Individual Patterns of Complexity in Cystic Fibrosis Lung Microbiota, Including Predator Bacteria, over a 1-Year Period

ABSTRACT Cystic fibrosis (CF) lung microbiota composition has recently been redefined by the application of next-generation sequencing (NGS) tools, identifying, among others, previously undescribed anaerobic and uncultivable bacteria. In the present study, we monitored the fluctuations of this ecosy...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Juan de Dios Caballero, Rafael Vida, Marta Cobo, Luis Máiz, Lucrecia Suárez, Javier Galeano, Fernando Baquero, Rafael Cantón, Rosa del Campo
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2017
Materias:	antibiotic consumption Bdellovibrio cystic fibrosis lung microbiota next-generation sequencing predator bacteria Vampirovibrio Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/7fee8c42cbc742938ce1ec460b1a184c
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:7fee8c42cbc742938ce1ec460b1a184c
record_format	dspace
spelling	oai:doaj.org-article:7fee8c42cbc742938ce1ec460b1a184c2021-11-15T15:51:50ZIndividual Patterns of Complexity in Cystic Fibrosis Lung Microbiota, Including Predator Bacteria, over a 1-Year Period10.1128/mBio.00959-172150-7511https://doaj.org/article/7fee8c42cbc742938ce1ec460b1a184c2017-11-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.00959-17https://doaj.org/toc/2150-7511ABSTRACT Cystic fibrosis (CF) lung microbiota composition has recently been redefined by the application of next-generation sequencing (NGS) tools, identifying, among others, previously undescribed anaerobic and uncultivable bacteria. In the present study, we monitored the fluctuations of this ecosystem in 15 CF patients during a 1-year follow-up period, describing for the first time, as far as we know, the presence of predator bacteria in the CF lung microbiome. In addition, a new computational model was developed to ascertain the hypothetical ecological repercussions of a prey-predator interaction in CF lung microbial communities. Fifteen adult CF patients, stratified according to their pulmonary function into mild (n = 5), moderate (n = 9), and severe (n = 1) disease, were recruited at the CF unit of the Ramón y Cajal University Hospital (Madrid, Spain). Each patient contributed three or four induced sputum samples during a 1-year follow-up period. Lung microbiota composition was determined by both cultivation and NGS techniques and was compared with the patients’ clinical variables. Results revealed a particular microbiota composition for each patient that was maintained during the study period, although some fluctuations were detected without any clinical correlation. For the first time, Bdellovibrio and Vampirovibrio predator bacteria were shown in CF lung microbiota and reduced-genome bacterial parasites of the phylum Parcubacteria were also consistently detected. The newly designed computational model allows us to hypothesize that inoculation of predators into the pulmonary microbiome might contribute to the control of chronic colonization by CF pathogens in early colonization stages. IMPORTANCE The application of NGS to sequential samples of CF patients demonstrated the complexity of the organisms present in the lung (156 species) and the constancy of basic individual colonization patterns, although some differences between samples from the same patient were observed, probably related to sampling bias. Bdellovibrio and Vampirovibrio predator bacteria were found for the first time by NGS as part of the CF lung microbiota, although their ecological significance needs to be clarified. The newly designed computational model allows us to hypothesize that inoculation of predators into the lung microbiome can eradicate CF pathogens in early stages of the process. Our data strongly suggest that lower respiratory microbiome fluctuations are not necessarily related to the patient’s clinical status.Juan de Dios CaballeroRafael VidaMarta CoboLuis MáizLucrecia SuárezJavier GaleanoFernando BaqueroRafael CantónRosa del CampoAmerican Society for Microbiologyarticleantibiotic consumptionBdellovibriocystic fibrosis lung microbiotanext-generation sequencingpredator bacteriaVampirovibrioMicrobiologyQR1-502ENmBio, Vol 8, Iss 5 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	antibiotic consumption Bdellovibrio cystic fibrosis lung microbiota next-generation sequencing predator bacteria Vampirovibrio Microbiology QR1-502
spellingShingle	antibiotic consumption Bdellovibrio cystic fibrosis lung microbiota next-generation sequencing predator bacteria Vampirovibrio Microbiology QR1-502 Juan de Dios Caballero Rafael Vida Marta Cobo Luis Máiz Lucrecia Suárez Javier Galeano Fernando Baquero Rafael Cantón Rosa del Campo Individual Patterns of Complexity in Cystic Fibrosis Lung Microbiota, Including Predator Bacteria, over a 1-Year Period
