{
  "abstract": "Background\n\nThe role of the lower airway microbiome in COVID-19-associated mortality remains poorly understood despite evidence implicating secondary pathogens and non-airway commensals. The influence of prior immunosuppression on the lower airway microbiome and its contribution to mortality in mechanically ventilated patients has been largely unexplored. Given that host-microbiome interactions are dynamic, we assessed longitudinal patterns in the respiratory microbiome associated with mortality and immunosuppression status.Results\n\nWe conducted longitudinal forecasting, differential abundance, and comparative network analyses of metatranscriptomic data from 604 upper and lower airway samples collected from 243 mechanically ventilated COVID-19 patients to profile key microbial factors associated with immunosuppression and clinical outcome. SARS-CoV-2 was enriched over time in immunosuppressed patients and in both immunosuppressed and immunocompetent patients who died, highlighting the need for aggressive viral infection control early in the disease course. Using longitudinal forecasting and differential abundance analyses, we observed a progressive increase in opportunistic pathogens, such as Staphylococcus aureus and Escherichia coli, among the taxa most predictive of mortality. Concurrently, immunosuppressed individuals exhibited a significant decrease in typical airway commensals alongside a restructuring and marked destabilization of the microbial community compared with their immunocompetent counterparts.Conclusions\n\nThese findings indicate that loss of airway microbiome stability in immunosuppressed patients constitutes an independent factor contributing to increased susceptibility to opportunistic pathogens and poor clinical outcomes. Video Abstract.",
  "abstract_shown": true,
  "affiliations": [
    "Systems Genomics Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.",
    "Division of Pulmonary and Critical Care Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.",
    "Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.",
    "Gutz Technologies, Corvina, CA, USA.",
    "Division of Pulmonary and Critical Care Medicine, VA New York Harbor Healthcare System, New York, NY, USA.",
    "Division of Rheumatology, Department of Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.",
    "Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, NYU Langone Health, New York, NY, USA.",
    "Systems Genomics Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA. elodie.ghedin@nih.gov."
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 14,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Matthew Chung"
    },
    {
      "affs": [
        1,
        2
      ],
      "name": "Clea R Barnett"
    },
    {
      "affs": [
        3
      ],
      "name": "Lars Hunger"
    },
    {
      "affs": [
        1,
        2
      ],
      "name": "Imran Sulaiman"
    },
    {
      "affs": [
        1,
        2,
        4
      ],
      "name": "Benjamin G Wu"
    },
    {
      "affs": [
        1,
        2
      ],
      "name": "Yonghua Li"
    },
    {
      "affs": [
        1,
        2,
        4
      ],
      "name": "Jun-Chieh J Tsay"
    },
    {
      "affs": [
        1,
        2
      ],
      "name": "Shari B Brosnahan"
    },
    {
      "affs": [
        2
      ],
      "name": "Cecilia J Chung"
    },
    {
      "affs": [
        1,
        2
      ],
      "name": "Luis Angel"
    },
    {
      "affs": [
        5
      ],
      "name": "Gregg J Silverman"
    },
    {
      "affs": [
        3
      ],
      "name": "James T Morton"
    },
    {
      "affs": [
        1,
        2,
        4,
        6
      ],
      "name": "Leopoldo N Segal"
    },
    {
      "affs": [
        7
      ],
      "name": "Elodie Ghedin"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/dhdvh1z6jzw9h.bib",
  "cited_by": 0,
  "doi": "10.1186/s40168-026-02462-1",
  "fulltext_url": "https://europepmc.org/articles/PMC13679178",
  "id": "dhdvh1z6jzw9h",
  "issns": [
    "2049-2618"
  ],
  "landing_url": "https://europepmc.org/article/MED/42897671",
  "language": "eng",
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "lcc",
      "QR100-130"
    ],
    [
      "openalex",
      "2725|COVID-19 Clinical Research Studies"
    ]
  ],
  "openalex": "W7170166078",
  "pdf_url": "https://europepmc.org/articles/PMC13679178?pdf=render",
  "pmcid": "PMC13679178",
  "pmid": "42897671",
  "published": "2026-07-01",
  "publisher": "BMC",
  "ris": "https://research.draconitic.com/paper/dhdvh1z6jzw9h.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:19:41Z",
      "native_id": "MED:42897671",
      "source": "europepmc",
      "url": "https://europepmc.org/article/MED/42897671"
    },
    {
      "first_seen": "2026-10-30T13:46:10Z",
      "native_id": "5e769149c5c54fc2ab16ea7fa8b287dd",
      "source": "doaj",
      "url": "https://doi.org/10.1186/s40168-026-02462-1"
    }
  ],
  "subjects": [
    {
      "field": "medicine",
      "origin": "openalex:2725|COVID-19 Clinical Research Studies",
      "subfield": "infectious-disease"
    }
  ],
  "title": "Immunosuppression is associated with loss of airway microbiome resilience in severe COVID-19.",
  "title_text": "Immunosuppression is associated with loss of airway microbiome resilience in severe COVID-19.",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T13:46:10Z",
  "url": "https://research.draconitic.com/paper/dhdvh1z6jzw9h",
  "venue": "Microbiome",
  "versions": []
}