Germs: as Much a Part of Us as DNA

“Men are from Mars; bacteria are from Uranus.” – J.A. Tetro, The Germ Code

germs and dna

My medical school microscope- it is still with me- and it provides me with much wonder looking at those tiny creatures we share our space with – bacteria

Here’s a pop quiz. The bacteria that occupy our guts are:
A) A foreign species, or
B) Every bit a part of us as any other organ of our body.
If you think of bacteria as a population of individual beings, then in our guts there are more bacteria than the number of human cells. That fact has led some to speculate that human beings have evolved simply as a bacterial transport system. However it is that you think of the bacteria that occupy our guts, the guts provide them a home and food, and bacteria are a de facto organ, synthesizing vitamin K, B, facilitating breakdown of carbohydrates, fats, bile, and just occupying space so “bad” bacteria (the bacteria that can do us harm) have no place to settle.

Let’s not think of bacteria in the guts as individual single-cell organisms. Instead, consider that those bacteria are every bit a part of the guts as the cells that transport glucose into the bloodstream. The bacteria in our gut can be thought of as an organ, as important as other organs to the gut like the liver or the pancreas. Damage them and the human suffers; and sometimes in our haste to get rid of infectious bacteria we can damage our gut bacteria with antibiotics.

Most people shudder when they hear we have millions times millions of bacteria in our guts. Because when they think of bacteria, they think of the one of the roughly 1,450 types of bacteria that can harm us, not the hundreds of bacteria that have been a part of us since our earliest memory.
In the written record of humans, we have identified bacteria as the pests that compete with us, that can kill us either through being better at competition, or are invading and destroying us. When the first man spotted bacteria in the earliest version of the microscope it was a wonder, little creatures that some thought of as angles or fairies. Later, when Pasteur identified bacteria as the cause of disease, we started a war with them. It is a war, by the way, that we cannot and must not win.

How We Acquire Our Bacteria

In the nine months in the womb our guts are sterile. They have no bacteria. As babies, we acquire bacteria, and as we acquire bacteria they start to work for us. Our mother has cultivated the bacteria that come into our guts; our first exposure to them happens when we pass through the birth canal. Our sterile intestines start to become inhabited with the bacteria from Mom.

This process isn’t random; that is, not just any bacteria from the environment will do. Think about this like making bread, a process which relies on another small organism, yeast, for the bread to rise. Most bread recipes do not rely on random chance for the right yeast from the environment; rather, you purchase the yeast from the store and add it at a specific time. Our parents have cultivated the gut bacteria we need, in the purest form of natural selection. For a human to thrive, the bacteria we cultivate must be the right ones, just like the peers your kids play with, the bacteria your child gets must be right.

The bacteria that occupies our body, from the skin to the guts, is called the microbiome. The Nobel Prize-winning microbiologist Joshua Lederberg coined the definition of “microbiome” as the “ecological community of commensal, symbiotic, and pathogenic microorganisms that literally share our body space.”

There is variability between humans as to the bacteria that occupy the guts. But looking at healthy people, researchers found that healthy guts have the same 450 types of bacteria. Those 450 types of bacteria are called the core of the microbiome. When you look at patients who have disease of their guts, some of those species are missing.

Every kiss from our mother, our father, our grandparents, becomes a means to inoculate the right bacteria into our guts. But it isn’t just the intimate contact with our parents that gets us their bacteria.

Most think the little boy is getting dirty – in fact, he is collecting germs – germs that will be a part of him, protect him, and stay with him for his lifetime

Any microbiologist will tell you that if you go into a house, on the carpet, on the silverware, on the counters, everywhere, are the shed bacteria that come from the people who live there. Watch any toddler explore; they put things into their mouths, which is the most primitive reflex. Hygienic parents react in horror and try to clean, but you cannot; it is impossible. In fact, that reflex, putting things in the mouth, is the perfect way to inoculate the guts with the shed bacteria of the humans raising the child.

The parents don’t know that picking up the toys on the floor and putting them in the mouth is just another way of getting good bacteria. They worry only about the bad things, the bad bacteria that can harm their baby.

These bacteria do things our highly specialized gut cells can’t do. Bacteria facilitate our ability to get energy from fiber, to produce vitamins B and K, and they offer protection of our guts from other bacteria that are not so nice.

Because of that it is easy to consider these bacteria as every bit as much a part of us as the endothelial cells that line the small bowel, the dendrite cells that are part of the immune system, or the islet cells of the pancreas producing insulin. Our DNA does not code for them, but like our DNA, we get these bacteria from our parents; it’s just transmitted in a different manner.

