{
  "abstract": "Background: Acute COVID-19 alters the airway microbiota. Whether these changes persist post-COVID-19 and contribute to long COVID is unknown. We aimed to describe the microbiota by long COVID severity and subtype, and identify links with inflammation.\n\nMethods: Adults were prospectively recruited to the longitudinal UK Post-hospitalisation COVID-19 study (PHOSP-COVID). Patients were grouped by previously described “severity clusters” (of ongoing health impairments) and symptom subgroups. Oral and sputum microbiota (at 6 months post-discharge) were characterised through 16S ribosomal RNA gene amplicon sequencing, and microbiota diversity was assessed. Co-occurrence network analysis identified keystone taxa. Associations between keystone taxa and plasma inflammatory proteins were assessed through Spearman's rank correlations.\n\nResults: 771 participants had their microbiota assessed. Of participants with oral rinses and “severity cluster” assignment (mean age 57.5 years), 278 out of 722 (38.5%) were women. The “very severe” cluster, in which disease was predominantly pulmonary in nature, was associated with a distinct microbiota profile post-COVID-19. Reduced lung function was associated with a distinct oral microbiota profile. Persistent neurocognitive symptoms were associated with a distinct oral microbiota profile, while gastrointestinal symptoms were associated with a distinct sputum microbiota profile. Microbiota keystone taxa shifted to a higher prevalence of lactic acid bacteria associated with worse health outcomes. Lactic acid bacteria abundance was associated with elevated blood inflammatory proteins.\n\nConclusion: Distinct oral and sputum microbiota profiles were associated with pulmonary function and with neurocognitive and gastrointestinal symptoms in long COVID. Shifts in keystone microbiota taxa linked with inflammation, based on worse health outcomes, suggest a potential role change for lactic acid bacteria, which may be associated with the host immune response.",
  "abstract_shown": true,
  "affiliations": [
    "University of Dundee, Ninewells Hospital and Medical School, Dundee, UK",
    "Department of Population Health Sciences, University of Leicester, Leicester, UK",
    "The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK",
    "NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK",
    "University Hospitals of Leicester NHS Trust, Leicester, UK",
    "Centre for Exercise and Rehabilitation Science, NIHR Leicester Biomedical Research Centre-Respiratory, University of Leicester, Leicester, UK",
    "Department of Respiratory Sciences, University of Leicester, Leicester, UK",
    "Therapy Department, University Hospitals of Leicester, NHS Trust, Leicester, UK",
    "Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK",
    "London School of Hygiene and Tropical Medicine, London, UK",
    "Roslin Institute, University of Edinburgh, Edinburgh, UK",
    "The Usher Institute, University of Edinburgh, Edinburgh, UK",
    "Royal Infirmary of Edinburgh, NHS Lothian, Edinburgh, UK",
    "School of Public Health, Imperial College London, London, UK",
    "Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK",
    "National Heart and Lung Institute, Imperial College London, London, UK",
    "Department of Psychiatry, University of Oxford, Oxford, UK",
    "Oxford Health NHS Foundation Trust, Oxford, UK",
    "Department of Psychological Medicine, Institute of Psychiatry, Psychology and Neuroscience, Kings College London, London, UK",
    "South London and Maudsley NHS Trust, London, UK",
    "Diabetes Research Centre, University of Leicester, Leicester, UK",
    "Population Health Sciences Institute, Newcastle University, Newcastle Upon Tyne, UK",
    "Newcastle upon Tyne Teaching Hospitals Trust, Newcastle upon Tyne, UK",
    "NIHR Oxford Health Biomedical Research Centre, University of Oxford, Oxford, UK",
    "University of Liverpool, Liverpool, UK",
    "The CRUK Liverpool Experimental Cancer Medicine Centre, Liverpool, UK",
    "Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK",
    "Imperial College Healthcare NHS Trust, London, UK",
