Human longevity and quality of life remain key societal drivers, but the healthcare burden of diet-related chronic diseases is economically unmanageable. In recent years, it has been proposed that the composition and abundance profiles of certain bacterial phyla in the gut are indicators of malnutrition, and ill health. But, how much does the gut microbiome and diet really contribute to outcomes? The description of three microbial enterotypes remains to be verified, as does its significance for health tested across continents and within people who migrate from one lifestyle to another. It is not simply that the diet of one region causes a dominance of microbes not found in another, or that it leads to adverse outcomes. Venezuelans have a diet different from Americans, yet life expectancy and causes of death are somewhat similar. Pregnant east African women have very different diets to Europeans, yet excluding infectious disease exposure, successful reproduction occurs in both. The microbiome has added another layer of complexity to nutrition management, but with modern sequencing platforms and bioinformatics tools, integration of this information will soon be feasible. In providing dietary recommendations, especially during pregnancy, more consideration is needed on reducing exposure to environmental toxins, encouraging intake of fermented foods and those designed to improve fetal and infant development. By focusing on the first 1000 days of life, it may be possible to improve how we produce and allocate food, and provide a newborn with the best chance of leading a productive life.