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Everything but the Kitchen Sink
Exploring the Human Microbiome
For the first half of geological time our ancestors were bacteria.
RICHARD DAWKINS
Don’t take this personally, but you are less than human. At least half of the genetic information that comprises your body and influences your mind—that which makes you feel most human—is actually not human. A substantial amount of your physical and genetic makeup, trillions of cells, are genetically “other.” These other living, and in the case of viruses, nonliving entities are collectively and loosely known as the human microbiome. As mentioned earlier, this collective is so important and has so much impact on our health, longevity, and quality of life that it’s often considered an organ in and of its own right. The little beings that comprise it include bacteria, fungi, and viruses, and we are only now, after hundreds of years of Western medicine and science, finally getting to know them. Our earliest glimpses into the microbial world started in the 1800s, but serious research didn’t really kick into gear until about a decade ago.
The more we learn about this world, the more questions arise. Fueling our curiosity is the hope that the information we glean will lead to the ability to cure diseases or alleviate their symptoms with manipulation of the microbiome. In fact, some scientists are coming to the conclusion that understanding the genetic material of our microbiome is as important as knowing all we can about the human genome. Below is a brief overview and introduction to some of what we currently do know, and some questions that arise as a result of our new knowledge.
We know our microbial inhabitants play a role in gene activation. They do not necessarily cause changes in the genetic material, but they can affect the way our genes express themselves, for better or for worse. They also affect estrogen levels in menstruating women. Maybe the gut microbiome plays a role in setting our biological clock. Maybe it causes menarche, or first menstruation, to begin, or perhaps an imbalance in the microbiome causes delayed onset. Could there be a community of metabolites specific to the microbes in the ovaries (which have microbiomes as well, and they may be different from left to right) and/or uterus we haven’t discovered yet that is responsible for communicating this timing to the brain? Is it possible that sterilized, hormonecontaining food in our diets creates a state of dysbiosis causing girls to start puberty prematurely? If that is the case, it may also play a role in male sexual development. It is conceivable because we know this happens elsewhere in nature. For example, there are sea creatures that don’t mature into adults without a microbial-triggered gene activation.1
We know the gut microbiome communicates with the brain, and that it plays a major role in our ability to experience a sense of wellbeing. We also know it plays a role in the inflammatory response, and that an imbalance in the gut microbiome can cause anxiety and keep us in the stress response of fight-or-flight. We know a bit about the passing on of microbes to newborns: the amniotic fluid, the umbilical cord blood, and the placenta all contain microbial communities; the vaginal canal colonizes an infant born naturally; and babies born by C-section are colonized by the bacterial environment from the mother’s abdominal skin and whatever is emitted by the delivering doctor or receiving nurse. Skin communities and vaginal communities are very different ecosystems. Studies show that C-section babies are more prone to obesity, asthma, and allergies later in life, so it seems probable there is a direct link between this statistic and skin colonization versus vaginal colonization.
In the case of various diseases, we know that specific communities are present in the guts of people with certain diagnoses, even if we don’t yet know what manifested first: the disease or the imbalance in the microbiome. We’ve learned that when we treat people with certain gastrointestinal disorders by using healthy microbial communities from healthy people, the diseased state improves overall in the person with the imbalance. There is much more to learn, and it seems a new study is being published almost daily, but we already know for sure that the microbiome helps maintain our homeostasis, our vitality, and our overall well-being.
By far the most researched and talked about microbiome is that residing in the gastrointestinal (GI) tract, commonly known as “gut flora.” It alone contains more than 3.3 million genes, contributing to and influencing our overall genetic makeup.2 (We will explore the GI microbiome in the next chapter.) The microbiome incorporates all of the nonhuman cells/microbes/critters on and in the body. You may have had some of those little microbes today in yogurt, kimchee, a fermented beverage, or probiotic supplement.
