Search

The composition of the gastrointestinal microbiota influences systemic immune responses, but how this affects infectious disease pathogenesis and antibiotic therapy outcome is poorly understood. This question is rarely examined in humans due to the difficulty in dissociating the immunologic effects of antibiotic-induced pathogen clearance and microbiome alteration. Here, we analyze data from two longitudinal studies of tuberculosis (TB) therapy (35 and 20 individuals) and a cross sectional study from 55 healthy controls, in which we collected fecal samples (for microbiome analysis), sputum (for determination of Mycobacterium tuberculosis (Mtb) bacterial load), and peripheral blood (for transcriptomic analysis). We decouple microbiome effects from pathogen sterilization by comparing standard TB therapy with an experimental TB treatment that did not reduce Mtb bacterial load. Random forest regression to the microbiome-transcriptome-sputum data from the two longitudinal datasets reveals that renormalization of the TB inflammatory state is associated with Mtb pathogen clearance, increased abundance of Clusters IV and XIVa Clostridia, and decreased abundance of Bacilli and Proteobacteria. We find similar associations when applying machine learning to peripheral gene expression and microbiota profiling in the independent cohort of healthy individuals. Our findings indicate that antibiotic-induced reduction in pathogen burden and changes in the microbiome are independently associated with treatment-induced changes of the inflammatory response of active TB, and the response to antibiotic therapy may be a combined effect of pathogen killing and microbiome driven immunomodulation., Antibiotic therapy can lead to pathogen clearance, but also to alterations in the gut microbiota and systemic immune responses. Here, the authors analyze data from patients with tuberculosis and healthy subjects to show that pathogen clearance and gut microbiota alterations are independently associated with antibiotic-induced changes of the inflammatory response of active tuberculosis.

Although the composition of the intestinal microbiota influences systemic immune responses, the contribution of this relationship to infectious disease pathogenesis and to the resolution of infectious diseases by antibiotic therapy is poorly understood. This question is rarely examined in humans due to the difficulty in dissociating the immunologic effects of antibiotic-induced pathogen clearance and salutary microbiome alteration. To address these questions in the context of Tuberculosis, we analyzed three independent human datasets from Haiti (two longitudinal treatment and one cross-sectional control), a prototypical infection remarkable for chronic inflammation, in which we had measured sputum TB bacterial load, gut microbiota composition, and peripheral blood transcriptomics. Using data from the longitudinal datasets combined with inflammatory pathway enrichment analysis, we determined that antibiotic treatment of TB, despite significantly perturbing the gut microbiota, dampens the proinflammatory signature characteristic of active TB. Contrarily, an investigational TB treatment that failed to clear TB, but that caused similar microbiota perturbations, exacerbated peripheral inflammation. To decouple the effects of antibiotic induced changes in the microbiota from Mtb sterilization as predictors of normalization of TB associated inflammation, we applied random forest regression to the microbiome-transcriptome-sputum data from the two longitudinal datasets. We found inflammatory renormalization is positively affected by both pathogen sterilization and by the abundance of health-associated Cluster IV and Cluster XIa Clostridia. Oppositely, increases in the abundance of commonly known pathobionts such as Bacilli and Proteobacteria clusters predict inflammatory exacerbation. We independently investigated and validated these microbiota-peripheral inflammatory signature associations by applying machine learning to the peripheral gene expression and microbiota profiling in an independent human cohort of 52 healthy control individuals. Together, our findings indicate that antibiotic-induced reduction in pathogen burden and changes in the microbiome are independently associated with treatment-induced changes of the inflammatory response of active TB, and more broadly indicate that response to antibiotic therapy may be a combined effect of pathogen killing and microbiome driven immunomodulation. Our results provide support to the hypothesis that there exists clear links between microbiome composition and host peripheral gene expression in humans that can be biologically elucidated using common and well validated molecular pathway analyses.