1
|
Human Microbiome Project Consortium.
Structure, function and diversity of the healthy human microbiome.
Nature. 486:207–214. 2012.PubMed/NCBI View Article : Google Scholar
|
2
|
Dy R and Sethi S: The lung microbiome and
exacerbations of COPD. Curr Opin Pulm Med. 22:196–202.
2016.PubMed/NCBI View Article : Google Scholar
|
3
|
Owyang C and Wu GD: The gut microbiome in
health and disease. Gastroenterology. 146:1433–1436. 2014.
|
4
|
Zheng J, Wu Q, Zou Y, Wang M, He L and Guo
S: Respiratory microbiota profiles associated with the progression
from airway inflammation to remodeling in mice with OVA-induced
asthma. Front Microbiol. 12(723152)2021.PubMed/NCBI View Article : Google Scholar
|
5
|
Littman DR and Pamer EG: Role of the
commensal microbiota in normal and pathogenic host immune
responses. Cell Host Microbe. 10:311–323. 2011.PubMed/NCBI View Article : Google Scholar
|
6
|
Fukuyama S, Hiroi T, Yokota Y, Rennert PD,
Yanagita M, Kinoshita N, Terawaki S, Shikina T, Yamamoto M, Kurono
Y and Kiyono H: Initiation of NALT organogenesis is independent of
the IL-7R, LTbetaR, and NIK signaling pathways but requires the Id2
gene and CD3(-)CD4(+)CD45(+) cells. Immunity. 17:31–40.
2002.PubMed/NCBI View Article : Google Scholar
|
7
|
Dickson RP, Erb-Downward JR, Freeman CM,
McCloskey L, Falkowski NR, Huffnagle GB and Curtis JL: Bacterial
topography of the healthy human lower respiratory tract. mBio.
8:e02287–16. 2017.PubMed/NCBI View Article : Google Scholar
|
8
|
Man WH, de Steenhuijsen Piters WA and
Bogaert D: The microbiota of the respiratory tract: Gatekeeper to
respiratory health. Nat Rev Microbiol. 15:259–270. 2017.PubMed/NCBI View Article : Google Scholar
|
9
|
Gleeson K, Eggli DF and Maxwell SL:
Quantitative aspiration during sleep in normal subjects. Chest.
111:1266–1272. 1997.PubMed/NCBI View Article : Google Scholar
|
10
|
Segal LN, Alekseyenko AV, Clemente JC,
Kulkarni R, Wu B, Gao Z, Chen H, Berger KI, Goldring RM, Rom WN, et
al: Enrichment of lung microbiome with supraglottic taxa is
associated with increased pulmonary inflammation. Microbiome.
1(19)2013.PubMed/NCBI View Article : Google Scholar
|
11
|
Eidi S, Kamali SA, Hajari Z, Fata A, Farid
Hosseini R, Naseri A and Bakhshaee M: Nasal and indoors fungal
contamination in healthy subjects. Health Scope. 5(e30033)2016.
|
12
|
Qin J, Li R, Raes J, Arumugam M, Burgdorf
KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, et al: A
human gut microbial gene catalogue established by metagenomic
sequencing. Nature. 464:59–65. 2010.PubMed/NCBI View Article : Google Scholar
|
13
|
Dai W, Wang H, Zhou Q, Li D, Feng X, Yang
Z, Wang W, Qiu C, Lu Z, Xu X, et al: An integrated respiratory
microbial gene catalogue to better understand the microbial
aetiology of Mycoplasma pneumoniae pneumonia. Gigascience.
8(giz093)2019.PubMed/NCBI View Article : Google Scholar
|
14
|
Mason MR, Preshaw PM, Nagaraja HN, Dabdoub
SM, Rahman A and Kumar PS: The subgingival microbiome of clinically
healthy current and never smokers. ISME J. 9:268–272.
2015.PubMed/NCBI View Article : Google Scholar
|
15
|
Sapkota AR, Berger S and Vogel TM: Human
pathogens abundant in the bacterial metagenome of cigarettes.
