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8. The Microbiome: What is it and Why?

Updated: Jun 1, 2021

A Brief Tour of the Human Body - Your skin is crawling

While it may make you queasy to know this, your digestive system may be just the tip of the proverbial iceberg. The microbial community in a single person’s gut has been estimated at 1000-1500 species with about 10,000 species worldwide, but the diversity of microbes so far identified in the human mouth is currently estimated at nearly 800 species[i] and diversity on the skin is very difficult to estimate, but may be equal to that. Bacteria do not easily conform to the concept of a “species” and because of their size we cannot merely look at them and determine their identity.

We typically identify bacteria by what molecules (“food”) they break down or by their genetic sequences. We can say one bacterium is different from another because they each decompose different molecules or we can say they are different because genetic sequencing indicates significant genetic differences between them. Either way is fine, but how different must they be to consider them different species?

Bacteria mutate and evolve so quickly that new “species” are emerging more or less constantly. In a remarkable demonstration from the Kishony Lab at Harvard Medical School,[ii] bacteria were placed at both ends of a large agar tray (like a super-sized Petri dish) that contained increasing amounts of antibiotic as one moved toward the center of the tray. Over the course of 10 days, bacteria grew toward each antibacterial boundary where growth slowed until mutations to tolerate the higher antibacterial content allowed mutant bacteria to move into the next section. In only 10 days, bacteria had evolved the capacity to live in agar that contained 1000 times the lethal concentration of antibiotic for the original bacteria.

This demonstration showed that huge populations of bacteria can quickly overcome incredibly toxic conditions and that mutations arise constantly, thereby increasing the chances of tolerating environmental stress. An interesting question is this: Are the bacteria at the beginning of the experiment and the bacteria at the end of the experiment still of the same species? The two strains of bacteria are adapted to very different conditions; the original cannot begin to tolerate the conditions the later strain can tolerate and the tolerant strain is probably non-competitive in the original environment. After a series of no less than four critically important mutations to the toxicity of the environment agar, should we consider the 1000x tolerant bacterial strain a new species?

The bacteria in our microbiome are faced with biochemical challenges in their environment every day. The digestive community must deal with every indigestible item we consume. The mouth community is exposed to mouthwash, toothpaste, alcohol, food, and spices. The skin community experiences soap, shampoo, skin lotion, antibacterial solutions, salt and chlorinated water, to name but a few.

The spices in our foods present interesting obstacles for bacteria and fungi. Nearly all of the chemical compounds in plants that make them taste good to humans are secondary compounds that plants produce to decrease the probability of herbivory. The flavors of plants are, in fact, toxins for insects, bacteria, and fungi, and we humans consume them because they enhance the taste of our food. If the toxins are not degraded in our mouth, stomach, or small intestine, they make their way into the colon where they may influence the environment of our microbiota. Do very spicy foods create gastric upset and diarrhea? They certainly can. Is it because they do something to YOU or is it because they disrupt the activities of the gut microbes? It’s more likely to be the latter.

Fortunately, your microbiome is quite capable of adjusting and adapting to adverse conditions. It may take a day or two, but it’s very likely that the consumption of antibacterial substances in our food pushes the gut microbes toward tolerating those chemicals. It is almost certain that the communities in our mouths and on our skin do the same. However, it is also true that if we manage to suppress the activities of our microbiome, to shift the abundances of different species, or to create an opportunity for new species to invade our bodies, we are likely to experience adverse consequences.

The known diversity of microbiota on the skin depends on sampling techniques, number of people sampled, region on the body, age and health of the person, and an unknown number of other factors including, of course, where in the world the study took place. For example, a 2009 study [iii] found 19 different phyla with 205 bacterial genera in samples from 20 sites on the body categorized by oily, moist or dry conditions. The researchers found that the bacterial complexity, diversity, and stability differed by the location on the body (with highest diversity behind the knee.) Although each volunteer in the study was more similar to themselves across the 20 samples locations than they were to other people, the researchers found considerable change in the bacterial communities when follow-up samples were taken 4-6 months later.

