What are biomes?

Teeming bacteria, viruses, and fungi live and thrive in nooks and crannies throughout a typically healthy human body. There are much more of “them” than there are of “us.” In fact, there are nine cells of this “foreign” microbial life for every one of your own cells.

These microbes reside in pockets metaphorically referred to as internal “rain forests” or “hidden zoos”—swarming with activity and sending signals to your brain and other tissues, greatly influencing how health unfolds. These pockets of microbial life are called “biomes.”

The most well-known biome occupies the warm, moist, nutrient-rich large intestine,known as your colon. This colonic biome is called the “microbiome.”

Your body has numerous biomes.

There are active biomes throughout your entire intestinal tract—inside your mouth, oral cavity and saliva, inside the stomach, small intestine, esophagus, liver, gallbladder, and bile ducts. You also have biomes inside your nasal cavities, breast tissue (in both genders), vaginal vault, placenta, seminal fluid, lungs, skin, and emerging research is demonstrating biomes in your brain and eye terrains. Cancerous tumor cells have their own biomes, too.

The combination of all the microorganisms that reside on or within all human tissues and fluids is collectively called the humanmicrobiota. Besides bacteria, fungi, and viruses, your microbiota is now known to house two new members, archaeaand protists. These are single-celled organisms that are just gaining recognition.

So the human microbiota, this influential foreign life within and on us, is more than only the bacteria we think about when we consider probiotics (healthy bacteria in a supplement form) and prebiotics (food that healthy bacteria eat).


Biomes “cross-talk”

They communicate. They affect each other. For example, healthy biomes send healthy messages to each other, acting synergistically to maintain overall biome health.

In contrast, unhealthy hidden pathogens proliferating deep within one biome can adversely effect other biomes. For example, your nasal biome, inside your sinuses, can be swallowed 24/7 and contribute to gut biome problems like SIBO in your small intestine and dysbiosis(more bad bugs than good bugs) in your large intestine. Thus, digestive woes may originate “up your nose.”

Your lung biome can affect your gut biome, and vice versa. Your vaginal (and perhaps prostate) biomes may influence your microbiome. And vice versa. Sometimes a woman’s recurrent vaginal yeast infections are being chronically “seeded” from candidiasis infections inside her colon.

Your gut biome might negatively cross-react with your immune system in your gut wall, and promoting widespread seemingly diverse issues from recurrent infections, mood and behavioral issues such as autism, or even suffering with sleep apnea!


Biome Beat

This “biome beat” —your microbial life-sending signals that influence other regions of your microbial life, affecting diverse tissues and overall health —is what I call your biome rhythm.

This cacophony of conversations between biomes at diverse locations throughout your body influences multiple levels of your health. Biome cross-dialoguescan affect mood, immune function, nutrient status, hormone health, cognition, perception of pain, and even your ability to stay well or fight off diseases like autoimmune disease, inflammatory bowel disease, cancer, or dementia.

As known job descriptions for biomes increase, scientific research is experiencing a biome madness. Research is hot and heavy.


Why doesn’t your immune system fight foreign biomes?

One question that arises is how an immune system, which normally “fights off” microbial infections by mounting vigorous immune responses, allows life-long colonization of these biomes throughout your entire body. Why doesn’t our immune system “kill” this foreign life? Since humans have powerful immune systems, how do these bacteria, viruses, and fungi flourish and remain with us? And how do these microbes keep from stay “good” and avert going “rogue?”

Three sets of scientists wanted to answer these questions. Harvard, Houston, and California researchers approached this issue by studying Bacterioides fragilis, known by its nickname: B. fragilis.

B. fragilis is a common “good bacterial” player, normally found in abundance in a healthy gut. A California Tech lab had already shown that when B. fragilis is growing robustly in the colon, it protects against neurologic diseases and inflammatory gut changes. It’s a defensive good bug. But exactly how does it form healthy colonies and how does our immune system allow it to flourish? Inquiring minds wanted to know.

These scientists used electron microscopes that allowed them to visualize that B. fragilis is produced and held in clumps inside niches immediately next to gut wall cells (epithelial cells), deep inside the thick layers of mucus that surround the gut wall. When enough B. fragilis hang out within these niches, they form healthy proliferating communities.

Why doesn’t our immune system stop them? These scientists found out that our immune system actually does the opposite: it “enables” them. How? B. fragilis proliferates by having supportive healthy “chit-chats” with our antibodies, the active soldiers in the body’s immune army, made by white blood cells.


Immune System as Enabler of Biomes

Secretory Immunoglobulin A (SIgA) is a protein, an immunoglobulin also known as an antibody, that “licks” what arrives inside you (your gut lumen) from the outside world in the form of food. As SIgA licks what arrives, it then “decides” if what it tastesis “friend” or “foe.”

