The Germ Theory of Disease

Copyright © Karl Dahlke, 2024

In 1675, Enter Anton van Leeuwenhoek was the first to observe bacteria through his improved microscope. Remember that bacteria are smaller than animal cells, so Hook's microscope, developed a decade earlier, was not up to the task. These little critters were everywhere, even in our food and drinking water. Well they had been there all along, and we coped for thousands of years, so people put the microscope away and tried not to think about it.

Bacteria were largely ignored for a century, until Marcus von Plenciz published his "germ theory of disease" in 1762. In his treatise, germs could refer to bacteria, now visible under the microscope, or other unidentified agents, that might carry disease from one person to another. However, such theories were rebuffed in favor of miasma, and other nonbiological explanations. Remember, the word malaria actually means "bad air", suggesting that night air, or moist air, or fetid air, must somehow cause the disease.

The germ theory wasn't particularly new. As so often happened, some of the Greek philosophers foresaw the germ theory of disease, two thousand years earlier. The historian, Thucydides, suggested, concerning the plague of Athens in 431 BC, that disease might spread from one infected person to another. If the people weren't in direct contact, perhaps the agent of transmission was a spore, that could somehow be dispersed through the air. Similarly, the Roman statesman Marcus Terentius Varro wrote, circa 40 BC, โ€œPrecautions must also be taken in the neighborhood of swamps โ€ฆ because there are bred certain minute creatures which cannot be seen by the eyes, which float in the air and enter the body through the mouth and nose and there cause serious diseases.โ€

During the middle ages, Other insightful physicians mentioned the possibility of contagions. Kircher suggested that the plague that ravaged Rome in 1656 was caused by micro organisms, which he thought he saw in the blood of plague victims, (though they were probably just white blood cells). Still, the germ theory of disease was largely ignored, or held in disdain.

By the early 1800's, vaccination against small pox could not be denied. This suggested a microscopic agent, possibly the same agent that produce cow pox in cows, might be responsible for one of the worst diseases in human history. Perhaps diseases are caused by germs after all. Furthermore, early vaccination could, in many cases, immunize people against these unseen "germs".

In 1847, Ignaz Semmelweis suggested that doctors wash their hands before delivering babies, especially since many of them had performed autopsies just prior. This reduced the incidents of puerperal fever dramatically. Despite this evidence, doctors still rejected, or quietly ignored, the practice of handwashing between patients.

Routine handwashing and sterilization did not take place until the 1880's. Joseph Lister, a british physician, actively promoted these practices, and recommended carbolic acid as a safe and effective antiseptic. When a wound was cleaned and sterilized, follow-on infection was much less likely. Since people died of infections at that time, this was a big deal. To this day, the name Lister is reflected in Listereen, the mouth wash that kills germs.

Beneficial Bacteria

With this backdrop, bacteria got a bum rap, and understandably so. However, during the 20th century, we learned that bacteria, or micro organisms in general, can be beneficial. They decompose dead material all around us, so that the nutrients and elements can be recycled into new life. They also live within us, in a harmonious relationship that we call symbiosis. Let's look at a few examples.

The Skunk

Recall our friend the skunk, whose spray is so noxious, it drives hungry predators away, and deters them in the future. The odoriferous compounds entrained within this spray are thiols - but the skunk can't produce these chemicals himself, he doesn't have the biochemistry. Instead, he harbors bacteria in his scent glands, in a symbiotic relationship. He gives them a warm home, and food, and protection, and in return they produce the thiols that the skunk needs for his spray. Without bacteria, the skunk would simply squirt water.

The Cow

The cow, and other herbivores, would starve to death without bacteria. ๐Ÿ„๐ŸŽ๐Ÿ‘๐Ÿ

The cow can't digest grass. Not well enough to survive anyways. Instead, he hosts a mixture of bacteria in his rumen, and the bacteria help digest the grass. Mostly, the bacteria break down the cellulose into its constituent sugar molecules. We don't have those bacteria in our gut, so we can't eat grass. There's energy in the grass, sure, but we can't get at it.