Another 2009 study [iv] sampled the bacterial community from 27 locations on the body and over two time periods and reached similar conclusions. One interesting observation was that similarity between sample sites depended on the side of the body they were on (left or right). A 2013 study [v] focused on fungal diversity from 14 sites on the body and found 130 genetic types. Although bacterial diversity differed more amongst the human individuals, fungal diversity in this study differed more by location on the body, with feet being the most diverse. Of perhaps greater interest was the observation that diversity was higher on people who used anti-fungal medications and that some fungal groups were anti-correlated with other groups, which suggested replacement or competitive effects.

These and many other studies have illustrated just how complex, diverse, and unpredictable the skin microbiota can be. It is probably not surprising that estimates for skin diversity were higher than those for either the mouth or gut, and this is likely due to the skin’s constant interaction with the external environment from which both the mouth and gut are buffered. The skin microbiome is to some degree the species pool from which the other microbiomes are drawn. What remains to be understood to any useful degree is what protection, if any, our skin microbiome affords our general health or even that of our skin.

And your mouth is alive

Although the bacteria of the large intestine (colon) receive the greatest attention, a large portion of the microbiome residing in our mouth is also considered important to our health. Even though van Leeuwenhoek’s discoveries concerning the mouth were not accepted initially, it quickly became apparent that there is an invisible world of animals (at least if you don’t have a microscope) and even a “clean” human is teeming with life.

The Human Oral Microbiome Database ( attempts to catalogue all of the identified bacteria in the human mouth. The numbers are ever changing as new samples and new techniques reveal previously unknown types, but the latest numbers are ~800 species of bacteria in ~200 genera. Only about half of the bacteria are named and about one third have never been cultured under laboratory conditions which complicates efforts to identify or name them and to figure out what they are up to.

The bacteria in the mouth appear to exist as a community of sorts. A 2010 study [vi] showed that although the mouth and gut harbor incredibly diverse assemblages of bacteria, there is very little similarity between them. One conclusion was that the presence of specific bacteria might not be random, but rather a result of interactions among species that results in a process of community “assembly”.

That is, the individual species do not exist in isolation, but are typically found in association with other specific bacterial species. One suspicion is that such community structure may have implications for the health of the mouth and consequently for diseases of the mouth. In other words, some mouth diseases may be contextual; an imbalance or disturbance to the normal mouth bacterial community, rather than of individual species of bacteria, may result in negative interactions with the teeth and tissues of the mouth.[vii]

Although the research on positive and negative interactions with mouth bacterial communities will likely be painstakingly slow, the goal will be to look for protective relationships correlated with some species and the loss of those protections when those species are absent.

As with the gut microbes, we can assume that the presence of some species represents a mutualistic association (much more on that later), one that provides some benefits to the human host, and those benefits are likely to take the form of protections from invasion by pathogenic species.[viii]

Such mutualisms are also likely to be very subtle, to vary with geographic region, culture, ethnicity, and even cuisine. Given the recent historical breakup of complex human social structures, such as the movement from rural to urban settings and the large and ongoing shifts of humans to different continents, our attempts to understand the subtleties of mutualisms involving mouth bacteria within particular regional or ethnic groups of people may turn out to be impossibly difficult.

Following our food

Our stomach is a very hostile place to most living things and very few organisms can survive passage from the throat through the stomach to the small intestine.[ix] In the stomach, food is mixed with acid, pepsin, and water to make a food slurry called chyme. The contents of chyme do not pass through the pyloric valve into the small intestine until they are reduced in size to smaller particles by the churning action of the stomach.

No food is digested in the stomach (in the sense that the food is not fully dissolved into component molecules), but some initial breakdown of protein does occur. The pepsinogen released by the stomach lining is activated by the release of hydrochloric acid and the activated pepsin begins to break down proteins, which are rather stubborn molecules to digest.