Environ Health Perspect. 118:351–356. 2010.PubMed/NCBI View Article : Google Scholar
|
16
|
Qin N, Liang P, Wu C, Wang G, Xu Q, Xiong
X, Wang T, Zolfo M, Segata N, Qin H, et al: Longitudinal survey of
microbiome associated with particulate matter in a megacity. Genome
Biol. 21(55)2020.PubMed/NCBI View Article : Google Scholar
|
17
|
Pereira EL, Madacussengua O, Baptista P
and Feliciano M: Assessment of indoor air quality in geriatric
environments of Southwestern Europe. Aerobiologia. 37:139–153.
2021.
|
18
|
Dong SR, Han YJ, Wu J, Zeng CL, Zhu KH,
Chen XJ, Liu YM, Zou XQ, Zheng SL, Wen ZH, et al: Distribution of
microbiota in fine particulate matter particles in Guangzhou,
China. Biomed Environ Sci. 33:306–314. 2020.PubMed/NCBI View Article : Google Scholar
|
19
|
Setti L, Passarini F, De Gennaro G,
Barbieri P, Perrone MG, Borelli M, Palmisani J, Di Gilio A, Torboli
V, Fontana F, et al: SARS-Cov-2RNA found on particulate matter of
Bergamo in Northern Italy: First evidence. Environ Res.
188(109754)2020.PubMed/NCBI View Article : Google Scholar
|
20
|
Brodie EL, DeSantis TZ, Parker JP,
Zubietta IX, Piceno YM and Andersen GL: Urban aerosols harbor
diverse and dynamic bacterial populations. Proc Natl Acad Sci USA.
104:299–304. 2007.PubMed/NCBI View Article : Google Scholar
|
21
|
Biswas K, Hoggard M, Jain R, Taylor MW and
Douglas RG: The nasal microbiota in health and disease: Variation
within and between subjects. Front Microbiol. 9(134)2015.PubMed/NCBI View Article : Google Scholar
|
22
|
Mariani J, Favero C, Spinazzè A, Cavallo
DM, Carugno M, Motta V, Bonzini M, Cattaneo A, Pesatori AC and
Bollati V: Short-term particulate matter exposure influences nasal
microbiota in a population of healthy subjects. Environ Res.
162:119–126. 2018.PubMed/NCBI View Article : Google Scholar
|
23
|
Ghebre MA, Pang PH, Diver S, Desai D,
Bafadhel M, Haldar K, Kebadze T, Cohen S, Newbold P, Rapley L, et
al: Biological exacerbation clusters demonstrate asthma and chronic
obstructive pulmonary disease overlap with distinct mediator and
microbiome profiles. J Allergy Clin Immunol. 141:2027–2036.e12.
2018.PubMed/NCBI View Article : Google Scholar
|
24
|
Dima E, Kyriakoudi A, Kaponi M,
Vasileiadis I, Stamou P, Koutsoukou A, Koulouris NG and Rovina N:
The lung microbiome dynamics between stability and exacerbation in
chronic obstructive pulmonary disease (COPD): Current perspectives.
Respir Med. 157:1–6. 2019.PubMed/NCBI View Article : Google Scholar
|
25
|
Opron K, Begley LA, Erb-Downward JR,
Freeman C, Madapoosi S, Alexis NE, Barjaktarevic I, Graham Barr R,
Bleecker ER, Bowler RP, et al: Lung microbiota associations with
clinical features of COPD in the SPIROMICS cohort. NPJ Biofilms
Microbiomes. 7(14)2021.PubMed/NCBI View Article : Google Scholar
|
26
|
Huang YJ, Sethi S, Murphy T, Nariya S,
Boushey HA and Lynch SV: Airway microbiome dynamics in
exacerbations of chronic obstructive pulmonary disease. J Clin
Microbiol. 52:2813–2823. 2014.PubMed/NCBI View Article : Google Scholar
|
27
|
Erb-Downward JR, Thompson DL, Han MK,
Freeman CM, McCloskey L, Schmidt LA, Young VB, Toews GB, Curtis JL,
Sundaram B, et al: Analysis of the lung microbiome in the ‘healthy’
smoker and in COPD. PLoS One. 6(e16384)2011.PubMed/NCBI View Article : Google Scholar
|
28
|
Tangedal S, Nielsen R, Aanerud M, Persson
LJ, Wiker HG, Bakke PS, Hiemstra PS and Eagan TM: Sputum microbiota
and inflammation at stable state and during exacerbations in a
cohort of chronic obstructive pulmonary disease (COPD) patients.
