Man, W. H., de Steenhuijsen Piters, W. A. A. & Bogaert, D. The microbiota of the respiratory tract: gatekeeper to respiratory health. Nat. Rev. Microbiol. 15, 259–270 (2017).
Olszak, T. et al. Microbial exposure during early life has persistent effects on natural killer T cell function. Science 336, 489–493 (2012).
Gollwitzer, E. S. et al. Lung microbiota promotes tolerance to allergens in neonates via PD-L1. Nat. Med. 20, 642–647 (2014).
Dickson, R. P., Martinez, F. J. & Huffnagle, G. B. The role of the microbiome in exacerbations of chronic lung diseases. Lancet 384, 691–702 (2014).
Hilty, M. et al. Disordered microbial communities in asthmatic airways. PLoS ONE 5, e8578 (2010).
Marsland, B. J. & Gollwitzer, E. S. Host-microorganism interactions in lung diseases. Nat. Rev. Immunol. 14, 827–835 (2014).
Liang, G. & Bushman, F. D. The human virome: Assembly, composition and host interactions. Nat. Rev. Microbiol. 19, 514–527 (2021).
Dickson, R. P., Erb-Downward, J. R. & Huffnagle, G. B. The role of the bacterial microbiome in lung disease. Expert Rev. Respir. Med. 7, 245–257 (2013).
Garcia-Nuñez, M. et al. Severity-related changes of bronchial microbiome in chronic obstructive pulmonary disease. J. Clin. Microbiol. 52, 4217–4223 (2014).
Makdisi, G. & Wang, I. W. Extra corporeal membrane oxygenation (ECMO) review of a lifesaving technology. J. Thorac. Dis. 7, E166–E176 (2015).
ARDS Definition Task Force et al. Acute respiratory distress syndrome: The Berlin Definition. JAMA 307, 2526–2533 (2012).
Fan, E. et al. An Official American Thoracic Society/European Society of Intensive Care Medicine/Society of Critical Care Medicine Clinical Practice Guideline: Mechanical ventilation in adult patients with acute respiratory distress syndrome. Am. J. Respir. Crit. Care Med. 195, 1253–1263 (2017).
Knaus, W. A., Draper, E. A., Wagner, D. P. & Zimmerman, J. E. APACHE II: A severity of disease classification system. Crit. Care Med. 13, 818–829 (1985).
Vincent, J. L. et al. The SOFA (Sepsis-related Organ Failure Assessment) score to describe organ dysfunction/failure. On behalf of the working group on sepsis-related problems of the European society of intensive care medicine. Intens. Care Med. 22, 707–710 (1996).
Kullberg, R. F. J. et al. Lung microbiota of critically ill patients with COVID-19 are associated with nonresolving acute respiratory distress syndrome. Am. J. Respir. Crit. Care Med. 206, 846–856 (2022).
Gaibani, P. et al. The lower respiratory tract microbiome of critically ill patients with COVID-19. Sci. Rep. 11, 10103 (2021).
Bakaletz, L. O. Viral-bacterial co-infections in the respiratory tract. Curr. Opin. Microbiol. 35, 30–35 (2017).
Qu, J. et al. Persistent bacterial coinfection of a COVID-19 patient caused by a genetically adapted pseudomonas aeruginosa chronic colonizer. Front. Cell. Infect. Microbiol. 11, 641920 (2021).
Kitsios, G. D. et al. Respiratory tract dysbiosis is associated with worse outcomes in mechanically ventilated patients. Am. J. Respir. Crit. Care Med. 202, 1666–1677 (2020).
Whelan, F. J. et al. The loss of topography in the microbial communities of the upper respiratory tract in the elderly. Ann. Am. Thorac. Soc. 11, 513–521 (2014).
Dickson, R. P. et al. Enrichment of the lung microbiome with gut bacteria in sepsis and the acute respiratory distress syndrome. Nat. Microbiol. 1, 16113 (2016).
Santacruz, A. et al. Gut microbiota composition is associated with body weight, weight gain and biochemical parameters in pregnant women. Br. J. Nutr. 104, 83–92 (2010).
Lamont, R. J., Koo, H. & Hajishengallis, G. The oral microbiota: Dynamic communities and host interactions. Nat. Rev. Microbiol. 16, 745–759 (2018).
Natalini, J. G., Singh, S. & Segal, L. N. The dynamic lung microbiome in health and disease. Nat. Rev. Microbiol. 21, 222–235 (2023).
Schmidt, M. et al. Mechanical ventilation management during extracorporeal membrane oxygenation for acute respiratory distress syndrome. An international multicenter prospective cohort. Am. J. Respir. Crit. Care Med. 200, 1002–1012 (2019).
Rozencwajg, S. et al. Ultra-protective ventilation reduces biotrauma in patients on venovenous extracorporeal membrane oxygenation for severe acute respiratory distress syndrome. Crit. Care Med. 47, 1505–1512 (2019).
Huang, J. et al. Venovenous extracorporeal membrane oxygenation promotes alveolar epithelial recovery by activating Hippo/YAP signaling after lung injury. J. Heart Lung Transpl. 41, 1391–1400 (2022).
Britton, N. et al. Respiratory fungal communities are associated with systemic inflammation and predict survival in patients with acute respiratory failure. MedRxiv 2023.05.11.23289861 (2023). [Preprint]
Zhang, P. et al. Pulmonary microbial composition in sepsis-induced acute respiratory distress syndrome. Front. Mol. Biosci. 9, 862570 (2022).
Viciani, E. et al. Critically ill patients with COVID-19 show lung fungal dysbiosis with reduced microbial diversity in patients colonized with Candida spp. Int. J. Infect. Dis. 117, 233–240 (2022).
Boxberger, M., Cenizo, V., Cassir, N. & La Scola, B. Challenges in exploring and manipulating the human skin microbiome. Microbiome 9, 125 (2021).
Nash, A. K. et al. The gut mycobiome of the Human Microbiome Project healthy cohort. Microbiome 5, 153 (2017).
Young, J. C. et al. Viral metagenomics reveal blooms of anelloviruses in the respiratory tract of lung transplant recipients. Am. J. Transplant. 15, 200–209 (2015).
Han, Y., Jia, Z., Shi, J., Wang, W. & He, K. The active lung microbiota landscape of COVID-19 patients through the metatranscriptome data analysis. Bioimpacts 12, 139–146 (2022).
Merenstein, C. et al. Signatures of COVID-19 severity and immune response in the respiratory tract microbiome. mBio 12, e0177721 (2021).
Frantzeskaki, F. G. et al. Cytomegalovirus reactivation in a general, nonimmunosuppressed intensive care unit population: Incidence, risk factors, associations with organ dysfunction, and inflammatory biomarkers. J. Crit. Care 30, 276–281 (2015).
Chiche, L. et al. Active cytomegalovirus infection is common in mechanically ventilated medical intensive care unit patients. Crit. Care Med. 37, 1850–1857 (2009).
Dickson, R. P. et al. Lung microbiota predict clinical outcomes in critically ill patients. Am. J. Respir. Crit. Care Med. 201, 555–563 (2020).
Dickson, R. P., Erb-Downward, J. R. & Huffnagle, G. B. Towards an ecology of the lung: New conceptual models of pulmonary microbiology and pneumonia pathogenesis. Lancet Respir. Med. 2, 238–246 (2014).
