Exposure to farm animals and pets, vaginal birth and breast milk, all of which have a potential microbial link, are putatively associated with a beneficial effect on the developing gut microbiome and host immune response. Factors such as urbanization (lack of microbial exposures), formula-only diet and antibiotic administration during the neonatal stage are associated with the development of subsequent chronic diseases such as asthma and atopy, putatively through the development of aberrant gut microbiomes.