Farming Your Biomes

The human biome is the community of microscopic organisms we carry around with us on every surface of our bodies, inside and outside. Almost all of them are important even if their presence just serves to crowd out pathogenic organisms. When everything is working well, the immune system keeps them in a careful balance between them and our own body cells. Many make a beneficial contribution to our well-being but sometimes unhelpful strains come along, similar to weeds, and upset the balance, make us sick, or even kill us.

Rather that let them grow wild and hope nature treats us well, we can actively care for them just as a farmer cares for his crops. Or we can also devastate them, similar to spraying agent orange on a forest. We can leave the gate open and let the wolves in to eat the sheep. In fact, most of us periodically poison them, carelessly taking large doses of antibiotics to treat a virus, or washing them with strong disinfectants and detergents like the beautiful people in the soap advertisements.

If we are smart, we can tend them and make a beautiful garden, or we can ignore them and create a briar patch.

Different Care for Different Biomes

Where Are They?

We actually have a lot of biomes, the environments where microbiota exist. They merge into one another following the contours of our skin into cavities and openings to our interior. They merge at the boundary of our skin into our nose, mouth, or ears on our top side and similarly into the orifices of our southern extremities. Colonization of every surface, internal or external, is highly variable depending on the nutrients available, health and immune system of the host (you), and physical effects like scrubbing, water, or chemicals.

The surfaces upon which organisms grow have one thing in common. They prevent our “friendly” organisms from invading into our inner spaces such as the blood vessels, brain, gut cavity, and joints. If they somehow penetrate the barrier, not all remain friendly.

The skin is one such barrier. Below the skin, our immune system constantly attempts to beep things in balance. When the barrier is breached, inflammation starts a complex process of containing the invading organisms or substance and repairing the damage.

Where the skin stops and continues into the openings such as our mouths and noses, the surface changes into a different kind of barrier called mucous membranes . Our gut, lungs, nose, mouth, and private parts are all lined with mucous membranes. Each has a different purpose and each needs to be cared for differently.

Biomes on the Skin

The skin is our largest organ. It has hundreds of different colonies of organisms that differ from person to person.

Every surface of the skin has its own unique colony. We ignore most of them until something goes wrong. For example the area between the toes of the feet is teaming with organisms. Sometimes fungi take over and we suffer from an infection we call athletes foot. When that happens, the organism invades through the skin barrier. Otherwise we just have normal stinky feet, which is also a product of organisms eating their food between our toes and excreting foul smelling volatile organic compounds. Good foot hygiene consists of doing things to keep the feet healthy. There is even a medical specialty called podiatry to help with the feet.

Another unique skin biome is in the arm pits. The skin in this area contains several types of glands, sometimes called sweat glands because that is one thing they produce. The major secreting glands are called ecctine, apocrine, and sebaceous mainly depending on their supposed type of secretions. Eccrine glands mostly excrete watery sweat that evaporates to keep us cool. Apocrine glands excrete water plus some oils. Sebaceous glands are associated with hair follicles and secrete oily substances.

While it is indisputable that sweat secreted from these glands serves to help us regulate our body temperature, the evolutionary origin, purpose, classification, and physiology of these glands remain a subject of debate.

Microorganisms thrive on the moisture and the oils. Stinky armpits is one reason people pay attention to the armpit microbiome. More often than not, a commercial product or perfume is applied to reduce the amount of water secreted or to mask odors. It may not be the best strategy.

Skin areas that have extra moisture have an increased number of organisms. The crotch is an obvious example. Smaller areas include skin folds, behind the ears, in the ear canal, eyelids, the crease at the side of the nose, and inside the navel to name a few.

One way to identify areas that have a lot of microorganisms is to simply rub an area and sniff it. If your senses are good, you can smell the difference between areas and even the right side and left side of the same areas.

In addition to visible surfaces, skin has microscopic openings like hair follicles that have very different colonies of organisms, even including tiny parasitic mites called Demodex folliculorum. Farming this part of your biome should include getting rid of the mites without killing good organisms or poisoning yourself.

Biomes of the Mucous Membranes

When you follow the skin into the mouth, nose, or other bodily openings, you go into the land of mucous membranes. The transition from skin to mucosa in the nose (nares) happens at about the distance you can poke your finger in to “pick” your nose. Up to that point, the skin has hair, the environment is moist, and it hosts microbes that can’t survive on the outside surface skin.

