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Pathogens: A Main Cause Of Illness & Aging?

“Our world is awash in microbes.”

Microbes thrive anywhere and everywhere in our world.

Can these microbes live in — and affect — our body’s health? Absolutely.

In fact, many scientists believe aging should be considered a disease — with pathogens playing a main role. Why?

Microbes can be found in our blood and tissues even before birth. Yet, in the age of antibiotics — and fewer deaths due to acute infection — we’ve forgotten that we absolutely live in a microbial world.

Surprisingly, there’s a wide variation in total microbial load inside each person.


Some people have three times (or more!) the bacterial DNA circulating in the body as other people. Thus, you and I may have hugely different pathogenic loads for our immune system to deal with. A higher pathogenic load certainly means more inflammation, insulin-resistance, fewer nutrients absorbed, higher bodily toxicity and hormonal dysregulation.

As we age, we see rising levels of bacterial toxins in our bloodstream and tissues.

“With the passage of time, the barriers responsible for keeping microbes out of us weaken.”

When our microbiome isn’t healthy, pathogens can directly suppress the immune system in order to survive — leading directly to a higher microbial presence in the body.

Your body’s microbiome depends on three things:

Science is beginning to understand the factors that influence your body-wide microbiome.

  • Your Environment
  • Your Habits
  • Your Immune Health

As humans, we have multiple microbiomes in and around the body. Our environment, habits, and immune system determine the health of these microbiomes.

Let’s explore how pathogens function in our world, how they shape our delicate microbiome, and what we can do to optimize our health, longevity, and recovery from chronic illness.

Microbes appear in every corner of human life, and microbes affect every aspect of human life.


Nature’s Microbiome

Did you know the entire world is one big microbiome? However, its characteristics change in each smaller location.

Let’s take a quick look at the microbiomes of the natural world we live in.

A Self-Regulating Microbiome

Nature is abundant with microbial life.

Microbes are (mostly) bacteria, fungus, and viruses — but they never grow unimpeded in nature. The outdoor microbiome is regulated via the following natural elements.

Microbiomes In Nature…

UV Light

UV light sterilizes exposed surfaces. Daily sunlight continually reduces the microbial count across the ground.


Ozone is known as “nature’s sterilizer.” It’s created by oxygen and light and kills microbes on contact.

Visible & Infrared Light

Visible light and heat kill or inhibit the growth of microbes. Microbes prefer darkness and moderate temperatures.

Microbial Diversity

Microbial diversity prevents any single species from dominating an environment.


Rainfall rinses surfaces and then evaporates or runs downhill, preventing stagnation.


The Indoor Microbiome

Microbially, the indoor environment is very different than the outdoor environment.

Completely Unregulated

Buildings do not have these natural elements — UV, ozone, or rainfall — to keep them clean. It’s dark inside walls, crawl spaces, attics, and closets.

Instead, buildings rely entirely on humans to maintain them.

Microbiomes Indoors

A Moist Building Is A Sick Building

Microbes only need one basic thing to thrive in our buildings: Moisture.

Modern building materials provide ample food for microbes — Just add moisture.

A Dry Building Is A Healthy Building

Clean, dry indoor habitats don’t let microbes grow.

Sure, microbes still abound indoors. They shouldn’t be thriving, but they’re absolutely still there.

All Buildings Have Microbes, Yes…

Researchers have discovered that there are similar numbers of microbial species 1) on indoor furniture and 2) in the Amazon rainforest.

So, microbial species are absolutely present indoors. If moisture is also present, nothing stops microbes from flourishing in our buildings.

Moisture Is Everywhere

Water is everywhere we look in buildings.

Water enters buildings via: plumbing pipes, air conditioners, sinks, drains, and washing machines.

Rainfall searches for a way inside: through roofs, gutters, windows, fireplaces, and at the foundation level.

85% of buildings had past water damage and 45% had current water leaks.

Hospitals Aren’t Sterile

Hospitals employ rigorous steps to filter air and kill pathogens, yet microbes are everywhere researchers look.

Underneath the bright lights and on the stainless steel gurneys lives a large community of microorganisms.

A separate study found that shower heads were also populated by opportunistic potential pathogens that are significantly different from microbes found elsewhere in patient rooms. These bacteria tend to form biofilms, persistent colonies of microbes… and can be next to impossible to kill.

Even Sterile Rooms Aren’t Sterile

Even in scientific “sterile rooms” we find that sterility is nearly impossible.

Microbes are incredibly stubborn and hardy. It can be very challenging to completely kill them.

‘“It’s very hard to clear out all of the microbes from a particular ecosystem,” Eisen says. …Simply put, sterility doesn’t exist.

Rethinking Sterile — The Hospital Microbiome

To Flourish, Microbes Need:

Hospitable living conditions:

  • Moisture In Buildings
  • Inside Humans


Humans “Shed Microbes Wherever We Go”

The human body is a walking zoo of microbial life — for better or worse.

