呼吸系统疾病与呼吸道微生态的研究进展

doi:10.12160/j.issn.1672-5190.2023.05.005

摘要/Abstract

摘要：

随着医学检验技术的发展，人们对呼吸道微生态有了进一步的认识，并开始对微生物组学与呼吸系统疾病之间的关系进行深入探索。越来越多的证据表明呼吸道微生物群与肺内环境稳定和疾病的发生有关，目前的研究着力寻找微生态失衡与慢性阻塞性肺疾病、哮喘、肺癌等呼吸系统疾病之间的因果关系及潜在机制。痰作为呼吸道微生态研究的首选样本，包含了丰富的微生态信息，并且极易获得。总结了呼吸道菌群的检测方法，综述了近年来呼吸道微生态的研究进展，探讨了呼吸道微生态与呼吸系统疾病发生发展的关系，以期为呼吸系统疾病的特异性诊断和治疗提供新的思路。

关键词: 呼吸道微生态, 呼吸系统疾病, 16S rDNA测序技术, 细菌光学检测方法

Abstract:

With the development of medical laboratory technology, people have gained deeper understanding of respiratory tract micro-ecology and begun to explore the relationship between microbiome and respiratory diseases. More and more evidence suggested that the respiratory tract microbiota is associated with the stability of the pulmonary environment and the occurrence of pulmonary diseases. The current research focused on exploring the causality and potential mechanisms between dysbiosis of respiratory tract microbiota and respiratory diseases such as chronic obstructive pulmonary disease, asthma, and lung cancer. Phlegm, as the preferred sample for respiratory tract micro-ecology research, contains rich micro-ecological information and is easily accessible. This paper summarizes the detection methods of respiratory tract bacterial flora, reviews the research progress of respiratory tract micro-ecology in recent years, and explores the relationship between respiratory tract micro-ecology and the occurrence and progression of respiratory diseases, in hoping to provide new ideas for the specific diagnosis and treatment of respiratory diseases.

Key words: respiratory tract micro-ecology, respiratory disease, 16S rDNA sequencing, bacterial optical detection method

中图分类号:

王静然, 李鹏飞, 刘苗, 陶艳琳, 刘亚男, 朱淑芬. 呼吸系统疾病与呼吸道微生态的研究进展[J]. 畜牧与饲料科学, 2023, 44(5): 30-38.

WANG Jingran, LI Pengfei, LIU Miao, TAO Yanlin, LIU Yanan, ZHU Shufen. Advances in Respiratory Diseases and Respiratory Tract Micro-ecology[J]. Animal Husbandry and Feed Science, 2023, 44(5): 30-38.

