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Argonne National Laboratory’s Microbiome Project: Surgery

Shortly after I’d written my last post (let’s not reflect on how long ago that was), I got tapped for a freelance project with Argonne National Laboratories. They have a YouTube series with Dr. Jack Gilbert called The Microbiome Project, and were looking to have a medical animation of what happens to gut bacteria during gastrointestinal surgery. I truly enjoy ruminating on the idea that we are all floating in and teaming with Pig-Pen-like clouds of our own complex, interacting filth, and could not have been more game to help out . This topic is so hot/right now, granted, I know it’s a topic that is attracting its fair share of nonsense and unbridled optimism, and the knowledge base is still in its infancy. Bacteria has a sort of intelligence that we ignore at our own peril. Surgical site infection is unacceptably common, though medicine has started to find ways to reduce it.

The microbiome of the colon

My content experts were gastrointestinal surgeons Dr. Kristi Guyton and Dr. John Alverdy from the University of Chicago, which is associated with Argonne. Their research has found that bowel surgery can compromise the gut microbiome in a number of way that can lead to infections, leaking wounds, and sepsis. I was to show a bowel being resected, which means a diseased part is cut out, and the ends reattached or anastomosed. Then, I needed to show the various types of bacteria increasing or decreasing, and then attacking the anastomotic line, leading to a frank hole.

Resected colon

I took the instructional liberty of portraying the bacteria as three bright colors and not the well, naturalistic color that one would find in the large bowel. It is also less dense for the sake of visibility. The benign bacteria are orange and yellow, while the “evil” collagen degrading bacteria is green. Yes, the green of Slimer or of the Teenage Mutant Ninja Turtles’ ooze. All types of bacteria are felled by invading oxygen (not good for anaerobes), and systemic antibiotics given before surgery don’t help microbiome matters either. Nutrients are shunted from the environment to the healing anastomotic line, and the “Slimer bacteria” follows. It degrades collagen, opens up the surgical wound, and creates peritoneal mayhem, not unlike the ballroom scene.

The collagen degrading bacteria attacking the anastomotic line


A hole forms in the anastomotic line

The solution turns out to be throwing Slimer some doughnuts to keep him distracted. The research team has found which nutrients are needed to make the different members of the microbiome “behave” so that anastomotic leaks don’t occur.

Dr. Guyton also discusses fecal transplants, which I think of as the grossest, simplest, but also most absurdly effective GI treatment in existence. The condition FMTs are commonly known to cure is c. Difficile infection, but they’re used in this setting prophylactically.

I am grateful to have worked with such wonderful people, and was super excited to see the final product! It’s pretty funny too.


Katie is an animator and illustrator of human innards living in Chicago.

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