Infants depend on breast milk for antibodies from their mother, but what they also get from their mother are bacteria that will be a part of them for all of their days. Amazingly, the antibodies in the mother’s breast milk do not contain antibodies against these bacteria; mom’s gut bacteria get a free pass. They get to arrive in the small bowel without worry of an immune system building up antibodies to them and ushering them out.

Like soldiers on the front lines who shout “Who goes there?” to identify an approaching person, there is a part of the gut immune system that has to determine what is “self” and what is not “self.” If the immune system is in overdrive and starts to make antibodies against its own tissue, the damage can be horrific. Making antibodies against one’s own tissue leads to autoimmune diseases like lupus, rheumatoid arthritis, Hashimoto’s Thyroiditis, and psoriasis. In those diseases the antibodies are made against normal tissue of the human, and the body is essentially at war with itself. The bugs we get from mom have a special place; her immunity that she passes from her breast milk won’t bother them, and they are our first probiotics.

The stomach of a newborn is not yet producing acid, making it a perfect place for bacteria to get their start. One of the reasons that honey should not be given to an infant is that there are spores in honey from the bacteria that can make botulism. In an older baby the acid will kill those spores, but in a newborn⎯up to about a year⎯ those spores could survive and hatch bacteria that produces the botulin toxin that can kill a baby.

By age one, the stomach has started to produce more and more acid, and the bacteria prefer to live in the small bowel, away from the harsh gastric juices of the stomach, and away from the digestive enzymes of the pancreas and bile from the liver. The stomach is a hostile environment for bacteria; it would be like living in a desert. Then as you get closer to the colon, very few things are there to hurt the bacteria. The farther from the stomach the bacteria go, the nicer the environment for the bacteria, and it gets positively delightful in the colon. For bacteria, the colon is like living on the oceanfront in San Diego: perfect climate, perfect conditions. That is why the further you get from the stomach, the higher the concentration of bacteria, to the point where when you look at the content of a bowel movement, a high percent of it is bacteria that have been shed.

The reason our gut bacteria are a part of us is because collectively they are like one of our organs. They are transmitted by our parents and are as genetically identical as the bacterial cells in our parents. Like some organs, we can live without them, although it is rare; and people who have sterile guts are far more prone to severe infections and other reactions.

Today researchers are looking at the microbiome of the colon, and they see the differences between people who eat meat and vegetables. This isn’t surprising that there would be a slightly different mix; after all, the bacteria that will thrive are the bacteria that can eat the food given to it.

The body recognizes these bacteria as “self,” meaning it does not make antibodies to combat them. At the same time, the gut bacteria affect the immune response to produce antibodies to other bacteria. Bacteria can also influence oral tolerance, in which the immune system can reduce an overactive response like those found in allergies and auto-immune diseases such as Crohn’s and ulcerative colitis.

They produce a number of vitamins we cannot produce ourselves, including vitamin K and some vitamin B. They help digest foods that other cells in the guts cannot break down, such as fiber, some proteins, and fats. They eat fiber and turn it into short chain fatty acids; these byproducts help regulate the gut, providing induction of growth of the epithelial cells that line the growth preventing over-proliferation of those cells.  The byproducts of some gut bacteria even inhibit the growth of cancer cells.

They form an immune barrier against harmful bacteria by occupying space. Think of gut bacteria as occupying seats in a stadium. The stadium represents an epithelial cell of the guts. There is limited space in a stadium, and once the seats are occupied there is no place for more bacteria to reside. Even if a few bacteria that are harmful occupy a few seats, they cannot cause a disturbance unless there are more of them. Just by occupying those stadium chairs, the gut bacteria prevent us from being infested with harmful bacteria.

By the time a child is three years old, the types of bacteria found stay pretty much the same. At this point most children are eating solid food, and the type of diet that a person has will determine the type of bacteria they will cultivate.

You have seen the television advertisements proclaiming how “probiotics” are good for your health. Why? Imagine, for example, you take antibiotics for an infection, knowing that the antibiotics will not only get rid of the bacteria that cause an infection, they will also get rid of the bacteria that normally occupy the gut. The concept behind probiotics is that they provide you with replacement good bacteria.

Many people, encouraged by TV ads, believe that eating probiotics is necessary and healthy for your gut. Probiotics sound great, heck, even the word sounds wonderful. The basis for probiotics is sound: Our guts have good bacteria, and sometimes antibiotics destroy the good bacteria and the bad bacteria take over.

The problem is that what is commercially available has not been proven to be beneficial. This is not to say probiotics are ineffective; probiotics are very effective, but what is marketed to consumers in food or pills may not be the same.

