Cargando…

Characterization and quantification of the fungal microbiome in serial samples from individuals with cystic fibrosis

BACKGROUND: Human-associated microbial communities include fungi, but we understand little about which fungal species are present, their relative and absolute abundances, and how antimicrobial therapy impacts fungal communities. The disease cystic fibrosis (CF) often involves chronic airway coloniza...

Descripción completa

Detalles Bibliográficos
Autores principales: Willger, Sven D, Grim, Sharon L, Dolben, Emily L, Shipunova, Anna, Hampton, Thomas H, Morrison, Hilary G, Filkins, Laura M, O‘Toole, George A, Moulton, Lisa A, Ashare, Alix, Sogin, Mitchell L, Hogan, Deborah A
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4236224/
https://www.ncbi.nlm.nih.gov/pubmed/25408892
http://dx.doi.org/10.1186/2049-2618-2-40
_version_ 1782345131340333056
author Willger, Sven D
Grim, Sharon L
Dolben, Emily L
Shipunova, Anna
Hampton, Thomas H
Morrison, Hilary G
Filkins, Laura M
O‘Toole, George A
Moulton, Lisa A
Ashare, Alix
Sogin, Mitchell L
Hogan, Deborah A
author_facet Willger, Sven D
Grim, Sharon L
Dolben, Emily L
Shipunova, Anna
Hampton, Thomas H
Morrison, Hilary G
Filkins, Laura M
O‘Toole, George A
Moulton, Lisa A
Ashare, Alix
Sogin, Mitchell L
Hogan, Deborah A
author_sort Willger, Sven D
collection PubMed
description BACKGROUND: Human-associated microbial communities include fungi, but we understand little about which fungal species are present, their relative and absolute abundances, and how antimicrobial therapy impacts fungal communities. The disease cystic fibrosis (CF) often involves chronic airway colonization by bacteria and fungi, and these infections cause irreversible lung damage. Fungi are detected more frequently in CF sputum samples upon initiation of antimicrobial therapy, and several studies have implicated the detection of fungi in sputum with worse outcomes. Thus, a more complete understanding of fungi in CF is required. RESULTS: We characterized the fungi and bacteria in expectorated sputa from six CF subjects. Samples were collected upon admission for systemic antibacterial therapy and upon the completion of treatment and analyzed using a pyrosequencing-based analysis of fungal internal transcribed spacer 1 (ITS1) and bacterial 16S rDNA sequences. A mixture of Candida species and Malassezia dominated the mycobiome in all samples (74%–99% of fungal reads). There was not a striking trend correlating fungal and bacterial richness, and richness showed a decline after antibiotic therapy particularly for the bacteria. The fungal communities within a sputum sample resembled other samples from that subject despite the aggressive antibacterial therapy. Quantitative PCR analysis of fungal 18S rDNA sequences to assess fungal burden showed variation in fungal density in sputum before and after antibacterial therapy but no consistent directional trend. Analysis of Candida ITS1 sequences amplified from sputum or pure culture-derived genomic DNA from individual Candida species found little (<0.5%) or no variation in ITS1 sequences within or between strains, thereby validating this locus for the purpose of Candida species identification. We also report the enhancement of the publically available Visualization and Analysis of Microbial Population Structures (VAMPS) tool for the analysis of fungal communities in clinical samples. CONCLUSIONS: Fungi are present in CF respiratory sputum. In CF, the use of intravenous antibiotic therapy often does not profoundly impact bacterial community structure, and we observed a similar stability in fungal species composition. Further studies are required to predict the effects of antibacterials on fungal burden in CF and fungal community stability in non-CF populations.
format Online
Article
Text
id pubmed-4236224
institution National Center for Biotechnology Information
language English
publishDate 2014
publisher BioMed Central
record_format MEDLINE/PubMed
spelling pubmed-42362242014-11-19 Characterization and quantification of the fungal microbiome in serial samples from individuals with cystic fibrosis Willger, Sven D Grim, Sharon L Dolben, Emily L Shipunova, Anna Hampton, Thomas H Morrison, Hilary G Filkins, Laura M O‘Toole, George A Moulton, Lisa A Ashare, Alix Sogin, Mitchell L Hogan, Deborah A Microbiome Research BACKGROUND: Human-associated microbial communities include fungi, but we understand little about which fungal species are present, their relative and absolute abundances, and how antimicrobial therapy impacts fungal communities. The disease cystic fibrosis (CF) often involves chronic airway colonization by bacteria and fungi, and these infections cause irreversible lung damage. Fungi are detected more frequently in CF sputum samples upon initiation of antimicrobial therapy, and several studies have implicated