Skip to main content

The Microbiome in Acute Lung Injury and ARDS

  • Chapter
  • First Online:
The Microbiome in Respiratory Disease

Part of the book series: Respiratory Medicine ((RM))

  • 767 Accesses

Abstract

The acute respiratory distress syndrome (ARDS) is a heterogeneous clinical entity of severe respiratory failure, which develops in response to various inflammatory insults and pathogenetic mechanisms. Clinical and biologic heterogeneity in ARDS has hampered the discovery of targeted and efficacious therapies, and clinical care has remained largely supportive. However, the established causal model of ARDS (i.e., an injurious exposure causing inflammatory lung damage) has not considered a potentially central determinant of pathogenesis: the microbiome. Accumulating evidence suggests that lung microbial communities are significantly altered in patients with ARDS, with dysbiosis accounting for variability in host inflammatory responses and clinical outcomes. In this chapter, we synthesize the ecological models, epidemiologic evidence from human studies, and experimental data from animal models to understand the role of the lung and gut microbiome in ARDS and outline research priorities for clinical translation of microbiome research to innovative care for ARDS.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 119.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Ashbaugh DG, Bigelow DB, Petty TL, Levine BE. Acute respiratory distress in adults. Lancet. 1967;2:319–23.

    Article  PubMed  CAS  Google Scholar 

  2. ARDS Definition Task Force, Ranieri VM, Rubenfeld GD, Thompson BT, Ferguson ND, Caldwell E, Fan E, Camporota L, Slutsky AS. Acute respiratory distress syndrome: the Berlin definition. JAMA. 2012;307:2526–33.

    Google Scholar 

  3. Bellani G, Laffey JG, Pham T, Fan E, Brochard L, Esteban A, Gattinoni L, van Haren F, Larsson A, McAuley DF, Ranieri M, Rubenfeld G, Thompson BT, Wrigge H, Slutsky AS, Pesenti A, LUNG SAFE Investigators, ESICM Trials Group. Epidemiology, patterns of care, and mortality for patients with acute respiratory distress syndrome in intensive care units in 50 countries. JAMA. 2016;315:788–800.

    Article  CAS  PubMed  Google Scholar 

  4. Hiscott J, Alexandridi M, Muscolini M, Tassone E, Palermo E, Soultsioti M, Zevini A. The global impact of the coronavirus pandemic. Cytokine Growth Factor Rev. 2020;53:1–9.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  5. Matthay MA, Leligdowicz A, Liu KD. Biological mechanisms of COVID-19 acute respiratory distress syndrome. Am J Respir Crit Care Med. 2020;202:1489–91.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  6. Rubenfeld GD, Caldwell E, Peabody E, Weaver J, Martin DP, Neff M, Stern EJ, Hudson LD. Incidence and outcomes of acute lung injury. N Engl J Med. 2005;353:1685–93.

    Article  PubMed  CAS  Google Scholar 

  7. Kojicic M, Li G, Hanson AC, Lee K-M, Thakur L, Vedre J, Ahmed A, Baddour LM, Ryu JH, Gajic O. Risk factors for the development of acute lung injury in patients with infectious pneumonia. Crit Care. 2012;16:R46.

    Article  PubMed  PubMed Central  Google Scholar 

  8. Matthay MA, Zemans RL, Zimmerman GA, Arabi YM, Beitler JR, Mercat A, Herridge M, Randolph AG, Calfee CS. Acute respiratory distress syndrome. Nat Rev Dis Primers. 2019;5:18.

    Article  PubMed  PubMed Central  Google Scholar 

  9. Thille AW, Esteban A, Fernández-Segoviano P, Rodriguez J-M, Aramburu J-A, Peñuelas O, Cortés-Puch I, Cardinal-Fernández P, Lorente JA, Frutos-Vivar F. Comparison of the Berlin definition for acute respiratory distress syndrome with autopsy. Am J Respir Crit Care Med. 2013;187:761–7.

    Article  PubMed  Google Scholar 

  10. Sjoding MW, Hofer TP, Co I, Courey A, Cooke CR, Iwashyna TJ. Interobserver reliability of the berlin ARDS definition and strategies to improve the reliability of ARDS diagnosis. Chest. 2018;153:361–7.

    Article  PubMed  Google Scholar 

  11. Acute Respiratory Distress Syndrome Network, Brower RG, Matthay MA, Morris A, Schoenfeld D, Thompson BT, Wheeler A. Ventilation with lower tidal volumes as compared with traditional tidal volumes for acute lung injury and the acute respiratory distress syndrome. N Engl J Med. 2000;342:1301–8.

    Article  Google Scholar 

  12. Guérin C, Reignier J, Richard J-C, Beuret P, Gacouin A, Boulain T, Mercier E, Badet M, Mercat A, Baudin O, Clavel M, Chatellier D, Jaber S, Rosselli S, Mancebo J, Sirodot M, Hilbert G, Bengler C, Richecoeur J, Gainnier M, Bayle F, Bourdin G, Leray V, Girard R, Baboi L, Ayzac L, PROSEVA Study Group. Prone positioning in severe acute respiratory distress syndrome. N Engl J Med. 2013;368:2159–68.

    Article  PubMed  CAS  Google Scholar 

  13. Calfee CS, Delucchi K, Parsons PE, Thompson BT, Ware LB, Matthay MA, NHLBI ARDS Network. Subphenotypes in acute respiratory distress syndrome: latent class analysis of data from two randomised controlled trials. Lancet Respir Med. 2014;2:611–20.

