title: Comparison of microbiomes from different niches of upper and lower airways in children and adolescents with cystic fibrosis.
abstract: Changes in the airway microbiome may be important in the pathophysiology of chronic lung disease in patients with cystic fibrosis. However, little is known about the microbiome in early cystic fibrosis lung disease and the relationship between the microbiomes from different niches in the upper and lower airways. Therefore, in this cross-sectional study, we examined the relationship between the microbiome in the upper (nose and throat) and lower (sputum) airways from children with cystic fibrosis using next generation sequencing. Our results demonstrate a significant difference in both α and β-diversity between the nose and the two other sampling sites. The nasal microbiome was characterized by a polymicrobial community while the throat and sputum communities were less diverse and dominated by a few operational taxonomic units. Moreover, sputum and throat microbiomes were closely related especially in patients with clinically stable lung disease. There was a high inter-individual variability in sputum samples primarily due to a decrease in evenness linked to increased abundance of potential respiratory pathogens such as Pseudomonas aeruginosa. Patients with chronic Pseudomonas aeruginosa infection exhibited a less diverse sputum microbiome. A high concordance was found between pediatric and adult sputum microbiomes except that Burkholderia was only observed in the adult cohort. These results indicate that an adult-like lower airways microbiome is established early in life and that throat swabs may be a good surrogate in clinically stable children with cystic fibrosis without chronic Pseudomonas aeruginosa infection in whom sputum sampling is often not feasible.
authors: Dept. of Infectious Diseases-Medical Microbiology and Hygiene, University Hospital Heidelberg, Heidelberg, Germany; Translational Lung Research Center Heidelberg (TLRC), Member of the German Center for Lung Research (DZL), Heidelberg, Germany.
authors: Sébastien
authors: S
authors: Boutin
authors: Department of Translational Pulmonology, University Hospital Heidelberg, Heidelberg, Germany; Div. of Pediatric Pulmonology & Allergology and Cystic Fibrosis Center, Dept. of Pediatrics, University Hospital Heidelberg, Heidelberg, Germany; Translational Lung Research Center Heidelberg (TLRC), Member of the German Center for Lung Research (DZL), Heidelberg, Germany.
authors: Simon Y
authors: SY
authors: Graeber
authors: Dept. of Infectious Diseases-Medical Microbiology and Hygiene, University Hospital Heidelberg, Heidelberg, Germany.
authors: Michael
authors: M
authors: Weitnauer
authors: Dept. of Infectious Diseases-Medical Microbiology and Hygiene, University Hospital Heidelberg, Heidelberg, Germany; Translational Lung Research Center Heidelberg (TLRC), Member of the German Center for Lung Research (DZL), Heidelberg, Germany.
authors: Jessica
authors: J
authors: Panitz
authors: Department of Translational Pulmonology, University Hospital Heidelberg, Heidelberg, Germany; Div. of Pediatric Pulmonology & Allergology and Cystic Fibrosis Center, Dept. of Pediatrics, University Hospital Heidelberg, Heidelberg, Germany; Translational Lung Research Center Heidelberg (TLRC), Member of the German Center for Lung Research (DZL), Heidelberg, Germany.
authors: Mirjam
authors: M
authors: Stahl
authors: Institute for Medical Informatics and Biometry, Technical University Dresden, Dresden, Germany.
authors: Diana
authors: D
authors: Clausznitzer
authors: Institute for Medical Informatics and Biometry, Technical University Dresden, Dresden, Germany.
authors: Lars
authors: L
authors: Kaderali
authors: CF & Airways Microbiology Group, Queen's University Belfast, Belfast, United Kingdom.
authors: Gisli
authors: G
authors: Einarsson
authors: CF & Airways Microbiology Group, Queen's University Belfast, Belfast, United Kingdom; School of Pharmacy, Queen's University Belfast, Belfast, United Kingdom.
authors: Michael M
authors: MM
authors: Tunney
authors: CF & Airways Microbiology Group, Queen's University Belfast, Belfast, United Kingdom; Centre for Infection & Immunity, School of Medicine, Dentistry & Biomedical Science, Queen's University Belfast, Belfast, United Kingdom.
authors: J Stuart
authors: JS
authors: Elborn
authors: Department of Translational Pulmonology, University Hospital Heidelberg, Heidelberg, Germany; Div. of Pediatric Pulmonology & Allergology and Cystic Fibrosis Center, Dept. of Pediatrics, University Hospital Heidelberg, Heidelberg, Germany; Translational Lung Research Center Heidelberg (TLRC), Member of the German Center for Lung Research (DZL), Heidelberg, Germany.
