Unique patterns of lower respiratory tract microbiota are associated with inflammation and hospital mortality in acute respiratory distress syndrome

Michihito Kyo, Keisuke Nishioka, Takaaki Nakaya, Yoshiko Kida, Yuko Tanabe, Shinichiro Ohshimo, Nobuaki Shime, Michihito Kyo, Keisuke Nishioka, Takaaki Nakaya, Yoshiko Kida, Yuko Tanabe, Shinichiro Ohshimo, Nobuaki Shime

Abstract

Background: The lung microbiome maintains the homeostasis of the immune system within the lungs. In acute respiratory distress syndrome (ARDS), the lung microbiome is enriched with gut-derived bacteria; however, the specific microbiome associated with morbidity and mortality in patients with ARDS remains unclear. This study investigated the specific patterns of the lung microbiome that are correlated with mortality in ARDS patients.

Methods: We analyzed the lung microbiome from the bronchoalveolar lavage fluid (BALF) of patients with ARDS and control subjects. We measured the copy numbers of 16S rRNA and the serum and BALF cytokines (interleukin [IL]-6, IL-8, receptor for advanced glycation end products, and angiopoietin-2).

Results: We analyzed 47 mechanically ventilated patients diagnosed with (n = 40) or without (n = 7; control) ARDS. The alpha diversity was significantly decreased in ARDS patients compared with that of the controls (6.24 vs. 8.07, P = 0.03). The 16S rRNA gene copy numbers tended to be increased in the ARDS group compared with the controls (3.83 × 106 vs. 1.01 × 105 copies/mL, P = 0.06). ARDS patients were subdivided into the hospital survivor (n = 24) and non-survivor groups (n = 16). Serum IL-6 levels were significantly higher in the non-survivors than in the survivors (567 vs. 214 pg/mL, P = 0.027). The 16S rRNA copy number was significantly correlated with serum IL-6 levels in non-survivors (r = 0.615, P < 0.05). The copy numbers and relative abundance of betaproteobacteria were significantly lower in the non-survivors than in the survivors (713 vs. 7812, P = 0.012; 1.22% vs. 0.08%, P = 0.02, respectively). Conversely, the copy numbers of Staphylococcus, Streptococcus and Enterobacteriaceae were significantly correlated with serum IL-6 levels in the non-survivors (r = 0.579, P < 0.05; r = 0.604, P < 0.05; r = 0.588, P < 0.05, respectively).

Conclusions: The lung bacterial burden tended to be increased, and the alpha diversity was significantly decreased in ARDS patients. The decreased Betaproteobacteria and increased Staphylococcus, Streptococcus and Enterobacteriaceae might represent a unique microbial community structure correlated with increased serum IL-6 and hospital mortality.

Trial registration: The institutional review boards of Hiroshima University (Trial registration: E-447-4, registered 16 October 2019) and Kyoto Prefectural University of Medicine (Trial registration: ERB-C-973, registered 19 October 2017) approved an opt-out method of informed consent.

Keywords: 16S rRNA; Acute respiratory distress syndrome; Bronchoalveolar lavage; Lung; Pneumonia; Sepsis.

Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
a 16S rRNA amplicon sequencing results of the main OTUs at the genus level. The microbiota indicated large variations among individuals. The non-survivor ARDS group presented fewer bacterial genera compared with the survivor and control groups. b Microbial community structures of the ARDS patients and controls using principle coordinates analysis. UniFrac distances were calculated after constructing the phylogenetic tree. Each dot and percentage of axes represent one sample and contribution rate, respectively. c Comparison of alpha diversity and Shannon diversity index indicating the bacterial diversity within one sample between ARDS patients and controls. Alpha diversities of the ARDS patients and non-surviving ARDS patients were significantly lower than those of the controls (*P < 0.05). ARDS, acute respiratory distress syndrome; OTU, operational taxonomic units
Fig. 2
Fig. 2
a (Left) 16S rRNA copy numbers from the BALF of ARDS patients were increased compared with the controls. (Right) 16S rRNA copy numbers from the BALF did not significantly differ between the BP and non-BP among ARDS. We compared the 10 patients with bacterial pneumonia to 30 patients with non-bacterial pneumonia. b Serum and BALF cytokine levels including IL-6, IL-8, RAGE and Ang-2 were compared between surviving and non-surviving ARDS patients. Serum IL-6 levels in 22 survivors were significantly increased compared with those of 13 non-survivors (*P < 0.05). We collected blood samples within 24 h after obtaining the BALF in 35 of ARDS patients. BALF cytokine levels were measured in 23 survivors and 15 non-survivors. ARDS, acute respiratory distress syndrome; BP, bacterial pneumonia; IL, interleukin; RAGE, receptor of advanced glycation end-products; Ang-2, Angiopoietin-2
Fig. 3
Fig. 3
a Correlation between alpha diversity (Shannon diversity index) and serum (in 22 survivors and 13 non-survivors) and BALF IL-6 (in 23 survivors and 15 non-survivors). No significant correlation was found between IL-6 and the Shannon diversity index. b Correlation between the copy numbers of 16S rRNA genes in the BALF and the serum and BALF IL-6. Increased copy numbers of 16S rRNA were correlated with increased serum IL-6. BALF, bronchoalveolar lavage fluid; IL, interleukin
Fig. 4
Fig. 4
a (Left) Copy numbers of the 16S rRNA genes of the Betaproteobacteria were not correlated with serum IL-6 in 22 surviving ARDS patients. (Right) Increased copy numbers of 16S rRNA genes in Betaproteobacteria were correlated with serum IL-6 in 13 non-surviving ARDS patients. b Copy numbers of 16S rRNA genes in the Betaproteobacteria in 16 non-surviving ARDS patients were significantly decreased compared with those of 24 surviving ARDS patients (*P < 0.05). c The relative abundances of Betaproteobacteria in 16 ARDS non-survivors were significantly decreased compared with those of 24 ARDS survivors (*P < 0.05). d Increased copy numbers of 16S rRNA genes of Staphylococcus, Streptococcus and Enterobacteriaceae were correlated with increased serum IL-6 levels in 13 non-surviving ARDS patients. e The ratio of Betaproteobacteria to Staphylococcus, Streptococcus and Enterobacteriaceae did not significantly differ between 24 survivors and 16 non-survivors of ARDS. f The ratio of Betaproteobacteria to the maximum value among Staphylococcus, Streptococcus and Enterobacteriaceae was significantly decreased in 16 non-survivors of ARDS compared with those of 24 survivors of ARDS (**P < 0.01). g Hazard ratio of the ratio of Betaproteobacteria to maximum value among Staphylococcus, Streptococcus and Enterobacteriaceae by the Cox proportional hazards model in 40 ARDS patients (**P < 0.01). IL, interleukin; ARDS, acute respiratory distress syndrome