    Article  PubMed  PubMed Central  Google Scholar 

  14. Sinha P, Delucchi KL, Thompson BT, McAuley DF, Matthay MA, Calfee CS, NHLBI ARDS Network. Latent class analysis of ARDS subphenotypes: a secondary analysis of the statins for acutely injured lungs from sepsis (SAILS) study. Intensive Care Med. 2018;44:1859–69.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  15. Kitsios GD, Yang L, Manatakis DV, Nouraie M, Evankovich J, Bain W, Dunlap DG, Shah F, Barbash IJ, Rapport SF, Zhang Y, DeSensi RS, Weathington NM, Chen BB, Ray P, Mallampalli RK, Benos PV, Lee JS, Morris A, McVerry BJ. Host-response subphenotypes offer prognostic enrichment in patients with or at risk for acute respiratory distress syndrome. Crit Care Med. 2019;47:1724–34.

    Article  PubMed  PubMed Central  Google Scholar 

  16. Calfee CS, Delucchi KL, Sinha P, Matthay MA, Hackett J, Shankar-Hari M, McDowell C, Laffey JG, O’Kane CM, McAuley DF, Irish Critical Care Trials Group. Acute respiratory distress syndrome subphenotypes and differential response to simvastatin: secondary analysis of a randomised controlled trial. Lancet Respir Med. 2018;6:691–8.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  17. Famous KR, Delucchi K, Ware LB, Kangelaris KN, Liu KD, Thompson BT, Calfee CS, Network ARDS. Acute respiratory distress syndrome subphenotypes respond differently to randomized fluid management strategy. Am J Respir Crit Care Med. 2017;195:331–8.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  18. Kitsios GD, Yang H, Yang L, Qin S, Fitch A, Wang X-H, Fair K, Evankovich J, Bain W, Shah F, Li K, Methé B, Benos PV, Morris A, McVerry BJ. Respiratory tract dysbiosis is associated with worse outcomes in mechanically ventilated patients. Am J Respir Crit Care Med. 2020;202:1666–77.

    Article  PubMed  PubMed Central  Google Scholar 

  19. Dickson RP, Schultz MJ, van der Poll T, Schouten LR, Falkowski NR, Luth JE, Sjoding MW, Brown CA, Chanderraj R, Huffnagle GB, Bos LDJ. Biomarker analysis in septic ICU patients (BASIC) consortium. Lung microbiota predict clinical outcomes in critically ill patients. Am J Respir Crit Care Med. 2020;201:555–63.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  20. Dickson RP. The microbiome and critical illness. Lancet Respir Med. 2016;4:59–72.

    Article  PubMed  Google Scholar 

  21. Kitsios GD, Morowitz MJ, Dickson RP, Huffnagle GB, McVerry BJ, Morris A. Dysbiosis in the intensive care unit: microbiome science coming to the bedside. J Crit Care. 2017;38:84–91.

    Article  PubMed  Google Scholar 

  22. Rynda-Apple A, Robinson KM, Alcorn JF. Influenza and bacterial superinfection: illuminating the immunologic mechanisms of disease. Infect Immun. 2015;83:3764–70.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  23. Garcia-Vidal C, Sanjuan G, Moreno-García E, Puerta-Alcalde P, Garcia-Pouton N, Chumbita M, Fernandez-Pittol M, Pitart C, Inciarte A, Bodro M, Morata L, Ambrosioni J, Grafia I, Meira F, Macaya I, Cardozo C, Casals C, Tellez A, Castro P, Marco F, García F, Mensa J, Martínez JA, Soriano A, COVID-19 Researchers Group. Incidence of co-infections and superinfections in hospitalized patients with COVID-19: a retrospective cohort study. Clin Microbiol Infect. 2021;27:83–8.

    Article  PubMed  CAS  Google Scholar 

  24. Markowicz P, Wolff M, Djedaïni K, Cohen Y, Chastre J, Delclaux C, Merrer J, Herman B, Veber B, Fontaine A, Dreyfuss D. Multicenter prospective study of ventilator-associated pneumonia during acute respiratory distress syndrome. Incidence, prognosis, and risk factors. ARDS study group. Am J Respir Crit Care Med. 2000;161:1942–8.

    Article  PubMed  CAS  Google Scholar 

  25. Messika J, La Combe B, Ricard J-D. Oropharyngeal colonization: epidemiology, treatment and ventilator-associated pneumonia prevention. Ann Transl Med. 2018;6:426.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  26. Price R, MacLennan G, Glen J, SuDDICU Collaboration. Selective digestive or oropharyngeal decontamination and topical oropharyngeal chlorhexidine for prevention of death in general intensive care: systematic review and network meta-analysis. BMJ. 2014;348:g2197.

    Article  PubMed  PubMed Central  Google Scholar 

  27. Magazine R, Rao S, Chogtu B. Prescribing patterns of drugs in acute respiratory distress syndrome (ARDS): an observational study. J Clin Diagn Res. 2015;9:FC01–4.

    PubMed  PubMed Central  Google Scholar 

  28. Micek ST, Schramm G, Morrow L, Frazee E, Personett H, Doherty JA, Hampton N, Hoban A, Lieu A, McKenzie M, Dubberke ER, Kollef MH. Clostridium difficile infection: a multicenter study of epidemiology and outcomes in mechanically ventilated patients. Crit Care Med. 2013;41:1968–75.

    Article  PubMed  Google Scholar 

  29. Prescott HC, Dickson RP, Rogers MAM, Langa KM, Iwashyna TJ. Hospitalization type and subsequent severe sepsis. Am J Respir Crit Care Med. 2015;192:581–8.

    Article  PubMed  PubMed Central  Google Scholar 

  30. Dickson RP. The lung microbiome and ARDS. It is time to broaden the model. Am J Respir Crit Care Med. 2018;197:549–51.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  31. Dickson RP, Erb-Downward JR, Huffnagle GB. Towards an ecology of the lung: new conceptual models of pulmonary microbiology and pneumonia pathogenesis. Lancet Respir Med. 2014;2:238–46.

