BibTex format
@article{Alferes:2026:10.1183/13993003.01162-2026,
author = {Alferes, de Lima Headley D and Richardson, H and Hennayake, C and Eke, Z and Stobo, J and Long, MB and Leavy, OC and Richardson, M and Elneima, O and McAuley, HJC and Shikotra, A and Singapuri, A and Sereno, M and Saunders, RM and Harris, VC and Houchen-Wolloff, L and Greening, NJ and Ntotsis, K and Lozano-Rojas, D and Guillen-Guio, B and Harrison, EM and Docherty, AB and Kerr, S and Lone, NI and Quint, JK and Sheikh, A and Thorpe, M and Zheng, B and Efstathiou, C and Taquet, M and Stewart, ID and Chalder, T and Davies, MJ and De, Soyza A and Geddes, JR and Greenhalf, W and Howard, LS and Jacob, J and Jenkins, RG and Man, WD-C and McCann, GP and Neubauer, S and Openshaw, PJM and Porter, JC and Rowland, MJ and Thomas, D and Toshner, M and Heller, S and Scott, JT and Semple, MG and Singh, SJ and Aul, R and Beirne, P and Bolton, CE and Brown, JS and Choudhury, G and Diar, Bakerly N and Easom, N and Echevarria, C and Fuld, J and Hurst, JR and Jones, M and Parekh, D and Pfeffer, P and Rahma},
doi = {10.1183/13993003.01162-2026},
journal = {Eur Respir J},
title = {Sputum and oral microbiota profiles are associated with long COVID severity and phenotype post-hospitalisation: a UK multicentre, prospective cohort study.},
url = {http://dx.doi.org/10.1183/13993003.01162-2026},
year = {2026}
}
RIS format (EndNote, RefMan)
TY - JOUR
AB - 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. METHODS: 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 6months 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. RESULTS: 771 participants had their microbiota assessed. Of participants with oral rinses and "severity cluster" assignment (mean age 57.5years), 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. CONCLUSION: 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 a
AU - Alferes,de Lima Headley D
AU - Richardson,H
AU - Hennayake,C
AU - Eke,Z
AU - Stobo,J
AU - Long,MB
AU - Leavy,OC
AU - Richardson,M
AU - Elneima,O
AU - McAuley,HJC
AU - Shikotra,A
AU - Singapuri,A
AU - Sereno,M
AU - Saunders,RM
AU - Harris,VC
AU - Houchen-Wolloff,L
AU - Greening,NJ
AU - Ntotsis,K
AU - Lozano-Rojas,D
AU - Guillen-Guio,B
AU - Harrison,EM
AU - Docherty,AB
AU - Kerr,S
AU - Lone,NI
AU - Quint,JK
AU - Sheikh,A
AU - Thorpe,M
AU - Zheng,B
AU - Efstathiou,C
AU - Taquet,M
AU - Stewart,ID
AU - Chalder,T
AU - Davies,MJ
AU - De,Soyza A
AU - Geddes,JR
AU - Greenhalf,W
AU - Howard,LS
AU - Jacob,J
AU - Jenkins,RG
AU - Man,WD-C
AU - McCann,GP
AU - Neubauer,S
AU - Openshaw,PJM
AU - Porter,JC
AU - Rowland,MJ
AU - Thomas,D
AU - Toshner,M
AU - Heller,S
AU - Scott,JT
AU - Semple,MG
AU - Singh,SJ
AU - Aul,R
AU - Beirne,P
AU - Bolton,CE
AU - Brown,JS
AU - Choudhury,G
AU - Diar,Bakerly N
AU - Easom,N
AU - Echevarria,C
AU - Fuld,J
AU - Hurst,JR
AU - Jones,M
AU - Parekh,D
AU - Pfeffer,P
AU - Rahman,NM
AU - Rowland-Jones,S
AU - Shah,AM
AU - Wootton,DG
AU - Lewis,K
AU - Heaney,LG
AU - Ho,L-P
AU - Horsley,A
AU - Marks,M
AU - Poinasamy,K
AU - Raman,B
AU - Wain,LV
AU - Evans,RA
AU - Brightling,CE
AU - Molyneaux,PL
AU - Chalmers,JD
AU - PHOSP-COVID,Collaborative Group
DO - 10.1183/13993003.01162-2026
PY - 2026///
TI - Sputum and oral microbiota profiles are associated with long COVID severity and phenotype post-hospitalisation: a UK multicentre, prospective cohort study.
T2 - Eur Respir J
UR - http://dx.doi.org/10.1183/13993003.01162-2026
UR - https://www.ncbi.nlm.nih.gov/pubmed/42860277
ER -