参考文献 65

[1]	HUFFNAGLE G B, DICKSON R P, LUKACS N W. The respiratory tract microbiome and lung inflammation: A two-way street[J]. Mucosal Immunology, 2017, 10(2): 299-306. doi: 10.1038/mi.2016.108 pmid: 27966551
[2]	SAEEDI P, SALIMIAN J, AHMADI A, et al. The transient but not resident (TBNR) microbiome: A Yin Yang model for lung immune system[J]. Inhalation Toxicology, 2015, 27(10): 451-461. doi: 10.3109/08958378.2015.1070220 pmid: 26307905
[3]	ROOKS M G, GARRETT W S. Gut microbiota, metabolites and host immunity[J]. Nature Reviews Immunology, 2016, 16(6): 341-352. doi: 10.1038/nri.2016.42 pmid: 27231050
[4]	PATTARONI C, WATZENBOECK M L, SCHNEIDEGGER S, et al. Early-life formation of the microbial and immunological environment of the human airways[J]. Cell Host and Microbe, 2018, 24(6): 857-865. doi: 10.1016/j.chom.2018.10.019
[5]	YAGI K, HUFFNAGLE G B, LUKACS N W, et al. The lung microbiome during health and disease[J]. International Journal of Molecular Sciences, 2021, 22(19): 10872. doi: 10.3390/ijms221910872
[6]	HUANG W Y, LEE M S, LIN L M, et al. Diagnostic performance of the Sputum Gram Stain in predicting sputum culture results for critically ill pediatric patients with pneumonia[J]. Pediatrics and Neonatology, 2020, 61(4): 420-425. doi: 10.1016/j.pedneo.2020.03.014
[7]	GU W, MILLER S, CHIU C Y. Clinical metagenomic next-generation sequencing for pathogen detection[J]. Annual Review of Pathology, 2019, 14:319-338. doi: 10.1146/annurev-pathmechdis-012418-012751 pmid: 30355154
[8]	DITZ B, CHRISTENSON S, ROSSEN J, et al. Sputum microbiome profiling in COPD: Beyond singular pathogen detection[J]. Thorax, 2020, 75(4): 338-344. doi: 10.1136/thoraxjnl-2019-214168 pmid: 31996401
[9]	JOHNSON J S, SPAKOWICZ D J, HONG B Y, et al. Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis[J]. Nature Communications, 2019, 10(1): 5029. doi: 10.1038/s41467-019-13036-1 pmid: 31695033
[10]	MÜLLER V, SOUSA J M, CEYLAN K H, et al. Identification of pathogenic bacteria in complex samples using a smartphone based fluorescence microscope[J]. RSC Advances, 2018, 8(64): 36493-36502. doi: 10.1039/C8RA06473C
[11]	ROMBOUTS S, NOLLMANN M. RNA imaging in bacteria[J]. FEMS Microbiology Reviews, 2021, 45(2): fuaa051. doi: 10.1093/femsre/fuaa051
[12]	FRICKMANN H, ZAUTNER A E, MOTER A, et al. Fluorescence in situ hybridization (FISH) in the microbiological diagnostic routine laboratory:A review[J]. Critical Reviews in Microbiology, 2017, 43(3): 263-293. doi: 10.3109/1040841X.2016.1169990
[13]	ZHU H Y, ISIKMAN S O, MUDANYALI O, et al. Optical imaging techniques for point-of-care diagnostics[J]. Lab on a Chip, 2013, 13(1): 51-67. doi: 10.1039/c2lc40864c pmid: 23044793
[14]	MENEGHEL J, PASSOT S, JAMME F, et al. FTIR micro-spectroscopy using synchrotron-based and thermal source-based radiation for probing live bacteria[J]. Analytical and Bioanalytical Chemistry, 2020, 412(26): 7049-7061. doi: 10.1007/s00216-020-02835-x pmid: 32839857
[15]	ZARNOWIEC P, LECHOWICZ Ł, CZERWONKA G, et al. Fourier transform infrared spectroscopy (FTIR) as a tool for the identification and differentiation of pathogenic bacteria[J]. Current Medicinal Chemistry, 2015, 22(14): 1710-1718. pmid: 25760086
[16]	SHI H M, SUN J J, HAN R R, et al. The strategy for correcting interference from water in Fourier transform infrared spectrum based bacterial typing[J]. Talanta, 2020, 208:120347. doi: 10.1016/j.talanta.2019.120347
[17]	QUINTELAS C, FERREIRA E C, LOPES J A, et al. An overview of the evolution of infrared spectroscopy applied to bacterial typing[J]. Biotechnology Journal, 2018, 13(1): 201700449.
