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. 2016 Dec 28;11(12):e0168860.
doi: 10.1371/journal.pone.0168860. eCollection 2016.

Effects of Propidium Monoazide (PMA) Treatment on Mycobiome and Bacteriome Analysis of Cystic Fibrosis Airways during Exacerbation

Linh Do Ngoc Nguyen  1 , Pieter Deschaght  2 , Sophie Merlin  3   4 , Alexandre Loywick  3   4 , Christophe Audebert  3   4 , Sabine Van Daele  5 , Eric Viscogliosi  1 , Mario Vaneechoutte  2 , Laurence Delhaes  1   6
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Effects of Propidium Monoazide (PMA) Treatment on Mycobiome and Bacteriome Analysis of Cystic Fibrosis Airways during Exacerbation

VSports注册入口 - Linh Do Ngoc Nguyen et al. PLoS One. .

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. VSports手机版.

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 V体育安卓版. 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. .

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Conflict of interest statement (V体育安卓版)

Sophie Merlin, Alexandre Loywick and Christophe Audebert are employed by GenesDiffusion. There are no patents, products in development or marketed products to declare in relation with our study. This does not alter our adherence to all the PLOS ONE policies on sharing data and materials, as detailed online in the guide for authors V体育ios版.

Figures

Fig 1
Fig 1. Comparison of the enumeration of P. aeruginosa cells between cultures and qPCRs of PMA-treated and untreated sputum samples.
Fig 2
Fig 2. Venn diagram representing number of shared and specific bacterial (A) and fungal (B) genera between PMA-treated and untreated samples.
In each case, the first 5 most prevalent genera are listed.
Fig 3
Fig 3. Global distribution of bacterial (A) and fungal (B) genera between PMA-treated (inner ring) and untreated groups (outer ring).
All genera are ordered in descending relative abundance.
Fig 4
Fig 4. Effect of PMA on the composition of bacteriome of each sample.
(A): Relative abundance of bacterial genera of each sample (“yes” or “no” indicates the samples with or without PMA-pretreatment). (B): PCA plot of the first two components of bacteriome of samples with and without PMA-pretreatment. Each marker represents treatment conditions (filled triangle symbols PMA-treated samples, filled square symbols untreated samples). Each color represents a given sputum sample (G040.I: light blue; G040.II: aqua; G040.III: dark blue; G088.I: yellow green; G088.II: chartreuse; G088.III: dark green; G172.II: orange; G172.III: dark orange; G014.I: grey; G014.II: dark grey; G014.III: black; G176.I: red; G176.II: firebrick; G176.III: dark red).
Fig 5
Fig 5. Effect of PMA on the composition of mycobiome of each sample.
(A): Relative abundance of fungal genera of each sample (“yes” or “no” indicates the samples with or without PMA-pretreatment). (B): PCA plot of the first two components of mycobiome of samples with and without PMA-pretreatment. Each marker represents treatment conditions (filled triangle symbols PMA-treated samples, filled square symbols untreated samples). Each color represents a given sputum sample (G040.III: dark blue; G088.II: chartreuse; G088.III: dark green; G172.I: yellow; G172.II: orange; G172.III: dark orange; G014.II: dark grey; G014.III: black; G176.II: firebrick; G176.III: dark red).
See this image and copyright information in PMC

References

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