Sputum and oral microbiota profiles are associated with long COVID severity and phenotype post-hospitalisation: a UK multicentre, prospective cohort study.

Authors

Daniela Alferes de Lima Headley, Hollian Richardson, Chandani Hennayake, Zsofia Eke, Jamie Stobo, Merete B Long, Olivia C Leavy, Matthew Richardson, Omer Elneima, Hamish J C McAuley, Aarti Shikotra, Amisha Singapuri, Marco Sereno, Ruth M Saunders, Victoria C Harris, Linzy Houchen-Wolloff, Neil J Greening, Kimon Ntotsis, Daniel Lozano-Rojas, Beatriz Guillen-Guio, Ewen M Harrison, Annemarie B Docherty, Steven Kerr, Nazir I Lone, Jennifer K Quint, Aziz Sheikh, Mathew Thorpe, Bang Zheng, Claudia Efstathiou, Maxime Taquet, Iain D Stewart, Trudie Chalder, Melanie J Davies, Anthony De Soyza, John R Geddes, William Greenhalf, Luke S Howard, Joseph Jacob, R Gisli Jenkins, William D-C Man, Gerry P McCann, Stefan Neubauer, Peter J M Openshaw, Joanna C Porter, Matthew J Rowland, David Thomas, Mark Toshner, Simon Heller, Janet T Scott, Malcolm G Semple, Sally J Singh, Raminder Aul, Paul Beirne, Charlotte E Bolton, Jeremy S Brown, Gourab Choudhury, Nawar Diar Bakerly, Nicholas Easom, Carlos Echevarria, Jonathan Fuld, John R Hurst, Mark Jones, Dhruv Parekh, Paul Pfeffer, Najib M Rahman, Sarah Rowland-Jones, Ajay M Shah, Daniel G Wootton, Keir Lewis, Liam G Heaney, Ling-Pei Ho, Alex Horsley, Michael Marks, Krisnah Poinasamy, Betty Raman, Louise V Wain, Rachael A Evans, Christopher E Brightling, Philip L Molyneaux, James D Chalmers, PHOSP-COVID Collaborative Group

Published in

The European respiratory journal. Oct 11, 2026. Epub Oct 11, 2026.

Abstract

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.
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.
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.
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.

PMID:
42860277
Bibliographic data and abstract were imported from PubMed on 12 Oct 2026.

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