In nutrition, the long-standing paradigm has been that it’s primarily the human part of our body that we need to take into account when we set out to design a healthy diet, and in this model a lot of focus is placed on how we should structure our diet in order to provide our human cells with an optimal supply of amino acids, fats, carbohydrates, water, vitamins, minerals, and all of the other compounds found in our daily food. But what has become increasingly clear over the last decade is that this approach is incomplete—this model only accounts for the dietary needs of the human part of our body, while neglecting the microbial part; a part that is vastly larger in terms of both cell and gene count.  

To really be able to design a healthy diet for Homo sapiens sapiens, as well as for other multicellular organisms carrying microbial communities, we not only have to consider the dietary requirements of the human host, but also the dietary needs of the microbial symbionts living within the host. Together, the host and all of its microbial symbionts is defined as a holobiont—whereas the collective genetic material of this holobiont, in essence the human genome plus the microbiome, is called the hologenome. This changing perspective of the human self has important implications for a wide range of disciplines within science, health, and medicine—and nutrition is not spared.

Microbes Need Food, Too

Imagine you sit down for a dinner of mashed potatoes, steamed broccoli, salmon, lightly cooked onions, and some melted butter. Once consumed, most of these foods’ nutrients will be digested and absorbed in the upper part of your gastrointestinal tract. 

For example, in the oral cavity, the enzyme salivary amylase will initiate the breakdown of the starch found in the potatoes. This process continues as the starch molecules—and the shorter-chain carbohydrates that are released during enzyme-facilitated hydrolysis—travel down the esophagus, into the stomach, and over to the duodenum (the first part of the small intestine). Once arrived, the sugars that are released during the breakdown of starch are absorbed into systemic circulation and proceed to travel out to your body’s various cells—the fate of their use will depend on the existing needs of your various tissues along the body. 

A similar digestion route is taken by many of the other nutrients you consumed during dinnertime. For example, the salmon’s and butter’s proteins and fats are largely broken down by host-produced enzymes and absorbed in the small intestine. However, not all of the compounds found in your nutrient-dense dinner follow this type of digestive path. 

When it comes to the macronutrients, the human genome “only” codes for enzymes that facilitate the breakdown of starch (with the exception of resistant starch), monosaccharides, disaccharides (some exceptions exist), fats, and proteins. In other words, the human host doesn’t produce all the enzymes that are needed to break down the wide diversity of nonstarch polysaccharides and oligosaccharides found in the plants, and certain animals, that we regularly eat. As such, we depend on the genetic information contained within the gut microbiota to extract anything we can use from these indigestible (to the human host) carbohydrates. 

It’s long been known that, without the help of gut microorganisms, the human body is incapable of extracting energy from these types of carbohydrates, which are classified as dietary fiber. However, what we’re now learning is that this microbe-facilitated digestion of otherwise-indigestible carbohydrates is vastly more important to our health and well-being than previously thought. Moreover, it has become clear that it’s not just the fibers we eat that interact with our gut bugs, playing a role in shaping the community of microorganisms we harbor in the tube that runs through our body. Recent research has made it clear that pretty much everything we eat affects the microbiome in some way. 

Simple sugars, fats, and even proteins can have a profound impact on our gut bugs.3, 4, 13 If you eat whole, unprocessed foods, rich in omega-3 fatty acids and low in simple sugars, you positively contribute to shaping a healthy community of gut bacteria—whereas if you drink a sugar-filled beverage or consume a meal high in very fatty and low-in-fiber foods, you may unknowingly trigger unfavorable changes in your gut microbiota’s composition. Even a single meal can initiate sweeping effects, changing the intraluminal gut environment favoring the growth of proinflammatory microorganisms, which can then lead to the translocation of bacterial endotoxins from the gut into systemic circulation.4, 13

Recent research has made it clear: Besides dietary fibers, the gut microbiota plays a direct role in the degradation of a wide range of food-derived compounds, including gluten,15 phytate,6 various phytochemicals,8 and omega-3 fatty acids,11 to name a few. In other words, our gastrointestinal tract’s bacteria are a bridge between the food we eat and our human self.

