An Ifnar1 allele impairs the colonization of gut bacteria and promotes tuberculosis

Both host genetics and gut microbiome have important effects on human health, yet how host genetics regulates gut bacteria and further determines disease susceptibility remains unclear. Here, we find that gut microbiome pattern of active tuberculosis (TB) patients is characterized by a reduction of core species found across healthy controls, particularly Akkermansia muciniphila (A. muciniphila). Oral treatments of A. muciniphila or palmitoleic acid, an A. muciniphila-derived metabolite, strongly inhibit TB infection through epigenetically inhibiting TNF-α. We use three independent cohorts comprising 6512 individuals and identify that single-nucleotide polymorphism rs2257167 “G” allele of type I interferon (IFN-I) receptor 1 (Ifnar1) contributes to stronger IFN-I signaling, impaired colonization and abundance of A. muciniphila, reduced production of palmitoleic acid, higher TNF-α, and much severer TB disease in humans and transgenic mice. Thus, host genetics are critical in modulating structure and functions of gut microbiome and gut microbial metabolites, which further determines disease susceptibility.