‘”Most of the microbes present in the hospital environment, however, arrive via humans, whether brought in on the soles of our shoes, on our cell phones, or our bodies themselves. Like Pigpen’s permanent aura of dirt in the “Peanuts” cartoon, humans are surrounded by a cloud of microbes. “Humans shed microbes wherever we go,” Gilbert says.

The Human Touch

A human is transferring microbes to the environment. Every object we touch, the furniture we use, and the floor underneath us receives microbes when we use the space.

“Each time we touch an object, we can (and do) transfer millions of microbes from our body to the environment. Because the types of microbes available to be transferred vary from person to person and body part to body part, different surfaces are likely to host different species. Objects such as computer keyboards, light switches, and soap dispensers are continually reseeded with microbes from our hands each time they are touched. Restrooms, on the other hand, are dominated by microorganisms associated with the gastrointestinal and urogenital tracts.”


Indoor Items Acquire Microbes

The Classroom Study

One study analyzed the microbiome of a classroom, with surprising findings: Each surface was home to a different combination of species, depending on how humans touched the surface:

  • Floors had outdoor species from shoes.
  • Chairs had microbial species from — literally — our digestive and urogenital tracts and skin.
  • Cell phones, light switches, and keyboards were populated with microbes from the hands (and whatever they touched).

“Your” Hospital Room

Back in the hospital, researchers found that a room’s microbiome was rapidly affected by the people in the room.

Within hours of a new patient’s arrival, the microbes in a room changed to reflect the composition of the latest inhabitant. “Within hours, the new person’s microbiome became the dominant force in that room.


Indoor Microbes Aren’t Thriving, They’re Waiting

…Waiting For Better Conditions

Microbes in clean, dry buildings mostly just want a more hospitable place to live.

The built environment appears to be more of a waiting room for these potentially harmful bacteria until better conditions are present.

In a well-maintained and well-designed building, microbes lack needed moisture and food to eat and grow.

The microbes in healthy buildings are surviving — but they’re waiting for better conditions.

What might “better conditions” look like for a microbe? Where might they go?

Moist buildings provide good conditions for microbes. Are people also “good conditions?”


Environmental Microbes Colonize Humans

…for better and for worse.

Your Room, But “Its” Microbes

We don’t simply “seed” the buildings we inhabit — they “seed” us, too.

We, as humans, acquire our personal microbiome from our environment. Unfortunately, as we’ll see, not all environments have a healthy microbiome.

More can be learned about how built environment design influences proliferation or transmission of such infectious microorganisms.
Key Takeaways
  • The health of a building directly impacts the health of its occupants.
  • How buildings are designed (and maintained) controls whether a building is “healthy” or not.


Environmental Microbes Colonize…

The Gut

You can improve the health of your gut microbiome.

To truly thrive, microbes need a warm, moist place with ample food supply. Fortunately for them, the human body is meets all of those demands. The main residence for microbes: The human digestive tract.

The Infant Study

In this study, stool samples taken from infants in the NICU reflected the same microbial species present throughout the NICU.

‘Brooks and colleagues collected fecal samples from the NICU newborns every three days. For each fecal sample, they also collected 33 environmental samples from around the NICU. The main species of bacteria they found in the infants’ guts (Staphylococcus epidermidisKlebsiella pneumoniaeBacteroides fragilis, and Escherichia coli) were found throughout the NICU, suggesting the hospital environment may have been the source of these microbes.

This finding suggests the microbes in the hospital were directly colonizing the digestive tracts of the infants — and it didn’t take long to happen, just mere days.

Environmental microbes colonize the guts of humans of all ages.


Environmental Microbes Colonize…

The Mouth

You can improve the health of your mouth’s microbiome.

Nine areas of the mouth have distinct microbiomes. Image:

There are between in 200-300 microbial species in the typical mouth.

Roughly 100 billion organisms can be found in a single gram of dental plaque.

Dental plaque and the surface of the tongue are among the densest microbial habitats on Earth. Bacteria are pretty much wall to wall in there.

The simple act of eating, drinking, and breathing means we take in “all of the other microorganisms from the planet.”

From The Mouth… To Gut

All those microbes in the mouth travel straight to the gut, anytime we swallow.

A Trillion Microbes Swallowed, Daily

Every day, people swallow more than a trillion microbes, but only a small fraction of these bacteria is able to survive the digestive juices and thrive in the gut. The transmission of bacteria along the gastrointestinal tract has long been associated with diseases such as colorectal cancer and inflammatory bowel disease. Now, scientists have found that even in healthy people, many mouth microbes are able to reach the gut and colonize it.

Down the hatch — We swallow trillions of microbes each day.

Environmental microbes certainly colonize the gut in healthy people, swallowed via the mouth.

