A prevalent and culturable microbiota links ecological balance to clinical stability of the human lung after transplantation

Sudip Das, Eric Bernasconi, Angela Koutsokera, Daniel Adrien Wurlod, Vishwachi Tripathi, Germán Bonilla-Rosso, John David Aubert, Marie France Derkenne, Louis Mercier, Céline Pattaroni, Alexis Rapin, Christophe von Garnier, Benjamin J. Marsland, Philipp Engel, Laurent P. Nicod

Research output: Contribution to journalArticleResearchpeer-review

30 Citations (Scopus)


There is accumulating evidence that the lower airway microbiota impacts lung health. However, the link between microbial community composition and lung homeostasis remains elusive. We combine amplicon sequencing and bacterial culturing to characterize the viable bacterial community in 234 longitudinal bronchoalveolar lavage samples from 64 lung transplant recipients and establish links to viral loads, host gene expression, lung function, and transplant health. We find that the lung microbiota post-transplant can be categorized into four distinct compositional states, ‘pneumotypes’. The predominant ‘balanced’ pneumotype is characterized by a diverse bacterial community with moderate viral loads, and host gene expression profiles suggesting immune tolerance. The other three pneumotypes are characterized by being either microbiota-depleted, or dominated by potential pathogens, and are linked to increased immune activity, lower respiratory function, and increased risks of infection and rejection. Collectively, our findings establish a link between the lung microbial ecosystem, human lung function, and clinical stability post-transplant.

Original languageEnglish
Article number2126
Number of pages17
JournalNature Communications
Issue number1
Publication statusPublished - Dec 2021

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