That's really not outside the realm of possibility for something to change the microbiome. That's a quarter pound of bread, two servings and about 280 kcal on the loaf I have in front of me. That's a reasonable amount for someone to consume as part of a normal diet.

We know small changes in diet can have a large effect on the microbiome. For example, adding seaweed to a mouse diet can select for microbes with the ability to digest particular polysaccharides within seaweed (https://www.nature.com/articles/s41586-018-0092-4). A company spun out of the Sonnenburg lab at Stanford is using this tech for microbiome therapeutics in humans (Novome). Those mice were given 10% seaweed by weight, so that serving of sourdough is right in the same range.

My point is, the researchers designing these experiments know what they're doing, and they're well thought out. You can't criticize something if you don't know the details of the field.