Everyone knows about standard types of yogurt and pickles and whatnot - there is a whole world of legume ferments (mainly beans) that use much more 'advanced' types of microorganisms. Examples would be things like Natto from Japan mentioned in the article (using Bacillus Subtilis). Unlike the simple yeasts that break down milk sugars in yogurt and produce various organic acids (like acetic acid for example) the bacteria in Natto can consume the resistant starch in beans and produce short chain fatty acids like Butyrate (very beneficial for health) AND can break down the complete protein in soybeans into their constituent amino acids. I believe Natto originally came about because cooked and cooled soybeans were then wrapped in rice leaves for transport and Bacillus Subtilis happens to naturally live on those leaves.
It is also really unfortunate that in the west we miss out on tons of fungi based foods (not talking about anything psychedelic here) as many mushrooms contain tons of prebiotic fiber like substances that feed the probiotics already found in our gut.