Cultivating Your Microbiome

Ayurvedic and Chinese Practices for a Healthy Gut and a Clear Mind

Bridgette Shea

• Publisher: Healing Arts Press
• Year: 2020
• Print ISBN: 9781620557808
• eBook ISBN: 9781620557815
• Topic: Medicine
• Subtopic: Alternative & Complementary Medicine

A holistic guide to improving your gut flora for better physical and emotional health • Explores the influence of the gut microbiome and the mesentery on all other bodily systems, especially the brain and immune system • Explains the central role of the digestive system in Ayurveda and traditional Chinese medicine and how these systems treat the microbiome • Presents herbal remedies, acupuncture and acupressure techniques, and dietary methods to restore balance to your gut flora, including a microbiome reset In traditional medicine, such as Indian Ayurveda and Chinese medicine, the digestive system and microbiome are recognized as the foundation for good health. Our internal flora influences our immune system, brain function, hormonal balance, cravings, sleep, mood, inflammatory response, digestion, nutrient assimilation, and elimination. In this holistic guide to cultivating a healthy microbiome and managing gut health naturally, Bridgette Shea explores digestive functioning from the perspectives of both Western science and traditional medicine. She examines Ayurvedic and Chinese medicine principles on digestion and constitution types. She reveals how, in addition to describing what we now call the microbiome, traditional Chinese medicine also has long recognized the importance of an abdominal organ that modern science has only recently ­acknowledged: the mesentery, the tissues that connect and support the internal organs. Going beyond probiotics and prebiotics, the author presents practices from Ayurveda and Chinese medicine to reestablish balance in your internal microbiome, support the mesentery, improve digestion and elimination, and restore a clear mind and strong immune system. She explains how to read your symptoms, from brain fog and fatigue to congestion and stool quality, and offers herbal remedies, acupuncture and acupressure techniques, and dietary methods to improve your internal health, including a microbiome dietary reset. Revealing the diverse role that our inner microbial colonies play in keeping us happy and healthy, this book shows that by changing your microbiome, you can greatly improve your physical, emotional, and mental health.

PART I

Modern Science Meets Ancient Wisdom

1

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...

Table of contents

• Cover Image
• Title Page
• Dedication
• Epigraph
• Acknowledgments
• Table of Contents
• Preface
• Introduction: The Fascinating World of Microbes
• Part 1. Modern Science Meets Ancient Wisdom
• Part 2. Practices for Daily Living
• Glossary
• Footnotes
• Endnotes
• Bibliography
• About the Author
• About Inner Traditions • Bear & Company
• Books of Related Interest
• Copyright & Permissions
• Index