You have SIgA antibodies throughout all your mucous membranes to protect you from bad stuff that might gain entry. But SIgA doesn’t fight B. fragilis. Not only does it lick B. fragilis and decide it’s not a foe, SIgA allows B. fragilis to stay hidden in its niches, where it lays low to protect you from inflammation.

In fact, SIgA assists B. fragilis to stay anchored to the epithelial surface. This ensures that B. fragilis will multiply and thrive.


Good Biofilms

B. fragilis wears a “coat.” This coat is a matrix surrounding the bug’s body (so to speak), often referred to as a biofilm.Most biofilms are thought to protect “bad” pathogens from our surveillant immune system. In this way biofilms have been thought of as ominous characteristics of pathogens that contribute to disease.

But our antibodies realize B. fragilis is a protective player—and that its biofilm is not dangerous. As the Beatle’s song says, your immune system can simply allow bugs it deems good, to . . . “Let them be.”

By the way, B. fragilis’s healthy biofilm is made up of carbs. Not all carbs are bad. Signals from the immune system allow B. fragilis to be anchored to the gut wall by the “carb-covering” sticking to the epithelial niche.

The study of immunology has historically been in the context of pathogenic (dangerous) bacteria and their dangerous biofilms. The focus has been on how our immune systems defend us, trying to not let bad bugs do us in.


New Job Description of Immunity

But biomes are giving us a brand new perspective of our immune system. The immune system is not just a defense system, it’s now also being seen as a biome promoter system. The human immune system has an active “immune recognition” of beneficial bugs that “helps” biomes rather then “hinders” them.

In this new perspective of immunity, antibodies are more than weapons; they are collaborative “signalers” to biomes.

A healthy gut, containing healthy amounts of B. fragilis, puts you at less risk of neurologic disorders like Multiple Sclerosis and fewer gut issues like ulcerative colitis, Crohn’s disease, or even recurrent diverticulitis (infected pouches in the lining of the large intestine).

Just as one bad apple can adversely affect good apples, it’s becoming clear than any “bad” biome can make a distant biome ill. And is a suggestion of an immune system that is not enabling good microbial life because it’s distracted by chronic infections elsewhere.

Forward-thinking functional docs now consider taking nasal swabs, testing for fungi and bacterial infections in the sinuses as the origin or major contributor to chronic dysbiosis further south in the colon, or infections in far off, seemingly unrelated tissues, like chronic vaginal, skin, or respiratory infections.


Biome Summary

The critical point is that biomes influence distant biomes and distant tissues.

  • We have biomes throughout our bodies.
  • Biomes cross-talk.
  • Biomes cross-talk with our antibodies.
  • Life is about healthy conversations.
  • An in-the-know practitioner should be assessing how these conversations are working “for” or “against” you.

As a practitioner, I measure the level of your SIgA in a comprehensive stool test. This gives me an idea of how well you are care-taking your B. fragilis and other healthy gut microbial life.

A body with excessive unhealthy inflammation, can put your protective SIgA, and thus your biomes, at risk.


Inflammation vs. Biomes

Where can unhealthy inflammation come from? You can have excessive inflammation if you are fighting cancer, just finishing radiation, going through an autoimmune flare, in the middle of a major depressive disorder, under severe stress such as a court battle or relationship woes, if you are battling an acute flare up of any disease or severe injury. All these types of life events can elevate the level of inflammation inside your tissues.

Inflammation is often diagnosed by inflammatory “markers,” such as sedimentation rate, the number of your platelets in your blood, your level of ferritin, and another pretty well known marker called “high sensitivity C reactive protein” (hs-CRP).

When your hs-CRP rises, this demonstrates that your body is awash with inflammation.

Where does this extra CRP come from? The CRP molecule is a protein. When it elevates, it needs to make more of itself. It does this by scavenging proteins from your SIgA. As your inflammation rises, and your hs-CRP rises, it does so at the expense of lowering your SIgA.

The lower your SIgA, the more your gut wall thins. This is called gut atrophy, or gut wall thinning. Seventy to eighty percent of your immune system lives inside your gut wall. As your gut wall thins, immune function wanes. Less SIgA means less enabling of healthy microbial life. Good gut bugs like B. Fragilis, wane in number. This leaves you more vulnerable to disease.

You wake up one morning and the doctor says you have this disease or that. But for a number of months or years, the processes mentioned above were going on silently. But you and your doc didn’t know this.

