Episodic Aspiration with Oral Commensals Induces a MyD88-dependent, Pulmonary T-Helper Cell Type 17 Response that Mitigates Susceptibility to Streptococcus pneumoniae

Intranasal immunization with the commensal Streptococcus mitis confers protective immunity against pneumococcal lung infection

(2019) Sudhanshu Shekhar et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Dysregulated Lung Commensal Bacteria Drive Interleukin-17B Production to Promote Pulmonary Fibrosis through Their Outer Membrane Vesicles

(2019) Daping Yang et al.   IMMUNITY

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

The Lung Microbiota of Healthy Mice are Highly Variable, Cluster by Environment, and Reflect Variation in Baseline Lung Innate Immunity

(2018) Robert P. Dickson et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

Of Mice and Men . . . and Microbes: Conclusions and Cautions from a Murine Study of the Lung Microbiome and Microbiome-immune Interactions

(2018) John E. McGinniss et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

Airway Microbiota Is Associated with Up-Regulation of the PI3K Pathway in Lung Cancer

(2018) Jun-Chieh J Tsay et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

IL-17–producing ST2 + group 2 innate lymphoid cells play a pathogenic role in lung inflammation

(2018) Ting Cai et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

The lung tissue microbiota of mild and moderate chronic obstructive pulmonary disease

(2018) Alexa A. Pragman et al.   Microbiome

Early-Life Formation of the Microbial and Immunological Environment of the Human Airways

(2018) Céline Pattaroni et al.   Cell Host & Microbe

Transcriptionally Active Lung Microbiome and Its Association with Bacterial Biomass and Host Inflammatory Status

(2018) Lili Ren et al.   mSystems

On-going Mechanical Damage from Mastication Drives Homeostatic Th17 Cell Responses at the Oral Barrier

(2017) Nicolas Dutzan et al.   IMMUNITY

Bacterial Topography of the Healthy Human Lower Respiratory Tract

(2017) Robert P. Dickson et al.   mBio

Inflammatory Cytokine Pattern Is Sex-Dependent in Mouse Cutaneous Melanoma Experimental Model

(2017) Mihaela Surcel et al.   Journal of Immunology Research

Comparing microbiotas in the upper aerodigestive and lower respiratory tracts of lambs

(2017) Laura Glendinning et al.   Microbiome

Effect of Advanced HIV Infection on the Respiratory Microbiome

(2016) Homer L. Twigg et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

Airway Microbiota Determines Innate Cell Inflammatory or Tissue Remodeling Profiles in Lung Transplantation

(2016) Eric Bernasconi et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Randomised, double-blind, placebo-controlled trial with azithromycin selects for anti-inflammatory microbial metabolites in the emphysematous lung

(2016) Leopoldo N Segal et al.   THORAX

Enrichment of the lung microbiome with oral taxa is associated with lung inflammation of a Th17 phenotype

(2016) Leopoldo N. Segal et al.   Nature Microbiology

Host Response to the Lung Microbiome in Chronic Obstructive Pulmonary Disease

(2015) Marc A. Sze et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

The airway microbiome in patients with severe asthma: Associations with disease features and severity

(2015) Yvonne J. Huang et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

Sexual dimorphisms in leukocyte trafficking in a mouse peritonitis model

(2015) E. Kay et al.   JOURNAL OF LEUKOCYTE BIOLOGY

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

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

(2014) Susannah J Salter et al.   BMC BIOLOGY

Segmented Filamentous Bacteria Antigens Presented by Intestinal Dendritic Cells Drive Mucosal Th17 Cell Differentiation

(2014) Yoshiyuki Goto et al.   IMMUNITY

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Causal analysis approaches in Ingenuity Pathway Analysis

(2013) Andreas Krämer et al.   BIOINFORMATICS

The murine lung microbiome in relation to the intestinal and vaginal bacterial communities

(2013) Kenneth Barfod et al.   BMC MICROBIOLOGY

T Cell-Derived IL-17 Mediates Epithelial Changes in the Airway and Drives Pulmonary Neutrophilia

(2013) L. K. Fogli et al.   JOURNAL OF IMMUNOLOGY

MyD88 Signaling in CD4 T Cells Promotes IFN-  Production and Hematopoietic Progenitor Cell Expansion in Response to Intracellular Bacterial Infection

(2013) Y. Zhang et al.   JOURNAL OF IMMUNOLOGY

The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote

(2013) Yang Liao et al.   NUCLEIC ACIDS RESEARCH

Enrichment of lung microbiome with supraglottic taxa is associated with increased pulmonary inflammation

(2013) Leopoldo N Segal et al.   Microbiome

The Lung Tissue Microbiome in Chronic Obstructive Pulmonary Disease

(2012) Marc A. Sze et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

The Lung Microbiome in Moderate and Severe Chronic Obstructive Pulmonary Disease

(2012) Alexa A. Pragman et al.   PLoS One

PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers

(2011) William A. Walters et al.   BIOINFORMATICS

Analysis of the Lung Microbiome in the “Healthy” Smoker and in COPD

(2011) John R. Erb-Downward et al.   PLoS One

Chlamydia pneumoniae Infection and Risk for Lung Cancer

(2010) A. K. Chaturvedi et al.   CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION

Airway microbiota and bronchial hyperresponsiveness in patients with suboptimally controlled asthma

(2010) Yvonne J. Huang et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

Induction of Colonic Regulatory T Cells by Indigenous Clostridium Species

(2010) K. Atarashi et al.   SCIENCE

Induction of Intestinal Th17 Cells by Segmented Filamentous Bacteria

(2009) Ivaylo I. Ivanov et al.   CELL

T cell–intrinsic role of Nod2 in promoting type 1 immunity to Toxoplasma gondii

(2009) Michael H Shaw et al.   NATURE IMMUNOLOGY