Unfortunately, in chronic illness and aging, stomach acid weakens. This allows a higher percentage of microbes to survive and reach the gut.

A common mouth bacterium known as Fusobacterium… can enter the body through the cheek cells, and it probably gets into the colon just by being swallowed.

Folks living and working in a sick building experience an elevated number of harmful microbes being swallowed — and surviving to the gut.

There’s an intimate link between the health of your environment, your gut, and your mouth.

Microbes Colonize Poor Dental Work

It is not uncommon for dental work to be performed in such a way that allows microbes to reside inside your tooth.

Wisdom teeth extraction can result in something called “cavitations” where microbes become trapped in the socket and the continue living, inside the gums, after the wound heals over. This infection seems to be able to cause broad, mysterious health problems as the microbes continually enter the bloodstream, causing infectious symptoms.

Root canals are commonly considered risky, simply because they leave dead material in the mouth. Dead material cannot be regenerated and has no immune function. Therefore, these areas are prime real estate for microbes to find safe harbor — and from there attack the rest of your body.


Environmental Microbes Colonize…

The Nose

You can improve the health of your nasal microbiome.

The quality of air you breathe directly affects the microbiome of your entire body.

Breathing Traps Microbes

Your nose is essentially a filter, removing all manner of tiny stuff from the air.

During [breathing], the [nasal] airways are exposed to pollutants, aeroallergens, microbes, and fungal spores.

Nasal inspiration… extracts dust, bacteria, and other contaminants from [the air].

Blowing the nose is essential for removing these microbes, but it cannot remove hardy pathogens completely. In the immune-suppressed body, the nose is an incredibly hospitable home for pathogens.

Two Important Variables

The health of your nasal microbiome is affected by your 1) environment and 2) your personal hygiene. An unhealthy nasal microbiome is correlated with many other important diseases.

A Better Nasal Microbiome Improves The Whole Body

According to Dr. Gerald Berke, chief of head and neck surgery at UCLA, folks struggling with chronic infection (and allergies) have “tremendous” improvement from once or twice daily nasal rinses [source].

Physical removal of pathogens via nasal rinsing is the single most effective tool for improving the nasal microbiome.

Other nasal products like Xlear sprays are also very important for keeping the nasal passages clear — and can demonstrably reduce pathogen count in the nose.

Xylitol significantly reduces the number of bacteria in the nasal passages.


Environmental Microbes Colonize…

The Skin & Scalp

Healthy Skin Microbes Should Create A Barrier Against Pathogens

Healthy skin is an excellent barrier against the outside world — keeping microbes, toxins, and other substances outside your body.

Your skin is “colonized by a diverse collection of microorganisms — including bacteria, fungi, viruses — as well as mites.”

Our skin is always shedding dead skin cells, which feed microbes.

“Symbiotic microorganisms occupy a wide range of skin niches and protect against invasion by more pathogenic or harmful organisms.”

Bathing does not fully remove these microbes from the skin, and as soon as we leave the shower, the skin is exposed to more environmental microbes.

Air Quality Harms Skin Barrier

Poor air quality, too, causes inflammation in the skin and results in the skin’s barrier becoming more permeable — letting microbes into the body and bloodstream.

Therefore, sick buildings and toxic work sites can harm the skin and body via elevated skin permeability, inflammation, and pathogenic exposure. This will be especially important for those struggling with chronic illness, and aging.

The Scalp Microbiome

The scalp is densely populated by microbes, is especially oily, and is notoriously difficult to truly clean.

Fungus seems especially comfortable living on the scalp. One 2018 study found that:

Bacteria On Scalp

Typical bacteria contributed to scalp health by synthesizing biotin, other B-vitamins and amino acids.

Fungus On Scalp

Fungi on the scalp were “takers” of nutrients from the scalp.


The scalp also appears to be an easy entry point for microbes to enter the body. Acne and scabs on the scalp can be clear signs that unhealthy microbes are residing in the area. Spending time in sick buildings is a main risk factor for the scalp microbiome.

Continue reading for steps to improve your scalp microbiome.


Dysbiosis Anywhere Weakens The Whole Body

Symbiosis -vs- Dysbiosis

A healthy microbiome means that microbes are working synergistically with the host’s body. The population in any microbiome needs to consist of mostly beneficial microbes and with very few harmful pathogens.

A healthy microbiome is in a state of ‘symbiosis.’

However, keeping pathogens at bay in our body’s microbiomes can be a difficult task — especially as we age or deal with chronic illness.

As a result, pathogens become more active in our microbiome, spreading around the body and wreaking havoc: causing inflammation, toxicity, nutrient malabsorption, hormonal disruption, circadian disruption, and more.

An unhealthy microbiome is in a state of ‘dysbiosis.’

Microbes Spread

The microbes in any microbiome hardly stay put. They grow, multiply and look for better opportunities to thrive.

