Faecal Microbiota Transplantation Restores <em>Mycobacterium tuberculosis</em> Control in Mice Pre-Treated with Anti-Tuberculosis Antibiotics

Background: Anti-tuberculosis (anti-TB) antibiotics alter the gut microbiome, potentially affecting the host physiology and immune response. Here, we investigated the impact of anti-TB antibiotics on host gut microbiota, immune response, and Mtb control. Methods: We pre-treated mice with isoniazid, rifampicin, pyrazinamide, and ethambutol (HRZE) for two months, followed by intranasal Mtb infection five days post-HRZE cessation. HRZE pre-treated mice received faecal microbiota transplants (FMT) or phosphate-buffered sa-line (PBS) pre- and post-infection. Faecal DNA was isolated, and 16S rRNA gene se-quencing was performed. Mycobacterial burden, histology, and immune response were assessed in tissues four weeks post-infection. Results: We observed an enrichment of Bacteroides, Alistipes, Alloprevotella, Paraprevotella, and Colidextribacter, and depletion of Clostridia UCG 014, Roseburia, Ruminococcus, and Rikenellaceae RC9 gut group in HRZE pre-treated Mtb-exposed mice compared to infected mice without HRZE (control group). HRZE pre-treatment followed by Mtb infection was associated with marked ileal histo-morphological damage compared to infection alone. Furthermore, gut microbiota alter-ations in HRZE pre-treated mice were associated with poor control of the mycobacterial burden, reduced frequencies of CD4+ T and CD68+ macrophage cell populations, and altered release of IFN-γ, IL-6, and PD-1. Notably, although not completely, FMT improved ileal features, normalised microbiota taxa abundance, lowered Mtb burden, and rescued impaired immune phenotypes. Conclusions: These data highlight the untoward con-sequences of recent anti-TB antibiotics for host control of subsequent Mtb infection and suggest a potential therapeutic avenue for mitigating the effects of HRZE-induced mi-crobiota dysbiosis through FMT or probiotics-associated host-directed therapies to prevent TB recurrence.