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How Fruits Restore the Microbiome – Revealing an Evolutionary Secret about Our Gut!

The microbiome is an essential part of our health and is tightly linked to the food we eat and to other environmental influences. Unfortunately, we are exposed to uncountable synthetic and harmful substances and antimicrobial agents daily. There are thousands of ways that the toxic world and unnatural lifestyle can unbalance our gut bacteria – but what can we do to restore it?

We all have tried probiotics with more or less success, but our friendly bacteria can only thrive in a suitable milieu and healthy gut environment. Here, evolution can help us with an important piece of this puzzle: FRUITS! Why fruits?

Our natural diet is highly frugivorous, and, by flooding the gut with the foods that we have naturally adapted to eat, we also feed and sustain our symbiotic bacteria! No wonder fruits do have extremely beneficial effects on the microbiome!

Here we dive into some aspects of what fruits can do for our gut health:

It is safe to say that – generally – edible fruits are beneficial for the microbiome and intestinal health! This is nothing new. Tropical countries and cultures have a long history with the wealth of fruits and their positive effects on the gut – and health in general. Regions that typically use fruits and fruit diets as medicine are indigenous from the Amazon, Caribbean, and the Western Indo-Pacific region.

However, the true reason and magnitude for fruit being the key factor in our digestion and the microbiome is a mind-boggling, and well-kept, evolutionary secret!

The microbiome is essential for health and digestion. It basically is our extra set of genetics: The bacterial genome and its biochemical functions are our highly variable, adaptable extra genetics. Therefore, “our” bacteria perform tasks that we are unable to do – for example, B12 production, vitamin K2, folate, biotin, and other B vitamins. This is one reason why we feel the consequences of an unhealthy diet and anything that harms our microbiome.

If you struggle with digestion, and intestinal health or just don’t see much benefits from your probiotic supplements, this article just might give you the missing piece of the puzzle!

The microbiome health secret: Why are fruits the key?

Why is it the fruits, in particular, that are the absolute key food for the microbiome? Because humans are biological frugivores! We come from a frugivorous ancestry and still are specialized fruit-eaters biologically. This is why our intestinal tract is the healthiest on a diet high in fruits, and beneficial bacteria need fruits to thrive and reach their functional optimum.

Our species originated in tropical forests. Our closest relatives – all apes – are highly frugivorous, and our species-specific diet is still high in fruits, as we, biologically, have remained frugivores! Thus, nothing can substitute fruits in great quantities, also for the microbiome! When adopting a diet high in fruits, we notice a change in digestion as one of the benefits!

Humans have a digestion and microbiome like frugivorous apes

Like chimpanzees and all the other great apes, humans have distinct adaptations for fruit-eating: a few examples are complex hands for fruit handling, dental structure, lips, and our positive sensory experience with ripe fruits (attractive look, smell, and taste) and biochemical features such as the loss of vitamin C genes. This is a unique trait shared by highly frugivorous animals.

Moreover, humans have a digestive anatomy that is typical for a frugivore:

“Anthropoids, including all great apes, take most of their diet from plants, and there is general consensus that humans come from a strongly herbivorous ancestry. Though gut proportions differ, overall gut anatomy and the pattern of digestive kinetics of extant apes and humans are very similar.”

K. Milton

Humans have also been shown to have a nearly identical microbiome to wild (frugivorous) chimpanzees when living in a natural environment (Gomez et al., 2019).

Watch this video of humans and chimps eating tropical fruits together – the similarity of dietary preferences is fascinating!

Not convinced yet that we are frugivores, but curious? Read more here.

Restoring health: You can shape the microbiome!

Our intestinal bacteria stand or fall with environmental exposures: Foods, but also other substances we ingest, are the main determinants of our intestinal bacterial colonization.

The microbiome is shaped by the environment more than it is determined by genetics (read more here)! This is good and bad news at the same time: It means we can restore our microbiome’s health, but it also means that, our symbiotic microbes are threatened by the many harmful environmental exposures we face today!

We all have heard that processed foods, preservatives, and antimicrobial substances harm the microbiome – and thus should be avoided! While this sounds like bad news, the amazing news is that the right foods can restore the intestinal microbial community to natural conditions:

As mentioned above, the human microbiome naturally is identical to to chimpanzees when living in a natural environment. What changes our microbiome is a “modern” polluted environment and diet (Sharma et al., 2020). Thus, humans naturally have a microbiome typical for a frugivorous primate, when living and eating according to their dietary ancestry.

