Much of the prior century was spent applying the latest emerging technologies toward managing pregnancy, childbirth, and infant development. The idea was that each change was significantly improving the health of our children across their lifetime. But it is now clear that with several of the adopted practices, there have been unintended consequences. We have run the risk of losing certain distinct advantages that were inherently embedded in ancient cultures and practices. Among these were the microbial-rich experiences of natural childbirth, breastfeeding, and agrarian living. These practices permitted children to acquire a complete microbiome thereby facilitating immune development and appropriate later-life immune responses. Perceived technology-associated benefits such as scheduled Caesarian births, urban sanitized living, and earlier and ever increasing vaccine burdens have helped to reduce the burden of some childhood illnesses. But recent studies suggest that they have also produced serious, unanticipated consequences for today’s children: an increased likelihood for human-microbiome incompleteness, lifelong immune dysfunction, and inflammation-promoted chronic disease. This review will examine recent evidence suggesting that a more effective blending of ancient practices and remedies with modern technology and medical knowledge could help to restore the human-microbiome super organism to its historic status, improve pediatric immune homeostasis and reduce risk of later-life chronic diseases.