{
  "abstract": "Pulmonary tuberculosis (TB) is associated with systemic alterations extending beyond the lungs, yet the longitudinal impact of anti-tuberculosis therapy (ATT) on gut ecosystem recovery remains poorly understood. Here, we performed a longitudinal multi-omics analysis of gut microbial and metabolic dynamics in pulmonary TB patients (n=8) followed at baseline, 1, 6, and 8 months of ATT, compared with healthy household contacts (HHCs; n=8). Shotgun metagenomics, functional profiling, untargeted fecal metabolomics, resistome, plasmidome, virome, and microbiome-metabolome integration analyses were performed to characterize disease-associated alterations and treatment-associated recovery. Active, treatment-naive TB was characterized by reduced microbial diversity, altered community structure, depletion of beneficial commensals, and disruption of microbial functional pathways and metabolic profiles. During ATT, microbial diversity and functional/metabolic features progressively recovered; however, post-treatment profiles remained distinct from HHCs, indicating incomplete ecological restoration after microbiological cure. Microbiome-metabolome analysis revealed associations between altered bacterial taxa and metabolites involved in amino acid metabolism, bile acid transformation, oxidative stress, and host-microbial metabolic interactions. In contrast, resistome and mobile genetic element profiles demonstrated greater stability throughout treatment. HHCs exposed to index TB cases maintained relative gut ecosystem stability over time. Bacterial-AMR correlation analysis identified taxon-specific resistance associations among gut bacteria. Together, these findings provide a longitudinal systems-level view of gut ecosystem remodeling during TB and highlight that restoration of microbial homeostasis extends beyond pathogen clearance.",
  "abstract_shown": true,
  "affiliations": [
    "BRIC-National Institute of Immunology"
  ],
  "article_type": "PUBLISHAHEADOFPRINT",
  "arxiv": null,
  "author_total": 13,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "A. Pant"
    },
    {
      "name": "S. K. Yadav"
    },
    {
      "name": "J. Srinivasan"
    },
    {
      "name": "S. K. Gupta"
    },
    {
      "name": "B. P. Gurjar"
    },
    {
      "name": "P. Jana"
    },
    {
      "name": "D. Talukdar"
    },
    {
      "name": "S. P. Babu"
    },
    {
      "name": "S. Sarkar"
    },
    {
      "name": "Y. Kumar"
    },
    {
      "name": "D. Mohanty"
    },
    {
      "name": "B. Das"
    },
    {
      "name": "G. A. Arimbasseri"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/21f925x95tttk.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.10.05.26364754",
  "fulltext_url": "https://www.medrxiv.org/content/10.64898/2026.10.05.26364754v1.full",
  "id": "21f925x95tttk",
  "issns": [],
  "landing_url": "https://www.medrxiv.org/content/10.64898/2026.10.05.26364754v1",
  "language": null,
  "licence": "CC-BY-NC-ND",
  "licence_label": "CC BY-NC-ND",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by-nc-nd/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "medrxiv",
      "infectious diseases"
    ],
    [
      "openalex",
      "1312|Gut microbiota and health"
    ]
  ],
  "openalex": "W7220898175",
  "pdf_url": "https://www.medrxiv.org/content/10.64898/2026.10.05.26364754v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-10-05",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/21f925x95tttk.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:20:20Z",
      "native_id": "10.64898/2026.10.05.26364754",
      "source": "medrxiv",
      "url": "https://www.medrxiv.org/content/10.64898/2026.10.05.26364754v1"
    }
  ],
  "subjects": [
    {
      "field": "medicine",
      "origin": "medrxiv:infectious diseases",
      "subfield": "infectious-disease"
    }
  ],
  "title": "Longitudinal Multi-omics Reveals Persistent Gut Microbial and Metabolic Dysbiosis Following Anti-Tuberculosis Therapy",
  "title_text": "Longitudinal Multi-omics Reveals Persistent Gut Microbial and Metabolic Dysbiosis Following Anti-Tuberculosis Therapy",
  "type": "preprint",
  "updated_at": "2026-10-30T12:20:20Z",
  "url": "https://research.draconitic.com/paper/21f925x95tttk",
  "venue": "medRxiv",
  "versions": []
}