Bacteria and other organisms are unlikely to survive the acid stomach environment unless they are adapted to it or protected from it in some way. For example, some parasite eggs and bacterial spores can pass through as can certain immature and adult parasites. Bacteria that cause different forms of gastritis are able to make it safely to the small and large intestines. Bacillary (bacterial) dysentery and amoebic (protozoan) dysentery are two examples.

And there is one bacterium that takes up residence in the stomach lining: Helicobacter pylori. H. pylori can penetrate the lining of the stomach resulting in inflammation and the symptoms of that infection traditionally have been called an ulcer. However, there are no known beneficial bacteria or microbes that inhabit the stomach and it is not considered part of the microbiome.[x]

The small intestine receives the contents of the stomach and is immediately bathed in a variety of enzymes that break down carbohydrates (amylases), fats (lipases) and proteins (proteases). The pH of the acidic chyme is quickly raised by digestive secretions, such as bile salts, in the upper small intestine and pH is nearly neutral through the lower small intestine. Bacteria are found in relatively low density in the small intestine, and the body’s antibacterial lymphocytes work to keep the numbers low in this aerobic and nutrient-rich environment. If the presence of bacteria in the small intestine is a typical indicator of pathogens, the body would do well to keep that area clean.

Not until the small intestine joins the large intestine (the colon) is the intestinal microbiome found in all its glory. Once the remnants of the last meal (i.e., the parts that are not easily digested) pass through the ileo-cecal valve into the colon, the bacteria go to work on them. This undigested material is the only food for the microbiome of the lower digestive tract.

There are hundreds to thousands of species of bacteria in every colon. It is certainly possible that the colonization of the colon is just a natural coincidence. After all, the gut environment is full of food for bacteria, the pH is neutral, it’s warm and dark, and we were just going to excrete that indigestible stuff anyway.

The indigestible material is very durable and moves through the small intestine pretty quickly, so chemical break down of the undigested food wasn’t likely to happen on its own. It would be natural for bacteria that are adapted to low-oxygen environments would find and take advantage of the unused resources. This is always the case in every ecosystem; unused resources do not go unused for long because they provide a niche for any organisms that can make use of them as food. However, the accumulation of a highly diverse and stable microbiome is very unlikely to be accidental and we’ll consider some reasons later.

Different sections of our digestive system are separated from each other and the outside world by sphincter muscles, which are circular muscles that can open and close to allow and prevent movement of materials. The esophageal sphincter at the top of the stomach prevents our most recent meal and beverages from coming out of our mouth when we hang upside down on the monkey bars at the playground. The pyloric sphincter meters the release of chyme into the small intestine from the stomach.

The ileocecal sphincter separates the large and small intestines and is important for preventing the bacteria in the large intestine from entering the small intestine. And perhaps the most notorious sphincter, the anal sphincter, separates the outside world from our inside world (just as the esophageal sphincter does at the other end). Other examples of sphincter muscles are those that dilate the pupil of the eye and prevent urine from escaping the bladder into the urethra.

At any rate, our internal world is not fully separated from the outer world and bacteria move into us and through us all the time. In fact, our digestive system is not truly internal anyway. Our mouth is the opening of a tube that winds and turns and bends back on itself and then eventually terminates at the anus. What we put into our mouth is not ever truly inside us; it is moving through us in a tube and our body extracts nutrients from it by diffusion. When nutrients are absorbed into our body from the digestive tract, it is in the form of small molecules that pass into some part of the circulatory system, but the food we eat is always technically outside our body.

Therefore, the bacteria inhabiting our colon are not really inside us so much as being carried along inside the tube that passes through us. Many bacteria do move from the outside to the true inside, into our tissues, organs, and circulatory system. Some are escorted by carrier cells and end up in particular places for particular purposes (more on that later), but others are definitely out of place and may be pathogenic. The bacteria that remain in the intestine are there for a variety of reasons.

There are several scenarios describing the interactions between two coexisting organisms, especially when one is inside the other. If one organism benefits from the interaction and the other is harmed, we call that a parasitic relationship. One organism gains nutrients and the other loses some vitality as a result. The parasite concept is a familiar one and many examples come to mind, such as ticks, leeches, tapeworms, and heartworms. Viruses can be cellular parasites because they make use of resources in the cells without providing any benefit to the host.