PLoS One. 14(e0222449)2019.PubMed/NCBI View Article : Google Scholar
|
29
|
Huang WC, Wu MF and Huang CC, Liu SY, Chen
HC, Chen YY, Hsu JY and Huang CC: Dynamics of the lung microbiome
in intensive care patients with chronic obstructive pulmonary
disease and community-acquired pneumonia. Sci Rep.
10(11046)2020.PubMed/NCBI View Article : Google Scholar
|
30
|
Huang YJ, Nariya S, Harris JM, Lynch SV,
Choy DF, Arron JR and Boushey H: The airway microbiome in patients
with severe asthma: Associations with disease features and
severity. J Allergy Clin Immunol. 136:874–884. 2015.PubMed/NCBI View Article : Google Scholar
|
31
|
Hilty M, Burke C, Pedro H, Cardenas P,
Bush A, Bossley C, Davies J, Ervine A, Poulter L, Pachter L, et al:
Disordered microbial communities in asthmatic airways. PLoS One.
5(e8578)2010.PubMed/NCBI View Article : Google Scholar
|
32
|
Kloepfer KM, Lee WM, Pappas TE, Kang TJ,
Vrtis RF, Evans MD, Gangnon RE, Bochkov YA, Jackson DJ, Lemanske RF
Jr and Gern JE: Detection of pathogenic bacteria during rhinovirus
infection is associated with increased respiratory symptoms and
asthma exacerbations. J Allergy Clin Immunol. 133:1301–1307.e3.
2014.PubMed/NCBI View Article : Google Scholar
|
33
|
McCauley KE, Flynn K, Calatroni A, DiMassa
V, LaMere B, Fadrosh DW, Lynch KV, Gill MA, Pongracic JA, Khurana
Hershey GK, et al: Seasonal airway microbiome and transcriptome
interactions promote childhood asthma exacerbations. J Allergy Clin
Immunol. 150:204–213. 2022.PubMed/NCBI View Article : Google Scholar
|
34
|
Perez-Losada M, Authelet KJ, Hoptay CE,
Kwak C, Crandall KA and Freishtat RJ: Pediatric asthma comprises
different phenotypic clusters with unique nasal microbiotas.
Microbiome. 6(179)2018.PubMed/NCBI View Article : Google Scholar
|
35
|
Teo SM, Tang HHF, Mok D, Judd LM, Watts
SC, Pham K, Holt BJ, Kusel M, Serralha M, Troy N, et al: Airway
microbiota dynamics uncover a critical window for interplay of
pathogenic bacteria and allergy in childhood respiratory disease.
Cell Host Microbe. 24:341–352.e5. 2018.PubMed/NCBI View Article : Google Scholar
|
36
|
Rogers GB, Zain NM, Bruce KD, Burr LD,
Chen AC, Rivett DW, McGuckin MA and Serisier DJ: A novel microbiota
stratification system predicts future exacerbations in
bronchiectasis. Ann Am Thorac Soc. 11:496–503. 2014.PubMed/NCBI View Article : Google Scholar
|
37
|
Araújo D, Shteinberg M, Aliberti S,
Goeminne PC, Hill AT, Fardon TC, Obradovic D, Stone G, Trautmann M,
Davis A, et al: The independent contribution of Pseudomonas
aeruginosa infection to long-term clinical outcomes in
bronchiectasis. Eur Respir J. 51(1701953)2018.PubMed/NCBI View Article : Google Scholar
|
38
|
Amati F, Simonetta E, Gramegna A, Tarsia
P, Contarini M, Blasi F and Aliberti S: The biology of pulmonary
exacerbations in bronchiectasis. Eur Respir Rev.
