One of the big problems with our food supply is that so much of what we consume has become overly sanatized, packaged, and barcoded LOL. (I often tell people who want to alter their diet, eat better, and improve some existing health problems, that the best thing they can do is go on a "bar code" free diet. Just eat what they feel is healthy and fresh but nothing with a bar code on it!) Maybe this will become the new fad diet--The Dr Phil Bar Code Free Diet Plan!
The problem is that so many of the commercial outlets for food distribution have overly sanitized and processed our foods to aid in distribution and profit making. Take Trader Joe's (in the States) for example. Most of what they sell (even with their organic produce) is overly washed, packaged, bar coded, etc. To get this stuff to market, most is picked way early and thus the nutrient content is also impacted. This has been the trend for groceries for a number of years now.
From a "how can this really benefit your microbiome perspective," this is basically sterile food. The good microbes have been taken away. A much better thing is to grow your own organics or to shop for your produce at local farmer's markets, just lightly rinse off what you eat, and then enjoy. Produce harvested this way is likely much more beneficial. What's becoming very important and the conversation we need to be having isn't just what we eat or avoid but the quality and source of what we eat.
I think articles like the above and new research that is being published about foods and the microbiome are starting to really shine the light on this.