All foods contain bacteria, and there is simply no additional benefit to buying foods that claim to contain probiotics. The food supplement industry is unregulated as far as making claims of health. One yogurt, Dannon’s Activia, went too far and was fined $21 million and had to agree to stop making exaggerated health claims. The Federal Trade Commission (FTC) charged that the claims made by Dannon were not substantiated, such as saying that probiotics were good for “irregularities.” The companies can make vague statements, but not specific performance claims. The reason: they have never tested the yogurt, and they cannot assure that the type and amount of “helpful” bacteria are present.

Here’s the problem. Clinical studies show some bacteria are good for certain illnesses but not for others. So we should treat bacteria like we do medicine: Certain medicines are good for some issues but not others. For the bacteria to work you need a certain “dose” of bacteria (too little won’t work, and too much can make you sick—just as with any drug you take). When you buy yogurt or pills that contain probiotics, you have no idea if it’s the right bug or if it contains the right number of bugs. Studies have shown that yogurts and pills bought off the shelf and tested often do not contain the bugs that are helpful, or even the bugs that are stated to be present. And sometimes the bugs in these products are already dead. At some point in the future these bacteria will be prescribed, like a drug⎯but it will be a very specific bacteria, for a very specific disease, and a very specific number of bacteria. (5,6,7)

If you enjoy eating yogurt, just buy a good organic brand with active cultures. Don’t bother with the more expensive “probiotic” brands unless you get a kick out of wasting your money.

A good way to get probiotics is to kiss. The bacteria you get from your partner’s mouth is free, and it’s more fun. (8) When babies are born their intestines are sterile and devoid of bacteria. Moms kiss their children and begin the process of passing on bacteria to their children. These are the bacteria that will colonize the gut, and provide important functions for the child. Kissing provides the first, best, and ultimate probiotics. Perhaps that is why babies are so cute and kissable⎯it’s nature’s way of helping us help them.

Killer Peach Ice Cream

She made the best peach ice cream on the East Coast. Her formula was simple: get fresh peaches, ripe from the tree. Carefully cut them up to almost a puree, but make certain that all the juices are collected, so keep scooping the juice into a bowl. Added was a bit of lemon and some salt, and then the ice cream was made with fresh heavy cream from the local dairy.

Mary’s peach ice cream was always a family favorite. Other employers worked hard to hire this amazing cook away, and often they succeeded. Mary left one place after the family became sick, not wishing to be sick herself, she said. Mary was never ill in her life, she said, and she didn’t like to be around sick people. And wherever Mary went people got sick, and some of them died. It was common in the early 1900s for typhoid to be fatal; there were no antibiotics, so typhoid fever would kill some because the bacteria were highly virulent. They would take up residence in the gut and even cause the gut to perforate, which, in the early 1900’s, meant death.
One family began to suspect that the Irish maid, Mary, was the source of their illness, so they hired Dr. George Soper to investigate. He suspected she was the source of the outbreak, as did the family.

Mary Mallon later would be called Typhoid Mary. She was a carrier of the salmonella bacteria that caused typhoid fever. Eventually the law caught up with Mary Mallon, and they did the only thing they could: she was hospitalized and quarantined for thee years until a judge set her free on condition she not gain employment as a cook. She agreed, only to take a job as a cook and make an entire hospital ill. In 1915 she was quarantined and spent the remainder of her days isolated. She did enjoy some celebrity as “Typhoid Mary,” and when she died the autopsy revealed that her gallbladder was filled with the bacteria Salmonella, that cause typhoid..

Mary herself was never ill, but the salmonella were able to hide inside the immune cells called Macrophages. Typhoid fever is spread when people don’t wash after going to the bathroom, and the peach ice cream made the perfect nutrient source for the bacteria. Even the freezing of the ice cream didn’t kill the bacteria, but it did stop them from growing just long enough until they got into the new person’s gut, where they would flourish, and cause illness.

Dr. Terry Simpson About Dr. Terry Simpson
Dr. Terry Simpson received his undergraduate and graduate degrees from the University of Chicago where he spent several years in the Kovler Viral Oncology laboratories doing genetic engineering. He found he liked people more than petri dishes, and went to medical school. Dr. Simpson, a weight loss surgeon is an advocate of culinary medicine. The first surgeon to become certified in Culinary Medicine, he believes teaching people to improve their health through their food and in their kitchen. On the other side of the world, he has been a leading advocate of changing health care to make it more "relationship based," and his efforts awarded his team the Malcolm Baldrige award for healthcare in 2011 for the NUKA system of care in Alaska and in 2013 Dr Simpson won the National Indian Health Board Area Impact Award. A frequent contributor to media outlets discussing health related topics and advances in medicine, he is also a proud dad, husband, author, cook, and surgeon “in that order.” For media inquiries, please visit

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