真菌微生物组在慢性呼吸道疾病发生发展中的作用
|
摘要
呼吸道微生物组与慢性呼吸道疾病的相关研究现为一个焦点,测序技术的应用可以更全面地阐述微生物群落结构。现呼吸道微生物组学研究主要集中于细菌微生物组与慢性呼吸道疾病的关系上,尤其是急性发作、用药与微生物群落的关系;也有少数研究呼吸道微生物组与肺癌的关系。而测序技术应用于呼吸道真菌微生物组学研究比较缺乏。但目前部分研究表明真菌在慢性呼吸道疾病发生发展过程中扮演着重要角色,如真菌与喘息症状、耐药等相关,也参与了宿主黏膜免疫反应,并且阐述了真菌菌群失调与真菌感染两个观点,证实真菌菌群的动态变化在人体健康与疾病状态中作用重大。因此,从整体群落结构全面了解并阐述真菌微生物组与呼吸道疾病的关系有助于进一步探讨疾病发病机制,辅助临床诊疗工作。我们将阐述真菌微生物组在慢性呼吸道疾病发生发展中的作用以及二代测序在真菌微生物组学中的应用。
引文
[1]SETHI S,MURPHY T F.Infection in the pathogenesis andcourse of chronic obstructive pulmonary disease[J].N Engl JMed,2008,359(22):2355-2365.
[2]DJUKANOVIC R,GADOLA S D.Virus infection,asthma,andchronic obstructive pulmonary disease.[J].N Engl J Med,2008,359(19):2062-2064.
[3]ILIEV I D,LEONARDI I.Fungal dysbiosis:immunity and inter-actions at mucosal barriers.[J].Nat Rev Immunol,2017,17(10):635-646.
[4]SETHI S,EVANS N,GRANT B J,et al.New strains of bacteriaand exacerbations of chronic obstructive pulmonary disease.[J].N Engl J Med,2002,347(7):465-471.
[5]GOW N A,NETEA M G.Medical mycology and fungal immunol-ogy:new research perspectives addressing a major world healthchallenge[J].Philos Trans R Soc Lond B Biol Sci,2016,371(1709).pii:20150462.
[6]LATGéJ P.Aspergillus fumigatus and aspergillosis.[J].ClinMicrobiol Rev,1999,12(2):310-350.
[7]NGUYEN L D,VISCOGLIOSI E,DELHAES L.The lung myco-biome:an emerging field of the human respiratory microbiome[J].Front Microbiol,2015,6:89.
[8]FISHER M C,HENK D A,BRIGGS C J,et al.Emerging fungalthreats to animal,plant and ecosystem health.[J].Nature,2012,484(7393):186-194.
[9]AMIN R,DUPUIS A,AARON S D,et al.The effect of chronicinfection with Aspergillus fumigatus on lung function and hospi-talization in patients with cystic fibrosis[J].Chest,2010,137(1):171-176.
[10]VERWEIJ P E,LESTRADE P P,MELCHERS W J,et al.Azole resistance surveillance in Aspergillus fumigatus:benefi-cial or biased[J].J Antimicrob Chemother,2016,71(8):2079-2082.
[11]PANIZ-MONDOLFI A,TALHARI C,SANDER HOFFMANNL,et al.Lobomycosis:an emerging disease in humans and del-phinidae[J].Mycoses,2012,55(4):298-309.
[12]VAN WOERDEN H C,GREGORY C,BROWN R,et al.Differ-ences in fungi present in induced sputum samples from asthmapatients and non-atopic controls:a community based case con-trol study[J].BMC Infect Dis,2013,13:69.
[13]SUDFELD C R,DASENBROOK E C,MERZ W G,et al.Preva-lence and risk factors for recovery of filamentous fungi in individ-uals with cystic fibrosis[J].J Cyst Fibros,2010,9(2):110-116.
[14]DELHAES L,MONCHY S,FRéALLE E,et al.The airway mi-crobiota in cystic fibrosis:a complex fungal and bacterial com-munity-implications for therapeutic management[J].PLo S One,2012,7(4):e36313.
[15]KRAMER R,SAUER-HEILBORN A,WELTE T,et al.Cohortstudy of airway mycobiome in adult cystic fibrosis patients:dif-ferences in community structure between fungi and bacteria re-veal predominance of transient fungal elements[J].J Clin Micro-biol,2015,53(9):2900-2907.