There is also a mycobiome, or fungal microbiome, that we have less information about, but as is the case with the bacterial colonies we harbor, we are learning more about it every day. Some people take a probiotic supplement containing Saccharomyces boulardii in order to stop diarrhea associated with antibiotic use, or to crowd out an overgrowth of candida. There is also a high concentration of fungal helpers in the ear canal that are believed to keep the rest of the ear’s microbial communities in check.3
In addition to the microbiome and mycobiome, our bodies also include a virome. The virome is a diverse collection of viruses that interact with the microbiome and affect us in ways we don’t yet fully understand. Some sophisticated studies show these interactions may enhance or block infection, but the role viruses play in assisting our health has been little studied. Unfortunately, there are limitations to the technology available for this research.4 Since we don’t know much about the virome, and have little information about the mycobiome, we will focus on the best-researched aspect of the microbiome in this text, our beneficial bacteria.
The Skin You’re In
There are microbiomes all over and in the human body. Let’s start with the one on the largest organ: the skin. Living in follicles and glands as well as on the surface, the skin microbiome helps to protect against infection, and some scientists believe the microbial inhabitants on the skin may train killer T cells in their work of finding and destroying foreign, infected, or damaged cells.5 This is aligned with the teaching in Chinese medicine that the skin contains a first line of defense in the immune system against potentially invading pathogens. This immunity in Chinese medicine is called wei qi, or defensive qi. Practitioners assess the functioning and quality of the defensive qi, and if it is deficient, can utilize acupuncture, diet, and herbal remedies to strengthen it. The skin microbiome has very similar friendly bacteria to the oral and gut microbiomes; they mostly differ in proportions particular to their classification by phylum.6
Not only is the skin colonized by microbes (bacteria, viruses, fungi), it is a home to mites as well. All of these players in the homeostasis of the skin make contributions to our good health in ways that our own human genome falls short.
The skin microbiome is affected by the environment, and studies have shown the presence of humidity and heat increases microbial counts on the back, armpits, and feet.7 This makes sense from an Eastern medicine perspective. It is taught in Eastern medicine that like increases like, and that external environmental conditions influence the body’s environment. It is also suspected that everything we apply to our skin affects the microbiome; it’s just unclear exactly how at this time. We know that what we apply may alter the condition of the skin, so common sense speaks to the likelihood of microbial modification as a result. Are we feeding our good critters? Killing off the beings that live on us, regardless of their function? Altering the composition of colonies, and therefore altering their symbiotic effects on our health and well-being? This is food for thought the next time you reach for antibacterial soap or put some artificially fragranced lotion on your skin. What shampoo do you use? What lotion do you put on your face? Remember, in addition to being a protective barrier, the skin is a sponge. Much of what goes on it passes through it as well. Anyone who has had hormonal imbalances corrected by a tiny patch can attest to the power of absorbing something through the skin, as can those with skin sensitivities, such as a wool allergy. The skin breathes and interacts with its environment without our even knowing it.
Handwashing for Health
Maybe washing our hands to stay healthy works in ways we hadn’t considered, not just by removing microbes so they don’t enter through our nose, eyes, or mouth but ridding ourselves of microbes, or their metabolites, that otherwise might be absorbed through the skin or send messages to the gut and immune system through it.
The fact that the skin absorbs was known to the ancient Chinese and Indians, and is incorporated into a slew of treatments in both systems of medicine. In Eastern treatments, poultices, soaks, and topical treatments are the norm. They are advised for anything from nervous disorders to skin ailments, and from beauty treatments to traumatic injuries. I won’t go over them in any detail here, as most are indicated for specific purposes according to diagnosis. What I can say is that in both Chinese medicine and Ayurveda, the skin is very important in both diagnosis and treatment. My guess is that one way poultices, soaks, and topical treatments work is to alter the microbiome in the area of focus, restoring homeostasis to the region—or to the region that correlates internally to that place on the body.
Most directly, researchers are finding a correlation between dysbiosis, or what is thought to be a pathological imbalance in the microbiome, internally and externally, and such skin issues as dermatitis, psoriasis, and eczema. In Eastern medicine, much can be told by the color, texture, temperature, sensitivity, laxity, density, markings, and moistness of the skin, as well as of the nails and hair.
Essential Oils, Friend or Foe?
Things to Consider before Using
We perceive substances called oils to be benign, as we use them regularly for cooking and nourishing our skin. In this more general sense of the word we are talking about bioavailable, unconcentrated oil. In contrast, essential oils are practically pharmaceutical-grade consolidations of plants and resins.