Intestinal bacteria also can be transferred between individuals and even our pets! This is why we see some extraordinary treatments like fecal transplants actually being helpful, as the receiver re-populates and shapes the microbiome.

Fruits feed the microbiome: inulin and fructans

Fruits not only feed us, but they also feed the bacteria in the gut, balancing the microbiome and contributing to gut health. Bananas are probably the most familiar example of fruits that accelerate intestinal healing, but other fruits – like mangoes and lychees – help modulate the microbiome and improve gut dysbiosis with their polyphenols and fructans:

Symbiotics are the latest name for functional supplements to restore the microbiome. They are composed of prebiotics (food for beneficial bacteria) and probiotics (beneficial bacterial strains). The polysaccharides (fructans) found in fruits are the natural prebiotics (food) of our friendly gut bacteria: fructans are fermented by the microbiome and in particular boost the growth of beneficial bifidobacteria populations (Flamm et al., 2001).

Prominent prebiotics are inulin and other fructans (oligofructose), which are mainly found in fruits! Inulin has been shown to balance the microbiome by increasing beneficial and decreasing harmful bacteria populations (Hoffman et al., 2019). Fructans in general improve the profile of intestinal bacteria, as well as mucosa health (tight junctions) (Liu et al., 2016).

Inulin is one of many types of polysaccharides: the strand is made up of multiple fructose molecules in a row and one glucose molecule in the end.

Fructans are only one of many beneficial compounds of naturally occurring fructose. Fructose from fruits also serves as an easily-available energy carrier for our cells – a fact that is easily forgotten in times of war against sweetness and sugar!

High intake of vitamin C is essential for the microbiome

Nothing can substitute the benefits of a diet high in vitamin C – which is a diet high in fruits – also for intestinal health! What is evident from the standpoint of our evolutionary history and ethnobotanical knowledge as frugivores, is increasingly being supported by studies:

“High-dose vitamin C supplementation for two weeks shows microbiota-modulating effects in healthy individuals, with several beneficial shifts of bacterial populations.”

Otten et al. 2021

Why is eating more vitamin C than we get in an average diet so important? If we do not eat a high-fruit diet, we cannot reach the amount of vitamin C that we have evolved to eat! To illustrate how essential this is, we can look at the evolution of vitamin C: Frugivores, like all apes, including humans, have lost their functional vitamin C genes (read more here) because they get plenty of vitamin C via their diet! All mammal and bird species, that do not consume much fruits, produce the vitamin themselves and do not need to get it from external sources. Now, imagine, you are a frugivore without vitamin C genes, but you do not eat high quantities of food that contain vitamin C – a recipe for health trouble! This is what happens to most of us today:

The circumstances that we have adopted a cooked-food, low-raw diet due to cultural shifts, without re-gaining our functional genes, has left us with chronic vitamin C deficiencies – and far-reaching health implications, which includes the microbiome: Adopting a high-fruit diet is actually the prerequisite for a healthy intestinal microbiome!

Polyphenols in fruits boost “good” bacteria, while reducing the “bad”

Polyphenols are interesting plant molecules and are also found in abundance in fruits: color, smell, and taste molecules are only a few of the many diverse functions of this chemical group. The secondary metabolites are a way for the plant to communicate, like attracting animals with pigments and fruits. Bitter or toxic polyphenols are a way for plants to defend themselves from herbivores.

But what do polyphenols have to do with our microbiome? Some of those molecules that we ingest are actually natural antibiotics and they have been shown to improve the bacterial composition of our gut:

Dietary polyphenols can modulate the composition of intestinal microbes, and in turn, gut microbes catabolize polyphenols to release bioactive metabolites… Polyphenols can selectively inhibit the growth of pathogenic bacteria. 

Wang et al 2022

Evolution and ecology of polyphenolic plant metabolites: Polyphenols can be beneficial for our health, but also toxic – depending on the evolutionary past that we share with the plant! Mutualistic relationships result in beneficial molecules, while an antagonistic situation can result in chemical defense molecules of plants.

Many polyphenols have evolved in plants as a defense mechanism against insects and microbial disease – which is why polyphenolic compounds can act as antimicrobial agents in humans. This is only one way they can be beneficial. However, some plants – i.e., toxic berries – have developed defense molecules against humans as a foraging predators.

How much fruit – and what types of fruit – to feed your microbiome?