    Article  PubMed  PubMed Central  Google Scholar 

  32. Dickson RP, Erb-Downward JR, Huffnagle GB. Homeostasis and its disruption in the lung microbiome. Am J Physiol Lung Cell Mol Physiol. 2015;309:L1047–55.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  33. Dickson RP, Erb-Downward JR, Freeman CM, McCloskey L, Beck JM, Huffnagle GB, Curtis JL. Spatial variation in the healthy human lung microbiome and the adapted island model of lung biogeography. Ann Am Thorac Soc. 2015;12:821–30.

    Article  PubMed  PubMed Central  Google Scholar 

  34. Cox MJ, Ege MJ, von Mutius E. The lung microbiome. In: Cox MJ, Ege MJ, von Mutius E, editors. . Sheffield: European Respiratory Society; 2019.

    Chapter  Google Scholar 

  35. The theory of island biogeography (Book, 2001) [WorldCat.org]. At https://www.worldcat.org/title/theory-of-island-biogeography/oclc/45202069.

  36. Kitsios GD, McVerry BJ. Host-microbiome interactions in the subglottic space. Bacteria ante Portas! Am J Respir Crit Care Med. 2018;198:294–7.

    Article  PubMed  Google Scholar 

  37. Powell J, Garnett J, Mather M, Cooles F, Nelson A, Verdon B, Scott J, Jiwa K, Ruchaud-Sparagano M-H, Cummings S, Perry J, Wright S, Wilson J, Pearson J, Ward C. Excess mucin impairs subglottic epithelial host defense inmechanically ventilated patients. Am J Respir Crit Care Med. 2018;198:340.

    Article  PubMed  CAS  Google Scholar 

  38. Deitch EA. Gut-origin sepsis: evolution of a concept. Surgeon. 2012;10:350–6.

    Article  PubMed  PubMed Central  Google Scholar 

  39. Steed H, Macfarlane GT, Blackett KL, Macfarlane S, Miller MH, Bahrami B, Dillon JF. Bacterial translocation in cirrhosis is not caused by an abnormal small bowel gut microbiota. FEMS Immunol Med Microbiol. 2011;63:346–54.

    Article  PubMed  CAS  Google Scholar 

  40. Wu H, Kuzmenko A, Wan S, Schaffer L, Weiss A, Fisher JH, Kim KS, McCormack FX. Surfactant proteins A and D inhibit the growth of gram-negative bacteria by increasing membrane permeability. J Clin Invest. 2003;111:1589–602.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  41. Günther A, Siebert C, Schmidt R, Ziegler S, Grimminger F, Yabut M, Temmesfeld B, Walmrath D, Morr H, Seeger W. Surfactant alterations in severe pneumonia, acute respiratory distress syndrome, and cardiogenic lung edema. Am J Respir Crit Care Med. 1996;153:176–84.

    Article  PubMed  Google Scholar 

  42. Ayzac L, Girard R, Baboi L, Beuret P, Rabilloud M, Richard JC, Guérin C. Ventilator-associated pneumonia in ARDS patients: the impact of prone positioning. A secondary analysis of the PROSEVA trial. Intensive Care Med. 2016;42:871–8.

    Article  PubMed  CAS  Google Scholar 

  43. Timsit J-F, Esaied W, Neuville M, Bouadma L, Mourvllier B. Update on ventilator-associated pneumonia. [version 1; peer review: 2 approved]. F1000Res. 2017;6:2061.

    Article  PubMed  PubMed Central  Google Scholar 

  44. Sender R, Fuchs S, Milo R. Are we really vastly outnumbered? Revisiting the ratio of bacterial to host cells in humans. Cell. 2016;164:337–40.

    Article  PubMed  CAS  Google Scholar 

  45. Young VB. The role of the microbiome in human health and disease: an introduction for clinicians. BMJ. 2017;356:j831.

    Article  PubMed  Google Scholar 

  46. Mittal R, Coopersmith CM. Redefining the gut as the motor of critical illness. Trends Mol Med. 2014;20:214–23.

    Article  PubMed  Google Scholar 

  47. Adelman MW, Woodworth MH, Langelier C, Busch LM, Kempker JA, Kraft CS, Martin GS. The gut microbiome’s role in the development, maintenance, and outcomes of sepsis. Crit Care. 2020;24:278.

    Article  PubMed  PubMed Central  Google Scholar 

  48. Carney S, Clemente J, Cox MJ, Dickson RP, Huang YJ, Kitsios GD, Kloepfer KM, Leung JM, LeVan TD, Molyneaux PL, Moore BM, O’Dwyer DN, Segal LN, Garantziotis S. Methods in lung microbiome research. An American Thoracic Society working group report. Am J Respir Cell Mol Biol. 2020;62:283–99.

    Google Scholar 

  49. Bauer TT, Torres A, Ewig S, Hernández C, Sanchez-Nieto JM, Xaubet A, Agustí C, Rodriguez-Roisin R. Effects of bronchoalveolar lavage volume on arterial oxygenation in mechanically ventilated patients with pneumonia. Intensive Care Med. 2001;27:384–93.

    Article  PubMed  CAS  Google Scholar 

  50. Wahidi MM, Shojaee S, Lamb CR, Ost D, Maldonado F, Eapen G, Caroff DA, Stevens MP, Ouellette DR, Lilly C, Gardner DD, Glisinski K, Pennington K, Alalawi R. The use of bronchoscopy during the coronavirus disease 2019 pandemic: CHEST/AABIP guideline and expert panel report. Chest. 2020;158:1268–81.

    Article  PubMed  CAS  Google Scholar 

  51. Canadian Critical Care Trials Group. A randomized trial of diagnostic techniques for ventilator-associated pneumonia. N Engl J Med. 2006;355:2619–30.

