Bacterial infections present a significant threat to neonates. Increasingly, studies demonstrate associations between human diseases and the microbiota, the communities of microorganisms on or in the body. A "healthy" microbiota with a great diversity and balance of microorganisms can resist harmful pathogens and protect against
infections, whereas a microbiota suffering from
dysbiosis, can predispose to pathogen colonization and subsequent
infection. For decades, strategies such as bacterial interference, decolonization,
prebiotics, and probiotics have been tested to reduce Staphylococcus aureus disease and other
infections in neonates. More recently, microbiota transplant has emerged as a strategy to broadly correct
dysbiosis, promote colonization resistance, and prevent
infections. This paper discusses the benefits of a healthy neonate's microbiota, exposures that alter the microbiota, associations of
dysbiosis and
neonatal disease, strategies to prevent
dysbiosis, such as microbiota
transplantation, and presents a framework of microbiome manipulation to reduce Staphylococcus aureus (S. aureus) and other
infections in neonates.