An Adaptable Organ

Humans don’t evolve as single organisms—rather, we evolve as holobionts. Mothers pass on microorganisms to their children during birth, breastfeeding, and other forms of contact. Moreover, during our lifetime, the microbial communities in and on our body change in response to various forms of stimuli, altering as we are exposed to, and as we pick up, bacteria from the surrounding world.

When contemplating the complex subject of human nutrition, this bacterial interconnectivity is extremely important to keep in mind—because the dynamic nature of the human microbiome allows us to adjust to dietary changes much more rapidly, and this would not be the case if we were solely relying on changes within the human genome. 

For example, post infancy, many of people are incapable of digesting lactose, because they don’t produce sufficient amounts of the enzyme that facilitates the hydrolysis of lactose into galactose and glucose, a process which facilitates the absorption across the intestinal wall and which finally lets the sugar be used by cells in the body. 

What most people don’t know is that the microbiota can provide the digestive functions these people lack, because these microorganisms have the capability to produce a wide range of enzymes. By eating microbes that have lactose-digesting capabilities, lactose-intolerant individuals can overcome—or at least significantly lessen the severity of—their intolerance, that is simply by consuming foods with abundant amounts of living organisms, like yogurt and kefir.2, 7, 10 Once ingested, these microbes then continue to colonize the gut, transferring lactase-encoding genes to bacteria already present in the intestine, thereby providing functions that the human host initially lacks. Many other similar examples exist. 

I’m very much a proponent of hunter-gatherer Paleolithic-style diets. That said, the Paleo-diet nutrition philosophy has some potential flaws, one of which is that it doesn’t adequately account for the fact that, when we change our diet, the human microbiome can adapt rapidly. While our human genome is still largely the same as that of the Paleolithic man, the microbiome is not. This does not mean that the concept of a Paleo diet has no merit (it absolutely does!), it just means that we should keep in mind that we all harbor a complex community of microorganisms that interacts with the food we eat and that can evolve at a pace far exceeding that of the human genome. 

Nutritional Take-away 

The human body is best viewed as a superorganism—or holobiont—composed of a human host imbued with trillions of microorganisms. These extraterrestrials play a unique role in the digestion and metabolism of food—and, as the nonnatives that they are, they too have their own dietary needs, which are different from that of their human host. 

As such, the task of designing a healthy diet must not only consider the dietary requirements of the human host, but also the nutritional needs of the microbiota. Moreover, we have to consider how our food choices affect the structure and makeup of the community of microorganisms in our gut—we have to make the leap from human nutrition to holobiont nutrition.

This insight adds another layer of complexity to the already-dense study and application of nutrition. That said, the key principles of evolution and biology remain. As long as we stick to the evolutionary model, we’re on safe grounds. The relationship between man and the symbionts that colonize his body was shaped over millions of years of evolution. 

Over the last several years, studies with the purpose of mapping “the non-Westernized microbiome” have been carried out among traditional populations such as the Hadza (a group of hunter-gatherers in Tanzania, Africa), the Tunapuco (a traditional agricultural community from the Andean highland), and the BaAka (a group of rainforest hunter-gatherers).1, 5, 9, 12 These studies concur that individuals leading traditional lifestyles house a much greater diversity of microbes than Westerners, including species that are never found in the guts of modern, industrialized people. Examinations of ancient coprolites and analyses of the microbiomes of many different primate species further support the idea that human microbiomes have deviated from the ancestral state at an accelerated rate.14 

Today, there is a conflict between the human genome and the human microbiome, in the sense that the human genome has been unable to keep up with the rapid and recent changes in diet and microbiome composition. In order to restore a peaceful relationship between the human host and its symbionts, we must restructure our modern diets, with the aim of more closely resembling the diets that conditioned the human genetic makeup. 

