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The metabolic footprint of the airway bacterial community in cystic fibrosis
BACKGROUND: Progressive, chronic bacterial infection of the airways is a leading cause of death in cystic fibrosis (CF). Culture-independent methods based on sequencing of the bacterial 16S rRNA gene describe a distinct microbial community that decreases in richness and diversity with disease progre...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5493850/ https://www.ncbi.nlm.nih.gov/pubmed/28666467 http://dx.doi.org/10.1186/s40168-017-0289-z |
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author | Narayanamurthy, Vaishnavi Sweetnam, John M. Denner, Darcy R. Chen, Lena W. Naureckas, Edward T. Laxman, Bharathi White, Steven R. |
author_facet | Narayanamurthy, Vaishnavi Sweetnam, John M. Denner, Darcy R. Chen, Lena W. Naureckas, Edward T. Laxman, Bharathi White, Steven R. |
author_sort | Narayanamurthy, Vaishnavi |
collection | PubMed |
description | BACKGROUND: Progressive, chronic bacterial infection of the airways is a leading cause of death in cystic fibrosis (CF). Culture-independent methods based on sequencing of the bacterial 16S rRNA gene describe a distinct microbial community that decreases in richness and diversity with disease progression. Understanding the functional characteristics of the microbial community may aid in identifying potential therapies and may assist in management, but current methods are cumbersome. Here, we demonstrate the use of an oxidative metabolic assay as a complement to sequencing methods to describe the microbiome in the airways of patients with CF. METHODS: Expectorated sputum was collected from 16 CF subjects and 8 control subjects. The Biolog Gen III Microplate was used in a community-level physiological profiling (CLPP)-based assay to examine oxidative metabolic activity. 16S rRNA V4 amplicon sequencing was used to characterize the taxonomy and diversity of the samples. Correlations were then identified among the oxidative activity and taxonomy data. In an additional paired analysis, sputum from seven CF subjects were collected at two separate clinic visits and compared for oxidative activity, taxonomy, and diversity. RESULTS: Significant differences in oxidative metabolic activity, microbial taxonomy, and diversity were found between the CF and control sputum samples. Oxidative activity correlated positively with total genera but not with other measures of diversity or taxonomy, demonstrating that the metabolic assay complements the structural aspects of the microbiome. As expected, Pseudomonas was significantly enriched in CF samples, while Streptococcus and Prevotella were similarly abundant in both CF and control samples. Paired analysis of CF samples at separate clinic visits revealed comparable oxidative activity that correlated with similar stability in taxonomy and diversity. CONCLUSIONS: The CLPP assay used in this study complements existing sequencing methods to delineate the oxidative metabolic footprint of the CF airway bacterial community. This method may be useful to study the CF microbial community over time and with changes in disease state. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s40168-017-0289-z) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-5493850 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-54938502017-07-05 The metabolic footprint of the airway bacterial community in cystic fibrosis Narayanamurthy, Vaishnavi Sweetnam, John M. Denner, Darcy R. Chen, Lena W. Naureckas, Edward T. Laxman, Bharathi White, Steven R. Microbiome Short Report BACKGROUND: Progressive, chronic bacterial infection of the airways is a leading cause of death in cystic fibrosis (CF). Culture-independent methods based on sequencing of the bacterial 16S rRNA gene describe a distinct microbial community that decreases in richness and diversity with disease progression. Understanding the functional characteristics of the microbial community may aid in identifying potential therapies and may assist in management, but current methods are cumbersome. Here, we demonstrate the use of an oxidative metabolic assay as a complement to sequencing methods to describe the microbiome in the airways of patients with CF. METHODS: Expectorated sputum was collected from 16 CF subjects and 8 control subjects. The Biolog Gen III Microplate was used in a community-level physiological profiling (CLPP)-based assay to examine oxidative metabolic activity. 16S rRNA V4 amplicon sequencing was used to characterize the taxonomy and diversity of the samples. Correlations were then identified among the oxidative activity and taxonomy data. In an additional paired analysis, sputum from seven CF subjects were collected at two separate clinic visits and compared for oxidative activity, taxonomy, and diversity. RESULTS: Significant differences in oxidative metabolic activity, microbial taxonomy, and diversity were found between the CF and control sputum samples. Oxidative activity correlated positively with total genera but not with other measures of diversity or taxonomy, demonstrating that the metabolic assay complements the structural aspects of the microbiome. As expected, Pseudomonas was significantly enriched in CF samples, while Streptococcus and Prevotella were similarly abundant in both CF and control samples. Paired analysis of CF samples at separate clinic visits revealed comparable oxidative activity that correlated with similar stability in taxonomy and diversity. CONCLUSIONS: The CLPP assay used in this study complements existing sequencing methods to delineate the oxidative metabolic footprint of the CF airway bacterial community. This method may be useful to study the CF microbial community over time and with changes in disease state. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s40168-017-0289-z) contains supplementary material, which is available to authorized users. BioMed Central 2017-06-30 /pmc/articles/PMC5493850/ /pubmed/28666467 http://dx.doi.org/10.1186/s40168-017-0289-z Text en © The Author(s). 2017 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. 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 | Short Report Narayanamurthy, Vaishnavi Sweetnam, John M. Denner, Darcy R. Chen, Lena W. Naureckas, Edward T. Laxman, Bharathi White, Steven R. The metabolic footprint of the airway bacterial community in cystic fibrosis |
title | The metabolic footprint of the airway bacterial community in cystic fibrosis |
title_full | The metabolic footprint of the airway bacterial community in cystic fibrosis |
title_fullStr | The metabolic footprint of the airway bacterial community in cystic fibrosis |
title_full_unstemmed | The metabolic footprint of the airway bacterial community in cystic fibrosis |
title_short | The metabolic footprint of the airway bacterial community in cystic fibrosis |
title_sort | metabolic footprint of the airway bacterial community in cystic fibrosis |
topic | Short Report |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5493850/ https://www.ncbi.nlm.nih.gov/pubmed/28666467 http://dx.doi.org/10.1186/s40168-017-0289-z |
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