28(190055)2019.PubMed/NCBI View Article : Google Scholar
|
39
|
Aksamit TR, O'Donnell AE, Barker A,
Olivier KN, Winthrop KL, Daniels MLA, Johnson M, Eden E, Griffith
D, Knowles M, et al: Adult patients with bronchiectasis: A first
look at the US bronchiectasis research registry. Chest.
151:982–992. 2017.PubMed/NCBI View Article : Google Scholar
|
40
|
Guan WJ, Gao YH, Xu G, Lin ZY, Tang Y, Li
HM, Lin ZM, Zheng JP, Chen RC and Zhong NS: Aetiology of
bronchiectasis in Guangzhou, Southern China. Respirology.
20:739–748. 2015.PubMed/NCBI View Article : Google Scholar
|
41
|
Mac Aogain M, Narayana JK, Tiew PY, Ali
NABM, Yong VFL, Jaggi TK, Lim AYH, Keir HR, Dicker AJ, Thng KX, et
al: Integrative microbiomics in bronchiectasis exacerbations. Nat
Med. 27:688–699. 2021.PubMed/NCBI View Article : Google Scholar
|
42
|
Richter AG, Stockley RA, Harper L and
Thickett DR: Pulmonary infection in Wegener granulomatosis and
idiopathic pulmonary fibrosis. Thorax. 64:692–697. 2009.PubMed/NCBI View Article : Google Scholar
|
43
|
Molyneaux PL, Cox MJ, Willis-Owen SA,
Mallia P, Russell KE, Russell AM, Murphy E, Johnston SL, Schwartz
DA, Wells AU, et al: The role of bacteria in the pathogenesis and
progression of idiopathic pulmonary fibrosis. Am J Respir Crit Care
Med. 190:906–913. 2014.PubMed/NCBI View Article : Google Scholar
|
44
|
Molyneaux PL, Cox MJ, Wells AU, Kim HC, Ji
W, Cookson WO, Moffatt MF, Kim DS and Maher TM: Changes in the
respiratory microbiome during acute exacerbations of idiopathic
pulmonary fibrosis. Respir Res. 18(29)2017.PubMed/NCBI View Article : Google Scholar
|
45
|
Warheit-Niemi HI, Edwards SJ, SenGupta S,
Parent CA, Zhou X, O'Dwyer DN and Moore BB: Fibrotic lung disease
inhibits immune responses to staphylococcal pneumonia via impaired
neutrophil and macrophage function. JCI Insight.
7(e152690)2022.PubMed/NCBI View Article : Google Scholar
|
46
|
D'Alessandro-Gabazza CN, Kobayashi T,
Yasuma T, Toda M, Kim H, Fujimoto H, Hataji O, Takeshita A,
Nishihama K, Okano T, et al: A Staphylococcus pro-apoptotic peptide
induces acute exacerbation of pulmonary fibrosis. Nat Commun.
11(1539)2020.PubMed/NCBI View Article : Google Scholar
|
47
|
Cremers AJ, Zomer AL, Gritzfeld JF,
Ferwerda G, van Hijum SA, Ferreira DM, Shak JR, Klugman KP,
Boekhorst J, Timmerman HM, et al: The adult nasopharyngeal
microbiome as a determinant of pneumococcal acquisition.
Microbiome. 2(44)2014.PubMed/NCBI View Article : Google Scholar
|
48
|
Chonmaitree T, Jennings K, Golovko G,
Khanipov K, Pimenova M, Patel JA, McCormick DP, Loeffelholz MJ and
Fofanov Y: Nasopharyngeal microbiota in infants and changes during
viral upper respiratory tract infection and acute otitis media.
