The human respiratory tract microbial community structures in healthy and cystic fibrosis infants

Lung function and microbiota diversity in cystic fibrosis

(2020) Leah Cuthbertson et al.   Microbiome

The quest for absolute abundance: The use of internal standards for DNA‐based community ecology

(2020) Joshua G. Harrison et al.   Molecular Ecology Resources

The effect of 16S rRNA region choice on bacterial community metabarcoding results

(2019) Yu. S. Bukin et al.   Scientific Data

Laboratory contamination over time during low‐biomass sample analysis

(2019) Laura S. Weyrich et al.   Molecular Ecology Resources

Mucus accumulation in the lungs precedes structural changes and infection in children with cystic fibrosis

(2019) Charles R. Esther et al.   Science Translational Medicine

Direct Lung Sampling Indicates That Established Pathogens Dominate Early Infections in Children with Cystic Fibrosis

(2019) Peter Jorth et al.   Cell Reports

Establishing microbial composition measurement standards with reference frames

(2019) James T. Morton et al.   Nature Communications

The influence of the microbiome on respiratory health

(2019) Tomasz P. Wypych et al.   NATURE IMMUNOLOGY

Upper versus lower airway microbiome and metagenome in children with cystic fibrosis and their correlation with lung inflammation

(2019) Mariana E. Kirst et al.   PLoS One

The future of cystic fibrosis care: a global perspective

(2019) Scott C Bell et al.   Lancet Respiratory Medicine

Efficacy and safety of the elexacaftor plus tezacaftor plus ivacaftor combination regimen in people with cystic fibrosis homozygous for the F508del mutation: a double-blind, randomised, phase 3 trial

(2019) Harry G M Heijerman et al.   LANCET

Elexacaftor–Tezacaftor–Ivacaftor for Cystic Fibrosis with a Single Phe508del Allele

(2019) Peter G. Middleton et al.   NEW ENGLAND JOURNAL OF MEDICINE

Assessing the performance of different approaches for functional and taxonomic annotation of metagenomes

(2019) Javier Tamames et al.   BMC GENOMICS

Best practices for analysing microbiomes

(2018) Rob Knight et al.   NATURE REVIEWS MICROBIOLOGY

Interpretation of biological experiments changes with evolution of the Gene Ontology and its annotations

(2018) Aurelie Tomczak et al.   Scientific Reports

Initial acquisition and succession of the cystic fibrosis lung microbiome is associated with disease progression in infants and preschool children

(2018) Marianne S. Muhlebach et al.   PLoS Pathogens

Differences in the lower airway microbiota of infants with and without cystic fibrosis

(2018) Katherine B. Frayman et al.   Journal of Cystic Fibrosis

Respiratory Bacterial Culture Sampling in Expectorating and Non-expectorating Patients With Cystic Fibrosis

(2018) Hanneke Eyns et al.   Frontiers in Pediatrics

Contamination in Low Microbial Biomass Microbiome Studies: Issues and Recommendations

(2018) Raphael Eisenhofer et al.   TRENDS IN MICROBIOLOGY

Airway microbiota across age and disease spectrum in cystic fibrosis

(2017) Edith T. Zemanick et al.   EUROPEAN RESPIRATORY JOURNAL

Where less may be more: how the rare biosphere pulls ecosystems strings

(2017) Alexandre Jousset et al.   ISME Journal

The microbiota of the respiratory tract: gatekeeper to respiratory health

(2017) Wing Ho Man et al.   NATURE REVIEWS MICROBIOLOGY

The lower airway microbiota in early cystic fibrosis lung disease: a longitudinal analysis

(2017) Katherine B Frayman et al.   THORAX

Microbiome Datasets Are Compositional: And This Is Not Optional

(2017) Gregory B. Gloor et al.   Frontiers in Microbiology

The Microbiome and the Respiratory Tract

(2016) Robert P. Dickson et al.   Annual Review of Physiology

Sensitivity and correlation of hypervariable regions in 16S rRNA genes in phylogenetic analysis

(2016) Bo Yang et al.   BMC BIOINFORMATICS

Centrifuge: rapid and sensitive classification of metagenomic sequences

(2016) Daehwan Kim et al.   GENOME RESEARCH

Assignment of function to a domain of unknown function: DUF1537 is a new kinase family in catabolic pathways for acid sugars

(2016) Xinshuai Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Inherent bacterial DNA contamination of extraction and sequencing reagents may affect interpretation of microbiota in low bacterial biomass samples

(2016) Angela Glassing et al.   Gut Pathogens

Airway Microbiota in Bronchoalveolar Lavage Fluid from Clinically Well Infants with Cystic Fibrosis

(2016) Theresa A. Laguna et al.   PLoS One

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

Analysis of the Upper Respiratory Tract Microbiotas as the Source of the Lung and Gastric Microbiotas in Healthy Individuals

(2015) Christine M. Bassis et al.   mBio

Lung microbiota across age and disease stage in cystic fibrosis

(2015) Bryan Coburn et al.   Scientific Reports

Reagent and laboratory contamination can critically impact sequence-based microbiome analyses

(2014) Susannah J Salter et al.   BMC BIOLOGY

ForceAtlas2, a Continuous Graph Layout Algorithm for Handy Network Visualization Designed for the Gephi Software

(2014) Mathieu Jacomy et al.   PLoS One

Deciphering microbial interactions and detecting keystone species with co-occurrence networks

(2014) David Berry et al.   Frontiers in Microbiology

The microbiome in pediatric cystic fibrosis patients: the role of shared environment suggests a window of intervention

(2014) Thomas H Hampton et al.   Microbiome

Induced sputum compared to bronchoalveolar lavage in young, non-expectorating cystic fibrosis children

(2013) Hannah Blau et al.   Journal of Cystic Fibrosis

Bioinformatics challenges in de novo transcriptome assembly using short read sequences in the absence of a reference genome sequence

(2013) Elsa Góngora-Castillo et al.   NATURAL PRODUCT REPORTS

Unique microbial communities persist in individual cystic fibrosis patients throughout a clinical exacerbation

(2013) Katherine E Price et al.   Microbiome

Eradication therapy for Pseudomonas aeruginosa colonization episodes in cystic fibrosis patients not chronically colonized by P. aeruginosa

(2012) Petra Schelstraete et al.   Journal of Cystic Fibrosis

Serial Analysis of the Gut and Respiratory Microbiome in Cystic Fibrosis in Infancy: Interaction between Intestinal and Respiratory Tracts and Impact of Nutritional Exposures

(2012) J. C. Madan et al.   mBio

Evaluation of different partial 16S rRNA gene sequence regions for phylogenetic analysis of microbiomes

(2010) Minseok Kim et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Baseline Characteristics and Factors Associated With Nutritional and Pulmonary Status at Enrollment in the Cystic Fibrosis EPIC Observational Cohort

(2010) Margaret Rosenfeld et al.   PEDIATRIC PULMONOLOGY

Treatment of early Pseudomonas aeruginosa infection in patients with cystic fibrosis: the ELITE trial

(2009) F. Ratjen et al.   THORAX