I just read this article about what palaeofaeces can tell us about how our gut microbiome has changed in more industrialised societies:

What 2,000-year-old poo says about our gut bugs

One of the influences on modern day gut microbiome is the use - or overuse - of antibiotics. Coincidentally, I just watched a medical documentary about that this week. Another is the modern diet in many developed countries, including lots of junk or fast foods.