The neonatal microbiome includes all the microorganisms living within or on the
surface of the newborn, as well as their genes (i.e., bacteria, fungi, and viruses), which are composed
mainly of bacteria. The majority of these microorganisms reside in the gastrointestinal
tract (GIT), which is known as the gut microbiome. They include trillions of microbes, which
exceed the total number of neonate cells. In this study, we have examined factors affecting neonatal
microbiome colonization, various phyla of the microbiome in neonates, and their characteristics.
In addition, we have discussed symbiosis and dysbiosis, precipitating diseases, breast
milk’s role in the neonatal gut microbiome, prebiotics, probiotics, postbiotics, and synbiotics, as
well as the airway or respiratory microbiome, and the main role of the neonatal microbiome. We
have also discussed neonatal mycobiome and neonatal virome, as well as the research done on
the neonatal microbiome.