    Article  Google Scholar 

  52. Torres A, Niederman MS, Chastre J, Ewig S, Fernandez-Vandellos P, Hanberger H, Kollef M, Bassi G, Luna CM, Martin-Loeches I, Paiva JA, Read RC, Rigau D, Timsit JF, Welte T, Wunderink R. International ERS/ESICM/ESCMID/ALAT guidelines for the management of hospital-acquired pneumonia and ventilator-associated pneumonia: guidelines for the management of hospital-acquired pneumonia (HAP)/ventilator-associated pneumonia (VAP). Eur Respir J. 2017;50:1700582.

    Article  PubMed  CAS  Google Scholar 

  53. Kalil AC, Metersky ML, Klompas M, Muscedere J, Sweeney DA, Palmer LB, Napolitano LM, O’Grady NP, Bartlett JG, Carratalà J, El Solh AA, Ewig S, Fey PD, File TM, Restrepo MI, Roberts JA, Waterer GW, Cruse P, Knight SL, Brozek JL. Management of Adults with Hospital-acquired and Ventilator-associated Pneumonia: 2016 clinical practice guidelines by the Infectious Diseases Society of America and the American Thoracic Society. Clin Infect Dis. 2016;63:e61–e111.

    Article  PubMed  PubMed Central  Google Scholar 

  54. Kalantar KL, Moazed F, Christenson SC, Wilson J, Deiss T, Belzer A, Vessel K, Caldera S, Jauregui A, Bolourchi S, DeRisi JL, Calfee CS, Langelier C. Metagenomic comparison of tracheal aspirate and mini-bronchial alveolar lavage for assessment of respiratory microbiota. Am J Physiol Lung Cell Mol Physiol. 2019;316:L578–84.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  55. Gattinoni L, Caironi P, Pelosi P, Goodman LR. What has computed tomography taught us about the acute respiratory distress syndrome? Am J Respir Crit Care Med. 2001;164:1701–11.

    Article  PubMed  CAS  Google Scholar 

  56. Erb-Downward JR, Thompson DL, Han MK, Freeman CM, McCloskey L, Schmidt LA, Young VB, Toews GB, Curtis JL, Sundaram B, Martinez FJ, Huffnagle GB. Analysis of the lung microbiome in the “healthy” smoker and in COPD. PLoS One. 2011;6:e16384.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  57. Jorth P, Staudinger BJ, Wu X, Hisert KB, Hayden H, Garudathri J, Harding CL, Radey MC, Rezayat A, Bautista G, Berrington WR, Goddard AF, Zheng C, Angermeyer A, Brittnacher MJ, Kitzman J, Shendure J, Fligner CL, Mittler J, Aitken ML, Manoil C, Bruce JE, Yahr TL, Singh PK. Regional isolation drives bacterial diversification within cystic fibrosis lungs. Cell Host Microbe. 2015;18:307–19.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  58. Valenzi E, Yang H, Sembrat JC, Yang L, Winters S, Nettles R, Kass DJ, Qin S, Wang X, Myerburg MM, Methé B, Fitch A, Alder JK, Benos PV, McVerry BJ, Rojas M, Morris A, Kitsios GD. Topographic heterogeneity of lung microbiota in end-stage idiopathic pulmonary fibrosis: the Microbiome in Lung Explants-2 (MiLEs-2) study. Thorax. 2020; https://doi.org/10.1136/thoraxjnl-2020-214770.

  59. Kitsios GD, Rojas M, Kass DJ, Fitch A, Sembrat JC, Qin S, Veraldi KL, Gibson KF, Lindell K, Pilewski JM, Methe B, Li K, McDyer J, McVerry BJ, Morris A. Microbiome in lung explants of idiopathic pulmonary fibrosis: a case-control study in patients with end-stage fibrosis. Thorax. 2018;73:481–4.

    Article  PubMed  Google Scholar 

  60. Jenkins G. A big beautiful wall against infection. Thorax. 2018;73:485.

    Article  PubMed  Google Scholar 

  61. Fair K, Dunlap DG, Fitch A, Bogdanovich T, Methé B, Morris A, McVerry BJ, Kitsios GD. Rectal swabs from critically ill patients provide discordant representations of the gut microbiome compared to stool samples. mSphere. 2019;4:e00358-19.

    Article  PubMed  PubMed Central  Google Scholar 

  62. Bansal S, Nguyen JP, Leligdowicz A, Zhang Y, Kain KC, Ricciuto DR, Coburn B. Rectal and naris swabs: practical and informative samples for analyzing the microbiota of critically ill patients. mSphere. 2018;3:e00219-18.

    Article  PubMed  PubMed Central  Google Scholar 

  63. Charlson ES, Diamond JM, Bittinger K, Fitzgerald AS, Yadav A, Haas AR, Bushman FD, Collman RG. Lung-enriched organisms and aberrant bacterial and fungal respiratory microbiota after lung transplant. Am J Respir Crit Care Med. 2012;186:536–45.

    Article  PubMed  PubMed Central  Google Scholar 

  64. Bassis CM, Erb-Downward JR, Dickson RP, Freeman CM, Schmidt TM, Young VB, Beck JM, Curtis JL, Huffnagle GB. Analysis of the upper respiratory tract microbiotas as the source of the lung and gastric microbiotas in healthy individuals. MBio. 2015;6:e00037.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  65. Goleva E, Jackson LP, Harris JK, Robertson CE, Sutherland ER, Hall CF, Good JT, Gelfand EW, Martin RJ, Leung DYM. The effects of airway microbiome on corticosteroid responsiveness in asthma. Am J Respir Crit Care Med. 2013;188:1193–201.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  66. Man WH, de Steenhuijsen Piters WAA, Bogaert D. The microbiota of the respiratory tract: gatekeeper to respiratory health. Nat Rev Microbiol. 2017;15:259–70.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  67. Segal LN, Alekseyenko AV, Clemente JC, Kulkarni R, Wu B, Gao Z, Chen H, Berger KI, Goldring RM, Rom WN, Blaser MJ, Weiden MD. Enrichment of lung microbiome with supraglottic taxa is associated with increased pulmonary inflammation. Microbiome. 2013;1:19.

