The principle behind modifying the gut microbiome to achieve good outcomes requires the intestinal flora to change: that means, for example, that some bacteria must die and some bacteria must proliferate. This is one of the main reasons why curcumin (from turmeric), for example, is the subject of much research in the field.

Anti-microbial properties don't apply equally to all species of microbes, and such selective action is essential for modulating the microbiome.

Disturbances of the gut flora do tend to lead to poorer outcomes more often than not, but this is not a hard rule. It's rather that complex machines are fragile, and most modifications done in flight lead to adverse outcomes: without prior knowledge and generally speaking, it's a bit like adding or removing a random line of code in a large application.

Fungi tend to compete with bacteria; if modern lifestyles generally tend to result in a overly fungus-heavy gut biome, a food with anti-fungal properties could restore healthy balance.