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Where is the line between good and bad microorganisms and why do we seem to know so much more about the bad ones?

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Gross, A. G., & Harmon, J. E. (2007). The Scientific Literature: A Guided Tour. Chicago, IL: University of Chicago Press.
Magnifying lenses like the ones in today’s microscopes gave us, of course, our first glimpses into the world of the microcosmos.

But it was not the first time people had guessed that there might be more to the world than met our eyes, particularly regarding illness. Marcus Terentius Varro, a Roman scholar in 30 BC, wrote about the need to be cautious around swamps “because there bred certain animalculae 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.” Marcus, thus, managed to guess at a reality that it would take thousands more years, and a great deal of debate to confirm.

Even now, when it comes to human understanding of our unseen neighbors, our focus is almost always driven by negative interactions. Our most vivid, collective encounters are also some of the most unpleasant: the sneezing, the coughing, the upset stomachs, the death evidence of an apparent tension between our bodies and the microbial world. This strange little guy is a parasitic flatworm, but for now, it’s in its cercarial form, a larva in search of a host—preferably animals like duck, geese, and raccoons—where it can feed on their blood and then mature into adulthood and release eggs through the infected animal’s waste.

From the eggs will emerge a ciliated larva that will seek out particular species of aquatic snails to serve as an intermediate host as they develop into their cercarial stage and complete the cycle. For all the hosts this parasite will go through, it turns out that we humans are not a particularly great one. They can infect us, and when they do, they will burrow into the skin and create little bumps, inciting an allergic reaction that produces a rash formally known as cercarial dermatitis, but it’s more frequently known as “swimmer’s itch” thanks to its aquatic origin.

But for the cercaria, the real challenge is that we just aren’t the right bodies to house its development into adulthood, and instead, it will die. The word “germs” might be the very first term many of us learn to describe microbes, an easy word that warns us from an early age that there are things we cannot see that nonetheless we must watch out for. And with medical necessity often shaping the direction of scientific research, their potential danger is further emphasized because it has inspired and shaped so much of our understanding of microorganisms.

And so we know a great deal about the microbes that can hurt us and next to nothing about the ones that can’t. But necessity is now driving us to better grasp the complexity of microbes in relation to us, the idea that they are only ever enemies is contradicted by our developing understanding of the organisms that live in and on us, not just as freeloaders, but potentially as part of our body’s mechanics. Words like “microbiome” and “probiotic” are now part of our understanding of the world, and also part of active research, though a far smaller part than research focused on pathogens.

But, and stop me if you’ve heard this before, it turns out, the world is bigger than humans, and beyond our own perimeters, there’s the importance of microbes to the world around us. What is known about that world is a tiny percentage of what there is to know. Now as we delve more into the balance between microbes that both help and harm, we do want to remind you that however harmless or beautiful or fascinating the microbes we show you here are, you should still wash your hands and get your shots, and having done away with that though, let’s remind you, most microbes cannot hurt you.

While it would be challenging to calculate the exact percentage of microbial species out there that are pathogenic and could potentially make us sick, estimates put it somewhere less than 1%. Figuring out whether the bacteria in our samples lie in that slim percentage would require isolating and growing them up in cultures so that we can sequence and properly identify them. But we just take the safe route and you know, we don’t drink the pond water.

Bacterial species do run a range as well, giving us everything from cheese to tetanus. For us though, their presence helps sustain the many bacteria-eaters we feature, and we keep them fed on droplets of milk, water from boiled hay, cooked rice, or even liquid plant fertilizer. Now Nematodes, on the other hand, might seem like a more clear cut danger.

More commonly known as roundworms, they are plentiful, with estimates counting them at around 60 billion nematodes for every person on Earth, and around 40,000 species in total. But it’s a select few of those species that are particularly notorious for humans, able to enter humans as eggs in contaminated food or as larva that can penetrate the skin depending on the species. So it’s understandable if you respond to the image of a nematode with some revulsion.

But the vastness of them means that their impact is so much more complex when you examine them across their different intersections with life, from ecosystems where they can move other microbes around the soil and cycle nutrients like nitrogen, to agriculture, where some nematode species may be pests while others are helpful controls of insect populations. But these complications aren’t always strictly about pathogens. We’ve featured Euglena here before, their twisty bodies both fascinating and seemingly harmless.

But in 2002, 21,000 striped bass died in a facility in North Carolina. The culprit? A bloom of Euglena sanguinea, which released a toxin called euglenophycin that is similar in structure to fire ant venom.

And yet this danger poses a potential as well, as scientists study the use of euglenophycin to fight cancer. And unlike nematodes, which we decidedly do not want to ingest, there is some culinary promise for Euglena. Like Euglena gracilis, which for all of its small size, manages to pack in large amounts of proteins and vitamins.

There’s an underlying question in this video about all these microbes we’ve seen: are they good? Or bad? Or neither?

The answer, of course, varies. We’re still grasping the extent of what it means to share a world with organisms that we weren’t able to even see until a few centuries ago, dealing not only with the consequences of their existence but also of our own response to what we’ve learned. Understanding bacteria and other microbes, for example, that helped us usher in the modern era of antibiotics, which has saved so many lives.

But antibiotic overuse has also led to the growing threat of antibiotic-resistant bacteria. We can’t not try to fight disease or find uses for microbes, just as we can’t not interact with the world around us. The challenge then of making use of our knowledge responsibly, of categorizing good and bad—whether at the scale of a microbe or much, much larger—hinges on our ability to identify our place among all of this, to better understand the complexities of the good and the bad of our own actions.

Thank you for coming on this journey with us as we explore the unseen world that surrounds us. And thank you of course to all of the people who support this channel at If you want to see more from our Master of Microscopes, James check our Jam and Germs on Instagram.

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