I've got Dr. Michael Ruscio's book coming: Healthy Gut, Healthy You: The Personalized Plan to Transform Your Health from the Inside Out (2018).

In the below video, he talks of recovered microbiatas from the paleolithic era - after 12 minutes.

referenced paper:

Phylotyping and Functional Analysis of Two Ancient Human Microbiomes

We examine two paleofecal samples originating from cave deposits in Durango Mexico and dating to approximately 1300 years ago.

The Gut; Diet, Flora, Health and Disease — Michael Ruscio, D.C., B.S. (AHS14)