    Article  PubMed  PubMed Central  Google Scholar 

  68. Morris A, Beck JM, Schloss PD, Campbell TB, Crothers K, Curtis JL, Flores SC, Fontenot AP, Ghedin E, Huang L, Jablonski K, Kleerup E, Lynch SV, Sodergren E, Twigg H, Young VB, Bassis CM, Venkataraman A, Schmidt TM, Weinstock GM, Lung HIV Microbiome Project. Comparison of the respiratory microbiome in healthy nonsmokers and smokers. Am J Respir Crit Care Med. 2013;187:1067–75.

    Article  PubMed  PubMed Central  Google Scholar 

  69. Segal LN, Clemente JC, Tsay J-CJ, Koralov SB, Keller BC, Wu BG, Li Y, Shen N, Ghedin E, Morris A, Diaz P, Huang L, Wikoff WR, Ubeda C, Artacho A, Rom WN, Sterman DH, Collman RG, Blaser MJ, Weiden MD. Enrichment of the lung microbiome with oral taxa is associated with lung inflammation of a Th17 phenotype. Nat Microbiol. 2016;1:16031.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  70. Dickson RP, Erb-Downward JR, Freeman CM, McCloskey L, Falkowski NR, Huffnagle GB, Curtis JL. Bacterial topography of the healthy human lower respiratory tract. MBio. 2017;8:e02287-16.

    Article  PubMed  PubMed Central  Google Scholar 

  71. Beck JM, Schloss PD, Venkataraman A, Twigg H, Jablonski KA, Bushman FD, Campbell TB, Charlson ES, Collman RG, Crothers K, Curtis JL, Drews KL, Flores SC, Fontenot AP, Foulkes MA, Frank I, Ghedin E, Huang L, Lynch SV, Morris A, Palmer BE, Schmidt TM, Sodergren E, Weinstock GM, Young VB, Lung HIV Microbiome Project. Multicenter comparison of lung and oral microbiomes of HIV-infected and HIV-uninfected individuals. Am J Respir Crit Care Med. 2015;192:1335–44.

    Article  PubMed  PubMed Central  Google Scholar 

  72. Lamarche D, Johnstone J, Zytaruk N, Clarke F, Hand L, Loukov D, Szamosi JC, Rossi L, Schenck LP, Verschoor CP, McDonald E, Meade MO, Marshall JC, Bowdish DME, Karachi T, Heels-Ansdell D, Cook DJ, Surette MG, PROSPECT Investigators, Canadian Critical Care Trials Group, Canadian Critical Care Translational Biology Group. Microbial dysbiosis and mortality during mechanical ventilation: a prospective observational study. Respir Res. 2018;19:245.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  73. Kitsios GD, Fitch A, Manatakis DV, Rapport SF, Li K, Qin S, Huwe J, Zhang Y, Doi Y, Evankovich J, Bain W, Lee JS, Methé B, Benos PV, Morris A, McVerry BJ. Respiratory microbiome profiling for etiologic diagnosis of pneumonia in mechanically ventilated patients. Front Microbiol. 2018;9:1413.

    Article  PubMed  PubMed Central  Google Scholar 

  74. Kelly BJ, Imai I, Bittinger K, Laughlin A, Fuchs BD, Bushman FD, Collman RG. Composition and dynamics of the respiratory tract microbiome in intubated patients. Microbiome. 2016;4:7.

    Article  PubMed  PubMed Central  Google Scholar 

  75. Kyo M, Nishioka K, Nakaya T, Kida Y, Tanabe Y, Ohshimo S, Shime N. Unique patterns of lower respiratory tract microbiota are associated with inflammation and hospital mortality in acute respiratory distress syndrome. Respir Res. 2019;20:246.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  76. Panzer AR, Lynch SV, Langelier C, Christie JD, McCauley K, Nelson M, Cheung CK, Benowitz NL, Cohen MJ, Calfee CS. Lung microbiota is related to smoking status and to development of acute respiratory distress syndrome in critically ill trauma patients. Am J Respir Crit Care Med. 2018;197:621–31.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  77. Dickson RP, Singer BH, Newstead MW, Falkowski NR, Erb-Downward JR, Standiford TJ, Huffnagle GB. Enrichment of the lung microbiome with gut bacteria in sepsis and the acute respiratory distress syndrome. Nat Microbiol. 2016;1:16113.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  78. Sinha P, Delucchi KL, McAuley DF, O’Kane CM, Matthay MA, Calfee CS. Development and validation of parsimonious algorithms to classify acute respiratory distress syndrome phenotypes: a secondary analysis of randomised controlled trials. Lancet Respir Med. 2020;8:247–57.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  79. Schmitt FCF, Lipinski A, Hofer S, Uhle F, Nusshag C, Hackert T, Dalpke AH, Weigand MA, Brenner T, Boutin S. Pulmonary microbiome patterns correlate with the course of the disease in patients with sepsis-induced ARDS following major abdominal surgery. J Hosp Infect. 2020; https://doi.org/10.1016/j.jhin.2020.04.028.

  80. Walsh DM, McCullough SD, Yourstone S, Jones SW, Cairns BA, Jones CD, Jaspers I, Diaz-Sanchez D. Alterations in airway microbiota in patients with PaO2/FiO2 ratio ≤ 300 after burn and inhalation injury. PLoS One. 2017;12:e0173848.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  81. Gorrie CL, Mirceta M, Wick RR, Edwards DJ, Thomson NR, Strugnell RA, Pratt NF, Garlick JS, Watson KM, Pilcher DV, McGloughlin SA, Spelman DW, Jenney AWJ, Holt KE. Gastrointestinal carriage is a major reservoir of Klebsiella pneumoniae infection in intensive care patients. Clin Infect Dis. 2017;65:208–15.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  82. Freedberg DE, Zhou MJ, Cohen ME, Annavajhala MK, Khan S, Moscoso DI, Brooks C, Whittier S, Chong DH, Uhlemann A-C, Abrams JA. Pathogen colonization of the gastrointestinal microbiome at intensive care unit admission and risk for subsequent death or infection. Intensive Care Med. 2018;44:1203–11.

