Clinical practices underlie COVID-19 patient respiratory microbiome composition and its interactions with the host.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
29 10 2021
29 10 2021
Historique:
received:
16
08
2021
accepted:
06
10
2021
entrez:
30
10
2021
pubmed:
31
10
2021
medline:
16
11
2021
Statut:
epublish
Résumé
Understanding the pathology of COVID-19 is a global research priority. Early evidence suggests that the respiratory microbiome may be playing a role in disease progression, yet current studies report contradictory results. Here, we examine potential confounders in COVID-19 respiratory microbiome studies by analyzing the upper (n = 58) and lower (n = 35) respiratory tract microbiome in well-phenotyped COVID-19 patients and controls combining microbiome sequencing, viral load determination, and immunoprofiling. We find that time in the intensive care unit and type of oxygen support, as well as associated treatments such as antibiotic usage, explain the most variation within the upper respiratory tract microbiome, while SARS-CoV-2 viral load has a reduced impact. Specifically, mechanical ventilation is linked to altered community structure and significant shifts in oral taxa previously associated with COVID-19. Single-cell transcriptomics of the lower respiratory tract of COVID-19 patients identifies specific oral bacteria in physical association with proinflammatory immune cells, which show higher levels of inflammatory markers. Overall, our findings suggest confounders are driving contradictory results in current COVID-19 microbiome studies and careful attention needs to be paid to ICU stay and type of oxygen support, as bacteria favored in these conditions may contribute to the inflammatory phenotypes observed in severe COVID-19 patients.
Identifiants
pubmed: 34716338
doi: 10.1038/s41467-021-26500-8
pii: 10.1038/s41467-021-26500-8
pmc: PMC8556379
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
6243Subventions
Organisme : Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)
ID : 12V9421N
Organisme : European Molecular Biology Organization (EMBO)
ID : ALTF 349-2019
Investigateurs
Yannick Van Herck
(Y)
Alexander Wilmer
(A)
Michael Casaer
(M)
Stephen Rex
(S)
Nathalie Lorent
(N)
Jonas Yserbyt
(J)
Dries Testelmans
(D)
Karin Thevissen
(K)
Informations de copyright
© 2021. The Author(s).
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