Great article. The current consensus is that we contain roughly an equal amount of microbial and human cells. The view that we were outnumbered 10 to 1 by bacteria was based on research that used colon populations to estimate the entire intestinal tract. The colon has very dense populations, hence the over-estimation.
Antibiotics save lives. They do wipe out our own microbial diversity, but sometimes this is necessary as we don't yet have an alternative. Staying alive with an unhealthy gut, is better than being dead.
Antibiotics are used needlessly in many cases, and because they are used so much, pathogens are developing resistance to them. Doctors need to reduce the number of prescriptions of antibiotics, but unfortunately they give into patient pressure and give them out when not required.
As you said, lots of fresh fruit and veg, high fibre diet, and possibly fermented foods such as kefir and kimchi, will lead to a healthy gut.