PLoS One. 12(e0180630)2017.PubMed/NCBI View Article : Google Scholar
|
49
|
Wu BG and Segal LN: The lung microbiome
and its role in Pneumonia. Clin Chest Med. 39:677–689.
2018.PubMed/NCBI View Article : Google Scholar
|
50
|
Soret P, Vandenborght LE, Francis F, Coron
N, Enaud R, Avalos M, Schaeverbeke T, Berger P, Fayon M, Thiebaut
R, et al: Respiratory mycobiome and suggestion of inter-Kingdom
network during acute pulmonary exacerbation in cystic fibrosis. Sci
Rep. 10(3589)2020.PubMed/NCBI View Article : Google Scholar
|
51
|
Tipton L, Ghedin E and Morris A: The lung
mycobiome in the next-generation sequencing era. Virulence.
8:334–341. 2017.PubMed/NCBI View Article : Google Scholar
|
52
|
Weaver D, Gago S, Bromley M and Bowyer P:
The human lung mycobiome in chronic respiratory disease:
Limitations of methods and our current understanding. Curr Fungal
Infect Rep. 13:109–119. 2019.
|
53
|
Runge S and Rosshart SP: The mammalian
metaorganism: A holistic view on how microbes of all Kingdoms and
niches shape local and systemic immunity. Front Immunol.
12(702378)2021.PubMed/NCBI View Article : Google Scholar
|
54
|
Speirs JJ, van der Ent CK and Beekman JM:
Effects of Aspergillus fumigatus colonization on lung function in
cystic fibrosis. Curr Opin Pulm Med. 18:632–638. 2012.PubMed/NCBI View Article : Google Scholar
|
55
|
Tiew PY, Dicker AJ, Keir HR, Poh ME, Pang
SL, Mac Aogáin M, Chua BQY, Tan JL, Xu H, Koh MS, et al: A
high-risk airway mycobiome is associated with frequent exacerbation
and mortality in COPD. Eur Respir J. 57(2002050)2021.PubMed/NCBI View Article : Google Scholar
|
56
|
Sovran B, Planchais J, Jegou S, Straube M,
Lamas B, Natividad JM, Agus A, Dupraz L, Glodt J, Da Costa G, et
al: Enterobacteriaceae are essential for the modulation of colitis
severity by fungi. Microbiome. 6(152)2018.PubMed/NCBI View Article : Google Scholar
|
57
|
Liu H, Liang Z, Cao N, Tan X, Liu Z, Wang
F, Yang Y, Li C, He Y, Su J, et al: Airway bacterial and fungal
microbiome in chronic obstructive pulmonary disease. bioRxiv. 2020:
2020.10.05.327536.
|
58
|
Mac Aogáin M, Chandrasekaran R, Lim AYH,
Low TB, Tan GL, Hassan T, Ong TH, Hui Qi Ng A, Bertrand D, Koh JY,
et al: Immunological corollary of the pulmonary mycobiome in
bronchiectasis: The CAMEB study. Eur Respir J.
52(1800766)2018.PubMed/NCBI View Article : Google Scholar
|
59
|
Máiz L, Nieto R, Cantón R, Gómez G, de la
Pedrosa E and Martinez-García MÁ: Fungi in Bronchiectasis: A
concise review. Int J Mol Sci. 19(142)2018.PubMed/NCBI View Article : Google Scholar
|
60
|
Camargo CN, Carraro E, Granato CF and
Bellei N: Human rhinovirus infections in symptomatic and
asymptomatic subjects. Braz J Microbiol. 43:1641–1645.
2012.PubMed/NCBI View Article : Google Scholar
|
61
|
Biancardi E, Fennell M, Rawlinson W and
Thomas PS: Viruses are frequently present as the infecting agent in
acute exacerbations of chronic obstructive pulmonary disease in
patients presenting to hospital. Intern Med J. 46:1160–1165.
