The study doesn't show this: it compares humans (who happen to live in cities) to primates (who definitely don't live in cities). It doesn't compare between human populations.
Ironically, cities (particularly affluent ones, but in general) probably have better access to fresh and healthy produce than do medium or low-income rural areas. Some of that is supply and demand (the economics of moving bulk produce favor large population clusters), and some of it is pricing (affluent consumers prefer cities and suburbs on average). You can see these trends in the USDA's Food Atlas[1], which shows lots of rural areas with poor access to produce.
Based on the way my body responds and reviewing lab results after trying different diets, I am of the opinion that it has more to do with processed foods versus minimally/unprocessed foods. I don’t think whether it is plant or meat/dairy based really matters that much nutritionally. Enriched flour, is plant based but by no means do I believe that to be healthy. Same goes for sausage and bacon, too processed. N of 1 but since I stopped consuming processed food and stopped worrying about cholesterol while restricting calories, eating plenty of fruit & veggies, and exercising, I have actually lowered my ldl cholesterol by 40 points. Triglycerides were fine. Dr was thrilled, didn’t have the heart to tell her I didn’t follow her advice.
Having lived both in the city and fairly rural, I can say that access to a healthy and varied diet is much much easier in the city. Both when it came to restaurants and buying and cooking food.
"Cities are unnatural therefore they contain less natural foods" is the West Coast/boomer environmentalism mindset, so this is actually a California moment.
City dwellers tend to eat a lot more unhealthy foods. They also eat a lot less vegetables, fruit and nuts than their rural country(wo)men.
You want more microbes in your gut? Eat more plant-based food.