> an increase in Bifidobacterium abundance. (Was not clear on a first read if that is necessarily always positive).

The total effect of a microbiome is not an additive function of the individual species. These species interact in highly complex ways. Some species might normally release factors that are detrimental to health, but their behaviour is suppressed by other species present in the flora. Therefore the individual species are not of therapeutic relevance; due to limitations in our understanding, each flora must be considered as a whole.