Borreliosis and doxycycline treatment disrupt gut microbiota and immune responses in nonhuman primates

<i>Borrelia burgdorferi</i> (Bb) is the spirochete that causes Lyme disease (LD). Transmission to humans occurs via bites of infected <i>Ixodes</i> spp. ticks. Doxycycline is often used to treat LD patients, which is sometimes delayed due to current diagnostic challenges. Recently, several lines of evidence show dysbiosis of the gut microbiome in LD patients, which may be a host factor contributing to pathogenesis and symptomology but is still an understudied area in the field. To address this knowledge gap, we longitudinally compared the immune response and gut microbial composition of Japanese macaques after intradermal infection with Bb strain 297 with or without doxycycline treatment. Immunological and microbial changes were monitored longitudinally using enzyme-linked immunosorbent assay, flow cytometry, single-cell genomics, and 16S amplicon sequencing assays. All Bb-inoculated animals seroconverted to produce Bb-specific antibodies. Borrelial DNA was undetected by real-time quantitative PCR in the skin, blood, and cerebrospinal fluid. Levels of CXCL13, a B cell chemoattractant, increased following infection but reached a nadir after treatment. The frequency of circulating immune cells remained constant over the course of the study, but gene expression analysis showed downregulation of antimicrobial genes in monocytes, dendritic cells, and B cells until late in infection, regardless of treatment. Infection and antibiotic treatment led to a loss of gut commensals important for maintaining gut integrity. Finally, untreated infected animals showed mononuclear myocarditis along with sporadic detection of borrelial DNA. Data from this study suggest aberrant B cell activity, myocarditis, and loss of important commensal microbes as factors contributing to symptoms of untreated Lyme disease.IMPORTANCELyme disease (LD) is caused by <i>Borrelia burgdorferi</i> (Bb) transmitted via tick bite. The incidence of LD is expanding in North America and Southeast Asia. LD patients are frequently misdiagnosed or receive delayed treatment due to the lack of sensitive diagnostic strategies. The pathophysiology of LD remains poorly understood because of challenges with clear infection timelines in clinical studies. Here, we utilize Japanese macaques to provide an in-depth longitudinal investigation into the host immunological and gut microbial changes in response to Bb infection. This work highlights CXCL13 as a potential Bb diagnostic marker, as well as host factors such as aberrant B cell activity, mononuclear myocarditis, and gut dysbiosis as potential therapeutic targets.