description	ABSTRACT Cystic fibrosis (CF) lung microbiota composition has recently been redefined by the application of next-generation sequencing (NGS) tools, identifying, among others, previously undescribed anaerobic and uncultivable bacteria. In the present study, we monitored the fluctuations of this ecosystem in 15 CF patients during a 1-year follow-up period, describing for the first time, as far as we know, the presence of predator bacteria in the CF lung microbiome. In addition, a new computational model was developed to ascertain the hypothetical ecological repercussions of a prey-predator interaction in CF lung microbial communities. Fifteen adult CF patients, stratified according to their pulmonary function into mild (n = 5), moderate (n = 9), and severe (n = 1) disease, were recruited at the CF unit of the Ramón y Cajal University Hospital (Madrid, Spain). Each patient contributed three or four induced sputum samples during a 1-year follow-up period. Lung microbiota composition was determined by both cultivation and NGS techniques and was compared with the patients’ clinical variables. Results revealed a particular microbiota composition for each patient that was maintained during the study period, although some fluctuations were detected without any clinical correlation. For the first time, Bdellovibrio and Vampirovibrio predator bacteria were shown in CF lung microbiota and reduced-genome bacterial parasites of the phylum Parcubacteria were also consistently detected. The newly designed computational model allows us to hypothesize that inoculation of predators into the pulmonary microbiome might contribute to the control of chronic colonization by CF pathogens in early colonization stages. IMPORTANCE The application of NGS to sequential samples of CF patients demonstrated the complexity of the organisms present in the lung (156 species) and the constancy of basic individual colonization patterns, although some differences between samples from the same patient were observed, probably related to sampling bias. Bdellovibrio and Vampirovibrio predator bacteria were found for the first time by NGS as part of the CF lung microbiota, although their ecological significance needs to be clarified. The newly designed computational model allows us to hypothesize that inoculation of predators into the lung microbiome can eradicate CF pathogens in early stages of the process. Our data strongly suggest that lower respiratory microbiome fluctuations are not necessarily related to the patient’s clinical status.
format	article
author	Juan de Dios Caballero Rafael Vida Marta Cobo Luis Máiz Lucrecia Suárez Javier Galeano Fernando Baquero Rafael Cantón Rosa del Campo
author_facet	Juan de Dios Caballero Rafael Vida Marta Cobo Luis Máiz Lucrecia Suárez Javier Galeano Fernando Baquero Rafael Cantón Rosa del Campo
author_sort	Juan de Dios Caballero
title	Individual Patterns of Complexity in Cystic Fibrosis Lung Microbiota, Including Predator Bacteria, over a 1-Year Period
title_short	Individual Patterns of Complexity in Cystic Fibrosis Lung Microbiota, Including Predator Bacteria, over a 1-Year Period
title_full	Individual Patterns of Complexity in Cystic Fibrosis Lung Microbiota, Including Predator Bacteria, over a 1-Year Period
title_fullStr	Individual Patterns of Complexity in Cystic Fibrosis Lung Microbiota, Including Predator Bacteria, over a 1-Year Period
title_full_unstemmed	Individual Patterns of Complexity in Cystic Fibrosis Lung Microbiota, Including Predator Bacteria, over a 1-Year Period
title_sort	individual patterns of complexity in cystic fibrosis lung microbiota, including predator bacteria, over a 1-year period
publisher	American Society for Microbiology
publishDate	2017
url	https://doaj.org/article/7fee8c42cbc742938ce1ec460b1a184c
work_keys_str_mv	AT juandedioscaballero individualpatternsofcomplexityincysticfibrosislungmicrobiotaincludingpredatorbacteriaovera1yearperiod AT rafaelvida individualpatternsofcomplexityincysticfibrosislungmicrobiotaincludingpredatorbacteriaovera1yearperiod AT martacobo individualpatternsofcomplexityincysticfibrosislungmicrobiotaincludingpredatorbacteriaovera1yearperiod AT luismaiz individualpatternsofcomplexityincysticfibrosislungmicrobiotaincludingpredatorbacteriaovera1yearperiod AT lucreciasuarez individualpatternsofcomplexityincysticfibrosislungmicrobiotaincludingpredatorbacteriaovera1yearperiod AT javiergaleano individualpatternsofcomplexityincysticfibrosislungmicrobiotaincludingpredatorbacteriaovera1yearperiod AT fernandobaquero individualpatternsofcomplexityincysticfibrosislungmicrobiotaincludingpredatorbacteriaovera1yearperiod AT rafaelcanton individualpatternsofcomplexityincysticfibrosislungmicrobiotaincludingpredatorbacteriaovera1yearperiod AT rosadelcampo individualpatternsofcomplexityincysticfibrosislungmicrobiotaincludingpredatorbacteriaovera1yearperiod
_version_	1718427347901743104

Individual Patterns of Complexity in Cystic Fibrosis Lung Microbiota, Including Predator Bacteria, over a 1-Year Period

Ejemplares similares