Essential oils are largely antimicrobial. As author and master herbalist David Crow points out, they are the distilled immune systems of plants. All the information that has come down through millennia to protect the plants is contained in each drop of oil. They have great potential for helping to keep us healthy when used in moderation in a balanced, well-informed manner. When overused, however, in addition to possibly triggering inflammatory reactions in the skin and respiratory systems, they may interfere with the beneficial microbes on the skin. These microbes knit together to form protective colony barriers against invaders, and excessive applications of essential oils have the potential to break those bonds. Additionally, some create photosensitivity and can result in bad burns if the skin is exposed to the sun. There is also the risk of irritating mucosal membranes if ingested. Essential oils are readily available but they are not all top quality, so think twice before ingesting them, and do so only at the behest of a qualified medical practitioner. I believe it is safest to use them selectively in a diffuser, occasionally in a carrier oil on the skin, or in small quantities in a steam inhalation to help clear the passages when the nose and sinuses are blocked.
Regional Differences
Each region of the skin has its own unique colonies in specific balance.
Navel. There is a question as to what ways the microbiome of the navel influences our health overall. A 2012 study of the navel microbiome found 1,458 bacteria previously unknown to science. One person in the study harbored extreme microbes previously thought present only in thermal vents and ice caps. It is now thought that laparoscopic surgery through the navel may introduce these microbes to the body’s interior.8 Experts recommend regularly cleaning the navel with soap and water and gentle rubbing, but caution against alcohol as a cleanser, as it can disrupt the area’s ecology.
Scalp. A recent clinical study showed that an imbalance in the bacterial community of the scalp may be implicated in the production of dandruff.9
Armpits and Genitals. I’m sure you can imagine how the communities on and around the armpits and genitals must be different from those on the forearm or face. The way these microbial communities utilize our bodily secretions is what causes each of our distinct odors.
Researchers have found that in the armpits of study participants, people who don’t use deodorant or antiperspirant had more than double the population of Corynebacterium. This microbe works with the body to maintain or restore balance, and is present in the vagina, fighting off pathogens. The study leaders divided participants into three groups: Some wore only antiperspirant, then stopped after several days; some wore deodorant, then stopped; and some wore neither. After stopping the study, the deodorantand antiperspirant-users had triple the staph microbes compared to non-users, and the fewest corynebacteria, the ones known to provide a strong defense against pathogens.10 They also exhibited the greatest diversity of microbes, which may be linked to better health in the gut, but is not necessarily so for the armpit.
Healthy armpits contain an enormous number of bacteria but not a great variety, according to scientist Chris Callewaert, an expert on armpit (axilla) microbes. In fact, a greater diversity of microbes in the armpits usually equates to worse body odor because increased diversity in this area usually means more diverse colonies of bad bacteria—the ones that produce a foul smell. Dr. Callewaert has been working with transplanting armpit microbial communities in order to address bad body odor. He’s found that people who are more genetically similar have greater success rates with the procedure, so he uses family members in his experiments.11 In preparation for the transplant, the armpits of the malodorous recipient are sterilized, while the sweeter-smelling donor is encouraged to let bacteria flourish. Then the donor microbe community is applied to the recipient’s armpits, which can’t be washed for a week. Dr. Callewaert reports semi-permanent to permanent results.12
Research from the University of York shows that staph is making the biggest contribution to foul underarm odor.13 A National Public Radio article describing the findings states, “Most deodorants [and antiperspirants] block sweat glands or kill off underarm bacteria. Blocking the sweat glands sometimes leads to irritated or swollen skin. And given all the new research into the complexity of the human microbiome, the researchers are a little anxious that deodorants may kill good bacteria, too.”14 They aren’t sure we should be killing any bacteria, as it can upset the balance, potentially allowing for the stink-causing staph and other potentially harmful species to run rampant. Instead, researchers are looking for ways to add friendly bacteria to the armpits that hopefully will colonize and take up more space and air than their stink-causing counterparts, crowding them out.
More research is needed to understand how the skin microbiome plays a role in various skin diseases, as well as how to encourage the dominance of helpful players and mitigate the offenders.
