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Microbiota and metabolite profiling reveal specific alterations in bacterial community structure and environment in the cystic fibrosis airway during exacerbation

Microbiota and metabolite profiling reveal specific alterations in bacterial community structure and environment in the cystic fibrosis airway during exacerbation
Microbiota and metabolite profiling reveal specific alterations in bacterial community structure and environment in the cystic fibrosis airway during exacerbation

Chronic polymicrobial infections of the lung are the foremost cause of morbidity and mortality in cystic fibrosis (CF) patients. The composition of the microbial flora of the airway alters considerably during infection, particularly during patient exacerbation. An understanding of which organisms are growing, their environment and their behaviour in the airway is of importance for designing antibiotic treatment regimes and for patient prognosis. To this end, we have analysed sputum samples taken from separate cohorts of CF and non-CF subjects for metabolites and in parallel, and we have examined both isolated DNA and RNA for the presence of 16S rRNA genes and transcripts by high-throughput sequencing of amplicon or cDNA libraries. This analysis revealed that although the population size of all dominant orders of bacteria as measured by DNA- and RNA- based methods are similar, greater discrepancies are seen with less prevalent organisms, some of which we associated with CF for the first time. Additionally, we identified a strong relationship between the abundance of specific anaerobes and fluctuations in several metabolites including lactate and putrescine during patient exacerbation. This study has hence identified organisms whose occurrence within the CF microbiome has been hitherto unreported and has revealed potential metabolic biomarkers for exacerbation.

1932-6203
Twomey, Kate B.
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Alston, Mark
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An, Shi Qi
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O'Connell, Oisin J.
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McCarthy, Yvonne
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Swarbreck, David
b9fca4d2-48fc-4593-a002-6fc101146be6
Febrer, Melanie
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Maxwell Dow, J.
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Plant, Barry J.
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Ryan, Robert P.
cd9f1e35-9ffe-456f-a64e-798b1f520298
Twomey, Kate B.
66d5fee3-2daf-4e66-ac8e-61ee0b49bd11
Alston, Mark
0af7ca7b-0722-4aa1-bc3d-9f4fe44276fa
An, Shi Qi
0e05f480-cec1-4c0e-bc1d-359d30ea9a6e
O'Connell, Oisin J.
7df41ecb-3395-490b-a00f-ba6f3c51acab
McCarthy, Yvonne
63ab1257-a428-427a-a560-30d6bd3922e3
Swarbreck, David
b9fca4d2-48fc-4593-a002-6fc101146be6
Febrer, Melanie
cdfa7831-01ec-4106-837e-5b345cf4a360
Maxwell Dow, J.
131815f4-de2d-4b5f-abd9-e1bfc3ce7bf3
Plant, Barry J.
10178115-7af4-4f4b-b2bc-45463080baf2
Ryan, Robert P.
cd9f1e35-9ffe-456f-a64e-798b1f520298

Twomey, Kate B., Alston, Mark, An, Shi Qi, O'Connell, Oisin J., McCarthy, Yvonne, Swarbreck, David, Febrer, Melanie, Maxwell Dow, J., Plant, Barry J. and Ryan, Robert P. (2013) Microbiota and metabolite profiling reveal specific alterations in bacterial community structure and environment in the cystic fibrosis airway during exacerbation. PLoS ONE, 8 (12), [e82432]. (doi:10.1371/journal.pone.0082432).

Record type: Article

Abstract

Chronic polymicrobial infections of the lung are the foremost cause of morbidity and mortality in cystic fibrosis (CF) patients. The composition of the microbial flora of the airway alters considerably during infection, particularly during patient exacerbation. An understanding of which organisms are growing, their environment and their behaviour in the airway is of importance for designing antibiotic treatment regimes and for patient prognosis. To this end, we have analysed sputum samples taken from separate cohorts of CF and non-CF subjects for metabolites and in parallel, and we have examined both isolated DNA and RNA for the presence of 16S rRNA genes and transcripts by high-throughput sequencing of amplicon or cDNA libraries. This analysis revealed that although the population size of all dominant orders of bacteria as measured by DNA- and RNA- based methods are similar, greater discrepancies are seen with less prevalent organisms, some of which we associated with CF for the first time. Additionally, we identified a strong relationship between the abundance of specific anaerobes and fluctuations in several metabolites including lactate and putrescine during patient exacerbation. This study has hence identified organisms whose occurrence within the CF microbiome has been hitherto unreported and has revealed potential metabolic biomarkers for exacerbation.

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journal.pone.0082432 - Version of Record
Available under License Creative Commons Attribution.
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Accepted/In Press date: 23 October 2013
e-pub ahead of print date: 17 December 2013

Identifiers

Local EPrints ID: 425814
URI: http://eprints.soton.ac.uk/id/eprint/425814
ISSN: 1932-6203
PURE UUID: 5c71aa71-7f2f-4a63-a7ba-c57dd0180774

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Date deposited: 05 Nov 2018 17:30
Last modified: 05 Jun 2024 18:44

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Contributors

Author: Kate B. Twomey
Author: Mark Alston
Author: Shi Qi An
Author: Oisin J. O'Connell
Author: Yvonne McCarthy
Author: David Swarbreck
Author: Melanie Febrer
Author: J. Maxwell Dow
Author: Barry J. Plant
Author: Robert P. Ryan

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