Genomics and functional dynamics of host-microbiome systems in humans

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Concurrent with industrialization, the human gut microbiome has drastically decreased in diversity and shifted in composition. However, to what extent transitioning from hunter-gatherer to industrialized lifestyles impacted host-microbiome interactions and host physiology is unknown. Here, we generate gut microbiome multi omics data coupled with host physiology from dozens of populations worldwide, ranging from hunter-gatherers to fully industrialized groups, and show that intestinal inflammation, humoral immune response and patterns of horizontal gene transfers (HGT) between bacteria strongly changed with industrialization. We reveal that industrialized gut microbiomes associate with elevated secretion of intestinal immunoglobulin A, despite lower levels of parasitic incidence. Furthermore, populations with hunter-gatherer lifestyles exhibit the lowest levels of intestinal inflammation. Finally, we show that gut bacteria within the microbiome of industrialized individuals exchange genes more frequently than in non-industrialized populations, potentially in response to increased environmental perturbations. Overall, our results suggest that industrialization perturbed our gut ecosystem and homeostasis on many levels, which could contribute to many chronic inflammation diseases.