References

    1. Bellani G, Laffey JG, Pham T, Fan E, Brochard L, Esteban A, et al. 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. doi: 10.1001/jama.2016.0291.
    1. Charlson ES, Bittinger K, Haas AR, Fitzgerald AS, Frank I, Yadav A, et al. Topographical continuity of bacterial populations in the healthy human respiratory tract. Am J Respir Crit Care Med. 2011;184:957–963. doi: 10.1164/rccm.201104-0655OC.
    1. Garzoni C, Brugger SD, Qi W, Wasmer S, Cusini A, Dumont P, et al. Microbial communities in the respiratory tract of patients with interstitial lung disease. Thorax. 2013;68:1150–1156. doi: 10.1136/thoraxjnl-2012-202917.
    1. Bousbia S, Papazian L, Saux P, Forel JM, Auffray JP, Martin C, et al. Repertoire of intensive care unit pneumonia microbiota. PLoS One. 2012;7:e32486. doi: 10.1371/journal.pone.0032486.
    1. Dickson RP, Erb-Downward JR, Freeman CM, McCloskey L, Falkowski NR, Huffnagle GB, et al. Bacterial topography of the healthy human lower respiratory tract. MBio. 2017;8. 10.1128/mBio.02287-16.
    1. Han MK, Zhou Y, Murray S, Tayob N, Noth I, Lama VN, et al. Lung microbiome and disease progression in idiopathic pulmonary fibrosis: an analysis of the COMET study. Lancet Respir Med. 2014;2:548–556. doi: 10.1016/S2213-2600(14)70069-4.
    1. Molyneaux PL, Cox MJ, Willis-Owen SA, Mallia P, Russell KE, Russell AM, et al. The role of bacteria in the pathogenesis and progression of idiopathic pulmonary fibrosis. Am J Respir Crit Care Med. 2014;190:906–913. doi: 10.1164/rccm.201403-0541OC.
    1. O'Dwyer DN, Ashley SL, Gurczynski SJ, Xia M, Wilke C, Falkowski NR, et al. Lung microbiota contribute to pulmonary inflammation and disease progression in pulmonary fibrosis. Am J Respir Crit Care Med. 2019;199:1127–1138. doi: 10.1164/rccm.201809-1650OC.
    1. Leitao Filho FS, Alotaibi NM, Ngan D, Tam S, Yang J, Hollander Z, et al. Sputum microbiome is associated with 1-year mortality following COPD hospitalizations. Am J Respir Crit Care Med. 2019;199:1205–1213. doi: 10.1164/rccm.201806-1135OC.
    1. Prevaes SM, de Winter-de Groot KM, Janssens HM, de Steenhuijsen Piters WA, Tramper-Stranders GA, Wyllie AL, et al. Development of the nasopharyngeal microbiota in infants with cystic fibrosis. Am J Respir Crit Care Med. 2016;193:504–515. doi: 10.1164/rccm.201509-1759OC.
    1. Dickson RP, Singer BH, Newstead MW, Falkowski NR, Erb-Downward JR, Standiford TJ, et al. Enrichment of the lung microbiome with gut bacteria in sepsis and the acute respiratory distress syndrome. Nat Microbiol. 2016;1:16113. doi: 10.1038/nmicrobiol.2016.113.
    1. Panzer AR, Lynch SV, Langelier C, Christie JD, McCauley K, Nelson M, et al. 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;197:621–631. doi: 10.1164/rccm.201702-0441OC.
    1. Segal LN, Alekseyenko AV, Clemente JC, Kulkarni R, Wu B, Gao Z, et al. Enrichment of lung microbiome with supraglottic taxa is associated with increased pulmonary inflammation. Microbiome. 2013;1:19. doi: 10.1186/2049-2618-1-19.
    1. Segal LN, Clemente JC, Tsay JC, Koralov SB, Keller BC, Wu BG, et al. Enrichment of the lung microbiome with oral taxa is associated with lung inflammation of a Th17 phenotype. Nat Microbiol. 2016;1:16031. doi: 10.1038/nmicrobiol.2016.31.
    1. Bernasconi E, Pattaroni C, Koutsokera A, Pison C, Kessler R, Benden C, et al. Airway microbiota determines innate cell inflammatory or tissue remodeling profiles in lung transplantation. Am J Respir Crit Care Med. 2016;194:1252–1263. doi: 10.1164/rccm.201512-2424OC.
    1. Force ADT, Ranieri VM, Rubenfeld GD, Thompson BT, Ferguson ND, Caldwell E, et al. Acute respiratory distress syndrome: the Berlin definition. JAMA. 2012;307:2526–2533.
