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I think the connection between gut bacteria and human health is one of the great developing medical stories of the current time. It is almost on par with the development of the germ theory of disease. Scientists are aware that most of the cells in your body are not human, but the role of bacteria in your body's function is only slowly being uncovered.
" Scientists are aware that most of the cells in your body are not human"

I guess that depends on the definition. How do you define a cell in the body as human and another cell as not human, when both are necessary for the human as a whole?

> How do you define a cell in the body as human and another cell as not human ...

by their genomes?

The human genome is complicated. Mitochondrial DNA is distinct from nuclear DNA. For the most part, people only get mitochondrial DNA from their mothers.
> How do you define a cell in the body as human and another cell as not human, when both are necessary for the human as a whole?

On that note, 'I' am in many ways a 'we'. I am an orchestra, a beautifully complex and rich interchange. As are you.

I understand wet markets can be transmission hubs for diseases. Could ancient cesspits house inordinately dangerous diseases as well?
I only have an undergrad in biochem with a few semesters of immunology/virology under my belt, so this is my uneducated understanding.

I would assume not for viruses.

Wet markets make zoonotic diseases more probable since they are an intersection for several disease reservoir populations. Novel viruses have more opportunity to jump species since the animals are often sourced from diverse wild populations, and many animals and humans are present together.

A septic system is used predominantly by one species - humans - that are already in close contact. They may aid the fecal-oral transmission route for an existing disease or be a breeding ground for bacteria, but I wouldn't expect novel viruses to arise here.

Edit : I might have misread the intent of your question. I wouldn't have expected these sources to generate novel viral diseases in the time in which they were used.

If you're wondering whether they sequester diseases that have been forgotten by the immune systems of people alive today, that seems quite possible. We're finding all sorts of interesting things in peat bogs and permafrost. If this environment adequately preserves bacteria or viruses, we might find something. I honestly have no idea about this kind of preservation, though.

There are already cases of archaeologists picking up ancient diseases from their finds...

Part of that I suspect is an (unofficial) tradition of licking archaeological finds for luck...

But they're so careful with those tiny brushes - seems totally counter to their field to contaminate the find.
When people are looking, the tiny brushes come out. When nobody's looking, it's shovels and excavators. The quicker you dig, the more artifacts you can find, and the more papers you can write and publish, leading to fame and fortune.
Isn't the licking to identify bone?
Wow, I assumed you were "yes-and"ing the parent commenter's joke, but it seems you're correct about the lick test.

Sounds like material for the pre-credits sequence of a low-budget horror movie.

>the parent commenter's joke

I'm quite sure that it wasn't a joke.