Eat as much fruit as you feel like, to feed your microbiome! As frugivores, we can hardly ever overdo it with fruits – and my family living in the tropics is living proof that fruits directly from trees can be eaten in kilos! Chimpanzees, for example, eat, on average, 70 % fruit. And, depending on the population and season, they live from fruits only for extended periods of time. The most beneficial fruits to integrate into a high-fruit diet – and probably to pamper your microbiome – are ripe tropical fruits, like bananas, mangoes, guava, lychee, papaya, etc., because they have coevolved with our ancestors and primates, in general. Find our free frugivore diet guide here.

All fruits offer the benefits of Vitamin C and the prebiotics mentioned above. However, some fruits are used for intestinal health, specifically in different cultures:

  • Constipation: Papaya, durian, plumes, mangoes, avocados
  • Diarrhea: Bananas, figs, papaya, guava
  • Anti-parasitic effect: papaya (fruit and seeds), durian

Add the good, and reduce the bad! Stay away from what is not supposed to be eaten! In practice this means, we need to stay away from harmful everyday toxins, but also, from foods that we have not evolved to eat!

A diet very high in fruit is the prerequisite for optimal gut colonization and a healthy microbiome. Fruits are probably the most overlooked and misunderstood food, with an enormous potential to not only aid the microbiome and intestinal health but generally boost our well-being and regeneration!

Such effects have been reported by a growing community of people that adopt a high-fruit diet – rediscovering our species-appropriate diet as frugivores!


  1. Hossain, K.S., Amarasena, S. and Mayengbam, S. (2022) ‘B vitamins and their roles in Gut Health’, Microorganisms, 10(6), p. 1168. doi:10.3390/microorganisms10061168. 
  2. Milton, K. (2004) ‘Ferment in the family tree: Does a frugivorous dietary heritage influence contemporary patterns of human ethanol use?’, Integrative and Comparative Biology, 44(4), pp. 304–314. doi:10.1093/icb/44.4.304. 
  3. Gomez, A. et al. (2019a) ‘Plasticity in the human gut microbiome defies evolutionary constraints’, mSphere, 4(4). doi:10.1128/msphere.00271-19. 
  4. Flamm, G. et al. (2001) ‘Inulin and oligofructose as dietary fiber: A review of the evidence’, Critical Reviews in Food Science and Nutrition, 41(5), pp. 353–362. doi:10.1080/20014091091841. 
  5. A. K. Sharma et al., Traditional human populations and nonhuman primates show parallel gut microbiome adaptations to analogous ecological conditions. mSystems5 (2020), doi:10.1128/msystems.00815-20.
  6. Hoffman, J.D. et al. (2019) ‘Dietary inulin alters the gut microbiome, enhances systemic metabolism and reduces neuroinflammation in an APOE4 mouse model’, PLOS ONE, 14(8). doi:10.1371/journal.pone.0221828. 
  7. Liu, T.-W. et al. (2016) ‘Nondigestible fructans alter gastrointestinal barrier function, gene expression, histomorphology, and the microbiota profiles of diet-induced obese C57BL/6J MICE’, The Journal of Nutrition, 146(5), pp. 949–956. doi:10.3945/jn.115.227504. 
  8. Otten, A.T. et al. (2021) ‘Vitamin C supplementation in healthy individuals leads to shifts of bacterial populations in the gut—a pilot study’, Antioxidants, 10(8), p. 1278. doi:10.3390/antiox10081278. 
  9. Boncler, M. et al. (2017) ‘A new approach for the assessment of the toxicity of polyphenol-rich compounds with the use of high content screening analysis’, PLOS ONE, 12(6). doi:10.1371/journal.pone.0180022. 
  10. Wang, X., Qi, Y. and Zheng, H. (2022) ‘Dietary polyphenol, gut microbiota, and health benefits’, Antioxidants, 11(6), p. 1212. doi:10.3390/antiox11061212. 
  11. Katsirma, Z. et al. (2021) ‘Fruits and their impact on the gut microbiota, gut motility and constipation’, Food & Function, 12(19), pp. 8850–8866. doi:10.1039/d1fo01125a. 
  12. Venancio, V.P. et al. (2018) ‘Polyphenol‐Rich Mango (Mangifera indica L.) ameliorate functional constipation symptoms in humans beyond equivalent amount of fiber’, Molecular Nutrition & Food Research, 62(12), p. 1701034. doi:10.1002/mnfr.201701034. 

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Martina Spaeni Lima, MSc

"We are frugivores - specialized fruit-eaters!" It was passion at first sight when I came across the intriguing concept that humans are adapted to a high-fruit diet, similar to chimpanzees...

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