We Are 90% Microbe and 10% Human – Assuming That We Only Need to Feed the Human Part of Our Body is One of the Biggest Fallacies in Human Nutrition

foodWhile the total weight of the microorganisms that live in and on the human body is quite small compared to the body weight of the human host, recent research has made it clear that more than 90% of the cells in the human body are microbial and that the genetic repertoire of these germs is more than 100 times greater than that of the human cells (1,2). The state of this microbiome (microbes and their genes) seems to largely determine if we are healthy or sick, and while it’s often assumed that the food we eat are supposed to fuel the single human organism, we now know that feeding the remaining 90% of the human superorganism might be equally as important.

Bacteria inhabit several organs in the human body, and each location has a specific microbiota made up of microorganisms that are able to live symbiotically with the human host in that specific environment. A new study even shows that microorganism are found in the brain, and that these microbes are very different from the species of bacteria that are found other places like the gut or vagina (3). Most of the organisms making up the human microbiome are found in the large intestine, and it also seems that this gut microbiota is especially important in regards to human health.

While alterations in the human microbiome often occur because of some type of exposure, like when hand sanitizers changes the composition of bacteria that live on the skin, a diet high in sugar upsets the balance of bacteria in the digestive tract or smoking disrupts the microbiota in the lungs, a lack of certain exposures can also negatively impact the composition of bacteria in the body. Feeding the right types of gut bugs with indigestible (by the human host) food ingredients is one of these things that seem to be especially important if we want to keep our good gut bacteria in charge.

Official dietary guidelines are incomplete

Conventional dietary advice often dictates that fiber is an essential part of the diet, but official guidelines are incomplete because they provide no information on the gut microbiome and how the bacterial communites are affected by the food you eat. Also, official dietary guidelines rarely distinguish between different types of fiber, and a lot of people end up getting the majority of indigestible carbohydrate in the form of grain fiber which also contain a wide range of gut-irritating substances such as gluten and lectins.

The avalanche of studies connecting the human microbiome to all sorts of diseases should slowly make it’s way into the field of nutrition and change how we look at the human diet.

Fermentable carbohydrates are the most important dietary component that feed gut bacteria

Fermentable carbohydrates are found primarily in plant-based foods.

Fermentable carbohydrates are found primarily in plant-based foods.

As we established in part 1 of the series on fermentable substrates, food ingredients that stimulate the growth of beneficial bacteria like bifidobacteria in the digestive system are called prebiotics. I also highlighted the fact that although only a few fermentable substrates such as inulin and oligofructose, lactulose, and resistant starch are officially classified as prebiotics, it seems that a lot of the complex carbohydrates found in fruits, vegetables and other whole foods have a beneficial effect on the activity and/or growth of beneficial bacteria in the colon (4).

While proteins, endogenous secretions, and sloughed cells may also serve as fermentable substrate for the colonic microbes, complex carbohydrates are the primary fuel for the bacteria in our bodies (5).

Prebiotics boost the immune system and prevent chronic disease


Prebiotics increase production of butyric acid, whick prevents leaky gut and inflammation.

The consumption of prebiotic fiber is associated with better immunity, increased absorption of certain minerals, proper bowel pH, suppressed growth of pathogens, and intestinal regularity. It seems that the increased production of Short-Chain Fatty Acids (SCFA’s) in the colon is especially important in regards to human health, as these SCFA’s are the primary fuel for the cells lining the gut, and play an essential part in the development and control of the immune system (6).

Recent research has implicated dysbiosis and increased intestinal permeability in most of the chronic diseases we see in todays society. Although it’s often hard to determine cause and effect, we already know that an inflammatory microbiota and increased translocation of bacterial endotoxins (endotoxemia associated with a leaky gut) are critical to the development and progression of chronic low-grade inflammation. Endotoxemia and chronic low-grade inflammation play an important role in chronic disease, and initiate disorders such as obesity, insulin resistance, and diabetes (7,8,9,10).

Probiotics and prebiotics are anti-inflammatory since they shift the balance of microbes living in the gut, and decrease colonic and plasma lipopolysaccharide concentrations (11,12). Since we know that most of the immune system is located in and around the gut, it’s hard to overstate the importance of a healthy and diverse gut microbiota.