    "Imperial College London, London, UK",
    "Centre for Medical Image Computing, University College London, London, UK",
    "Lungs for Living Research Centre, University College London, London, UK",
    "Royal Brompton and Harefield Clinical Group, Guy's and St Thomas’ NHS Foundation Trust, London, UK",
    "NHLI, Imperial College London, London, UK",
    "King's Centre for Lung Health, Faculty of Life Sciences and Medicine, King's College London, London, UK",
    "Department of Cardiovascular Sciences, University of Leicester, Leicester, UK",
    "Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK",
    "UCL Respiratory, Department of Medicine, University College London, Rayne Institute, London, UK",
    "University College London Hospital (UCLH) NIHR Biomedical Research Centre, and ILD Service UCLH, London, UK",
    "Wellcome–Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK",
    "Cambridge NIHR Biomedical Research Centre, Cambridge, UK"
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 80,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Daniela Alferes de Lima Headley",
      "orcid": "0000-0002-5125-1657"
    },
    {
      "affs": [
        0
      ],
      "name": "Hollian Richardson"
    },
    {
      "affs": [
        0
      ],
      "name": "Chandani Hennayake"
    },
    {
      "affs": [
        0
      ],
      "name": "Zsofia Eke"
    },
    {
      "affs": [
        0
      ],
      "name": "Jamie Stobo",
      "orcid": "0000-0003-4829-7440"
    },
    {
      "affs": [
        0
      ],
      "name": "Merete B. Long"
    },
    {
      "affs": [
        1,
        2
      ],
      "name": "Olivia C. Leavy"
    },
    {
      "affs": [
        2
      ],
      "name": "Matthew Richardson"
    },
    {
      "affs": [
        2
      ],
      "name": "Omer Elneima"
    },
    {
      "affs": [
        2
      ],
      "name": "Hamish J.C. McAuley",
      "orcid": "0000-0001-8997-0764"
    },
    {
      "affs": [
        3
      ],
      "name": "Aarti Shikotra"
    },
    {
      "affs": [
        2
      ],
      "name": "Amisha Singapuri"
    },
    {
      "affs": [
        2
      ],
      "name": "Marco Sereno"
    },
    {
      "affs": [
        2
      ],
      "name": "Ruth M. Saunders"
    },
    {
      "affs": [
        2,
        4
      ],
      "name": "Victoria C. Harris"
    },
    {
      "affs": [
        5,
        6,
        7
      ],
      "name": "Linzy Houchen-Wolloff",
      "orcid": "0000-0003-4940-8835"
    },
    {
      "affs": [
        2
      ],
      "name": "Neil J. Greening",
      "orcid": "0000-0003-0453-7529"
    },
    {
      "affs": [
        2
      ],
      "name": "Kimon Ntotsis"
    },
    {
      "affs": [
        2
      ],
      "name": "Daniel Lozano-Rojas"
    },
    {
      "affs": [
        1,
        2
      ],
      "name": "Beatriz Guillen-Guio",
      "orcid": "0000-0002-3703-1738"
    },
    {
      "affs": [
        8
      ],
      "name": "Ewen M. Harrison"
    },
    {
      "affs": [
        8
      ],
      "name": "Annemarie B. Docherty"
    },
    {
      "affs": [
        8,
        9
      ],
      "name": "Steven Kerr"
    },
    {
      "affs": [
        10,
        11
      ],
      "name": "Nazir I. Lone",
      "orcid": "0000-0003-2707-2779"
    },
    {
      "affs": [
        12
      ],
      "name": "Jennifer K. Quint",
      "orcid": "0000-0003-0149-4869"
    },
    {
      "affs": [
        13
      ],
      "name": "Aziz Sheikh"
    },
    {
      "affs": [
        8
      ],
      "name": "Mathew Thorpe"
    },
    {
      "affs": [
        14
      ],
      "name": "Bang Zheng"
    },
    {
      "affs": [
        15
      ],
      "name": "Claudia Efstathiou",
      "orcid": "0000-0001-6125-8126"
    },
    {
      "affs": [
        16,
        17
      ],
      "name": "Maxime Taquet"
    },
    {
      "affs": [
        15
      ],
      "name": "Iain D. Stewart",
      "orcid": "0000-0002-1340-2688"
    },
    {
      "affs": [
        18,
        19
      ],
      "name": "Trudie Chalder"
    },
    {
      "affs": [
        3,