    1. Akiyama K, Nishioka K, Khan KN, Tanaka Y, Mori T, Nakaya T, et al. Molecular detection of microbial colonization in cervical mucus of women with and without endometriosis. Am J Reprod Immunol. 2019;82:e13147. doi: 10.1111/aji.13147.
    1. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010;7:335–336. doi: 10.1038/nmeth.f.303.
    1. Shen W, Le S, Li Y, Hu F. SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation. PLoS One. 2016;11:e0163962. doi: 10.1371/journal.pone.0163962.
    1. Goleva E, Jackson LP, Harris JK, Robertson CE, Sutherland ER, Hall CF, et al. The effects of airway microbiome on corticosteroid responsiveness in asthma. Am J Respir Crit Care Med. 2013;188:1193–1201. doi: 10.1164/rccm.201304-0775OC.
    1. Bassis CM, Erb-Downward JR, Dickson RP, Freeman CM, Schmidt TM, Young VB, et al. Analysis of the upper respiratory tract microbiotas as the source of the lung and gastric microbiotas in healthy individuals. MBio. 2015;6:e00037. doi: 10.1128/mBio.00037-15.
    1. Nseir S, Zerimech F, Jaillette E, Artru F, Balduyck M. Microaspiration in intubated critically ill patients: diagnosis and prevention. Infect Disord Drug Targets. 2011;11:413–423. doi: 10.2174/187152611796504827.
    1. Poroyko V, Meng F, Meliton A, Afonyushkin T, Ulanov A, Semenyuk E, et al. Alterations of lung microbiota in a mouse model of LPS-induced lung injury. Am J Physiol Lung Cell Mol Physiol. 2015;309:L76–L83. doi: 10.1152/ajplung.00061.2014.
    1. Huffnagle GB, Dickson RP, Lukacs NW. The respiratory tract microbiome and lung inflammation: a two-way street. Mucosal Immunol. 2017;10:299–306. doi: 10.1038/mi.2016.108.
    1. Bingula R, Filaire M, Radosevic-Robin N, Bey M, Berthon JY, Bernalier-Donadille A, et al. Desired turbulence? Gut-lung Axis, immunity, and lung cancer. J Oncol. 2017;2017:5035371. doi: 10.1155/2017/5035371.
    1. Stanley D, Moore RJ, Wong CHY. An insight into intestinal mucosal microbiota disruption after stroke. Sci Rep. 2018;8:568. doi: 10.1038/s41598-017-18904-8.
    1. Kelly BJ, Imai I, Bittinger K, Laughlin A, Fuchs BD, Bushman FD, et al. Composition and dynamics of the respiratory tract microbiome in intubated patients. Microbiome. 2016;4:7. doi: 10.1186/s40168-016-0151-8.
    1. O'Dwyer DN, Dickson RP, Moore BB. The lung microbiome, immunity, and the pathogenesis of chronic lung disease. J Immunol. 2016;196:4839–4847. doi: 10.4049/jimmunol.1600279.
    1. Mouraux S, Bernasconi E, Pattaroni C, Koutsokera A, Aubert JD, Claustre J, et al. Airway microbiota signals anabolic and catabolic remodeling in the transplanted lung. J Allergy Clin Immunol. 2018;141:718–729. doi: 10.1016/j.jaci.2017.06.022.
    1. Knippenberg S, Ueberberg B, Maus R, Bohling J, Ding N, Tort Tarres M, et al. Streptococcus pneumoniae triggers progression of pulmonary fibrosis through pneumolysin. Thorax. 2015;70:636–646. doi: 10.1136/thoraxjnl-2014-206420.
    1. Stock CJ, Sato H, Fonseca C, Banya WA, Molyneaux PL, Adamali H, et al. Mucin 5B promoter polymorphism is associated with idiopathic pulmonary fibrosis but not with development of lung fibrosis in systemic sclerosis or sarcoidosis. Thorax. 2013;68:436–441. doi: 10.1136/thoraxjnl-2012-201786.
    1. Marri PR, Stern DA, Wright AL, Billheimer D, Martinez FD. Asthma-associated differences in microbial composition of induced sputum. J Allergy Clin Immunol. 2013;131:346–352. doi: 10.1016/j.jaci.2012.11.013.
    1. Teo SM, Mok D, Pham K, Kusel M, Serralha M, Troy N, et al. The infant nasopharyngeal microbiome impacts severity of lower respiratory infection and risk of asthma development. Cell Host Microbe. 2015;17:704–715. doi: 10.1016/j.chom.2015.03.008.

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