[18]	MAITY J P, KAR S, LIN C M, et al. Identification and discrimination of bacteria using Fourier transform infrared spectroscopy[J]. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 2013, 116:478-484. doi: 10.1016/j.saa.2013.07.062
[19]	GULIEV R R, SUNTSOVA A Y, VOSTRIKOVA T Y, et al. Discrimination of Staphylococcus aureus strains from coagulase-negative staphylococci and other pathogens by Fourier transform infrared spectroscopy[J]. Analytical Chemistry, 2020, 92(7): 4943-4948. doi: 10.1021/acs.analchem.9b05050
[20]	TYAGI D, MISHRA S K, ZOU B, et al. Nano-functionalized long-period fiber grating probe for disease-specific protein detection[J]. Journal of Materials Chemistry B, 2018, 6(3): 386-392. doi: 10.1039/c7tb02406a pmid: 32254518
[21]	SRINIVASAN R, UMESH S, MURALI S, et al. Bare fiber Bragg grating immunosensor for real-time detection of Escherichia coli bacteria[J]. Journal of Biophotonics, 2017, 10(2): 224-230. doi: 10.1002/jbio.v10.2
[22]	SRIVASTAVA S K, HAMO H B, KUSHMARO A, et al. Highly sensitive and specific detection of E. coli by a SERS nanobiosensor chip utilizing metallic nanosculptured thin films[J]. The Analyst, 2015, 140(9): 3201-3209. doi: 10.1039/C5AN00209E
[23]	KAUSHIK S, TIWARI U K, PAL S S, et al. Rapid detection of Escherichia coli using fiber optic surface plasmon resonance immunosensor based on biofunctionalized molybdenum disulfide (MoS2) nanosheets[J]. Biosensors and Bioelectronics, 2019, 126:501-509. doi: 10.1016/j.bios.2018.11.006
[24]	CHARLSON E S, BITTINGER K, HAAS A R, et al. Topographical continuity of bacterial populations in the healthy human respiratory tract[J]. American Journal of Respiratory and Critical Care Medicine, 2011, 184(8): 957-963. doi: 10.1164/rccm.201104-0655OC pmid: 21680950
[25]	HILTY M, BURKE C, PEDRO H, et al. Disordered microbial communities in asthmatic airways[J]. PLoS One, 2010, 5(1): e8578. doi: 10.1371/journal.pone.0008578
[26]	ERB-DOWNWARD J R, THOMPSON D L, HAN M K, et al. Analysis of the lung microbiome in the healthy smoker and in COPD[J]. PLoS One, 2011, 6(2): e16384. doi: 10.1371/journal.pone.0016384
[27]	CHEN X Y, QIU C. Respiratory tract mucous membrane microecology and asthma[J]. Annals of Translational Medicine, 2019, 7(18): 495. doi: 10.21037/atm.2019.09.06 pmid: 31700931
[28]	HALDAR K, GEORGE L, WANG Z, et al. The sputum microbiome is distinct between COPD and health, independent of smoking history[J]. Respiratory Research, 2020, 21(1): 183. doi: 10.1186/s12931-020-01448-3 pmid: 32664956
[29]	MAMMEN M J, SETHI S. COPD and the microbiome[J]. Respirology, 2016, 21(4): 590-599. doi: 10.1111/resp.12732 pmid: 26852737
[30]	The Global Initiative for Chronic Obstructive Lung Disease GOLD. Global strategy for the diagnosis, management and prevention of chronic obstructive pulmonary disease 2022 report[R/OL].(2021-11-15)[2023-05-09]. https://goldcopd.org/wp-content/uploads/2021/12/GOLD-REPORT-2022-v1.1-22Nov2021_WMV.pdf.
[31]	RITCHIE A I, WEDZICHA J A. Definition, causes, pathogenesis, and consequences of chronic obstructive pulmonary disease exacerbations[J]. Clinics in Chest Medicine, 2020, 41(3): 421-438. doi: S0272-5231(20)30040-X pmid: 32800196
[32]	SZE M A, DIMITRIU P A, SUZUKI M, et al. Host response to the lung microbiome in chronic obstructive pulmonary disease[J]. American Journal of Respiratory and Critical Care Medicine, 2015, 192(4): 438-445. doi: 10.1164/rccm.201502-0223OC pmid: 25945594