The Mouth
The mouth is called the gateway to the stomach in Eastern medicine, and it is the gatekeeper for potentially trillions of microbes entering the body—thousands per swallow.15 The mouth microbiome’s composition overlaps that of the colon’s by about 45 percent!16 Some researchers posit that what we eat affects our teeth less directly than it affects the healthy balance of mouth microbes. They believe that it isn’t sugar, for example, directly causing cavities, but the dysbiosis, or disruption to the healthy balance of the microbial communities in the mouth caused by sugar consumption that is the culprit.
There is increasing evidence in support of a direct connection between mouth health and systemic health. Basically, what is happening in the mouth is a reflection of what is going on in the rest of the body. This may also mean that what is happening in the mouth has a role to play in causing what’s happening in the rest of the body. Here we can again refer to Eastern medicine, which has the detailed evaluation tool of tongue diagnosis, which is tremendously limited in Western medicine. Tongue diagnosis is just what it sounds like: looking at the tongue to determine the state of the insides of the body and the functioning of the mind. The tongue’s coating, shape, and color reflect the quality of digestion and metabolism, the presence of toxins, and the state of the microbiome.
In addition, Eastern medicine hygiene techniques such as tongue scraping and oil pulling, or kavala, are being used more regularly now in the West with promising results. Although we don’t have much trial data, coconut oil, for example, contains vitamin E (an antioxidant) and has antibacterial and anti-fungal properties, as does sesame oil, which is traditionally recommended for oil pulling. Unlike many mainstream mouthwashes containing alcohol, which may contribute to dysbiosis, using oil may actually be nourishing to the friendly bacteria in the mouth. Beyond the oil’s potentially nourishing and antimicrobial properties, there may be something to how the oil’s viscosity changes during the pulling process, in addition to the sucking and swishing, that accounts for its numerous beneficial effects.
Many of us have heard the term leaky gut. The mouth may also have increased permeability of the membranes that allows pathogenic microbes to migrate into systemic circulation. This means leaky gut doesn’t just happen in the gut, but can happen across other membranes as well. This is just one way the mouth may affect the rest of the body, potentially leading to increased inflammation. Eastern medicine recognizes that disturbed physiological factors can come from pretty much anywhere and migrate to places in the body where they don’t belong, wreaking havoc.
In a recent interview for the blog Ask the Dentist, ethnopharmacologist Cass Nelson-Dooley answers a question about the connection between periodontal disease and inflammatory bowel disease. She states, “A mouth that is sick is seeding the entire GI tract with bad bugs every day.”17 This may be hugely problematic, especially if the beneficial microbes in the gut are not diverse enough or the gut is overrun with microbes that are creating imbalance in the system. Steven Lin, D.D.S., writes, “Probiotic strains of bacteria are known to perform protective functions in the mouth. For example, some strains release acids that keep the harmful bacteria that cause tooth decay under control. Others protect against strains that cause gum disease and bad breath.”18
So how do we maintain a good mouth environment? Eating a good diet is key, as is reducing or eliminating broad-spectrum mouthwashes that annihilate good bacteria as well as bad. In addition to oil pulling, if it isn’t contraindicated for your current presentation (which may include head or neck, including mouth, pathologies), maintaining consistency with tongue scraping, flossing, and brushing is, of course, critical. Breathing through your nostrils rather than your mouth is also beneficial for oral microbiome health. Breathing through the mouth may dry out the mucusa and contribute to dysbiosis.
A study released in January 2019 suggests a strong link between the bacteria Porphyromonas gingivalis, the bug that stimulates gingivitis—and Alzheimer’s disease. Not only is there a link, the study claims this microbe is a primary causative factor, being intimately tied to the amyloid plaques present in the brains of many Alzheimer’s patients. By-products of the microbe’s activity, called gingipains, were found in the majority of brains tested of people who died from the disease. As part of the study researchers infected mice orally with Porphyromonas gingivalis, then administered a gingipain inhibitor. It was found that the inhibitor was more effective at curing the mice of their gingivitis than the commonly administered antibiotic prescribed to humans.19 Although more research is needed, including human trials for the gingipain inhibitor, this is yet another example of the link between a member of the microbial community and its impact on health or disease, both locally and in other parts of the body.