2016.PubMed/NCBI View Article : Google Scholar
|
62
|
Harris AM, Hicks LA and Qaseem A: High
Value Care Task Force of the American College of Physicians and for
the Centers for Disease Control and Prevention. Appropriate
antibiotic use for acute respiratory tract infection in adults:
Advice for high-value care from the American college of physicians
and the centers for disease control and prevention. Ann Intern Med.
164:425–434. 2016.PubMed/NCBI View Article : Google Scholar
|
63
|
Osur SL: Viral respiratory infections in
association with asthma and sinusitis: A review. Ann Allergy Asthma
Immunol. 89:553–560. 2002.PubMed/NCBI View Article : Google Scholar
|
64
|
Burchill E, Lymberopoulos E, Menozzi E,
Budhdeo S, McIlroy JR, Macnaughtan J and Sharma N: The unique
impact of COVID-19 on human Gut microbiome research. Front Med
(Lausanne). 8(652464)2021.PubMed/NCBI View Article : Google Scholar
|
65
|
Thevaranjan N, Puchta A, Schulz C, Naidoo
A, Szamosi JC, Verschoor CP, Loukov D, Schenck LP and Jury J:
Age-associated microbial dysbiosis promotes intestinal
permeability, systemic inflammation, and macrophage dysfunction.
Cell Host Microbe. 21:455–466.e4. 2017.PubMed/NCBI View Article : Google Scholar
|
66
|
Dhar D and Mohanty A: Gut microbiota and
Covid-19-possible link and implications. Virus Res.
285(198018)2020.PubMed/NCBI View Article : Google Scholar
|
67
|
Chhibber-Goel J, Gopinathan S and Sharma
A: Interplay between severities of COVID-19 and the gut microbiome:
Implications of bacterial co-infections? Gut Pathog.
13(14)2021.PubMed/NCBI View Article : Google Scholar
|
68
|
Khatiwada S and Subedi A: Lung microbiome
and coronavirus disease 2019 (COVID-19): Possible link and
implications. Hum Microb J. 17(100073)2020.PubMed/NCBI View Article : Google Scholar
|
69
|
Fan J, Li X, Gao Y, Zhou J, Wang S, Huang
B, Wu J, Cao Q, Chen Y, Wang Z, et al: The lung tissue microbiota
features of 20 deceased patients with COVID-19. J Infect.
81:e64–e67. 2020.PubMed/NCBI View Article : Google Scholar
|
70
|
Johnson DW: Croup. BMJ Clin Evid.
2014(0321)2014.PubMed/NCBI
|
71
|
Llor C and Bjerrum L: Antibiotic
prescribing for acute bronchitis. Expert Rev Anti Infect Ther.
14:633–642. 2016.PubMed/NCBI View Article : Google Scholar
|
72
|
Fujiogi M, Camargo CA Jr, Bernot JP,
Freishtat RJ, Harmon B, Mansbach JM, Castro-Nallar E, Perez-Losada
M and Hasegawa K: In infants with severe bronchiolitis:
Dual-transcriptomic profiling of nasopharyngeal microbiome and host
response. Pediatr Res. 88:144–146. 2020.PubMed/NCBI View Article : Google Scholar
|
73
|
Greenberg SB: Viral respiratory infections
in elderly patients and patients with chronic obstructive pulmonary
disease. Dis Mon. 49:201–209. 2003.PubMed/NCBI View Article : Google Scholar
|
74
|
Seemungal T, Harper-Owen R, Bhowmik A,
Moric I, Sanderson G, Message S, Maccallum P, Meade TW, Jeffries
DJ, Johnston SL and Wedzicha JA: Respiratory viruses, symptoms, and
inflammatory markers in acute exacerbations and stable chronic
obstructive pulmonary disease. Am J Respir Crit Care Med.
164:1618–1623. 2001.PubMed/NCBI View Article : Google Scholar
|
75
|
Wat D: Impact of respiratory viral
infections on cystic fibrosis. Postgrad Med J. 79:201–203.
2003.PubMed/NCBI View Article : Google Scholar
|