Here’s a review on Cesarean and Vaginal births.
There’s a evidence that being inoculated with the mother’s intestinal flora affects the health of the infant. In Cesarean births, the infant is mostly inoculated with environmental bacteria instead, causing potential problems later in life.
As I understand it, it’s not an issue of exposure to the bacteria - they’re everywhere. Even antibiotics only cause a temporary imbalance.
The issue in diversity and type of gut flora is mostly what you feed them. Ancient hunter-gatherers ate a very wide variety of foods, and they ate different foods in different seasons. Very few people are still eating acorns, dandelion greens, fern shoots and insect grubs. Most of are eating some combination of only about a dozen major ingredients. On top of that, we’ve largely removed seasonality: only in modern humans is it possible to eat strawberries every day.
A less varied diet supports a less varied gut flora. The ones that like the food you eat will outcompete the ones that don’t like it. If you ate a little bit of everything, then each strain of gut flora would find something like they like and they would maintain a different population balance.