The Nose Knows
Within the nose there are very interesting and unexpected factors at play. We know that the nasal passages are lined with hairs that help filter potentially harmful entities and substances from entering deeper into the body, but did you know they also have ridges that affect your mood? The nose contains turbinates that swirl and shape the flow of air entering the body, and affect how it hits the back of the cavity, influencing the brain. This flow, if strong enough and nurtured with healthy breathing, can affect the limbic system and alter our mood. It may be that the microbes lining the nasal passages have a role to play in changing the shape of this landscape. In classical yoga, nose breathing is so important that there is a comprehensive system of breathing practices called swara that deals with different ways to regulate air flow through the nostrils. It helps to induce meditative and other mental states, and helps practitioners to identify and align with their biological clocks and other cycles of nature.
It is optimal to breathe through the nose instead of the mouth. This is not only good for the microbial communities helping to keep your mouth healthy, but also good practice for keeping your lungs healthy. Think about how dryness affects you when forced hot air is first turned back on during the winter. It wreaks havoc with people’s mucosal membranes. When the wetness dries, filtering is decreased and pathogens can more easily enter the deeper areas of the respiratory pathways. Additionally the dryness can affect the throat, cause coughing, and be just plain uncomfortable. It is therefore recommended to make a habit out of breathing in and out through the nose at all times of year. Breathing in through the nostrils, instead of the mouth, filters pathogens, dust, and other irritants. Exhaling through the nose allows the balmy, moist air from the lungs to rewarm and remoisten the nasal passages. What an ingenious, simple mechanism for self-regulation! Nature is incredibly efficient. This is the temperate, humid environment we want to cultivate for our nasal, sinus, bronchi, and lung mucusa and for our friendly microbes.
There is literally a bittersweet battle raging in your nose right now between bacteria that are working to keep each other in check. Different strains in the nasal cavity help to keep you healthy by secreting amino acids that activate taste receptors on your cells and prevent things like sinusitis from developing. Molecules on, or secreted by, bacteria can activate bitter taste receptors in the sinuses that produce antimicrobial molecules. Other bacteria directly or indirectly activate sweet receptors that produce further balancing results.20
Yes, you did just read that we have taste receptors on cells in our sinuses. As mentioned earlier, we have taste receptors on cells in lots of places in our bodies that are far removed from the tongue. In Eastern medicine, foods and medicines are classified by taste in order to intentionally alter, activate, or deactivate biological processes. One simple example of this is in using bitter medicinals to clear heat (inflammation) from the body. As explained above, this is exactly what is happening in the head naturally, via the microbiome, without our interference.
Eastern teachings specify which foods should be eaten for which internal environment or individual constitution at any given time of the year according to taste and thermogenic properties. In Western science there is less recognition, understanding, or even awareness of the influence of taste on our physiology. We tend to see food according to calories, macromolecules, and nutritive constituents. This is one of the reasons I encourage people to steer toward a diet that is steeped in Eastern wisdom. I see many diet plans and cookbooks that encourage eating for the microbiome but fall short of what we can be doing to optimize one’s microbiome as an individual. They do not take into account the digestibility of the food, the way the food is combined, how it is eaten, the season in which it is eaten, or the individual’s body type.
Microbiology has recognized that the tastes sweet and bitter carry out specific tasks in the nasal and sinus cavities. There are two theories that may help to explain it:
Scientists are studying how to better understand this phenomena so that they may utilize taste in the nose to help treat people suffering with chronic sinusitis.
Tricky Tonsils
The tonsils play an active role in immunity. Seated at the junction of the oroand nasopharynx are three sets of them: the adenoids, palatine tonsils, and lingual tonsils. This lymphatic/epithelial tissue is most popular for being removed in childhood, when it may become chronically inflamed and swell, leading to breathing difficulty. We may as a culture view them as disposable, but the tonsils filter and trap incoming pathogens from the mouth and nose. They also notify the immune system of the presence of a potential pathogen so the rest of the body can initiate preventive measures to stop their spread and catch them if they make a break. There are resident communities of friendly microbes in this area as well, and their balance may be key to preventing chronic tonsillitis.
Eye of the Beholder
The eyes also have a unique microbiome. A study done on mice and published in the journal Immunity shows commensal bacteria resident to the ocular surface, which keep the eyes free from infection. Researchers found that these microbes work by stimulating the production of interleukin, an immune-signaling protein. This is produced by mucosal immune cells, and its presence attracts white blood cells to an area to boost immunity. In this case the area is the cornea.22 Once again, as in the nose, the microbes living in and around us work with our human cells like a team to help keep us healthy.
