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Effects of propidium monoazide (PMA) treatment on mycobiome and bacteriome analysis of cystic fibrosis airways during exacerbation

Linh Do Ngoc Nguyen, Pieter Deschaght UGent, Sophie Merlin, Alexandre Loywick, Christophe Audebert, Sabine Van Daele UGent, Eric Viscogliosi, Mario Vaneechoutte UGent and Laurence Delhaes (2017) PLOS ONE. 11(12).
abstract
Introduction and Purpose : Propidium monoazide (PMA)-pretreatment has increasingly been applied to remove the bias from dead or damaged cell artefacts, which could impact the microbiota analysis by high-throughput sequencing. Our study aimed to determine whether a PMA-pretreatment coupled with high-throughput sequencing analysis provides a different picture of the airway mycobiome and bacteriome. Results and Discussion : We compared deep-sequencing data of mycobiota and microbiota of 15 sputum samples from 5 cystic fibrosis (CF) patients with and without prior PMA-treatment of the DNA-extracts. PMA-pretreatment had no significant effect on the entire and abundant bacterial community (genera expressed as operational taxonomic units (OTUs) with a relative abundance greater than or equal to 1%), but caused a significant difference in the intermediate community (less than 1%) when analyzing the alpha biodiversity Simpson index (p = 0.03). Regarding PMA impact on the airway mycobiota evaluated for the first time here; no significant differences in alpha diversity indexes between PMA-treated and untreated samples were observed. Regarding beta diversity analysis, the intermediate communities also differed more dramatically than the total and abundant ones when studying both mycobiome and bacteriome. Our results showed that only the intermediate (or low abundance) population diversity is impacted by PMA-treatment, and therefore that abundant taxa are mostly viable during acute exacerbation in CF. Given such a cumbersome protocol (PMA-pretreatment coupled with high-throughput sequencing), we discuss its potential interest within the follow-up of CF patients. Further studies using PMA-pretreatment are warranted to improve our "omic" knowledge of the CF airways.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
PSEUDOMONAS-AERUGINOSA, RESPIRATORY-INFECTIONS, CANDIDA-ALBICANS, SAMPLES, MICROBIOME, CELLS, RARE, QUANTIFICATION, ASPERGILLOSIS, COMMUNITIES
journal title
PLOS ONE
PLoS One
volume
11
issue
12
article number
e0168860
Web of Science type
Article
Web of Science id
000391222000081
ISSN
1932-6203
DOI
10.1371/journal.pone.0168860
UGent publication?
yes
classification
U
id
8516246
handle
http://hdl.handle.net/1854/LU-8516246
date created
2017-03-30 08:22:36
date last changed
2017-08-04 14:47:14
@article{8516246,
  abstract     = {Introduction and Purpose : Propidium monoazide (PMA)-pretreatment has increasingly been applied to remove the bias from dead or damaged cell artefacts, which could impact the microbiota analysis by high-throughput sequencing. Our study aimed to determine whether a PMA-pretreatment coupled with high-throughput sequencing analysis provides a different picture of the airway mycobiome and bacteriome. 
Results and Discussion : We compared deep-sequencing data of mycobiota and microbiota of 15 sputum samples from 5 cystic fibrosis (CF) patients with and without prior PMA-treatment of the DNA-extracts. PMA-pretreatment had no significant effect on the entire and abundant bacterial community (genera expressed as operational taxonomic units (OTUs) with a relative abundance greater than or equal to 1\%), but caused a significant difference in the intermediate community (less than 1\%) when analyzing the alpha biodiversity Simpson index (p = 0.03). Regarding PMA impact on the airway mycobiota evaluated for the first time here; no significant differences in alpha diversity indexes between PMA-treated and untreated samples were observed. Regarding beta diversity analysis, the intermediate communities also differed more dramatically than the total and abundant ones when studying both mycobiome and bacteriome. Our results showed that only the intermediate (or low abundance) population diversity is impacted by PMA-treatment, and therefore that abundant taxa are mostly viable during acute exacerbation in CF. Given such a cumbersome protocol (PMA-pretreatment coupled with high-throughput sequencing), we discuss its potential interest within the follow-up of CF patients. Further studies using PMA-pretreatment are warranted to improve our {\textacutedbl}omic{\textacutedbl} knowledge of the CF airways.},
  articleno    = {e0168860},
  author       = {Nguyen, Linh Do Ngoc and Deschaght, Pieter and Merlin, Sophie and Loywick, Alexandre and Audebert, Christophe and Van Daele, Sabine and Viscogliosi, Eric and Vaneechoutte, Mario and Delhaes, Laurence},
  issn         = {1932-6203},
  journal      = {PLOS ONE},
  keyword      = {PSEUDOMONAS-AERUGINOSA,RESPIRATORY-INFECTIONS,CANDIDA-ALBICANS,SAMPLES,MICROBIOME,CELLS,RARE,QUANTIFICATION,ASPERGILLOSIS,COMMUNITIES},
  number       = {12},
  title        = {Effects of propidium monoazide (PMA) treatment on mycobiome and bacteriome analysis of cystic fibrosis airways during exacerbation},
  url          = {http://dx.doi.org/10.1371/journal.pone.0168860},
  volume       = {11},
  year         = {2017},
}

Chicago
Nguyen, Linh Do Ngoc, Pieter Deschaght, Sophie Merlin, Alexandre Loywick, Christophe Audebert, Sabine Van Daele, Eric Viscogliosi, Mario Vaneechoutte, and Laurence Delhaes. 2017. “Effects of Propidium Monoazide (PMA) Treatment on Mycobiome and Bacteriome Analysis of Cystic Fibrosis Airways During Exacerbation.” Plos One 11 (12).
APA
Nguyen, L. D. N., Deschaght, P., Merlin, S., Loywick, A., Audebert, C., Van Daele, S., Viscogliosi, E., et al. (2017). Effects of propidium monoazide (PMA) treatment on mycobiome and bacteriome analysis of cystic fibrosis airways during exacerbation. PLOS ONE, 11(12).
Vancouver
1.
Nguyen LDN, Deschaght P, Merlin S, Loywick A, Audebert C, Van Daele S, et al. Effects of propidium monoazide (PMA) treatment on mycobiome and bacteriome analysis of cystic fibrosis airways during exacerbation. PLOS ONE. 2017;11(12).
MLA
Nguyen, Linh Do Ngoc, Pieter Deschaght, Sophie Merlin, et al. “Effects of Propidium Monoazide (PMA) Treatment on Mycobiome and Bacteriome Analysis of Cystic Fibrosis Airways During Exacerbation.” PLOS ONE 11.12 (2017): n. pag. Print.