title: Effects of Propidium Monoazide (PMA) Treatment on Mycobiome and Bacteriome Analysis of Cystic Fibrosis Airways during Exacerbation.
abstract: OBJECTIVE
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Institut Pasteur de Lille, Center for Infection and Immunity of Lille (CIIL), INSERM U1019, CNRS UMR 8204, University of Lille, Lille, France.
authors.forename: Linh Do Ngoc
authors.initials: LD
authors.lastname: Nguyen
authors.affiliation: Laboratory for Bacteriology Research, Faculty of Medicine & Health Sciences, Ghent University, Ghent, Belgium.
authors.forename: Pieter
authors.initials: P
authors.lastname: Deschaght
authors.affiliation: GenesDiffusion, Douai, France.|PEGASE, Biosciences, Institut Pasteur de Lille, Lille, France.
authors.forename: Sophie
authors.initials: S
authors.lastname: Merlin
authors.affiliation: GenesDiffusion, Douai, France.|PEGASE, Biosciences, Institut Pasteur de Lille, Lille, France.
authors.forename: Alexandre
authors.initials: A
authors.lastname: Loywick
authors.affiliation: GenesDiffusion, Douai, France.|PEGASE, Biosciences, Institut Pasteur de Lille, Lille, France.
authors.forename: Christophe
authors.initials: C
authors.lastname: Audebert
authors.affiliation: Department of Pediatrics and Genetics, Faculty of Medicine & Health Sciences, Ghent University, Ghent, Belgium.
authors.forename: Sabine
authors.initials: S
authors.lastname: Van Daele
authors.affiliation: Institut Pasteur de Lille, Center for Infection and Immunity of Lille (CIIL), INSERM U1019, CNRS UMR 8204, University of Lille, Lille, France.
authors.forename: Eric
authors.initials: E
authors.lastname: Viscogliosi
authors.affiliation: Laboratory for Bacteriology Research, Faculty of Medicine & Health Sciences, Ghent University, Ghent, Belgium.
authors.forename: Mario
authors.initials: M
authors.lastname: Vaneechoutte
authors.affiliation: Institut Pasteur de Lille, Center for Infection and Immunity of Lille (CIIL), INSERM U1019, CNRS UMR 8204, University of Lille, Lille, France.|Parasitology-Medical Mycology Department, Regional Hospital Center, Faculty of Medicine, Lille, France.
authors.forename: Laurence
authors.initials: L
authors.lastname: Delhaes
mesh_terms: D000293:Adolescent; D000328:Adult; D000900:Anti-Bacterial Agents / Q000494:pharmacology; D001386:Azides / Q000494:pharmacology*; D044822:Biodiversity; D003550:Cystic Fibrosis / Q000188:drug therapy / Q000235:genetics / Q000382:microbiology*; D004269:DNA, Bacterial / Q000235:genetics; D018450:Disease Progression; D005260:Female; D005541:Forced Expiratory Volume; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008168:Lung / Q000187:drug effects / Q000382:microbiology* / Q000503:physiopathology; D008297:Male; D054892:Metagenome; D064307:Microbiota / Q000187:drug effects / Q000235:genetics*; D008875:Middle Aged; D000072761:Mycobiome / Q000187:drug effects / Q000235:genetics*; D011419:Propidium / Q000031:analogs & derivatives* / Q000494:pharmacology; D011446:Prospective Studies; D012137:Respiratory System / Q000187:drug effects / Q000378:metabolism / Q000382:microbiology*; D013183:Sputum / Q000382:microbiology; D055815:Young Adult
chemical_list: D000900:Anti-Bacterial Agents; D001386:Azides; D004269:DNA, Bacterial; C533957:propidium monoazide; D011419:Propidium