It’s mainly mucus, from a piece of mouse colon that was cut open and gently flushed out, leaving the inner mucus layer attached. The actual mucus is black here by default but there is another channel you can turn on in the sidebar to see it.

On top of it we added bacteria (green) and bacteria sized beads (red). On the bottom are colon lining cells (blue).

The inner mucus layer of the colon was generally thought to be impenetrable to bacteria, serving as a way to protect you from the trillions of bacteria in the gut.

It turns out that actually, it’s really easy for bacteria to swim through mucus by using flagella. We found some bacterial mutants that swim through mucus (the green ones). The red beads serve as a control marking the top of the mucus since they can’t get through the mucus.

Find this and other images in my paper: https://pmc.ncbi.nlm.nih.gov/articles/PMC11784811/

The real question is then - if they can get through the mucus at any time, why don’t they? And there are various theories about this - which I’m happy to elaborate on this you want. The basic idea is there is a risk whenever you cross the mucus (you get closer to the immune system) and mucus actually feeds and tames bacteria over time by providing them with various sugars and things like that. But if they get desperate/starve, then they will cross.

Mucus is still a mystery - there are substructures within mucus, take a look at this image for example:

https://mucus-atlas-viewer.pazimzadeh.chatgpt.site/?sample=f...

And here is a good paper too from my collaborator (who actually took these images) who discovered a sub-type of mucus and mucus-producing cells:

https://pubmed.ncbi.nlm.nih.gov/33859001/