[33]	SU L F, QIAO Y X, LUO J M, et al. Characteristics of the sputum microbiome in COPD exacerbations and correlations between clinical indices[J]. Journal of Translational Medicine, 2022, 20(1): 76. doi: 10.1186/s12967-022-03278-x pmid: 35123490
[34]	WANG J, CHAI J M, SUN L N, et al. The sputum microbiome associated with different sub-types of AECOPD in a Chinese cohort[J]. BMC Infectious Diseases, 2020, 20(1): 610. doi: 10.1186/s12879-020-05313-y pmid: 32811432
[35]	SOCKRIDER M, FUSSNER L. What is asthma?[J]. American Journal of Respiratory and Critical Care Medicine, 2020, 202(9): 25-26.
[36]	HOLGATE S T, WENZEL S, POSTMA D S, et al. Asthma[J]. Nature Reviews Disease Primers, 2015, 1:15025. doi: 10.1038/nrdp.2015.25 pmid: 27189668
[37]	MARRI P R, STERN D A, WRIGHT A L, et al. Asthma-associated differences in microbial composition of induced sputum[J]. Journal of Allergy and Clinical Immunology, 2013, 131(2): 346-352. doi: 10.1016/j.jaci.2012.11.013
[38]	ABDEL-AZIZ M I, VIJVERBERG S J H, NEERINCX A H, et al. The crosstalk between microbiome and asthma:Exploring associations and challenges[J]. Clinical and Experimental Allergy, 2019, 49(8): 1067-1086. doi: 10.1111/cea.v49.8
[39]	The Lancet. Lung cancer: Some progress, but still a lot more to do[J]. The Lancet, 2019, 394(10212): 1880.
[40]	SUNG H, FERLAY J, SIEGEL R L, et al. Global cancer statistics 2020:GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries[J]. CA:a Cancer Journal for Clinicians, 2021, 71(3): 209-249. doi: 10.3322/caac.v71.3
[41]	MAO Q X, JIANG F, YIN R, et al. Interplay between the lung microbiome and lung cancer[J]. Cancer Letters, 2018, 415:40-48. doi: S0304-3835(17)30760-7 pmid: 29197615
[42]	JIN J, GAN Y C, LIU H Y, et al. Diminishing microbiome richness and distinction in the lower respiratory tract of lung cancer patients: A multiple comparative study design with independent validation[J]. Lung Cancer, 2019, 136:129-135. doi: S0169-5002(19)30623-3 pmid: 31494531
[43]	LIU H X, TAO L L, ZHANG J, et al. Difference of lower airway microbiome in bilateral protected specimen brush between lung cancer patients with unilateral lobar masses and control subjects[J]. International Journal of Cancer, 2018, 142(4): 769-778. doi: 10.1002/ijc.v142.4
[44]	LEDERER D J, MARTINEZ F J. Idiopathic pulmonary fibrosis[J]. New England Journal of Medicine, 2018, 378(19): 1811-1823. doi: 10.1056/NEJMra1705751
[45]	GUENTHER A, KRAUSS E, TELLO S, et al. The European IPF registry (eurIPFreg):Baseline characteristics and survival of patients with idiopathic pulmonary fibrosis[J]. Respiratory Research, 2018, 19(1): 141. doi: 10.1186/s12931-018-0845-5
[46]	O′DWYER D N, ASHLEY S L, GURCZYNSKI S J, et al. Lung microbiota contribute to pulmonary inflammation and disease progression in pulmonary fibrosis[J]. American Journal of Respiratory and Critical Care Medicine, 2019, 199(9): 1127-1138. doi: 10.1164/rccm.201809-1650OC pmid: 30789747
[47]	INVERNIZZI R, WU B G, BARNETT J, et al. The respiratory microbiome in chronic hypersensitivity pneumonitis is distinct from that of idiopathic pulmonary fibrosis[J]. American Journal of Respiratory and Critical Care Medicine, 2021, 203(3): 339-347. doi: 10.1164/rccm.202002-0460OC
[48]	NTOLIOS P, TZILAS V, BOUROS E, et al. The role of microbiome and virome in idiopathic pulmonary fibrosis[J]. Biomedicines, 2021, 9(4): 442. doi: 10.3390/biomedicines9040442
[49]	CASTELLANI C, ASSAEL B M. Cystic fibrosis: A clinical view[J]. Cellular and Molecular Life Sciences, 2017, 74(1): 129-140. doi: 10.1007/s00018-016-2393-9 pmid: 27709245