    Article  PubMed  PubMed Central  Google Scholar 

  83. Zaborin A, Smith D, Garfield K, Quensen J, Shakhsheer B, Kade M, Tirrell M, Tiedje J, Gilbert JA, Zaborina O, Alverdy JC. Membership and behavior of ultra-low-diversity pathogen communities present in the gut of humans during prolonged critical illness. MBio. 2014;5:e01361–14.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  84. Ravi A, Halstead FD, Bamford A, Casey A, Thomson NM, van Schaik W, Snelson C, Goulden R, Foster-Nyarko E, Savva GM, Whitehouse T, Pallen MJ, Oppenheim BA. Loss of microbial diversity and pathogen domination of the gut microbiota in critically ill patients. Microb Genom. 2019;5:e000293.

    PubMed Central  Google Scholar 

  85. Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature. 2012;486:207–14.

    Article  CAS  Google Scholar 

  86. McDonald D, Ackermann G, Khailova L, Baird C, Heyland D, Kozar R, Lemieux M, Derenski K, King J, Vis-Kampen C, Knight R, Wischmeyer PE. Extreme dysbiosis of the microbiome in critical illness. mSphere. 2016;1:e00199-16.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  87. Burmeister DM, Johnson TR, Lai Z, Scroggins S, DeRosa M, Jonas RB, Zhu C, Scherer E, Stewart RM, Schwacha MG, Jenkins DH, Eastridge BJ, Nicholson SE. The gut microbiome distinguishes mortality in trauma patients upon admission to the emergency department. J Trauma Acute Care Surg. 2020; https://doi.org/10.1097/TA.0000000000002612.

  88. Shimizu K, Yamada T, Ogura H, Mohri T, Kiguchi T, Fujimi S, Asahara T, Yamada T, Ojima M, Ikeda M, Shimazu T. Synbiotics modulate gut microbiota and reduce enteritis and ventilator-associated pneumonia in patients with sepsis: a randomized controlled trial. Crit Care. 2018;22:239.

    Article  PubMed  PubMed Central  Google Scholar 

  89. Aardema H, Lisotto P, Kurilshikov A, Diepeveen JRJ, Friedrich AW, Sinha B, de Smet AMGA, Harmsen HJM. Marked changes in gut microbiota in cardio-surgical intensive care patients: a longitudinal cohort study. Front Cell Infect Microbiol. 2019;9:467.

    Article  PubMed  CAS  Google Scholar 

  90. Yadava K, Pattaroni C, Sichelstiel AK, Trompette A, Gollwitzer ES, Salami O, von Garnier C, Nicod LP, Marsland BJ. Microbiota promotes chronic pulmonary inflammation by enhancing IL-17A and autoantibodies. Am J Respir Crit Care Med. 2016;193:975–87.

    Article  PubMed  CAS  Google Scholar 

  91. Poroyko V, Meng F, Meliton A, Afonyushkin T, Ulanov A, Semenyuk E, Latif O, Tesic V, Birukova AA, Birukov KG. Alterations of lung microbiota in a mouse model of LPS-induced lung injury. Am J Physiol Lung Cell Mol Physiol. 2015;309:L76–83.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  92. O’Dwyer DN, Ashley SL, Gurczynski SJ, Xia M, Wilke C, Falkowski NR, Norman KC, Arnold KB, Huffnagle GB, Salisbury ML, Han MK, Flaherty KR, White ES, Martinez FJ, Erb-Downward JR, Murray S, Moore BB, Dickson RP. Lung microbiota contribute to pulmonary inflammation and disease progression in pulmonary fibrosis. Am J Respir Crit Care Med. 2019;199:1127–38.

    Article  PubMed  PubMed Central  Google Scholar 

  93. Basic M, Bleich A. Gnotobiotics: past, present and future. Lab Anim. 2019;53:232–43.

    Article  PubMed  CAS  Google Scholar 

  94. Dickson RP, Erb-Downward JR, Falkowski NR, Hunter EM, Ashley SL, Huffnagle GB. The lung microbiota of healthy mice are highly variable, cluster by environment, and reflect variation in baseline lung innate immunity. Am J Respir Crit Care Med. 2018;198:497–508.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  95. Barfod KK, Roggenbuck M, Hansen LH, Schjørring S, Larsen ST, Sørensen SJ, Krogfelt KA. The murine lung microbiome in relation to the intestinal and vaginal bacterial communities. BMC Microbiol. 2013;13:303.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  96. Matute-Bello G, Frevert CW, Martin TR. Animal models of acute lung injury. Am J Physiol Lung Cell Mol Physiol. 2008;295:L379–99.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  97. Matute-Bello G, Downey G, Moore BB, Groshong SD, Matthay MA, Slutsky AS, Kuebler WM, Acute Lung Injury in Animals Study Group. An official American Thoracic Society workshop report: features and measurements of experimental acute lung injury in animals. Am J Respir Cell Mol Biol. 2011;44:725–38.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  98. Uhlig S, Kuebler WM. Difficulties in modelling ARDS (2017 Grover conference series). Pulm Circ. 2018;8:2045894018766737.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  99. McCoy KD, Geuking MB, Ronchi F. Gut microbiome standardization in control and experimental mice. Curr Protoc Immunol. 2017;117:23.1.1–23.1.13.