In Eastern medicine the eyes are the window to the soul. The vibrance and vitality the eyes exude reflect the shen, or spirit, the state of mental and emotional health of the individual.
Vagina Chronicles
Let’s move more deeply into the body now and explore what we know about the internal microbiomes. The vagina hosts a complex microbiome of bacteria, viruses, and fungi. In this environment, diversity is key. The job of the primary bacterial colonizer in the vaginal canal, Lactobacillus, is to interact with the host’s own cells to keep mucus production in balance and protect from invaders.23 This creates an acidic environment that helps protect against things like sexually transmitted infections, bacterial vaginosis, and pelvic inflammatory disease. It also helps guard against the overgrowth of potentially harmful bacteria, viruses, and yeasts that might otherwise become too abundant.24
Although research is needed, it is now known that pretty much everything can disturb the vaginal microbiome’s balance, including menstruation. Things as seemingly unrelated to this area of the body as what goes into our mouths can adversely affect our vaginal microbial balance. Antibiotics are notorious for wiping out Lactobacillus. Any woman who has taken a course of antibiotics and ended up with a vaginal yeast infection knows very well just how related it all is. Decreasing the numbers of certain lactobacilli allows other critters—in this case, candida—to thrive. Hormonal contraceptives and excessive alcohol consumption also affect the vaginal microbiome, as do diet and aging. I think it makes sense, given all the science available, that any birth control affects the vaginal microbiome, even those that aren’t believed to create systemic reactions. Anything that enters the vagina may change its microbial composition. That includes substances from sexual activity, like semen and lubricants. For this reason, it is generally recommended to avoid douching.25
Once the microbial composition of the vaginal canal is compromised, undesirable entities can enter into even deeper places—the uterus, fallopian tubes, and ovaries. There is some evidence that vaginal dysbiosis, or a resulting infection, can even affect a woman’s fertility, or if she does get pregnant, the fetus.26 Some reports cite the presence of adverse bacteria in the uterus causing recurrent miscarriage.
Recurrent Miscarriage in Chinese Medicine
In Chinese medicine, many female fertility issues and recurrent miscarriages are considered the result of patterns that may be correctable with bodywork modalities, including acupuncture, and medicinal preparations (herbal formulas). Instead of addressing the issue as a defect of the woman’s hormonal or immune system, Chinese medicine sees it as the result of an imbalance in the woman’s constitutional factors and internal environment, which may be associated with complications from one of several pathogenic influences such as excess heat, cold, dampness, phlegm, or dryness. This imbalance may be caused by or result in fluid or vitality circulation issues or one or more of these pathogenic influences being lodged in the uterus. Such an influence might be classified by modern science as the result of unchecked microbial agents entering the upper reproductive tract.
Research indicates there is indeed a placental microbiome, an area that, up until recently, was believed to be sterile. In addition, some experts believe the placenta can be contaminated by microbes that may affect the growth and development of the fetus, and potentially lead to preterm labor and delivery.27 Much more research needs to be done, as we don’t currently know what the role of the mother’s microbiome is in fetal development, let alone what the composition of a healthy, life-supporting womb environment should be.
In the Womb and Beyond
As we noted earlier, there is a marked difference in the microbiomes of newborns born vaginally and those born by Cesarean section. Those born without intervention are colonized by the mother’s vaginal microbiome through the mouth, face, and bodily exposure. Babies born via C-section are largely colonized, at least initially, by microbial entities from the mother’s skin. Any attending delivery personnel who come into contact with the infant may also transfer microbes. C-section babies are shown to be more prone to developing allergies and asthma, and there is speculation that it might be due to having skin and gut microbiomes that largely resemble the mother’s skin versus her vagina. Because of this, some people are now swabbing the vaginal canal of C-section mothers and administering a smear of beneficial colonies to the newborn’s mouth, face, and body. In one experiment, those born by C-section and inoculated after birth with their mother’s vaginal microbiome were shown after one month to have a gut microbiome that more resembled the mother’s vagina.28
There is strong evidence that even before a baby is born it is being programmed by the mother’s microbiome, and that the mother’s microbial metabolites influence the brain development of her fetus.29 A researcher at the University of Michigan who studies fMRI scans of babies has observed that the amygdala’s connections to the rest of the brain structures are stronger in those with a less diverse microbial gut composition.30 The amygdala is the primitive part of the brain that gets activated to respond to strong emotional states, such as fear and anger. This finding may indicate that the microbiome has a strong influence on how a baby develops its personality, and perhaps whether it is more prone to experience strong emotions, such as fear and anger.31
The Bladder
The bladder was formerly believed to be sterile, but now we know that it too has a microbiome, and that there is a distinct connection between the urinary and vaginal microbiomes. The bladder microbiome is influenced by diet and lifestyle factors, and altered by urinary tract disease. It is also associated with urinary incontinence in women. Researchers are hopeful that further exploration of the urinary tract microbiome will create treatment options other than antibiotics for women with recurrent urinary tract infections.32 Studies are currently underway in hopes of discovering whether or not the urinary microbiome also has a role to play in bladder cancer.
