Abstract Bacteria deliver a significant functionality (e.g., metabolic capability) in the gut microbiome of humans; however, Archaea and microeukaryotes (fungi and protozoans) exert important influences that are only starting to be explored. These polymicrobial interactions help regulate the expansion and overgrowth of opportunistic organisms, and serve important roles in shaping immune responses. Fungal communities, for example, can be acquired vertically during birth or from the environment and serve important roles in shaping the composition of bacterial communities in ways that are not yet fully understood. Extremely and very low birth weight (E/VLBW) preterm infants are born with very immature immune systems and are particularly vulnerable to invasive infections, so they are often treated with broad-spectrum antibiotics and antifungals. These premature infants spend the most amount of time in the neonatal intensive care units and experience a variety of stressors. The use of broad-spectrum antimicrobials likely has long-term impacts on the developing bacterial and fungal communities that colonize the infant gut, and this in turn may impact long-term health. And because the metabolic potential of the gut microbiome is a product of the interactions of prokaryotic and eukaryotic microbes, there is an urgent need for ‘microbiome’ studies to incorporate more comprehensive approaches (e.g., multi-omic) to capture the gene products and signature metabolites impacting functional interaction networks. We have shown that prematurity among E/VLBW infants includes a significant dysbiosis that likely impacts key metabolite signatures that may influence nutrient sensing and/or calorie processing capabilities, in ways that can impact growth and development. This study will leverage banked temporal stool samples from E/VLBW infants, many of which were followed until the age of 4, to evaluate functional metabolic networks via metagenomic sequencing and metabolomics. Early changes to the microbiome may also contribute to or predispose later health, such as metabolic dysfunction and obesity. We propose that the products of a perturbed E/VLBW infant gut microbiome are linked to long-term health consequences that are not yet fully understood, but likely include effects on nutrient sensing, metabolic processing of caloric intake, and subsequent growth in the first few years of life.