    Article  Google Scholar 

  100. Ashley SL, Sjoding MW, Popova AP, Cui TX, Hoostal MJ, Schmidt TM, Branton WR, Dieterle MG, Falkowski NR, Baker JM, Hinkle KJ, Konopka KE, Erb-Downward JR, Huffnagle GB, Dickson RP. Lung and gut microbiota are altered by hyperoxia and contribute to oxygen-induced lung injury in mice. Sci Transl Med. 2020;12:eaau9959.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  101. Wienhold S-M, Macrì M, Nouailles G, Dietert K, Gurtner C, Gruber AD, Heimesaat MM, Lienau J, Schumacher F, Kleuser B, Opitz B, Suttorp N, Witzenrath M, Müller-Redetzky HC. Ventilator-induced lung injury is aggravated by antibiotic mediated microbiota depletion in mice. Crit Care. 2018;22:282.

    Article  PubMed  PubMed Central  Google Scholar 

  102. Kapur R, Kim M, Rebetz J, Hallström B, Björkman JT, Takabe-French A, Kim N, Liu J, Shanmugabhavananthan S, Milosevic S, McVey MJ, Speck ER, Semple JW. Gastrointestinal microbiota contributes to the development of murine transfusion-related acute lung injury. Blood Adv. 2018;2:1651–63.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  103. Sze MA, Tsuruta M, Yang S-WJ OY, Man SFP, Hogg JC, Sin DD. Changes in the bacterial microbiota in gut, blood, and lungs following acute LPS instillation into mice lungs. PLoS One. 2014;9:e111228.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  104. Xiang M, Fan J. Pattern recognition receptor-dependent mechanisms of acute lung injury. Mol Med. 2010;16:69–82.

    Article  PubMed  CAS  Google Scholar 

  105. Williams AE, José RJ, Mercer PF, Brealey D, Parekh D, Thickett DR, O’Kane C, McAuley DF, Chambers RC. Evidence for chemokine synergy during neutrophil migration in ARDS. Thorax. 2017;72:66–73.

    Article  PubMed  Google Scholar 

  106. Zemans RL, Matthay MA. What drives neutrophils to the alveoli in ARDS? Thorax. 2017;72:1–3.

    Article  PubMed  Google Scholar 

  107. Bradley BT, Maioli H, Johnston R, Chaudhry I, Fink SL, Xu H, Najafian B, Deutsch G, Lacy JM, Williams T, Yarid N, Marshall DA. Histopathology and ultrastructural findings of fatal COVID-19 infections in Washington State: a case series. Lancet. 2020;396:320–32.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  108. Leiva-Juárez MM, Kolls JK, Evans SE. Lung epithelial cells: therapeutically inducible effectors of antimicrobial defense. Mucosal Immunol. 2018;11:21–34.

    Article  PubMed  CAS  Google Scholar 

  109. Yang D, Chen X, Wang J, Lou Q, Lou Y, Li L, Wang H, Chen J, Wu M, Song X, Qian Y. Dysregulated lung commensal bacteria drive interleukin-17B production to promote pulmonary fibrosis through their outer membrane vesicles. Immunity. 2019;50:692–706.e7.

    Article  PubMed  CAS  Google Scholar 

  110. Alessandro-Gabazza CND, Kobayashi T, Yasuma T, Toda M, Kim H, Fujimoto H, Hataji O, Takeshita A, Nishihama K, Okano T, Okano Y, Nishii Y, Tomaru A, Fujiwara K, Alessandro VFD, Abdel-Hamid AM, Ren Y, Pereira GV, Wright CL, Hernandez A, Fields CJ, Yau PM, Wang S, Mizoguchi A, Fukumura M, Ohtsuka J, Nosaka T, Kataoka K, Kondoh Y, et al. A staphylococcus pro-apoptotic peptide induces acute exacerbation of pulmonary fibrosis. Nat Commun. 2020;11:1539.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  111. Vieira R d S, Castoldi A, Basso PJ, Hiyane MI, NOS C, Almeida RR. Butyrate attenuates lung inflammation by negatively modulating th9 cells. Front Immunol. 2019;10:67.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  112. Sencio V, Barthelemy A, Tavares LP, Machado MG, Soulard D, Cuinat C, Queiroz-Junior CM, Noordine M-L, Salomé-Desnoulez S, Deryuter L, Foligné B, Wahl C, Frisch B, Vieira AT, Paget C, Milligan G, Ulven T, Wolowczuk I, Faveeuw C, Le Goffic R, Thomas M, Ferreira S, Teixeira MM, Trottein F. Gut dysbiosis during influenza contributes to pulmonary pneumococcal superinfection through altered short-chain fatty acid production. Cell Rep. 2020;30:2934–2947.e6.

    Article  PubMed  CAS  Google Scholar 

  113. Dang AT, Marsland BJ. Microbes, metabolites, and the gut-lung axis. Mucosal Immunol. 2019;12:843–50.

    Article  PubMed  CAS  Google Scholar 

  114. Ericsen AJ, Lauck M, Mohns MS, DiNapoli SR, Mutschler JP, Greene JM, Weinfurter JT, Lehrer-Brey G, Prall TM, Gieger SM, Buechler CR, Crosno KA, Peterson EJ, Reynolds MR, Wiseman RW, Burwitz BJ, Estes JD, Sacha JB, Friedrich TC, Brenchley JM, O’Connor DH. Microbial translocation and inflammation occur in hyperacute immunodeficiency virus infection and compromise host control of virus replication. PLoS Pathog. 2016;12:e1006048.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  115. Beitler JR, Goligher EC, Schmidt M, Spieth PM, Zanella A, Martin-Loeches I, Calfee CS, Cavalcanti AB, ARDSne(x)t Investigators. Personalized medicine for ARDS: the 2035 research agenda. Intensive Care Med. 2016;42:756–67.

    Article  PubMed  PubMed Central  Google Scholar 

  116. Meyer NJ, Calfee CS. Novel translational approaches to the search for precision therapies for acute respiratory distress syndrome. Lancet Respir Med. 2017;5:512–23.