[50]	MUHLEBACH M S, ZORN B T, ESTHER C R, et al. Initial acquisition and succession of the cystic fibrosis lung microbiome is associated with disease progression in infants and preschool children[J]. PLoS Pathogens, 2018, 14(1): e1006798. doi: 10.1371/journal.ppat.1006798
[51]	CUTHBERTSON L, WALKER A W, OLIVER A E, et al. Lung function and microbiota diversity in cystic fibrosis[J]. Microbiome, 2020, 8(1): 45. doi: 10.1186/s40168-020-00810-3 pmid: 32238195
[52]	HURLEY M N, AMIN ARIFF A H, BERTENSHAW C, et al. Results of antibiotic susceptibility testing do not influence clinical outcome in children with cystic fibrosis[J]. Journal of Cystic Fibrosis, 2012, 11(4): 288-292. doi: 10.1016/j.jcf.2012.02.006 pmid: 22436723
[53]	FLUME P A, CHALMERS J D, OLIVIER K N. Advances in bronchiectasis:Endotyping, genetics, microbiome, and disease heterogeneity[J]. The Lancet, 2018, 392(10150): 880-890. doi: 10.1016/S0140-6736(18)31767-7
[54]	CHALMERS J D, CHANG A B, CHOTIRMALL S H, et al. Bronchiectasis[J]. Nature Reviews Disease Primers, 2018, 4:45. doi: 10.1038/s41572-018-0042-3 pmid: 30442957
[55]	AMATI F, SIMONETTA E, GRAMEGNA A, et al. The biology of pulmonary exacerbations in bronchiectasis[J]. European Respiratory Review, 2019, 28(154): 190055. doi: 10.1183/16000617.0055-2019
[56]	ROGERS G B, VAN DER GAST C J, CUTHBERTSON L, et al. Clinical measures of disease in adult non-CF bronchiectasis correlate with airway microbiota composition[J]. Thorax, 2013, 68(8): 731-737. doi: 10.1136/thoraxjnl-2012-203105 pmid: 23564400
[57]	LEE S H, LEE Y, PARK J S, et al. Characterization of microbiota in bronchiectasis patients with different disease severities[J]. Journal of Clinical Medicine, 2018, 7(11): 429. doi: 10.3390/jcm7110429
[58]	NAIDOO C C, NYAWO G R, WU B G, et al. The microbiome and tuberculosis: State of the art, potential applications, and defining the clinical research agenda[J]. The Lancet Respiratory Medicine, 2019, 7(10): 892-906. doi: 10.1016/S2213-2600(18)30501-0
[59]	HU Y F, KANG Y, LIU X, et al. Distinct lung microbial community states in patients with pulmonary tuberculosis[J]. Science China Life Sciences, 2020, 63(10): 1522-1533. doi: 10.1007/s11427-019-1614-0
[60]	HU Y F, CHENG M, LIU B, et al. Metagenomic analysis of the lung microbiome in pulmonary tuberculosis - A pilot study[J]. Emerging Microbes and Infections, 2020, 9(1): 1444-1452. doi: 10.1080/22221751.2020.1783188
[61]	HARPER A, VIJAYAKUMAR V, OUWEHAND A C, et al. Viral infections, the microbiome, and probiotics[J]. Frontiers in Cellular and Infection Microbiology, 2021, 10:596166. doi: 10.3389/fcimb.2020.596166
[62]	LI C X, LIU H Y, LIN Y X, et al. The gut microbiota and respiratory diseases: New evidence[J]. Journal of Immunology Research, 2020, 2020:2340670.
[63]	SHI C Y, YU C H, YU W Y, et al. Gut-lung microbiota in chronic pulmonary diseases: Evolution, pathogenesis, and therapeutics[J]. Canadian Journal of Infectious Diseases and Medical Microbiology, 2021, 2021:1-8.
[64]	JAMALKANDI S A, AHMADI A, AHRARI I, et al. Oral and nasal probiotic administration for the prevention and alleviation of allergic diseases, asthma and chronic obstructive pulmonary disease[J]. Nutrition Research Reviews, 2021, 34(1): 1-16. doi: 10.1017/S0954422420000116
[65]	PEI C X, WU Y C, WANG X M, et al. Effect of probiotics, prebiotics and synbiotics for chronic bronchitis or chronic obstructive pulmonary disease:A protocol for systematic review and meta-analysis[J]. Medicine, 2020, 99(45): e23045. doi: 10.1097/MD.0000000000023045