Modern World Influences on the Microbiome and Their Consequences for Immune-Mediated Disease

Abstract

(...) It is increasingly clear that our microbiomes, defined as the collective genomes of the microbes (including bacteria, bacteriophage, fungi, viruses, protozoa, and helminths) that populate our bodies, profoundly influence all aspects of our physiology. Humans have coevolved with the microbes that inhabit their skin and mucosal surfaces (1). Twenty-first century human microbiomes differ substantially from those that colonized our ancestors, as demonstrated by sequence analysis of ancient paleofeces (2) or of samples collected from living indigenous populations (3). In particular, the lifestyle changes associated with industrialization, including increased sanitation, antibiotic use, consumption of processed foods, and urban living, have reduced microbial diversity and altered both community structure and function (4). Some losses may be more consequential than others; it is now clear that the depletion of microbial metabolites beneficial to host health is associated with a rapid rise in noncommunicable chronic diseases (NCCDs) (5). To stem the tide of NCCDs, we need a better understanding of how microbes, and their metabolites, influence host immunity. Much of the current literature is based on associations of bacterial taxa and disease with little evidence for causality. Because the diets and geocultural practices of human societies are highly diverse, we don’t even have a clear definition for a healthy microbiome. In keeping with the focus of The Journal of Immunology, the outstanding contributions to this special collection add to our understanding of the microbiome’s influence on immunity. (...)