Testes
Researchers have found that healthy testes are home to a diversity of microbes from four major families. Like the bladder, the testes were previously believed to be a sterile environment, but access to new technologies has now given scientists the tools to “discover” these diverse microbial inhabitants. They do so by tracking them through their DNA.33
There is evidence that an imbalance in the testes microbiome may play a significant role not only in some male fertility issues, but also in production of sperm. Men with a certain condition that doesn’t allow sperm to exit the body with the semen were found to have decreased microbial diversity. Further, men who produced no sperm had only one group of microbes present.34 This makes me think of how Eastern traditions prescribe moderation in sexual activity, particularly for men, as it is believed that overindulgence can weaken the essence. Perhaps this is because too much sexual activity damages microbial diversity. Western researchers also think there may be a link between microbiomes in other places in the body and prostate issues, but more studies are needed.
The Lungs
Another site in the body previously believed to be sterile is the lung environment. Forgive me for being critical here, but why would we think anything in the body is sterile? It seems a childish notion. There is hardly a place on Earth, if any, that is not inhabited by microbes. Even the most extreme environments harbor thriving resident communities. All creatures have mites and bugs on them and in them. We are no different.
The ecosystem in the lungs is particularly fascinating because it changes with every breath. Having a background in yoga, and a particular interest in the mental, emotional, psychospiritual, and physical dynamics of the breath, I find this realm very interesting. Unlike the other microbiomes, including the one in the gut when it’s healthy, the lungs have a bidirectional means of transporting and exchanging microbes. This means that instead of one primary direction of movement (as in the case of the GI tract where microbes travel from the mouth, in one direction, to the anus), the lungs bring in and send out. The respiratory pathway has two entrances that also serve as exits. As a serious student of the breath, I know that we have immense influence over our respiratory health, that we can alter it consciously, and that the quality of our respiration has a direct effect on our physical, mental, and emotional well-being. It follows that it may also directly influence the quality and/or activity of the microbiome both in the lungs and the gut.
In an article citing a study done of the lung microbiome in 2017, Robert P. Dickson, M.D., states, “The lungs are our largest interface with the outside environment, with 70 square meters of surface area. That’s thirty times the size of the skin and twice the size of the gastrointestinal tract.”35 As it turns out, the lung microbiome most closely resembles that of the mouth. Researchers believe this happens largely as a result of microaspiration, or the inhalation of microbes into the upper reaches of the lungs. There are mechanisms in place that don’t allow much to enter, and it seems that what does get in also exits. Although some microbes do inhabit the deeper air sacs, called “alveoli,” researchers think the lung microbiome is largely a transient community kept in check by both the host’s immune system and the ability to expel the microbes via coughing and ciliary action. It’s when the immune system is weakened for some reason, or microbial inhabitants overstay their welcome, that the microbiome becomes dysbiotic and causes infection or disease.36 I think researchers are likely to discover that the lung microbiome is comprised of more residents than they currently believe. Curiously, the lungs of some critically ill patients contain the microbial inhabitants of the gut, which indicates the importance of strong immunity.37 It also suggests that there may be a mode of travel from the gut to the lungs for these microbes. From an Eastern medicine perspective these communities of microbes would travel via the circulation, fluid pathways, meridians, and san jiao.