    Article  PubMed  PubMed Central  Google Scholar 

  117. Yang L, Haidar G, Zia H, Shah F, Rapport S, McVerry B, Morris A, O’Grady J, Kitsios GD. Metagenomic identification of severe pneumonia pathogens in mechanically-ventilated patients: a feasibility and clinical validity study. Respir Res 2019;20:265–77.

    Google Scholar 

  118. Charalampous T, Kay GL, Richardson H, Aydin A, Baldan R, Jeanes C, Rae D, Grundy S, Turner DJ, Wain J, Leggett RM, Livermore DM, O’Grady J. Nanopore metagenomics enables rapid clinical diagnosis of bacterial lower respiratory infection. Nat Biotechnol. 2019;37:783–92.

    Article  PubMed  CAS  Google Scholar 

  119. Langelier C, Kalantar KL, Moazed F, Wilson MR, Crawford ED, Deiss T, Belzer A, Bolourchi S, Caldera S, Fung M, Jauregui A, Malcolm K, Lyden A, Khan L, Vessel K, Quan J, Zinter M, Chiu CY, Chow ED, Wilson J, Miller S, Matthay MA, Pollard KS, Christenson S, Calfee CS, DeRisi JL. Integrating host response and unbiased microbe detection for lower respiratory tract infection diagnosis in critically ill adults. Proc Natl Acad Sci U S A. 2018;115:E12353–62.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  120. Kitsios GD. Translating lung microbiome profiles into the next-generation diagnostic gold standard for pneumonia: a clinical Investigator’s perspective. mSystems. 2018;3:e00153-17.

    Article  PubMed  PubMed Central  Google Scholar 

  121. Pendleton KM, Erb-Downward JR, Bao Y, Branton WR, Falkowski NR, Newton DW, Huffnagle GB, Dickson RP. Rapid pathogen identification in bacterial pneumonia using real-time metagenomics. Am J Respir Crit Care Med. 2017;196:1610–2.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  122. Villar J, Ferrando C, Martínez D, Ambrós A, Muñoz T, Soler JA, Aguilar G, Alba F, González-Higueras E, Conesa LA, Martín-Rodríguez C, Díaz-Domínguez FJ, Serna-Grande P, Rivas R, Ferreres J, Belda J, Capilla L, Tallet A, Añón JM, Fernández RL, González-Martín JM, dexamethasone in ARDS network. Dexamethasone treatment for the acute respiratory distress syndrome: a multicentre, randomised controlled trial. Lancet Respir Med. 2020;8:267–76.

    Article  PubMed  CAS  Google Scholar 

  123. O’Dwyer DN, Dickson RP, Moore BB. The lung microbiome, immunity, and the pathogenesis of chronic lung disease. J Immunol. 2016;196:4839–47.

    Article  PubMed  CAS  Google Scholar 

  124. Cookson WOCM, Cox MJ, Moffatt MF. New opportunities for managing acute and chronic lung infections. Nat Rev Microbiol. 2018;16:111–20.

    Article  PubMed  CAS  Google Scholar 

  125. Wunderink RG. Turning the phage on treatment of antimicrobial-resistant pneumonia. Am J Respir Crit Care Med. 2019;200:1081–2.

    Article  PubMed  PubMed Central  Google Scholar 

  126. Shankar-Hari M, Fan E, Ferguson ND. Acute respiratory distress syndrome (ARDS) phenotyping. Intensive Care Med. 2019;45:516–9.

    Article  PubMed  CAS  Google Scholar 

  127. Britton N, Kitsios G, Fitch A, Methe B, McVerry BJ, Morris AM. The composition of the lung mycobiome in adult critically ill patients. B98 new developments in lung microbiome. American Thoracic Society; 2020. p A4252. https://doi.org/10.1164/ajrccm-conference.2020.201.1_MeetingAbstracts.A4252.

  128. Kuntz TM, Gilbert JA. Introducing the microbiome into precision medicine. Trends Pharmacol Sci. 2017;38:81–91.

    Article  PubMed  CAS  Google Scholar 

  129. Mohammed A, Alghetaa H, Zhou J, Chatterjee S, Nagarkatti P, Nagarkatti M. Protective effects of Δ9-tetrahydrocannabinol against enterotoxin-induced acute respiratory distress syndrome is mediated by modulation of microbiota. Br J Pharmacol. 2020; https://doi.org/10.1111/bph.15226.

  130. Schuijt TJ, Lankelma JM, Scicluna BP, de Sousa e Melo F, Roelofs JJTH, de Boer JD, Hoogendijk AJ, de Beer R, de Vos A, Belzer C, de Vos WM, van der Poll T, Wiersinga WJ. The gut microbiota plays a protective role in the host defence against pneumococcal pneumonia. Gut. 2016;65:575–83.

    Article  PubMed  CAS  Google Scholar 

  131. Prakash A, Sundar SV, Zhu Y-G, Tran A, Lee J-W, Lowell C, Hellman J. Lung ischemia-reperfusion is a sterile inflammatory process influenced by commensal microbiota in mice. Shock. 2015;44:272–9.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Georgios D. Kitsios .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2022 The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Nature Switzerland AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Kitsios, G.D., Franz, C., McVerry, B.J. (2022). The Microbiome in Acute Lung Injury and ARDS. In: Huang, Y.J., Garantziotis, S. (eds) The Microbiome in Respiratory Disease. Respiratory Medicine. Humana, Cham. https://doi.org/10.1007/978-3-030-87104-8_11

Download citation

  • DOI: https://doi.org/10.1007/978-3-030-87104-8_11

  • Published:

  • Publisher Name: Humana, Cham

  • Print ISBN: 978-3-030-87103-1

  • Online ISBN: 978-3-030-87104-8

  • eBook Packages: MedicineMedicine (R0)

Publish with us

Policies and ethics