Mucous membranes are considerably thinner than skin and are adapted to absorb nutrients, water, or air into the blood stream. They also have mechanisms to keep the bacteria at bay, keeping them on the outside while allowing substances to pass to the inside.

The organisms found in the different regions of the gut, or lungs, or nose gradually change as the function of the mucous membranes changes. So in the nose and lungs, organisms that tolerate oxygen predominate, while in the large intestine, a vast number of bacteria exist, some that tolerate oxygen and others that oxygen kills. Keep in mind that it is not just bacteria that live on mucous membranes; it also includes fungus,viruses, and parasites.


The stomach is a marvelous place. We commonly think of it as a place to catch the food we eat, and then mechanically and chemically break it down. But it is also like a Venus fly trap. It catches and kills bugs.

Its low pH (1-2) means it is highly acidic. Think of pH as the “power of hydrogen.” Hydrochloric acid (HCl) in the stomach not only breaks down the molecular structure of the food we eat, it kills most living things we eat too. Most but not all!

The large intestine contains more bacteria per square inch than almost any place on earth. How did they all get there? How did they get past the stomach?

Although highly acidic and toxic to most organisms, stomach acid is easily diluted or neutralized by our actions. The questionable habit of taking antacid tablets or proton pump inhibitors, may provide temporary relief from eating the wrong thing, it can also serve as a high pH path for bad bugs to get into your lower gut. The same thing happens with overeating, also called gluttony, one of the seven deadly sins.

Even if you are careful and don’t overeat or take antacids, there a a few microbes that can actually live in and around your stomach. The amazing bacterium Helicobacter pylori (H. pylori) is one you can pick up in childhood, live with all your life, and maybe not even suffer from the ulcers that it causes in millions of people. In fact, perhaps as many as half the world’s population may be infected with it. Infection is the correct word to use with H. pylori because it is not a friend. Fortunately now doctors are looking for it and can kill it with antibiotics, along with a lot of your friendly bacteria. Nevertheless the collateral damage may be worth it and you can carefully nurture your good bugs back.


Major rule for skin biomes: Leave us alone!

The primary objective of skin care is to keep the barrier healthy and intact. Yet people carelessly allow the skin barrier to be breached. An obvious breach is when it is cut, scraped, or blistered. Fortunately, the skin can adapt to constant physical abuse by thickening to form calluses. It can adapt instead of breaking down as it does with bed sores. But old age, smoking, pressure spots, immobility, and poor skin hygiene make it difficult to adapt.

Penetration by Chemicals

There is an interesting solvent called DMSO that demonstrates how careful we should be about what we allow to touch our skin. Within seconds of applying DMSO to the skin, many people can taste a garlic-like flavor in the mouth. Some solvents can breach the skin or allow other things to be carried through the skin. Two examples besides DMSO are ordinary alcohol (ethanol) and oleic acid, a fatty acid that we get in our “diet.” Health food fans know about oleic acid because its a big part of their favorite triglyceride in olive oil. A triglyceride is how mother nature tames fatty acids by hooking them up to a glycerol molecule.

unsaturated fat triglyceride (C55H98O6). Left part: glycerol; right part, from top to bottom: palmitic acid, oleic acid, alpha-linolenic acid.

Consider carefully the creams and salves and potions you apply to your skin. Many of them not only harm your skin, they also penetrate the skin and harm the real you inside your skin! Then when your inside is really messed up, the outside will show it.

Cosmetics manufacturers often include fatty acids and triglycerides as surfactants and opacifying agents in their preparations. Microbes, both friendly and pathogenic, have cell membranes and walls that surfactants can break those down. It’s OK to kill the bad ones but unfortunately surfactants are not selective; they disrupt the biome. Don’t hurt the good guys!

Nevertheless there are skin care products that act as a temporary barrier to help your skin heal from trauma and even assault from pathogens including fungus. Hint: the pH of healthy skin is around 4.5-5, slightly acidic making it less attractive to fungi.


Most teenagers suffer from skin problems as hormones change and they become careless about the food they consume.

