Flesh-Eating Bacteria and Microscopic Warfare: Personifying the Microbiome

Necrotizing faciitis, also referred to as flesh-eating disease, is caused by a range of bacteria that live on your skin and in your nasal cavity every day. While some cases happen in perfectly healthy individuals, some studies have been shown to correlate the risks with autoimmune diseases, diabetes, and alcoholism. The part that blew my mind was that nothing could be done, and nobody was sure about the cause. See the necrotizing faciitis causing bacteria are opportunistic pathogens. They are little friends that use our bodies as their ecosystem, then randomly decide to burn down their home. Well, they sneak their way into a cut or scrape and decide to become the infamous flesh-eating bacteria. The plant pathogen, Pseudomonas syringae, has a very similar story. P. syringae is a foliar plant pathogen that has a wide host range from trees to agricultural crops. Like the flesh-eating bacteria above, P. syringae exists as an opportunistic plant pathogen. It is found ubiquitously on the surfaces of plants. Also like the flesh-eating bacteria, we do have a few conditions that correlate to disease, but we don’t exactly know what makes them turn on their hosts. In plant pathology, we are reminded constantly that disease is the exception, not the rule. What makes one pathovar of P. syringae act as a pathogen, and what keeps one from behaving this way. To figure out what causes this exception, we need to step into the shoes of the bacteria. Bacteria that exist on us and plants live in a microscopic world with many interactions much like our own. I like to think of the bacteria world as a war.

Possible reasons personified microbes would have to change their niches:  (This list is not exhaustive just a fun mind game)

  • A bacterium could be stressed because their niche is being taken away from them by two allied microbes. This could look something like when the United States won the Revolutionary War with the help of France.
  • It could also be a more indirect ally situation like when many European countries were invading the Americas simultaneously. Even though they weren’t working together per-say, the Natives were getting pressure from may different people invading their established niche. Maybe its possible flesh-eating bacteria and P. syringae are getting booted out of their established area, so they decide to go rogue and become a pathogen?
  • Another possibility could be just a good old fashion enemy. The bacteria could have unrest with one other type of microbe in the area. They could have a Hatfield and McCoy turf war full of trickery and violence. The microbe could decide in the end that instead of skin or leaf surface, a different nearby tissue would be a better place to live.
  • Maybe there’s a famine causing chaos. A once rich with nutrient niche is now depleted of a key nutrient, so it is having to battle microbes in the area that it normally doesn’t fight. This can even include microbes of its own kind. This could be personified by natural disasters. Your normal environment is ruined, and you decide the best option is to find another place to call home temporarily.
  • The microbes could be getting “hacked” and false signals are making them believe they need to change niches. Maybe this is the human equivalent to being brainwashed. The most conspiracy theory of the personified microbe predictions.
  • There could be no other reason for changing environments other that exploiting resources for your own personal gain. Maybe the grass looks greener in the other niche. Maybe there’s another microbe over there enticing you with signals to leave your home.


For me, I think it is important to think of microbes not just as a set of genes but also as a behavioral organism or even a population of organisms that interact. We know individual genes can code for and affect many different phenotypic properties, so it is unreasonable to only view the microbiome as a set of genes. Evolution has created organisms with properties that cannot be limited to only the total of its genes. This is why I find it useful to personify the organisms and communities. While it’s fun to think about the different personified versions of microbe war, we can’t leave out how heritable microbial behaviors are. In any case, it is best for a microbe to predict what is happening in its environment. The diversity of being plastic keeps your survival chances higher when your environment isn’t a perfect stable bubble. While we don’t see microbes as conscious, maybe we can see their genes as a program for a computer black jack game. The computer game is programed to make decisions based on the code written. Even using the best statistics it still may choose an action that will make it lose, but having a prewritten code at least gives standards for what action is reasonable. Its no secret that I admire Richard Feynman. He was interviewed and said in regards to physics, but it still is relevant,

“The world is strange. The whole universe is very strange, but you see when you look at the details that the rules of the game are very simple – the mechanical rules by which you can figure out exactly what is going to happen when the situation is simple. It is like a chess game. If you are in a corner with only a few pieces involved, you can work out exactly what is going to happen, and you can always do that when there are only a few pieces. And yet in the real game there are so many pieces that you can’t figure out what is going to happen – so there is a kind of hierarchy of different complexities. It is hard to believe. It is incredible! In fact, most people don’t believe that the behavior of, say, me is the result of lots and lots of atoms all obeying very simple rules and evolving into such a creature that a billion years of life has produced…. There is such a lot in the world. There is so much distance between the fundamental rules and the final phenomena that it is almost unbelievable that the final variety of phenomena can come from such a steady operation of such simple rules.”

Our genes remember patterns that help them replicate in our environment. We get to keep the genetic blue print that we have evolved over the history of the human life. Our DNA tells a story about our environment and where we have been as a species. Microbes have an even longer history with the environment, and they have more complex ways of replicating and sharing genetic information than animals. Their computer programed black jack game has had to upload and lose many different parameters over the years. Our bodies are just playing a black jack game with a standard decks of 52 playing cards and one set of rules. They play the black jack with standard cards, some UNO decks, the monopoly chance cards, and multiple types of dice with many sets of rules. They are experts at the game of adaption. We have just been playing it for a few hundred thousand years in our current form. Microbes are plastic enough to survive in deep sea vents, ice sheets, and the human gut. We have to live on the greenish brown 25% of earth’s surface or at least something very similar. Trying to understand behavior of microbes by only personifying them is like trying to understand a game of black jack with several types of cards and dice without a rule book. We don’t know all the ways they communicate and interact. 150 years ago we just settled on germ theory as the cause of infectious disease. For now, we will remain puzzled with necrotizing fasciitis and rapid microbe adaption to our actions. We will for as long as microbes keep showing us all the different types of cards and dice they have been programed to play the game of survival with. We have many exciting discoveries ahead of us as we understand the rules and interactions of the microbiome, and to finish in Feynman’s words from the same interview as above,

“It has to do with curiosity. It has to do with people wondering what makes something do something. And then to discover, if you try to get answers, that they are related to each other – that things that make the wind make the waves, that the motion of water is like the motion of air is like the motion of sand. The fact that things have common features. It turns out more and more universal. What we are looking for is how everything works. What makes everything work.”


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