If one organism benefits, but the other is not harmed, we call that a commensal relationship. These relationships are a popular subject for animal shows on TV. One example is the birds that use the backs of rhinos or giraffes as a perch as they look for insects that are stirred up by movements of the larger animals. The birds benefit, but the large herbivores are indifferent to their presence.

Finally, when both organisms benefit from their interactions, this is called a mutualistic relationship. While we certainly don’t know enough to categorize all of the bacteria in the human gut in terms of the relationship, it would appear that a large number of bacteria are probably mutualists in that they provide some benefit to their human host. In return, we provide a provide safe, well-stocked, amenable environment for bacteria. Whether or not these mutualisms are necessary (i.e., obligate) relationships or just opportunistic (i.e., facultative) relationships is not well known. (I'll describe the nature of mutualisms later.)

Just how beneficial are these bacteria to us? How important are they to us? What is the consequence of having too many or too few of them? Can a non-pathogenic bacteria become pathogenic if conditions change? Can we survive without them? Where do they come from in case we need more? These questions and more are the subject of intense research scrutiny, several diet plans, rapidly growing pharmaceutical sales, and a growing number of very interesting books.

What is known is essentially this: a healthy gut microbiome protects us from pathogenic bacteria, provides vitamins and nutrients that we do not (or cannot) get from our food, alters our blood chemistry, stimulates our immune system, and manages our waste products prior to defecation. Bacteria are so abundant, they make up about 60% of the weight of our feces. That is, bacterial biomass in our solid waste is greater than the indigestible remains of our food! While hundreds of species may be common at any one time, the majority are from 30-40 species [xi] and about 30% from a single genus [xii]. Keep in mind that these bacteria are necessary and beneficial and not to be confused with the disease-causing bacteria that come to mind when one is usually discussing bacteria.

[i] Dewhirst, Floyd E., Tuste Chen, Jacques Izard, Bruce J. Paster, Anne CR Tanner, Wen-Han Yu, Abirami Lakshmanan, and William G. Wade. "The human oral microbiome." Journal of bacteriology 192, no. 19 (2010): 5002-5017. [ii] [iii] Elizabeth A. Grice, et al. 2009. Topographical and temporal diversity on the human skin microbiome. Science 324:1190-1192. [iv] Elizabeth A. Costello, et al. 2009. Bacterial community variation in human body habitats across space and time. Science 326:1694-1697. [v] Keisha Findley, et al. 2013. Topographic diversity of fungal and bacterial communities in human skin. Nature [vi] Elisabeth M Bik1, Clara Davis Long1, Gary C Armitage2, Peter Loomer2, Joanne Emerson3,7, Emmanuel F Mongodin4, Karen E Nelson3, Steven R Gill5, Claire M Fraser-Liggett4 and David A Relman. 2010. Bacterial diversity in the oral cavity of 10 healthy individuals. The ISME Journal 4:962-974. [vii] Howard F. Jenkinson, Richard J. Lamont. 2005. Oral microbial communities in sickness and in health. Trends in Microbiology 13:598-595. [viii] See Chapter 5 for more details. [ix] DeAnna E. Beasley et al. 2015. The Evolution of Stomach Acidity and Its Relevance to the Human Microbiome. PLoS ONE, July 2015 [x] Gianluca Ianiro et al. 2015. Gastric microbiota. Helicobacter 20(S1):68-71. [xi] Beaugerie, Laurent; Petit, Jean-Claude (2004). "Antibiotic-associated diarrhoea". Best Practice & Research Clinical Gastroenterology. 18(2): 337–52. doi:10.1016/j.bpg.2003.10.002 [xii] Sears, Cynthia L. (2005). "A dynamic partnership: Celebrating our gut flora". Anaerobe. 11(5): 247–51. doi:10.1016/j.anaerobe.2005.05.001

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