Here is the best way to treat acne: Stop eating junk food. Starve if necessary, but eliminate sugar, simple carbohydrates, and all vegetable oils. If you know what simple carbohydrates and vegetable oils are, you will quickly realize that it is everything that you and most Americans eat. Increasingly it is what the rest of the world eats, and they too are getting acne, along with heart disease, cancer, and Alzheimers.

After you have corrected what you eat and you still have acne, go to a good board certified dermatologist. If she praises you for your diet, you know you are on the right track. Eating correctly may also help correct accompanying hormone problems.

Appropriate treatment will correct what your immune system was temporarily unable to correct. It should be relatively short term treatment to get the microbes and immune system back under control.

Washing Skin

Skin needs to be washed because … Well you know why it needs to be washed. And with soap, right?

Here is the problem (rub?). Skin produces protective oils. Skin also has bacteria that you need to protect. They get washed away by soap and detergents, but if the soap or detergent is on for a very short time. little damage is done. Different skin biomes can tolerate exposure to soaps for longer or shorter times.

Avoid so called “harsh” detergents containing powerful antibacterial chemicals like tetrachlorosalicylanilide (TCSA), and bactericidal cationic surfactants like benzalkonium and cetylpyridinium, among many others. Cationic surfactants have a high potential for pulmonary toxicity if inhaled.

Anionic surfactants aren’t as bad. They are still irritating to the skin but not as toxic to bacteria. Nevertheless they are common in various kinds of creams, toothpaste, shampoo, and even in prepared foods! They are everywhere so it’s hard to avoid them but you should use them sparingly.

Common Toothpaste Ingredients

One of the most common is sodium lauryl sulfate; also its cousin sodium lauryl ether sulfate. When using toothpaste, remember its the mechanical brushing that is most useful so use the toothpaste sparingly. Toothpaste foams and makes you feel and taste good. Fluoride may helpful too but not in excess. It is a metabolic poison.

Non-ionic and amphoteric surfactants are the least dangerous. Non-ionic surfactants like decyl glucoside don’t foam very well and adding an amphoteric surfactant like coco betaine helps make it foam. Consumers don’t seem to like soaps that don’t make bubbles. But think about it. Are bubbles really necessary?

Read the labels of products you use directly on you or in you. Get to know some of the long unfamiliar names.

(Continued in Next Column)


Minor Skin Biomes

Inner Nose and Mucosa of Nasal Cavity

The biome in and around the nose is a place where it’s easy to make mistakes. Most of the mistakes are because we have dirty hands and we pick at our faces and we pick our noses. Staphylococcus bacteria are commonly found on the skin or in the nose. Most of the time they don’t cause problems or result in relatively minor skin infections if we are careful. But when we aggressively squeeze pimples and pick the inside of our noses with dirty fingernails, the chance of developing nasty infections increases dramatically.

Because everyone picks their noses, its worth mentioning that there are 3 biomes to understand, the one under your fingernail, the one on the skin lining the inside of your nose, and the mucous membrane that is generally too far away for your dirty finger to reach. Everyone’s fingernails are loaded with organisms and it’s hard to know what is there at any given time. Where has your hand been? Assume the worse.

Your nostrils lead into the nasal vestibule, which leads to the nasal cavity behind the vestibule. Hair follicles inside your nose harbor different bacteria that on the skin or deeper inside the nose.

The nose is an important one to understand because soon after the skin (epithelium) inside the nose stops, you transition to a tender (non-keratinized) type of epithelium, and then on to mucous membranes in the nasal cavity. The organisms on each of these surfaces are quite different.

We aren’t going to suggest how to treat pimples or pick your nose. Just be aware that there is probably a better way that the one you learned when you were 3 years old. Now you know there are special biomes there that require special care.

Naval (Belly Button)

Seriously! Your naval has its own little biome. Put your finger in it and smell your finger. The bacteria produce that unique fragrance. It’s not disgusting as long as you don’t make somebody else smell it. Leave it alone.

It’s wise to avoid piercings anywhere on the skin, including the naval. The small biome in the moist naval environment isn’t big enough to withstand a lot of abuse. It can become infected with yeast, staph, or strep. Wash regularly to flush debris away but avoid detergents; just rinse thoroughly. If it gets infected, consult a dermatologist.

