrate, acetate, and propionate. These SCFAs are then taken in by the intestinal walls into the bloodstream, where they have different metabolic functions, including as energy sources for important organs — including the brain (Flint et al., 2012).
What makes SCFAs special is not just their calorie amount but how easily they can be used. Unlike fat or protein, which need multiple steps to metabolize, SCFAs are readily available energy. Some SCFAs can even cross the blood-brain barrier and affect neurotransmitter production, directly adding to brain function and structure.
Key Study: Brain Models + Microbiome Simulation
A significant study in 2024 brought this theory into sharper focus. Using detailed metabolic models, researchers simulated early human energy use in two situations — one with a gut microbiome and one without. The results showed that models that included a microbiome showed a 25% decrease in the metabolic cost of keeping a large brain (Zhou et al., 2024).
Put simply, early hominins could have bigger brains without eating much more food, if they had the “right” types of gut microbes. The simulations also showed that SCFAs could have made up 7–12% of total daily energy intake in these ancient diets, a considerable amount not previously accounted for in development-energy calculations.
The importance of this model is deep. While it doesn’t state cause — i.e., microbes directly caused brain growth — it supports the idea that the presence of gut microbes made larger brains biologically possible. It changes the question from “How could we afford bigger brains?” to “Who helped pay the metabolic bill?”
Hominin Diets + High-Fiber Intake
If fermentation was so important, did early humans actually eat the right types of food to support this process? Evidence suggests yes. Analyses of fossilized dental plaque — basically ancient tartar — and very small plant particles stuck in human ancestors’ teeth showed traces of fibrous plant matter. These include starch granules from tubers, grass seeds, nuts, and even wild legume types (Henry et al., 2011).
Such diets are clearly different from the common picture of early humans as mainly meat-eating hunters. While meat likely provided important nutrients and calories, many early Homo species were opportunistic omnivores and used whatever was available — especially fibrous roots and tubers. These food sources are exactly what fiber-loving gut bacteria thrive on. The more of this material that was eaten, the more SCFAs gut bacteria could make — a biologically efficient way to get energy from material that is otherwise hard to digest.
It is interesting that these foods were high-volume but low-calorie before fermentation. Without gut microbes, digesting them would give little benefit. However, with microbes, early humans gained a metabolic advantage, getting access to previously unavailable calories and making a repeating pattern between diet, microbes, and brain fuel.
SCFAs and Brain Benefit Beyond Development
The benefits of SCFAs are not just something from the distant past. Today, we understand that these compounds continue to have an active role in brain health. Several SCFAs can directly affect the central nervous system. Butyrate, for example, has anti-inflammation properties and is related to keeping blood-brain barrier integrity. Some SCFAs also affect epigenetic gene expression, possibly affecting neurodevelopmental patterns.
Research has indicated that SCFAs help control mood, anxiety, and thinking functions by changing neurotransmitter systems like serotonin and dopamine. New findings in psychiatry even suggest that SCFA deficits could be factors in disorders like depression, brain degeneration, and autism spectrum disorders.
Evidence from both animal and human studies suggests that SCFAs may act as signals that affect brain plasticity, memory forming, and neurogenesis — the making of new neurons. In short, SCFAs are not just leftovers from digestion — they’re important biochemical assets in supporting and improving brain health.
Microbiome Development With Us
One reason this microbial partnership succeeded in humans could be co-development. As our diets changed and became more varied and fibrous, so did our microbial partners. Over time, humans had microbiomes that became best suited for fiber fermentation and SCFA production.
Studies comparing gut bacteria across primates indicate that microbiomes often develop at the same time as host species. In one study, researchers discovered that chimpanzees and gorillas, even though they live in the same geographic area and even eat some of the same things, had different gut microbiomes, suggesting these microbial groups are made for the specific biology of the host (Moeller et al., 2016).
This type of host-specific microbial development likely happened throughout human history. Our ancestors’ changing food habits, social structures (such as food sharing), and migration patterns all shaped and were shaped by our internal microbial worlds.
Comparison with Other Primates
Why didn’t closely related species like chimpanzees follow the same path of brain growth? The answer may be in a mix of diet, gut structure, and microbial makeup.
Chimpanzees often eat high-sugar fruits and less complex fiber than early humans. Their colons are also relatively shorter, meaning less time for fermentation. Also, their gut microbiota is made up of different bacterial types not specialized in making the high amounts of SCFAs found in humans.
So, even if you made the calorie intake the same between a chimp and a human, the metabolic conversion rate might be very different. The microbial tools are simply not the same. In humans, the combined effect of fiber-rich diets and a well-organized microbial system may have made a unique body advantage, allowing for the extra energy needed to build larger and more complex brains.
