Medicine For People!

April 2018: Germs - The Surprising Truth

Human Germ Colony

Germs: The Surprising Truth

  • What is a Germ?
  • Myths about Germs
  • All these Myths are Wrong
  • Germs are usually our friends
  • We Need Germs

What is a Germ?

American usage defines a germ as any microorganism that can cause disease. In medicine we call these pathogens, from the Greek words pathos for suffering and genes for "producer of." Pathogens include bacteria, viruses, fungi, single-celled creatures such as trichomonas, and proteins called prions (such as those that cause mad cow disease). In this newsletter we are mostly concerned with bacteria, although the principles apply to most pathogens.

Myths about Germs

Most people believe the following about germs:

  • There is nothing good about a germ
  • We want to avoid them
  • Germs make us sick
  • Germs always give us infections
  • Antibiotics kill them

All These Myths are False

First off, let me explain the difference between colonization and infection1. Understanding this will help you understand why the myths listed above are not always true.

We say that germs that live in us and on us without causing illness have colonized us. Only when they move into our tissues do we concern ourselves with infection.

Here is an image of a new human being in process of being colonized. The trillions of germs that co-exist within and on our bodies are called the microbiome, about which more in a moment.

Human Germ Colony


In this picture, some bacteria have caused an infection. It is has invaded just a fraction of an inch, meaning that like most acne whiteheads it is being contained by the person's immune system. We call this a localized infection.


In the picture below, the bacteria have escaped the barn. Such an invasive infection can kill or maim. You can see a small piece of gauze protruding from the skin, helping antibiotic treatment by maintaining an escape route for pus and allowing the abscess to heal from the bottom up.

Invasive Infection

But for every invasive infection, there are thousands of children out there getting cuts and scrapes or eating dirt with no harm resulting.

Let's address the most common myths about germs...

There is nothing good about a germ.

Many germs are helpful! We often use germs as medicine. For example, those in the know treat children's colic with Lactobacillus reuteri. Bloody diarrhea in children (necrotizing enteritis) and adults (ulcerative colitis) often improve when treated with capsules containing normal intestinal germs—which you know as probiotics.

Certain viruses infect and destroy bacteria, including bacteria dangerous to us such as Staphylococcus aureus, which you have heard of as "staph." These viruses, called bacteriophages, can cure infections when antibiotics fail.2

Germs make us sick.

Most of the time, no, they don't. We spend our entire life not only surrounded by germs but hosting huge numbers inside our bodies. There are communities of specific types of bacteria living in our ears, in our tears, in our sinuses and noses, in our intestines, on our feet, our skin, you name it.

Germs always give us infections.

Most of the bacteria on our skin are normal residents. If anything, they protect us by crowding out invasive bacteria such as staph and Streptococcus pyogenes ("strep").

If we get a cut or scratch, some of these bacteria may invade a fraction of an inch and cause some redness and tenderness in that area. These localized infections, as pictured above, are readily dealt with by a person's immune system and usually go away by themselves in a few days. Hot soaks can help speed the process.

Sometimes bacteria invade the deep tissues and cause tissue destruction or even move into the bloodstream. These invasive infections are more likely in people with diabetes or some form of immune system insufficiency.

But most of the time, the trillions of bacteria living in us and around us leave us alone. As with the millions of people living alongside each other in a large city, each tends to their own affairs.

We want to avoid them.

Actually, not always. And in fact, we can't avoid them—for example, during childbirth. We used to think that a mother's womb provided a sterile environment for her developing baby, but now we have identified particular bacteria that live within the normal womb.3

When a baby is born, it is pushed through a vagina teeming with Lactobacillus, which it swallows. This helps the baby start its own healthy intestinal bacterial colony. Babies are usually born face down, rubbing their little noses and mouths across mom's anus, picking up Escherichia coli and other valuable and normal colonic bacteria to add to their collection. Evidence suggests that mothers harbor beneficial intestinal bacteria such as Bifidobacter in their milk ducts prior to birth and begin transferring these to their baby with the first suckling.4

How wonderful nature is, making it so easy for a baby to get all the bacteria it needs as it enters the world! A nurse friend scheduled for a repeat C section recently told me that her birth plan includes a purposeful transfer of vaginal juices into baby's mouth to help replicate nature's work in this regard.

