Tetracycline Antibiotics Induce Biosynthesis of Pro-Inflammatory Metabolites in the Immunobiotic <i>Bacteroides dorei</i>

The human gut microbiome consists of diverse microbes that communicate through small molecules. Numerous recent studies have demonstrated links between gut microbiota and host physiological processes; however, the underlying metabolites remain elusive in part because laboratory conditions do not replicate the native environment of these bacteria. Herein, we focused on <i>Bacteroides dorei</i>, a predominant and representative member of human gut microbiota, to interrogate the chemical composition and possible biological functions of its secondary metabolome. Using UPLC-MS-guided high-throughput elicitor screening (HiTES), we examined how the metabolome of this commensal bacterium responds to hundreds of FDA-approved drug molecules that the host may intake. We identified low-dose tetracyclines as pleiotropic inducers of the <i>B. dorei</i> secondary metabolome, leading to the identification and structural elucidation of six serine-glycine dipeptide lipids, named doreamides A-F, and two 6-<i>N</i>-acyladenosines. The induced doreamides and <i>N</i>-acyladenosines exhibited pro-inflammatory activities, upregulating tumor necrosis factor α (TNFα), interleukin (IL)-1β, IL-6, and IL-10 in macrophages. Doreamides also triggered production of cathelicidin, which inhibits the growth of multiple bacteria tested but not <i>B. dorei</i>. Our results show that low-dose antibiotics can perturb the secondary metabolome of gut bacteria, and that these induced metabolites can exert immunomodulatory effects and restructure the microbiome.