External Ear

Each ear has its own biome. Both sides are usually quite similar. It’s a small biome and is easily disrupted, usually by too much water entering the auditory canal, as when swimming. Both excessive moisture and trauma impair the canal’s natural defenses causing the infection called otitis externa.

Earwax effectively protects the auditory canal from harmful organisms. There are genetic differences between people who produce thin oily ear wax and others who produce hard wax. Hard wax producers soon learn to deal with wax, which can become too thick. Persons with thin ear wax have little to do but wipe excess water from the ears after bathing.

Sometimes an ear becomes infected chronically as opposed to a rather transitory otitis externa. Chronic seborrheic dermatitis of the ear canal is such a condition. In 1881, Dr. Lloyd Storrs demonstrated that this condition could be cured by transplanting wax from the opposite ear to the affected ear. Recurrent bacterial and fungal ear infections have been successfully treated this way by simple restoring the healthy biome.

Biomes of Mucous Membranes

A mucous membrane is a layer of cells that line internal body cavities including the mouth, nasal cavity, esophagus, stomach, small and large intestines, trachea and lungs, and urogenital tracts. And eyelids.

The mucus they secrete serves many purposes besides being a slimy lubricant. Mucus is an integral part of the environment of each biome. It serves as both a barrier to organisms and a protective layer for some. It the eye it’s primarily a lubricant. In the nose it serves to flush out inhaled dirt and debris. In the mouth it lubricates the tissues and food as it is swallowed.

Here we will briefly discuss some major activities needed to keep mucous membranes healthy. In almost all cases, the less we interfere with them, the better they perform.


Don’t smoke. Don’t vape. Don’t breath dirty air, including industrial contaminants, solvent vapors, toxic gas, etc.. Get enough sunlight at high noon to make vitamin D or take vitamin D3 as a supplement.

There is a lot more that can be said about the lungs but we will deal with some of that when we discuss breathing and nutrition.

Generally the lungs are an inhospitable place for microorganisms. Lung cells secrete an antimicrobial peptide called cathelicidin (among others) that effectively eliminates invading organisms. Adequate vitanin D is needed to produce enough cathelicidin. Despite peptides that kill invaders, the lungs have a resident population of microorganisms that resemble those in the mouth.


The mouth is like Grand Central Station for germs. Think about where your mouth has been and what you have put in it. We will try not to imagine what you are thinking.

The important inhabitants of your intestines got there through your mouth. It’s actually a good thing that microbes enter through your mouth. There are many safeguards to sort them out later.

Successful farming of the biome of your mouth is as simple as receiving regular dental care and brushing and flossing your teeth to reduce the bacterial load. Mouthwash is counter productive. Don’t chew tobacco. Your dentist will tell you all of the things you should do.

The mouth is also where you consume the food that nourishes both you and your biome in the gut. It’s under your conscious control, so the mouth is where you need to resolve the complex questions of food as entertainment, nutrition, and socialization.

Mouth Biome and Your Brain

Research into the brain and disorders like Alzheimer’s and Parkinson Disease is beginning to reveal that the mouth biome may be implicated in brain health. Namely, the terrible food that feeds the microbes that cause gum disease and cavities may also be slowly destroying your brain. Now scientists suggest creating a healthy mouth biome by eliminating the same foods that destroy the gut biome. Sugar and simple carbohydrates are the culprits.

Additionally people do terrible things to their mouths. They suck on sugary mints for sweet breath. They smoke cigarettes. They use mouthwash that kills 99.9% of germs, as if that were a good thing. It isn’t! They don’t floss.

Some people inadvertently breath through their mouths, possibly because the nasal cavity is swollen and “dysbiotic.” Despite popular cultural ideas, the mouth is not an essential part of the human reproductive system. Sexually transmitted disease are not a good member of any biome. Google to see if there is a relationship between dementia and Chlamydia, or just go to this paper on PubMed or this one. Then ask to see what the difference is between Chlamydia pneumoniae and Chlamydia trachomatis.

The science that explains the relationship between our bodies, and our greater own body that includes the bacteria, fungi, and viruses, is in its infancy. Someday we will understand how take care of ourselves, including our bugs. We cannot survive without the good ones and the bad ones regularly kill us.


Gut Biome