Western diets starve gut microbiota

Western diets devoid of prebiotic fiber only feed 10% of our cells.

Western diets devoid of prebiotic fiber only feed 10% of our cells.

The western dietary pattern is characterized by high intakes of refined and processed food where most of the prebiotic fiber has been removed during the production process. Refined grains, meat, vegetable oils, and dairy are staple foods in the industrialized world and contain virtually no prebiotic fiber. These foods are therefore broken down and absorbed in the small intestine, leaving the gut microbes in the large intestine starving for food.

While some traditional cultures such as The Inuit had a limited intake of prebiotic fiber and still maintained good health, it’s clear that a diet devoid of prebiotic fiber in combination with acellular carbohydrates, antibiotics, and other factors present in the industrialized wreacks havoc on the gut microbiota.

Sources of prebiotics

Inulin and some types of oligosaccharides


Onions and garlic contain prebiotic fructans.

Inulin and oligosaccharides such as fructooligosaccharides are polymers of fructose molecules that have long been recognized for their prebiotic effect.  Oligofructose is often classified as a short-chain prebiotic that’s broken down quickly in the right side of the colon, while inulin is a long-chain prebiotic that’s fermented more slowly.  These fermentable substrates stimulate the growth of beneficial bacteria like bifodobacteria and lactobacillus in the large intestine (5). Sources of inulin and prebiotic oligosaccharides include chicory, asparagus, artichoke, onions, garlic, and leeks (13).

Resistant starch


Green bananas are a source of resistant starch.

Resistant starch is subdivided into 4 fractions (RS1, RS2, RS3, and RS4) based on different characteristics such as structure and type of resistance towards enzymes produced by the human host. Besides being a potent prebiotic that significantly increase the levels of short-chain fatty acids in the colon, RS also has an effect on postprandial glycemia, hormonal response, and satiety (14,15,16,17).

Good sources of resistant starch include green bananas, potato starch, legumes and potatoes. The resistant starch content of foods like beans and potatoes increase when they are cooked and then allowed to cool for several hours (retrograded starch) (18).

Are whole grains a good source of prebiotic fiber?

Whole grains provide a fair amount of fermentable carbohydrates, but grain fiber also contains toxins and antinutrients that could negatively impact health (19,20,21,22,23).

Alterations in the human microbiome has been linked to increased incidence of grain- and gluten-related disorders, and may explain why some people tolerate grains better than others.

Traditional food processing techniques such as soaking, sprouting and fermentation increase the bioavailability of many nutrients and reduce or eliminate many toxins and antinutrients.


It seems that most people benefit from having a diverse intake of plant foods.

Most people benefit from increasing their prebiotic intake from plant-based foods.

Although specifically eating food with plenty of oligosaccharides and resistant starch will provide the optimal environment for the colonic microbiota, the primary takeaway is that most people benefit from having a diverse intake of vegetables, fiber-rich fruits, traditionally prepared legumes, and other plant-based foods. Supplements like potato starch or fructooligosaccharides can also be used to increase the intake of prebiotic fiber. The exception could be people with severely disrupted gut microbiota and/or small intestinal overgrowth, but few studies have investigated the use of prebiotics in cases of SIBO or severe gut dysbiosis.

Since the gut microbiota have to adjust to the increased intake of fermentable substrates, it’s usually advised to slowly increase the consumption of prebiotic fibers to avoid excessive flatulence or other gastrointestinal issues.

Different species of bacteria are able to utilize different types of fermentable substrates, and consuming several species of plants during the week could promote a more diverse microbiota. Minimally washed plants grown in quality soil (i.e., from your own garden, farmers market) are also a source of soil organisms that aid in the breakdown of polysaccharides. This notion that the bacteria found on the leaves of vegetables and other plant-based foods should actually be considered a part of the food suggests that modern food production (e.g., monocultures, pesticides, poor soil quality) and food safety (e.g., cleaning and/or boiling produce to remove bacteria) decrease microbial diversity in the gut and may contribute to poor breakdown of fermentable substrates.


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