authors: Marcus A
authors: MA
authors: Mall
authors: Dept. of Infectious Diseases-Medical Microbiology and Hygiene, University Hospital Heidelberg, Heidelberg, Germany; Translational Lung Research Center Heidelberg (TLRC), Member of the German Center for Lung Research (DZL), Heidelberg, Germany.
authors: Alexander H
authors: AH
authors: Dalpke
mesh_terms: D000293:Adolescent; D044822:Biodiversity; D002648:Child; D019295:Computational Biology; D003430:Cross-Sectional Studies; D003550:Cystic Fibrosis / Q000150:complications*; D066264:Datasets as Topic; D005260:Female; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008297:Male; D054892:Metagenome; D064307:Microbiota; D011446:Prospective Studies; D012141:Respiratory Tract Infections / Q000209:etiology* / Q000382:microbiology*; D012307:Risk Factors; D055815:Young Adult
references: PLoS One. 2010;5(6):e11044
references: 20585638
references: Proc Natl Acad Sci U S A. 2010 Apr 20;107(16):7503-8
references: 20363958
references: J Clin Microbiol. 2006 Oct;44(10):3665-73
references: 17021095
references: Science. 2009 Dec 18;326(5960):1694-7
references: 19892944
references: Science. 1999 May 21;284(5418):1318-22
references: 10334980
references: PLoS One. 2010;5(10):e15406
references: 21048977
references: Klin Padiatr. 1988 Nov-Dec;200(6):451-6
references: 3236750
references: Am J Respir Crit Care Med. 2008 May 1;177(9):995-1001
references: 18263800
references: Nat Rev Microbiol. 2012 Dec;10(12):841-51
references: 23147702
references: Bioinformatics. 2011 Aug 15;27(16):2194-200
references: 21700674
references: Am J Respir Crit Care Med. 2013 May 15;187(10):1067-75
references: 23491408
references: J Clin Microbiol. 2006 Jul;44(7):2601-4
references: 16825392
references: J Cyst Fibros. 2011 Jun;10 Suppl 2:S53-66
references: 21658643
references: Acta Pathol Microbiol Scand Suppl. 1977;(262):1-96
references: 411327
references: J Pediatr. 1993 Jan;122(1):1-9
references: 8419592
references: Pediatr Pulmonol. 2003 Nov;36(5):439-46
references: 14520728
references: Thorax. 2011 Jul;66(7):579-84
references: 21270069
references: Cell Host Microbe. 2007 Aug 16;2(2):119-29
references: 18005726
references: J Cyst Fibros. 2010 Mar;9(2):130-4
references: 20110197
references: Am J Respir Crit Care Med. 2003 Oct 15;168(8):918-51
references: 14555458
references: Clin Microbiol Rev. 2004 Jan;17(1):57-71
references: 14726455
references: Am J Respir Crit Care Med. 2011 Oct 15;184(8):957-63
references: 21680950
references: J Microbiol Methods. 2004 Oct;59(1):117-25
references: 15325758
references: PLoS One. 2012;7(2):e30126
references: 22319561
references: J Infect Dis. 2001 Feb 1;183(3):444-52
references: 11133376
references: Infect Immun. 2007 May;75(5):2214-24
references: 17261614
references: Nature. 2006 Dec 21;444(7122):1022-3
references: 17183309
references: PLoS One. 2011;6(7):e22702
references: 21829484
references: Pulm Med. 2012;2012:746358
references: 22448327
references: J Cyst Fibros. 2008 Nov;7(6):523-30
references: 18693078
references: MBio. 2011;2(1):e00245-10
references: 21285435
references: J Cyst Fibros. 2010 Jan;9(1):51-8
references: 19939747
references: Clin Microbiol Rev. 2002 Apr;15(2):194-222
references: 11932230
references: PLoS One. 2012;7(9):e45001
references: 23049765
references: Br Med Bull. 1992 Oct;48(4):912-30
references: 1281036
references: J Cyst Fibros. 2003 Mar;2(1):29-34
references: 15463843
references: Transl Res. 2012 Oct;160(4):258-66
references: 22683412
references: Appl Environ Microbiol. 2009 Dec;75(23):7537-41
references: 19801464
references: Gastroenterology. 2004 Oct;127(4):1085-95
references: 15480987
references: Clin Microbiol Rev. 1991 Jan;4(1):35-51
references: 1900735
references: Emerg Infect Dis. 2002 Jul;8(7):692-6
references: 12095436
references: ISME J. 2012 Jan;6(1):31-45
references: 21716309
references: Nature. 2012 Jun 14;486(7402):207-14
references: 22699609
references: PLoS One. 2008;3(7):e2843
references: 18665227
references: J Cyst Fibros. 2011 Jun;10 Suppl 2:S75-8
references: 21658646