[16]FRACZEK M G,CHISHIMBA L,NIVEN R M,et al.Corticoste-roid treatment is associated with increased filamentous fungalburden in allergic fungal disease[J].J llergy Clin Immunol,2017,pii:S0091-6749(17)31732-3.
[17]DUPUY A K,DAVID M S,LI L,et al.Redefining the humanoral mycobiome with improved practices in amplicon-based tax-onomy:discovery of Malassezia as a prominent commensal[J].PLo S One,2014,9(3):e90899.
[18]FINDLEY K,OH J,YANG J,et al.Topographic diversity offungal and bacterial communities in human skin[J].Nature,2013,498(7454):367-370.
[19]NOVERR M C,FALKOWSKI N R,MCDONALD R A,et al.Development of allergic airway disease in mice following antibiot-ic therapy and fungal microbiota increase:role of host genetics,antigen,and interleukin-13[J].Infect Immun,2005,73(1):30-38.
[20]WHEELER M L,LIMON J J,BAR A S,et al.ImmunologicalConsequences of Intestinal Fungal Dysbiosis[J].Cell Host Mi-crobe,2016,19(6):865-873.
[21]KIM Y G,UDAYANGA K G,TOTSUKA N,et al.Gut dysbio-sis promotes M2 macrophage polarization and allergic airway in-flammation via fungi-induced PGE?[J].Cell Host Microbe,2014,15(1):95-102.
[22]CUI L,LUCHT L,TIPTON L,et al.Topographic diversity ofthe respiratory tract mycobiome and alteration in HIV and lungdisease[J].Am J Respir Crit Care Med,2015,191(8):932-942.
[23]THOMAS S,IZARD J,WALSH E,et al.The Host MicrobiomeRegulates and Maintains Human Health:A Primer and Perspec-tive for Non-Microbiologists[J].Cancer Res,2017,77(8):1783-1812.
[24]BUDDEN K F,GELLATLY S L,WOOD D L,et al.Emergingpathogenic links between microbiota and the gut-lung axis.[J].Nat Rev Microbiol,2017,15(1):55-63.
[25]MARSLAND B J,SALAMI O.Microbiome influences on allergyin mice and humans[J].Curr Opin Immunol,2015,36:94-100.
[26]肖亮,唐彤宇,徐红.肠道真菌与炎症性肠病的关系[J].实用医学杂志,2017,33(18):3151-3153.
[27]FUJIMURA K E,SITARIK A R,HAVSTAD S,et al.Neonatalgut microbiota associates with childhood multisensitized atopyand T cell differentiation[J].Nat Med,2016,22(10):1187-1191.
[28]WAINRIGHT P O,HINKLE G,SOGIN M L,et al.Monophylet-ic origins of the metazoa:an evolutionary link with fungi[J].Sci-ence,1993,260(5106):340-342.
[29]CASADEVALL A.Fungi and the rise of mammals.[J].PLo S Pat-hog,2012,8(8):e1002808.
[30]ILIEV I D,LEONARDI I.Fungal dysbiosis:immunity and inter-actions at mucosal barriers[J].Nat Rev Immunol,2017,17(10):635-646.
[31]CUTLER J E,DEEPE G S,KLEIN B S.Advances in combatingfungal diseases:vaccines on the threshold[J].Nat Rev Microbi-ol,2007,5(1):13-28.
[32]SZAJEWSKA H,KO?ODZIEJ M.Systematic review with metaanalysis:Saccharomyces boulardii in the prevention of antibiotic-associated diarrhoea[J].Aliment Pharmacol Ther,2015,42(7):793-801.
[33]MARTINS F S,VIEIRA A T,ELIAN S D,et al.Inhibition oftissue inflammation and bacterial translocation as one of the pro-tective mechanisms of Saccharomyces boulardii against Salmonel-la infection in mice[J].Microbes Infect,2013,15(4):270-279.
[34]LEWIS J D,CHEN E Z,BALDASSANO R N,et al.Inflamma-tion,Antibiotics,and Diet as Environmental Stressors of the GutMicrobiome in Pediatric Crohn′s Disease[J].Cell Host Microbe,2015,18(4):489-500.