        4,
        20
      ],
      "name": "Melanie J. Davies"
    },
    {
      "affs": [
        21,
        22
      ],
      "name": "Anthony De Soyza",
      "orcid": "0000-0002-8566-0344"
    },
    {
      "affs": [
        23,
        17
      ],
      "name": "John R. Geddes"
    },
    {
      "affs": [
        24,
        25,
        26
      ],
      "name": "William Greenhalf"
    },
    {
      "affs": [
        27,
        28
      ],
      "name": "Luke S. Howard",
      "orcid": "0000-0003-2822-210X"
    },
    {
      "affs": [
        29,
        30
      ],
      "name": "Joseph Jacob",
      "orcid": "0000-0002-8054-2293"
    },
    {
      "affs": [
        15
      ],
      "name": "R. Gisli Jenkins"
    },
    {
      "affs": [
        31,
        32,
        33
      ],
      "name": "William D-C. Man",
      "orcid": "0000-0002-3782-659X"
    },
    {
      "affs": [
        3,
        34
      ],
      "name": "Gerry P. McCann"
    },
    {
      "affs": [
        23,
        35
      ],
      "name": "Stefan Neubauer"
    },
    {
      "affs": [
        15
      ],
      "name": "Peter J.M. Openshaw",
      "orcid": "0000-0002-7220-2555"
    },
    {
      "affs": [
        36,
        37
      ],
      "name": "Joanna C. Porter",
      "orcid": "0000-0002-7307-169X"
    },
    {
      "affs": [
        38
      ],
      "name": "Matthew J. Rowland"
    },
    {
      "affs": [
        28
      ],
      "name": "David Thomas"
    },
    {
      "affs": [
        39
      ],
      "name": "Mark Toshner",
      "orcid": "0000-0002-3969-6143"
    },
    {
      "name": "Simon Heller"
    },
    {
      "name": "Janet T. Scott"
    },
    {
      "name": "Malcolm G. Semple",
      "orcid": "0000-0001-9700-0418"
    },
    {
      "affs": [
        2
      ],
      "name": "Sally J. Singh",
      "orcid": "0000-0002-9834-0366"
    },
    {
      "name": "Raminder Aul"
    },
    {
      "name": "Paul Beirne"
    },
    {
      "name": "Charlotte E. Bolton",
      "orcid": "0000-0002-9578-2249"
    },
    {
      "affs": [
        36
      ],
      "name": "Jeremy S. Brown"
    },
    {
      "name": "Gourab Choudhury"
    },
    {
      "name": "Nawar Diar Bakerly"
    },
    {
      "name": "Nicholas Easom"
    },
    {
      "name": "Carlos Echevarria"
    },
    {
      "name": "Jonathan Fuld"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/4pykpwc1d1t73.bib",
  "cited_by": 1,
  "doi": "10.1183/13993003.01162-2026",
  "fulltext_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC13735185/",
  "id": "4pykpwc1d1t73",
  "issns": [
    "0903-1936",
    "1399-3003"
  ],
  "landing_url": "https://doi.org/10.1183/13993003.01162-2026",
  "language": "en",
  "licence": "CC-BY-4.0",
  "licence_label": "CC BY 4.0",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "heading",
      "4"
    ],
    [
      "heading",
      "Original Research Article"
    ],
    [
      "heading",
      "Respiratory Infection"
    ],
    [
      "openalex",
      "2728|Long-Term Effects of COVID-19"
    ]
  ],
  "openalex": "W7221480796",
  "pdf_url": null,
  "pmcid": "PMC13735185",
  "pmid": "42860277",
  "published": "2026-11-05",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/4pykpwc1d1t73.ris",
  "sources": [
    {
      "first_seen": "2026-11-09T12:20:54Z",
      "native_id": "PMC13735185",
      "source": "pmc",
      "url": "https://doi.org/10.1183/13993003.01162-2026"
    }
  ],
  "subjects": [
    {
      "field": "medicine",
      "origin": "openalex:2728|Long-Term Effects of COVID-19",
      "subfield": "neurology"
    }
  ],
  "title": "Sputum and oral microbiota profiles are associated with long COVID severity and phenotype post-hospitalisation: a UK multicentre, prospective cohort study",
  "title_text": "Sputum and oral microbiota profiles are associated with long COVID severity and phenotype post-hospitalisation: a UK multicentre, prospective cohort study",
  "type": "peer-reviewed",
  "updated_at": "2026-11-09T12:20:54Z",
  "url": "https://research.draconitic.com/paper/4pykpwc1d1t73",
  "venue": "The European Respiratory Journal",
  "versions": []
}