The cow's rumen is large, holding 40 to 50 gallons of masticated grass and foliage. With the aid of bacteria and fungi, this mass ferments, before it moves on to the next chamber of the cow's stomach. The second chamber contains hydrochloric acid to further break down the food - the same acid we have in our stomachs. However, this acid would kill the bacteria, so the rumen is acid-free, and thereby fosters a variety of beneficial micro organisms.

Recall our earlier description of cellulose as a complex sugar polymer. The sugar molecule, glucose, is in the shape of a ring. It has some things hanging off of it but basically a ring. Honey has glucose, which is just these rings floating around free, and they taste sweet. Sugar hits the sweet receptors on your tongue. The same holds for an apple and other sweet fruits.

Did you connect rings together to make a paper chain for your Christmas tree? I did. Starch is a chain of these sugar molecules. It doesn't taste sweet any more, because it's locked up in a chain. Potatoes, noodles, rice, don't taste sweet, but there's lots of sugar in there, locked up in chains. We have the enzymes to break it apart into sugars, and then use the sugar for energy. We don't need bacteria, we can do it ourselves.

Cellulose, in plants and grass, is sugar molecules connected in chains. It sounds like starch, but the connection is different. It takes different chemistry to separate those rings, a different set of bolt cutters. We don't have it, and cows don't either, but cows enlist bacteria to help them take apart the cellulose into its sugars, and then they get their energy from there. Without this internal bacterial colony, the cow would not survive.

The Termite

The cow requires bacteria, along with some fungi, to digest its grass; it would starve without them. Well the termite eats wood, which is even tougher than grass. How does he digest his wood?

The termite has extremely sharp teeth, and can bite off a tiny speck of wood. It moves down to his abdomen, and there, it is broken down by protozoa. The termite has no ability, no biochemistry, to digest the wood himself. This is another example of symbiosis. The termite would starve without the protozoa, and the protozoa can't survive without the protection of the termite's gut.

There is a difference between this relationship and that of the cow. Remember your kingdoms of life: animals, plants, fungi, chromista (brown algae, seaweed, and kelp), protozoa, bacteria, and archaea. Cows rely on bacteria and fungi, calling upon two kingdoms of life, but termites rely on protozoa, a completely different kingdom of life. Protozoa aren't just everywhere, like bacteria, so how do they get the protozoa into their stomachs? Once hatched, the larva termites eat the feces of the adults, to prime their stomachs with the necessary protozoa. When a termite molts, shedding his exoskeleton in order to grow, he loses the protozoa. To get more protozoa, which he needs to survive, the termite ingests the feces of another termite, bringing more protozoa into his body.

This system has been in place for at least 100 million years, as determined by a termite trapped in amber, with protozoa in his gut. That is a span of time that we can hardly imagine.


We don't need bacteria to survive, but the bacteria on us, and in us, are often helpful. The bacteria that have taken up residence on our skin fight infections from other bacteria, and particularly fungi. The bacteria in our gut are even more important. They digest some of the food products that we cannot: oligosaccharides, fiber, and polyphenols. They create hormones that slow down digestion, and tell us we are full. In other words, these bacteria are a natural defense against overeating, obesity, and diabetes. Some of the compounds they produce have been compared to the modern drug Ozempic.

Mice can live without bacteria, as demonstrated by experiment. Some mice were placed in a sterile environment, directly from birth, and fed sterilized food and water. They survived, but they didn't thrive. In other words, they didn't do as well as their brothers and sisters who were raised in a natural, germy environment. Although the experiment has not been performed on humans, the same is probably true of us. We need the proper mix of bacteria on us, and in us, to remain in good health.

With this in mind, one should not wash with antibacterial products on a regular basis. Mild soap is fine; the bacteria we need can survive that. ๐Ÿงผ

If you are taking an antibiotic internally, to fight an infection, your doctor may advise you to stay away from milk and dairy products. There are three kinds of people: those who can digest milk on their own, those who can digest milk with the help of gut bacteria, and those who can't digest milk at all. If you belong to the middle group, the antibiotic will wipe away the helpful bacteria in your gut, and milk products, undigested, will lead to diarrhea. This may seem unusual, since you could digest milk before, but you lost your friends. They will come back however, and a few days after you stop taking the antibiotic, you will be able to drink milk again, in moderation. ๐Ÿฅ›