Antibiotics kill them.

Bacteria are clever little rascals. When we sprang the surprise of penicillin on them in the 1940s, for a long time we were winning many of the battles. But then bacteria evolved defenses, such as an enzyme that deactivates penicillin. All of a sudden, some the children we had been saving from death by meningitis started dying again, and we had to develop newer antibiotics.

Bacteria then developed cell membranes impermeable to the new antibiotics. When we overcame that, they deployed pumps in the membranes surrounding themselves. These pumps could remove newer antibiotics as fast as they seeped in, preventing them from poisoning the bacteria's metabolic machinery and allowing the bacteria to thrive even in an environment containing the antibiotic.

You can read more about this in this excellent Wikipedia article. Or you can just take a look at this diagram of a bacterium, which shows how different antibiotics disable the bacteria in different ways, and bacteria fight back with lively imagination. "Efflux" in the diagram, for example, refers to the pumping mechanism.

Invasive Infection


One last bacterial trick: Imagine a world in which you could hug your neighbor who is immune to anthrax and thereby acquire a piece of their DNA, a piece of DNA that would protect you and your descendants from that same illness. That is the world in which bacteria live. We worry about antibiotic use in animal husbandry, because bacteria in such animals (cows, sheep, chickens, etc.) are thus becoming immune to our antibiotics. If you eat those animal products these bacteria enter your intestine; mere contact with your friendly bacteria transfers the antibiotic resistance.5 Major concern these days? You betcha.

Fact: Germs are usually our Friends

Despite our concerns, we live, dear readers, in a world of almost always friendly germs.

And in the light of this new understanding, let me ask you to consider the impossible: the use of the most repulsive bacteria of all, those that live in our colon, to treat disease.

The disease in question is caused by a bacterium called Clostridium difficile (C diff in the trade). Some estimate that this particularly serious intestinal infection kills almost 30,000 people in the U.S. each year. Until recently we always started with antibiotics to kill C diff, but C diff can be so persistent that sometimes we have to remove the entire colon.

A more effective treatment that is becoming much more common these days (despite the yuck factor) is to take feces from a healthy person and insert them into the intestine of the C diff sufferer.6 We call this treatment fecal transplantation. The transplanted bacteria usually move happily into their new neighborhood and displace the disruptive C diff.

Oddly enough, this is not a new idea. The Chinese used feces to treat various illnesses thousands of years ago, calling it "yellow soup." (So read that menu carefully when you travel to China!) Bedouins used "fresh, warm camel feces" for dysentery. German soldiers attested to its value during WWII. 7 (Which I guess adds a concrete example to the adage that war is hell.)

We are continuing to learn what bacteria do for us. We know now that bacteria in our intestines produce chemical signals that can make us handle sugar improperly and store more calories. We have pretty decent evidence that fecal transplantation improves adult onset diabetes, low platelet counts, multiple sclerosis, and chronic fatigue syndrome.8 Case reports show that some people with Parkinson's disease have benefited.9 No doubt more exciting discoveries remain.

The Last Word: We Need Germs

Over the great time span of evolution we have evolved in company of a huge universe of micro-organisms. We share these microorganisms with the plants and creatures that we eat.

The biblical injunction for us to be stewards of this Earth is more appropriate than ever. We need to replace our fear of germs with respect for them and every living creature.










Thanks to Jody Bower and Michael Rienstra for their invaluable help editing this newsletter.



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Medicine for People! is published by Douwe Rienstra, MD at Port Townsend, Washington.