The present invention describes changes in bacterial gastrointestinal, cutaneous and nasal microbiota associated various mammalian medical conditions. Described are diagnostic tests that arise from combining phylogenetic information about the families,
genus, and species of the
microbiome and their relative abundance with the metabolic information contained in the metatranscriptome to determine the presence and absence of a
disease or medical condition. Provided are compositions of
bacteria, co-cultures of
bacteria and a carrier for use in treating the disclosed medical conditions. The described compositions restore or correct
disease- or medical condition-related imbalances in the
microbiome profile with culture-conditioned formulations in which the
transcriptome activity of the administered organisms is optimized. Alternatively, formulations of metabolites that drive changes in the metatranscriptome native to the
mammal that treat
disease or a medical condition or restore health are taught.