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

Nature Communications, 2021, vol. 12, issue 1, 1-17

Abstract: Abstract 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.

Date: 2021
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DOI: 10.1038/s41467-021-22344-4

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