the detection of fungi in sputum with worse outcomes. Thus, a more complete understanding of fungi in CF is required. RESULTS: We characterized the fungi and bacteria in expectorated sputa from six CF subjects. Samples were collected upon admission for systemic antibacterial therapy and upon the completion of treatment and analyzed using a pyrosequencing-based analysis of fungal internal transcribed spacer 1 (ITS1) and bacterial 16S rDNA sequences. A mixture of Candida species and Malassezia dominated the mycobiome in all samples (74%–99% of fungal reads). There was not a striking trend correlating fungal and bacterial richness, and richness showed a decline after antibiotic therapy particularly for the bacteria. The fungal communities within a sputum sample resembled other samples from that subject despite the aggressive antibacterial therapy. Quantitative PCR analysis of fungal 18S rDNA sequences to assess fungal burden showed variation in fungal density in sputum before and after antibacterial therapy but no consistent directional trend. Analysis of Candida ITS1 sequences amplified from sputum or pure culture-derived genomic DNA from individual Candida species found little (<0.5%) or no variation in ITS1 sequences within or between strains, thereby validating this locus for the purpose of Candida species identification. We also report the enhancement of the publically available Visualization and Analysis of Microbial Population Structures (VAMPS) tool for the analysis of fungal communities in clinical samples. CONCLUSIONS: Fungi are present in CF respiratory sputum. In CF, the use of intravenous antibiotic therapy often does not profoundly impact bacterial community structure, and we observed a similar stability in fungal species composition. Further studies are required to predict the effects of antibacterials on fungal burden in CF and fungal community stability in non-CF populations. BioMed Central 2014-11-03 /pmc/articles/PMC4236224/ /pubmed/25408892 http://dx.doi.org/10.1186/2049-2618-2-40 Text en Copyright © 2014 Willger et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/4.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research
Willger, Sven D
Grim, Sharon L
Dolben, Emily L
Shipunova, Anna
Hampton, Thomas H
Morrison, Hilary G
Filkins, Laura M
O‘Toole, George A
Moulton, Lisa A
Ashare, Alix
Sogin, Mitchell L
Hogan, Deborah A
Characterization and quantification of the fungal microbiome in serial samples from individuals with cystic fibrosis
title Characterization and quantification of the fungal microbiome in serial samples from individuals with cystic fibrosis
title_full Characterization and quantification of the fungal microbiome in serial samples from individuals with cystic fibrosis
title_fullStr Characterization and quantification of the fungal microbiome in serial samples from individuals with cystic fibrosis
title_full_unstemmed Characterization and quantification of the fungal microbiome in serial samples from individuals with cystic fibrosis
title_short Characterization and quantification of the fungal microbiome in serial samples from individuals with cystic fibrosis
title_sort characterization and quantification of the fungal microbiome in serial samples from individuals with cystic fibrosis
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4236224/
https://www.ncbi.nlm.nih.gov/pubmed/25408892
http://dx.doi.org/10.1186/2049-2618-2-40
work_keys_str_mv AT willgersvend characterizationandquantificationofthefungalmicrobiomeinserialsamplesfromindividualswithcysticfibrosis
AT grimsharonl characterizationandquantificationofthefungalmicrobiomeinserialsamplesfromindividualswithcysticfibrosis
AT dolbenemilyl characterizationandquantificationofthefungalmicrobiomeinserialsamplesfromindividualswithcysticfibrosis
AT shipunovaanna characterizationandquantificationofthefungalmicrobiomeinserialsamplesfromindividualswithcysticfibrosis
AT hamptonthomash characterizationandquantificationofthefungalmicrobiomeinserialsamplesfromindividualswithcysticfibrosis
AT morrisonhilaryg characterizationandquantificationofthefungalmicrobiomeinserialsamplesfromindividualswithcysticfibrosis
AT filkinslauram characterizationandquantificationofthefungalmicrobiomeinserialsamplesfromindividualswithcysticfibrosis
AT otoolegeorgea characterizationandquantificationofthefungalmicrobiomeinserialsamplesfromindividualswithcysticfibrosis
AT moultonlisaa characterizationandquantificationofthefungalmicrobiomeinserialsamplesfromindividualswithcysticfibrosis
AT asharealix characterizationandquantificationofthefungalmicrobiomeinserialsamplesfromindividualswithcysticfibrosis
AT soginmitchelll characterizationandquantificationofthefungalmicrobiomeinserialsamplesfromindividualswithcysticfibrosis
AT hogandeboraha characterizationandquantificationofthefungalmicrobiomeinserialsamplesfromindividualswithcysticfibrosis