Therefore, our body’s many different microbiomes are each connected to each other. Microbes from one travel all around the body, attempting to populate the other microbiomes.

The body has many microbiomes: mouth, gut, nose, skin, ears, vagina, and more.

Dysbiosis in one microbiome will ultimately, spread to other microbiomes — as chronic exposure to harmful microbes works to undermine the system. That is, unless steps are taken to reverse the process and restore symbiosis in the body’s microbiomes.

Sick Buildings

Sick buildings are becoming commonplace around the world — and with them comes elevated exposure to pathogens (harmful microbes).

Water-damaged buildings saturate their indoor space with fungal mold spores which readily live in nasal passages and colonize the mouth and gut. Mold also releases toxins that greatly harm the body.

Modern humans spend more time than ever indoors, breathing recycled air and exposed to a different set of microbes than our ancestors.

Seeing that we spend so much time indoors, we must make sure we are not doing so in a sick building. The results can be devastating to the entire microbiome and lead to many health challenges and diseases.


How To Improve Your Microbiomes

You can directly improve your microbiome via your habits.

The best news in all this? Microbiomes are not static. You can absolutely change yours.

The most critical is almost certainly the gut, and I recommend you start there. If that feels daunting (sometimes illness causes poor tolerance of gut supplements and foods), start with your mouth and nasal health.

Your environment is also an incredibly powerful way to transform your microbiome. The first step to improving your environment? Spending significant time outside each day.

Improving The Gut Microbiome

Restoring the health of the gut may seem like a terribly complicated process, but it really isn’t.

What matters is that you make “bad” microbes (pathogens) uncomfortable, while introducing and feeding “good” microbes (probiotics).

Therefore, focusing on light and heat, sunlight, gentle movement, the circadian rhythm and nutrition are excellent additional steps. They each boost blood flow and significantly boost immunity.

A Gut Supplement Regimen

A gut supplement regimen is also an important step, and it should consist of three components:

  • Prebiotics
  • Probiotics
  • Natural Antimicrobials
  • (IN WORST CASES: Prescription Antibiotics)

If your gut health is poor, you lack good microbes and have too many pathogens. Taking probiotics introduces good microbes, taking prebiotics can feed those good bugs, and natural antimicrobials help make the gut more hostile to pathogens that have gotten too comfortable.

When Nothing Else Works

In the worst of cases, it may be essential to do some sort of liquid fast for a few days, and take a combination of gut supplements to help remove problem microbes. Over time, the balance in the gut can shift to reflect a healthier microbiome.

If the liquid fast and gut supplement regimen doesn’t work, or is intolerable, prescription antibiotics may be necessary. Typical antibiotics and/or antifungals may be required. After the course of antibiotics, it’s imperitive that a strong gut supplement regimen is incorporated to continue building up the good flora in the gut.

Remember, the circadian rhythm, movement, light and nutrition all greatly impact the gut. Do not neglect these habits!

Improving The Mouth Microbiome

The Nose

  • Clean mouth after all meals or snacks
  • Products
  • Daily rinse, sprays

The Skin & Scalp

  • Medicated shampoos
  • Sunlight
  • Infrared Therapy
  • UV Therapy

Your Environment

  • Home
  • Work
  • Automobile
  • Get Outside A Lot

Other Places

  • Ears — Garlic oil?
  • Vagina — Probiotics

Proteins produced by microbes may interact with human cells and potentially function in altering barrier protection to the external environment.

The microbiota, which is the community of fungi, parasites, viruses, and bacteria, may increase mucosal barrier function through pathogen exclusion and activation of the innate and adaptive immune system

That microbial infections can influence the development and severity of allergic diseases is well established. Examples include Staphylococcus aureus or herpes simplex infection in atopic dermatitis (AD) and various respiratory viral infections in asthma. 

Damp building conditions promote the growth of mold, bacteria, and other microbial agents. Damp buildings may also contain other living organisms, such as dust mites and cockroaches (along with their associated microbial communities)

By separating themselves from the outdoors, humans may have eroded the diversity of their own, as well as their environmental, microbiomes.

In developed areas of the world, humans are born and spend the vast majority of their lives indoors, which may limit the diversity of microorganisms to which they are exposed. A building’s envelope (foundation, walls, windows, and roofs) separates the indoor and outdoor environments, thus reducing exposure to microorganisms that thrive outdoors and potentially increasing exposure to organisms that thrive indoors.

The diversity of the microbiomes of the built environments in which humans live may impact the microbiomes of their bodies. Studies have shown that humans who spend significant time outdoors or live in dwellings with more open building envelope designs that result in high levels of unfiltered or minimally filtered air exchange with the outdoors have more diverse microbiomes relative to those who live in dwellings with less open designs (Clemente et al., 2015Hanski et al., 2012).