[35]LIGUORI G,LAMAS B,RICHARD M L,et al.Fungal Dysbio-sis in Mucosa-associated Microbiota of Crohn′s Disease Patients[J].J Crohns Colitis,2016,10(3):296-305.
[36]HALWACHS B,MADHUSUDHAN N,KRAUSE R,et al.Criti-cal Issues in Mycobiota Analysis[J].Front Microbiol,2017,8:180.
[37]IRINYI L,SERENA C,GARCIA-HERMOSO D,et al.Interna-tional Society of Human and Animal Mycology(ISHAM)-ITS ref-erence DNA barcoding database--the quality controlled standardtool for routine identification of human and animal pathogenicfungi[J].Med Mycol,2015,53(4):313-337.
[2]DJUKANOVIC R,GADOLA S D.Virus infection,asthma,andchronic obstructive pulmonary disease.[J].N Engl J Med,2008,359(19):2062-2064.
[3]ILIEV I D,LEONARDI I.Fungal dysbiosis:immunity and inter-actions at mucosal barriers.[J].Nat Rev Immunol,2017,17(10):635-646.
[4]SETHI S,EVANS N,GRANT B J,et al.New strains of bacteriaand exacerbations of chronic obstructive pulmonary disease.[J].N Engl J Med,2002,347(7):465-471.
[5]GOW N A,NETEA M G.Medical mycology and fungal immunol-ogy:new research perspectives addressing a major world healthchallenge[J].Philos Trans R Soc Lond B Biol Sci,2016,371(1709).pii:20150462.
[6]LATGéJ P.Aspergillus fumigatus and aspergillosis.[J].ClinMicrobiol Rev,1999,12(2):310-350.
[7]NGUYEN L D,VISCOGLIOSI E,DELHAES L.The lung myco-biome:an emerging field of the human respiratory microbiome[J].Front Microbiol,2015,6:89.
[8]FISHER M C,HENK D A,BRIGGS C J,et al.Emerging fungalthreats to animal,plant and ecosystem health.[J].Nature,2012,484(7393):186-194.
[9]AMIN R,DUPUIS A,AARON S D,et al.The effect of chronicinfection with Aspergillus fumigatus on lung function and hospi-talization in patients with cystic fibrosis[J].Chest,2010,137(1):171-176.
[10]VERWEIJ P E,LESTRADE P P,MELCHERS W J,et al.Azole resistance surveillance in Aspergillus fumigatus:benefi-cial or biased[J].J Antimicrob Chemother,2016,71(8):2079-2082.
[11]PANIZ-MONDOLFI A,TALHARI C,SANDER HOFFMANNL,et al.Lobomycosis:an emerging disease in humans and del-phinidae[J].Mycoses,2012,55(4):298-309.
[12]VAN WOERDEN H C,GREGORY C,BROWN R,et al.Differ-ences in fungi present in induced sputum samples from asthmapatients and non-atopic controls:a community based case con-trol study[J].BMC Infect Dis,2013,13:69.
[13]SUDFELD C R,DASENBROOK E C,MERZ W G,et al.Preva-lence and risk factors for recovery of filamentous fungi in individ-uals with cystic fibrosis[J].J Cyst Fibros,2010,9(2):110-116.
[14]DELHAES L,MONCHY S,FRéALLE E,et al.The airway mi-crobiota in cystic fibrosis:a complex fungal and bacterial com-munity-implications for therapeutic management[J].PLo S One,2012,7(4):e36313.
[15]KRAMER R,SAUER-HEILBORN A,WELTE T,et al.Cohortstudy of airway mycobiome in adult cystic fibrosis patients:dif-ferences in community structure between fungi and bacteria re-veal predominance of transient fungal elements[J].J Clin Micro-biol,2015,53(9):2900-2907.
[16]FRACZEK M G,CHISHIMBA L,NIVEN R M,et al.Corticoste-roid treatment is associated with increased filamentous fungalburden in allergic fungal disease[J].J llergy Clin Immunol,2017,pii:S0091-6749(17)31732-3.
[17]DUPUY A K,DAVID M S,LI L,et al.Redefining the humanoral mycobiome with improved practices in amplicon-based tax-onomy:discovery of Malassezia as a prominent commensal[J].PLo S One,2014,9(3):e90899.
[18]FINDLEY K,OH J,YANG J,et al.Topographic diversity offungal and bacterial communities in human skin[J].Nature,2013,498(7454):367-370.
