Maternal nutrition is a key determinant of gut microbiome development and function, with implications for both maternal and infant health, particularly in the context of gestational diabetes mellitus (GDM). This study examined the effects of two dietary interventions—a conventional high-fat diet (CONV) and a complex carbohydrate-rich diet (CHOICE)—on the gut microbiomes of pregnant women with GDM and their infants. Using integrated metagenomic and metaproteomic analyses, the study aimed to assess not only taxonomic differences but also functional metabolic activities across the two dietary groups.

While metagenomic data showed no significant differences in microbial species composition or functional gene content between the CONV and CHOICE diets, metaproteomic analyses revealed marked differences in microbial protein expression. The CHOICE diet significantly increased microbial functional diversity and metabolic activity, particularly in pathways associated with energy production, amino acid metabolism, and short-chain fatty acid (SCFA) synthesis. In mothers, the metaproteome confirmed functional realization of these pathways, suggesting active metabolic contributions from key microbial species. In contrast, infants exhibited substantial metagenomic enrichment—especially of Bifidobacterium species—but minimal protein-level activity, indicating a developmental lag in microbial function.

These findings emphasize that dietary composition during pregnancy influences not just microbial presence but also metabolic output. The CHOICE diet promotes a more functionally diverse and metabolically active maternal microbiome, which may offer protective effects in GDM and facilitate the early colonization of beneficial microbes in infants. The study underscores the importance of incorporating functional data into microbiome analyses and supports the development of precision nutrition strategies to improve maternal and infant metabolic health outcomes.