As inflammation mounts and your hs-CRP elevates, your gut wall thins (gut atrophy), your SIgA wanes, and your ability to keep “licking” molecules to ascertain a threat or not, and inform your immune system or not, falters. And healthy microbes are less enabled to keep growing and having sustainable protective communities.

Illness seems to have come out of nowhere. But it’s been a hidden but active process.

The good news is that with nutrients and other functional medicine approaches, we can plump these immunoglobulins and your gut wall thickness and function back up again. And promote healing.

Isn’t functional medicine grand? It’s about fixing what’s wrong at the deepest cellular levels to try to achieve lifelong fixes. Not quick ones.

Allopathic medicine is great in the ICU and ER and with hip and eye surgery. But often with chronic health issues, it’s sadly only a Band-Aid. It uses meds to keep your symptoms, inflammation, and suffering at bay. But it’s not addressing gut wall thickness or rebooting your good immunoglobulin and gut wall function or your good bugs like B. fragilis, to get you well at a “root cause” level. And keep your biome madness serving you rather than adding to your suffering.

When you are diagnosed with an illness, you want to get rid of your pain and suffering, of course. But your main goal should be getting well once and for all. For example, insufficient SIgA is linked to other autoimmune diseases, not just M.S., like autoimmune thyroiditis or rheumatoid arthritis, type 1 diabetes, and more. In many of these diseases, suboptimal levels of SIgA and a thinned gut wall sustain illness rather than allowing you to put it in your rear view mirror once and for all.

You are a world unto yourself. When something goes wrong, it doesn’t make sense to protect this entire dynamic globe with a Band-Aid. You want to know where the problem is actually coming from and stop it at the source. Does part of your perfect “disease storm” come from consuming excess processed food, doing a poor job of digesting whatever you eat, mold exposure, or stealth infections (hidden infections that are distracting your immune system and damaging your biomes but you don’t know these battles are going on)? Assessing these potential contributors to illness is essential to getting well.

So is your air. What you breathe affects your health. And your biomes.


Pollution vs. Biomes

Recently the World Health Organization wrote that the planet’s air is toxic. The discussion further described how toxic air is a major contributor to diverse diseases from diabetes to cancer to dementia. And, hold on to your hats, air pollution is also being linked to “biome damage.”

Two Departments of Medicine in Canada have linked the rise of inflammatory bowel disease with urban air particulate matterthat is ingested through food and damages the SIgA/healthy bacteria cross-talks mentioned above.

Particulate pollution damages your biomes and makes it difficult for B. fragilis to prosper. Particulate pollution has been shown to damage intestinal barrier function and promote leaky gut.

Some of my gut patients are exposed to a perfect storm that manifests as ulcerative colitis or Crohn’s disease after moving into a new home that is right next to a major freeway, or after remodeling an office and being exposed to conventional materials and lots of unhealthy “out-gassing” from them.

Thus, part of total healing, even of your biome—aside from specific meds, probiotics, prebiotics, nutraceuticals, and foods—is finding out what might be “bad” in your air that’s bad for your biomes and taking steps to fix it.

  • We are intertwined. As above so below.
  • The earth’s body affects your body.
  • Your home air affects your body. And your biomes.

Much of us think of pollution as haze or out-gassing chemicals. Particulate matterpollution is poorly appreciated or understood. Particulate matter damages your biomes, and is being linked to an increased risk of respiratory diseases, dementia, infertility, cognitive and behavioral issues in kids, early adverse brain changes in kids, and more.

Be smart.

Control as much of the air you breathe as possible.

Spiritual leaders have been saying for millennia, we are all one. Turns out our microbiome is one with the world we walk through. True healing starts with awareness of this bigger picture.

Caretake your air.

Caretake your gut.

Caretake your biome rhythms.


Pollution Protective Resources

  1. You can get particulate matter pollution measured in your home by the amazing elbow grease of Terry Wright, CEO of pureairdoctor.com. Mr. Wright has recently launched a system to analyze your air (mold gasses deep in walls or pipes, volatile organic pollutants, and particulate matter) and then give your reasonably priced solutions to keep your home air (the air you have control over) safe for the brains, nervous systems, gut walls, and biomes of all your family members. Terry’s new home analysis system is called the ETA (Environmental Toxic Assessment System).

You get sent a box with what looks like two Alexa units and Terry helps you figure out where to put them in your home to start sleuthing out your air. If you use my code, you get discounts and free shipping; Terry made it even gentler on your pocketbook because you are part of my beloved tribe.

Berkson Pure Air doctor HEALTH PARTNER CODE: 247

Wright Way Environmental Technologies, Inc.


Email: [email protected]


  1. Check out my podcasts:
  1. If you want to dive deeper into biomes get my new 4.5 hour course, called Breasts, Biomes and Food.



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