One of the best ways to populate the microbiome with good bacteria is to eat what are called sour vegetables or fermented vegetables. This is valuable for all diets, not just plant based diets. One of the last hunter gatherer tribes on earth lives in Tanzania. When they kill an animal, the first thing they do is cut open the stomach and eat the contents raw. This gives them vitamins and minerals, but also repopulates their microbiome with good bacteria. I have never seen a Paleo diet proselytizer advocate this. Eating fermented vegetables is equivalent, and a lot more convenient.
There are lots of videos online about how to make fermented vegetables, but here is a simple recipe.
Clean and dry one of those 1 gallon or 5 quart plastic ice cream pails, with a lid. You can use glass or pottery (the traditional method), but polyethylene is used to hold reagents, so is adequate.
Chop enough vegetables into bite size chunks to fill the pail to within about 1 inch of the top. You can use cabbage, broccoli, cauliflower, brussel sprouts, carrots, onions, garlic, celery, radish, beets. You can use potatoes, if you place them at the bottom of the pail so they will not be exposed to air. The starch they contain will attract fungus if they are exposed. No fruit or tomatoes.
Place the chopped vegetables into the pail, placing the less dense vegetables like cabbage on the bottom (and potatoes), and denser ones like carrots and cauliflower on top.
When all the vegetables are in and compacted a little, place spices you want on the top. I use turmeric, thyme, oregano, rosemary, sage, basil, marjoram, and a teaspoon of chile powder. Be sure there is no salt in the spices, because it might be iodized and that will kill the ferment.
After the spices, add between 4 and 8 teaspoons of non-iodized salt. I experimented till I found the right amount that tastes good to me. It is very important that this be non-iodized salt, as the iodine is a bacteria killer. You might have heard of using tincture of iodine to sterilize water if there is no other way.
Add water until the vegetables are slightly floating. Pour it over the spices and salt so they move down into the mix with the water. The water you use is important. Use distilled or reverse osmosis water (like the kind from the machines outside grocery stores). These get rid of any chlorine in the water. Chlorine also kills bacteria, which is why it is added to drinking water, and thus is in tap water. Activated carbon filtration will also remove chlorine; those container style water filters like Pur contain activated carbon filters.
Take a plate that is roughly the circumference of the pail and place it on top of the vegetables with the hollow side up. Gently press down until the water rises to the level of the edge of the plate. That ensures that all the vegetables are under the water, necessary for anaerobic fermentation.
Place the lid on the pail. Press down on the center of the lid and lift the edge a little so the air can bleed out.
Put it in a cool place out of direct light. I use the oven, but that won't work if you are going to be baking.
Nothing much will happen for the first day. The bacteria from the vegetables are multiplying and getting established. By the second day you will notice that the lid begins to bulge up as the bacteria begin digesting the fiber in the vegetables. Bleed the gas off without taking the lid off, the same way as when you first put the lid on. If you want to get fancy you can use a lid with a check valve that will bleed the pressure without allowing air back in. Brewery stores should have them. The gas that comes off will be methane with a little hydrogen sulfide (rotten egg smell). No carbon dioxide because this is anaerobic. At peak ferment, you will have to bleed the gas about 3 or 4 times a day. Say morning, afternoon, night.
The ferment will be mostly over after a week, and you can then put the pail in the fridge. It will keep there for months, but you should probably eat the vegetables within a few months. You can eat them raw, and the liquid is delicious. I use a ladle to grab some to eat, and drink the juice. Don't place it back in the solution after you have touched it with your mouth without washing or you will introduce bacteria from your mouth that will probably cause mold. You can also cook the vegetables and juice, and it becomes pre-biotics. It kills the bacteria, but they act like a vaccine for your gut to recognize them, and become immune to them.
The first time you eat them, after a few hours you will find yourself farting a lot. That is the new bacteria establishing themselves in your gut, especially if you eat them with some fresh vegetables that they can feed on in your gut. The farts wont really smell as they will be mostly methane. After that, it won't happen again unless you upset your microbiome and have to reestablish it.