[19]NOVERR M C,FALKOWSKI N R,MCDONALD R A,et al.Development of allergic airway disease in mice following antibiot-ic therapy and fungal microbiota increase:role of host genetics,antigen,and interleukin-13[J].Infect Immun,2005,73(1):30-38.
[20]WHEELER M L,LIMON J J,BAR A S,et al.ImmunologicalConsequences of Intestinal Fungal Dysbiosis[J].Cell Host Mi-crobe,2016,19(6):865-873.
[21]KIM Y G,UDAYANGA K G,TOTSUKA N,et al.Gut dysbio-sis promotes M2 macrophage polarization and allergic airway in-flammation via fungi-induced PGE?[J].Cell Host Microbe,2014,15(1):95-102.
[22]CUI L,LUCHT L,TIPTON L,et al.Topographic diversity ofthe respiratory tract mycobiome and alteration in HIV and lungdisease[J].Am J Respir Crit Care Med,2015,191(8):932-942.
[23]THOMAS S,IZARD J,WALSH E,et al.The Host MicrobiomeRegulates and Maintains Human Health:A Primer and Perspec-tive for Non-Microbiologists[J].Cancer Res,2017,77(8):1783-1812.
[24]BUDDEN K F,GELLATLY S L,WOOD D L,et al.Emergingpathogenic links between microbiota and the gut-lung axis.[J].Nat Rev Microbiol,2017,15(1):55-63.
[25]MARSLAND B J,SALAMI O.Microbiome influences on allergyin mice and humans[J].Curr Opin Immunol,2015,36:94-100.
[26]肖亮,唐彤宇,徐红.肠道真菌与炎症性肠病的关系[J].实用医学杂志,2017,33(18):3151-3153.
[27]FUJIMURA K E,SITARIK A R,HAVSTAD S,et al.Neonatalgut microbiota associates with childhood multisensitized atopyand T cell differentiation[J].Nat Med,2016,22(10):1187-1191.
[28]WAINRIGHT P O,HINKLE G,SOGIN M L,et al.Monophylet-ic origins of the metazoa:an evolutionary link with fungi[J].Sci-ence,1993,260(5106):340-342.
[29]CASADEVALL A.Fungi and the rise of mammals.[J].PLo S Pat-hog,2012,8(8):e1002808.
[30]ILIEV I D,LEONARDI I.Fungal dysbiosis:immunity and inter-actions at mucosal barriers[J].Nat Rev Immunol,2017,17(10):635-646.
[31]CUTLER J E,DEEPE G S,KLEIN B S.Advances in combatingfungal diseases:vaccines on the threshold[J].Nat Rev Microbi-ol,2007,5(1):13-28.
[32]SZAJEWSKA H,KO?ODZIEJ M.Systematic review with metaanalysis:Saccharomyces boulardii in the prevention of antibiotic-associated diarrhoea[J].Aliment Pharmacol Ther,2015,42(7):793-801.
[33]MARTINS F S,VIEIRA A T,ELIAN S D,et al.Inhibition oftissue inflammation and bacterial translocation as one of the pro-tective mechanisms of Saccharomyces boulardii against Salmonel-la infection in mice[J].Microbes Infect,2013,15(4):270-279.
[34]LEWIS J D,CHEN E Z,BALDASSANO R N,et al.Inflamma-tion,Antibiotics,and Diet as Environmental Stressors of the GutMicrobiome in Pediatric Crohn′s Disease[J].Cell Host Microbe,2015,18(4):489-500.
[35]LIGUORI G,LAMAS B,RICHARD M L,et al.Fungal Dysbio-sis in Mucosa-associated Microbiota of Crohn′s Disease Patients[J].J Crohns Colitis,2016,10(3):296-305.
[36]HALWACHS B,MADHUSUDHAN N,KRAUSE R,et al.Criti-cal Issues in Mycobiota Analysis[J].Front Microbiol,2017,8:180.
[37]IRINYI L,SERENA C,GARCIA-HERMOSO D,et al.Interna-tional Society of Human and Animal Mycology(ISHAM)-ITS ref-erence DNA barcoding database--the quality controlled standardtool for routine identification of human and animal pathogenicfungi[J].Med Mycol,2015,53(4):313-337.