Energy Use of the Developing Brain
Developmental biology is about trade-offs. Growing a bigger brain is not free — it needs moving energy from other functions, like digestion, movement, or body keeping. Traditionally, scientists thought that early humans made up for this by reducing gut size (known as the expensive-tissue idea), or by increasing meat consumption.
However, this microbial idea suggests a third choice: instead of giving up organs or radically changing diets, we improved our internal energy systems through a symbiotic digestion way. The gut microbiome basically took over part of our metabolic load, acting as a built-in energy extraction plant that worked all the time to fuel our quickly growing thinking tools.
Points to Consider & Gaps in the Research
Of course, no theory is without limits. The 2024 model is based on simulations, not fossilized gut content. We can’t directly see ancient microbiomes since microorganisms don’t fossilize well. Instead, scientists guess at their existence by analyzing genetic data from modern humans and comparing it with current microbial systems in non-human primates.
Further, while SCFAs are known to support brain health, it’s still not clear how differences in their production and absorption play out in individual development. Questions also remain about the timing: did small bursts of microbial changes come before brain growth, happen at the same time, or come after?
Progress will depend on improvements in paleomicrobiology, ancient DNA analysis, and dietary archaeology. For now, the microbial-energy idea is a good possible answer to a very old mystery — but it needs more strong proof.
Modern Gut, Modern Brain?
Our microbial partnership did not stop with development. In modern humans, the gut microbiome continues to have an strong effect on brain processes. Studies in psychobiotics — a field that looks at how gut bacteria affect mental function — show possible links between microbial variety and thinking ability, mood control, stress resistance, and likelihood of getting psychiatric disorders.
Problems in gut flora, whether because of antibiotics, processed foods, or stress, have been related to results like poor memory, depression, anxiety, and brain diseases. Again, it seems that very small organisms have very large effects on mental health.
Can Diet Still Affect Brain Health via Microbes?
Definitely. Diets with lots of fermentable fibers and prebiotic compounds — found in foods like garlic, leeks, onions, bananas, and oats — help support good microbial populations. Fermented foods such as kimchi, miso, sauerkraut, yogurt, and kefir may act as natural probiotics, putting new types of helpful bacteria into the gut.
Even in adulthood, these diet changes can cause microbial changes within days or weeks. And these changes could affect not just digestion but mood, focus, and emotional control. Even though human studies differ in how strong the effect is, the direction is clear: your gut affects your brain, and your food decides your gut makeup.
Wider Impacts on Neuroscience & Psychology
This microbial-brain theory could change the base of neuroscience. We can no longer easily draw lines around the skull and say “thinking happens here.” Instead, our idea of self and awareness may now need to include trillions of very small organisms in our intestines.
This starts new areas that cross different fields. Psychologists must consider gut health as a factor in mental well-being. Brain doctors may treat inflammation with dietary probiotics. Anthropologists must include microbes in stories of human brain development. A new biological way of thinking is coming — one in which the person is seen not just as an organism, but as a superorganism: a partnership of human and microbial life.
Thinking With Our Guts
If this new theory is correct, then trillions of unseen partners helped shape your mind. Gut microbes, able to change fibrous food into energy that is easy to use, may have powered the developmental jump from just surviving to complex thought, music, language, and science.
Fire may have cooked our meals, but maybe it was fermentation in the gut that started the first brain sparks. As science gets better, the truth of this might become clearer—but for now, it gives a interesting reminder that even human genius might have microbial roots.
Citations
- Flint, H. J., Scott, K. P., Louis, P., & Duncan, S. H. (2012). The role of the gut microbiota in nutrition and health. Nature Reviews Gastroenterology & Hepatology, 9(10), 577–589. https://www.nature.com/articles/nrgastro.2012.156
- Henry, A. G., Brooks, A. S., & Piperno, D. R. (2011). Microfossils in calculus demonstrate consumption of plants and cooked foods in Neanderthal diets (Shanidar III, Iraq; Spy I and II, Belgium). Proceedings of the National Academy of Sciences, 108(2), 486–491. https://www.pnas.org/doi/abs/10.1073/pnas.1018033108
- Moeller, A. H., Peeters, M., Ndjango, J. B. N., Li, Y., Hahn, B. H., & Ochman, H. (2016). Sympatric chimpanzees and gorillas harbor convergent gut microbial communities. Science, 352(6287), 380–384. https://www.science.org/doi/10.1126/science.aaf3951
- Pontzer, H., et al. (2022). Encephalization and the energetic costs of brain size in humans and other primates. Science, 377(6610), 829–832. https://www.science.org/doi/10.1126/science.abn1731
- Zhou, D., et al. (2024). Microbiome-enhanced energy budgets and hominin brain-size evolution. Nature Ecology & Evolution. https://www.nature.com/articles/s41559-024-02456-3