Interesting factoids about the lung microbiome are that the ratio of bacterial to human cells in the lungs is 100 microbial cells to every 1000 host cells.38 Another is that we are subject to microbial lung colonization from birth. There is a shift in the microbial composition of the lungs in the infant over the first two weeks of life toward microbes that encourage resistance to allergens. These data suggest acquisition of a lung microbiome is an important early-life event necessary to protect the lung from injurious responses to inhaled antigens.39 I wonder just how early. There have been findings of microbes in the placenta, but more research is needed to understand their function: Are they alive? How do they get there? Do they influence the immune system or other development of the fetus?40 This also makes me wonder if the proteins secreted by the fetus that initiate labor could be triggered by microbial activity.
In researching the lungs, I was unable to find any reputable studies on the effects of intentional breathing techniques or of healthy breathing on the lung microbiome. If I had, it would be covered here in depth. It is interesting to me that a natural, healthy breath involves inhaling and exhaling through the nose, and that unconsciously breathing through the mouth on a regular basis is considered pathological. In addition to not allowing for optimal filtration of particles while mouth breathing, it may also be that mouth breathing allows for a greater number of microbes, more than would be inspired through nasal breathing, to enter the lungs. It makes sense that if this is the case, it would force the body to work harder to keep the communities in manageable numbers, overworking the immunity in this area and making it more difficult to stay healthy. In addition, mouth breathing is more likely to dry the mucosa that comes in contact with the inhaled air and in that way also affect microbial activity of the lungs and homeostasis.
The breathing exercises in yoga practices, categorized as kriyas (cleansing actions) and pranayama (vitality control), serve various purposes that benefit the health of the entire body-mind complex. There are specific exercises that assist one in releasing some of the older dead air in the bottom of the lungs and stale energy from the lungs in general that may be of great benefit to those who have issues with the cough reflex or ciliary action. These techniques may also increase gas exchange with pulmonary capillaries and prevent the development of additional dead space in the lungs. They may be just what the average, healthy person needs to keep ahead of pathogens in the winter months, or allergens at any time of year. Some of these exercises will be elaborated on in chapter 7.
Neti (nasal cleansing) pots are widely popular and are used quite extensively in the American yoga community. Although there are now variations on the shape and materials, a neti pot is a small container with a nasal spout that is used to flush salinated water through the nose via the nostrils, in order to filter out particles and mucus that may be stuck in the sinus cavity. When I was studying in India, two teachers from the same lineage, the one most American yoga practitioners are influenced by, cautioned against the use of neti pots. These teachers insisted that the saline, especially when neti pots are used regularly, gets into the lungs and can cause disease. Perhaps this is because the saline water is microaspirated and creates an imbalance in the lung tissue or its microbiome. If you do use a neti pot, it is recommended only to use sterile water. This caution comes after incidences made the news of pathogenic amoebas, believed to be transmitted to the brains of two people through the tap water in their neti pots, resulted in those people’s untimely deaths. I’m not advising against the use of neti pots, but I wouldn’t recommend trying it for the first time when you are sick, and I recommend moderation in usage.
Researchers suspect that the lung microbiome plays a primary role in our overall immunity and homeostasis. Maybe healthy humans harbor lung microbiomes not just because microbes are accidentally aspirated and our immunity is keeping them in check, but because they are helping to keep us healthy and alive. We know the diversity of symbiotic microbial communities is minimized in diseased lungs. Our scientific knowledge of connections among these microbes, their metabolites, gases in the respiratory tract, and our immune and other cells is grossly lacking. It is my sense that this ecosystem is just as important as the one in the gut or elsewhere in or on the body.
It has been my intention with this chapter to give you a substantial introduction to and understanding of some of the body’s microbiomes. By no means could everything be covered in this chapter, but I hope I’ve given you enough to be in awe of the microbiome and how it works. If I’ve left an area untouched in this chapter, keep in mind that this is merely an overview, and we will revisit some of these areas later in the book when exploring how Eastern medicine treats the microbiome holistically. I hope this has opened your eyes to the extent of the microbiomes of your body, and the importance of their balance in your good health. Next we will turn to the gastrointestinal microbiome, which gets its own chapter since it is the one we know the most about, including how it is connected to and influences the body, brain, and mind.