Culture-enriched metagenomic sequencing enables in-depth profiling of the cystic fibrosis lung microbiota

Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome

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Environment dominates over host genetics in shaping human gut microbiota

(2018) Daphna Rothschild et al.   NATURE

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

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Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software

(2017) Alexander Sczyrba et al.   NATURE METHODS

A comprehensive evaluation of the sl1p pipeline for 16S rRNA gene sequencing analysis

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Longitudinal sampling of the lung microbiota in individuals with cystic fibrosis

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The Microbiome and the Respiratory Tract

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A method for culturing Gram-negative skin microbiota

(2016) Ian A. Myles et al.   BMC MICROBIOLOGY

The Microbiome in Cystic Fibrosis

(2016) Yvonne J. Huang et al.   CLINICS IN CHEST MEDICINE

Diversity is the question, not the answer

(2016) Ashley Shade   ISME Journal

PHASTER: a better, faster version of the PHAST phage search tool

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CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database

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Durable coexistence of donor and recipient strains after fecal microbiota transplantation

(2016) Simone S. Li et al.   SCIENCE

Stenotrophomonas maltophilia Phenotypic and Genotypic Diversity during a 10-year Colonization in the Lungs of a Cystic Fibrosis Patient

(2016) Arianna Pompilio et al.   Frontiers in Microbiology

Dysbiosis is not an answer

(2016) Scott W. Olesen et al.   Nature Microbiology

Culture of previously uncultured members of the human gut microbiota by culturomics

(2016) Jean-Christophe Lagier et al.   Nature Microbiology

In VitroCulture of Previously Uncultured Oral Bacterial Phylotypes

(2015) Hayley Thompson et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

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Personalized Nutrition by Prediction of Glycemic Responses

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Regional Isolation Drives Bacterial Diversification within Cystic Fibrosis Lungs

(2015) Peter Jorth et al.   Cell Host & Microbe

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Emerging bacterial pathogens and changing concepts of bacterial pathogenesis in cystic fibrosis

(2015) Michael D. Parkins et al.   Journal of Cystic Fibrosis

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

(2015) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

Application of metagenomics in the human gut microbiome

(2015) Wei-Lin Wang et al.   WORLD JOURNAL OF GASTROENTEROLOGY

Compact graphical representation of phylogenetic data and metadata with GraPhlAn

(2015) Francesco Asnicar et al.   PeerJ

Curation, integration and visualization of bacterial virulence factors in PATRIC

(2014) Chunhong Mao et al.   BIOINFORMATICS

Biogeography and individuality shape function in the human skin metagenome

(2014) Julia Oh et al.   NATURE

A role for the gut microbiota in IBS

(2014) Stephen M. Collins   Nature Reviews Gastroenterology & Hepatology

Correlation between the human fecal microbiota and depression

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Cultivation-based multiplex phenotyping of human gut microbiota allows targeted recovery of previously uncultured bacteria

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Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible

(2014) Paul J. McMurdie et al.   PLoS Computational Biology

Host-associated bacterial taxa from Chlorobi, Chloroflexi, GN02, Synergistetes, SR1, TM7, and WPS-2 Phyla/candidate divisions

(2014) Anuj Camanocha et al.   Journal of Oral Microbiology

Urine Is Not Sterile: Use of Enhanced Urine Culture Techniques To Detect Resident Bacterial Flora in the Adult Female Bladder

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Genetic variation of a bacterial pathogen within individuals with cystic fibrosis provides a record of selective pressures

(2013) Tami D Lieberman et al.   NATURE GENETICS

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

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PANDAseq: paired-end assembler for illumina sequences

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Microbial culturomics: paradigm shift in the human gut microbiome study

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Metagenomics and metatranscriptomics: Windows on CF-associated viral and microbial communities

(2012) Yan Wei Lim et al.   Journal of Cystic Fibrosis

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Decade-long bacterial community dynamics in cystic fibrosis airways

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Generation of Multimillion-Sequence 16S rRNA Gene Libraries from Complex Microbial Communities by Assembling Paired-End Illumina Reads

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Does bacterial density in cystic fibrosis sputum increase prior to pulmonary exacerbation?

(2011) Franziska A. Stressmann et al.   Journal of Cystic Fibrosis

The skin microbiome

(2011) Elizabeth A. Grice et al.   NATURE REVIEWS MICROBIOLOGY

Unravelling the effects of the environment and host genotype on the gut microbiome

(2011) Aymé Spor et al.   NATURE REVIEWS MICROBIOLOGY

Fast Identification and Removal of Sequence Contamination from Genomic and Metagenomic Datasets

(2011) Robert Schmieder et al.   PLoS One

Culture Enriched Molecular Profiling of the Cystic Fibrosis Airway Microbiome

(2011) Christopher D. Sibley et al.   PLoS One

Universally Distributed Single-Copy Genes Indicate a Constant Rate of Horizontal Transfer

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Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice

(2011) A. L. Goodman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The genus Prevotella in cystic fibrosis airways

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Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Partitioning core and satellite taxa from within cystic fibrosis lung bacterial communities

(2010) Christopher J van der Gast et al.   ISME Journal

McKay agar enables routine quantification of the 'Streptococcus milleri' group in cystic fibrosis patients

(2010) C. D. Sibley et al.   JOURNAL OF MEDICAL MICROBIOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

The Effect of Diet on the Human Gut Microbiome: A Metagenomic Analysis in Humanized Gnotobiotic Mice

(2009) P. J. Turnbaugh et al.   Science Translational Medicine

Detection of Anaerobic Bacteria in High Numbers in Sputum from Patients with Cystic Fibrosis

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