I'd caution against drawing any conclusions about gut biome health and diet from the research so far. The field is very new and no causative outcomes have been linked to gut biome health. Here is an interview that provides a good overview of the literature from a researcher's perspective: https://www.youtube.com/watch?v=F9zPpAmmvE8
In terms of being completely self-sufficient in a temperate climate, it seems that calorie crops are the most critical component, with vegetables second but necessary for providing micronutrients. I suppose at some point you are going to have to make a tradeoff between efficiency and variety, as there may be only 2-3 calorie crops that are suitable for a home-scale gardener in a particular zone. Additionally, even among calorie crops, yields range widely. Based on what I'm reading in Jeavons' and Cox's The Sustainable Vegetable Garden
, here are what we see as the "moderate" biointensive yields of calorie crops that can be grown in my zone and I believe all the way north to you as well:
Potato (Irish) - 2lbs per sqft = 558 calories per sqft
Onions - 2lbs per sqft = 382 calories per sqft
Wheat - .1 lbs per sqft = 156 calories per sqft
Dry Beans - .1 lbs per sqft = 156 calories per sqft
Sweet Corn - .34 lbs per sqft = 133 calories per sqft
Now of course, there are lots of factors that can change those yields, but I'm more just using those as a baseline. So if I was aiming for pure self-sufficiency in a limited space, it would make sense for me to only grow potatoes as my calorie crop and then grow whatever varieties of veggies I feel like that will provide enough micronutrient yield. Of course I'd incorporate companion planting, closed loop systems, etc while trying to utilize as many permaculture principles as possible. If that strategy is taken, likely the bottleneck will be processing, as we've already discussed.
In my particular plan (work in progress), I may end up getting a good chunk of my leafy green nutrition from microgreens, so I'm unsure of how many vegetables I would grow other than the basics to provide variety and ingredients for meals (peppers, tomatoes, carrots, etc). I still have not done the calculations to plan out my spring garden yet, but I at least like that the book provides me with a baseline to plan off in terms of seeds, space, and yields (so I don't end up with the hundreds of pounds of zucchini problem).
I plan on supplementing the calories from my garden with fishing and hunting, so I still have to calculate what my garden caloric requirements would be. It's on my to do list.
Edit: The system wouldn't be very resilient with just one strain of a calorie crop, so I'd have to rely on a few different varieties to reduce risk of potato blight. TBD what my risk/reward framework is for my garden when I can just go to the store or dip into reserves if my crop fails.