The dietary template of our Paleolithic ancestors serves as a great starting point for achieving this objective. That said, since modern, domesticated fruits and vegetables tend to be markedly less fibrous than their wild counterparts, some people, in order to get their microbial symbionts to prosper, may find that they need to include smaller amounts of fiber-rich foods that are not traditionally viewed as Paleo (like lentils or oats) in their diet. 

Unfortunately, the conventional nutritional community has been slow to pick up on the importance of applying evolutionary biology to the study of nutrition. This is problematic for a number of reasons, one of which being that it’s impossible to understand how to properly fuel the human body—and even more so the human body plus its microbial symbionts—without an evolutionary framework. Hopefully, in a not-so-distant future, this will change, and terms such as holobiont nutrition, Paleolithic diets, and evolutionary mismatch will make their way into nutrition textbooks worldwide.


1 C. De Filippo, et al. “Impact of Diet in Shaping Gut Microbiota Revealed by a Comparative Study in Children from Europe and Rural Africa.” Proceedings of the National Academy of Sciences 107 (2010): 14691-6.

2 M. de Vrese, et al. “Probiotics–Compensation for Lactase Insufficiency.” The American Journal of Clinical Nutrition 73 (2001): 421s-29s.

3 Eirik Garnas. “10 Reasons Why You Shouldn’t Use Whey Protein Supplements.” Web (2015):

4 ———. “Don’t Believe the Hype: Eating a Lot of Butter, Bacon, and Other Fatty Foods Won’t Make You Healthy.” Web (2015):

5 A. Gomez, et al. “Gut Microbiome of Coexisting Baaka Pygmies and Bantu Reflects Gradients of Traditional Subsistence Patterns.” Cell Reports 14 (2016): 2142-53.

6 M. Haros, et al. “Phytate Degradation by Human Gut Isolated Bifidobacterium Pseudocatenulatum Atcc27919 and Its Probiotic Potential.” International Journal of Food Microbiology 135 (2009): 7-14.

7 S. R. Hertzler, and S. M. Clancy. “Kefir Improves Lactose Digestion and Tolerance in Adults with Lactose Maldigestion.” Journal of the American Dietetic Association 103 (2003): 582-7.

8 J. M. Laparra, and Y. Sanz. “Interactions of Gut Microbiota with Functional Food Components and Nutraceuticals.” Pharmacological Research 61 (2010): 219-25.

9 A. J. Obregon-Tito, et al. “Subsistence Strategies in Traditional Societies Distinguish Gut Microbiomes.” Nature Communications 6 (2015): 6505.

10 V. Ojetti, et al. “The Effect of Oral Supplementation with Lactobacillus Reuteri or Tilactase in Lactose Intolerant Patients: Randomized Trial.” European Review for Medical and Pharmacological Sciences 14 (2010): 163-70.

11 M. M. Pusceddu, et al. “N-3 Polyunsaturated Fatty Acids (Pufas) Reverse the Impact of Early-Life Stress on the Gut Microbiota.” PLoS One 10 (2015): e0139721.

12 S. L. Schnorr, et al. “Gut Microbiome of the Hadza Hunter-Gatherers.” Nature Communications 5 (2014): 3654.

13 I. Spreadbury. “Comparison with Ancestral Diets Suggests Dense Acellular Carbohydrates Promote an Inflammatory Microbiota, and May Be the Primary Dietary Cause of Leptin Resistance and Obesity.” Diabetes, Metabolic Syndrome and Obesity 5 (2012): 175-89.

14 R. Y. Tito, et al. “Insights from Characterizing Extinct Human Gut Microbiomes.” PLoS One 7 (2012): e51146.15 M. Zamakhchari, et al. “Identification of Rothia Bacteria as Gluten-Degrading Natural Colonizers of the Upper Gastro-Intestinal Tract.” PLoS One 6 (2011): e24455.