Profiling the airway in the macaque model of tuberculosis reveals variable microbial dysbiosis and alteration of community structure

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update

(2018) Enis Afgan et al.   NUCLEIC ACIDS RESEARCH

Fungi stabilize connectivity in the lung and skin microbial ecosystems

(2018) Laura Tipton et al.   Microbiome

Digitally Barcoding Mycobacterium tuberculosis Reveals In Vivo Infection Dynamics in the Macaque Model of Tuberculosis

(2017) Constance J. Martin et al.   mBio

Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy

(2017) Sivaranjani Namasivayam et al.   Microbiome

Effect of Advanced HIV Infection on the Respiratory Microbiome

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Gut Microbiota, Inflammation, and Colorectal Cancer

(2016) Caitlin A. Brennan et al.   Annual Review of Microbiology

The Microbiome and the Respiratory Tract

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

The respiratory tract microbiome and lung inflammation: a two-way street

(2016) G B Huffnagle et al.   Mucosal Immunology

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(2016) Christoph A. Thaiss et al.   NATURE

The Importance of First Impressions: Early Events in Mycobacterium tuberculosis Infection Influence Outcome

(2016) Anthony M. Cadena et al.   mBio

Longitudinal analysis of the lung microbiota of cynomolgous macaques during long-term SHIV infection

(2016) Alison Morris et al.   Microbiome

Topographic Diversity of the Respiratory Tract Mycobiome and Alteration in HIV and Lung Disease

(2015) Lijia Cui et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

Multicenter Comparison of Lung and Oral Microbiomes of HIV-infected and HIV-uninfected Individuals

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Sparse and Compositionally Robust Inference of Microbial Ecological Networks

(2015) Zachary D. Kurtz et al.   PLoS Computational Biology

Correlation between Either Cupriavidus or Porphyromonas and Primary Pulmonary Tuberculosis Found by Analysing the Microbiota in Patients’ Bronchoalveolar Lavage Fluid

(2015) Yuhua Zhou et al.   PLoS One

Early Changes by 18Fluorodeoxyglucose Positron Emission Tomography Coregistered with Computed Tomography Predict Outcome after Mycobacterium tuberculosis Infection in Cynomolgus Macaques

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The role of the microbiome in exacerbations of chronic lung diseases

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Dynamics and associations of microbial community types across the human body

(2014) Tao Ding et al.   NATURE

Aerosol Mycobacterium tuberculosis Infection Causes Rapid Loss of Diversity in Gut Microbiota

(2014) Kathryn Winglee et al.   PLoS One

PET/CT imaging reveals a therapeutic response to oxazolidinones in macaques and humans with tuberculosis

(2014) M. T. Coleman et al.   Science Translational Medicine

Towards an ecology of the lung: new conceptual models of pulmonary microbiology and pneumonia pathogenesis

(2014) Robert P Dickson et al.   Lancet Respiratory Medicine

Respiratory tract clinical sample selection for microbiota analysis in patients with pulmonary tuberculosis

(2014) Luz Botero et al.   Microbiome

Comparison of the Respiratory Microbiome in Healthy Nonsmokers and Smokers

(2013) Alison Morris et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

Sterilization of granulomas is common in active and latent tuberculosis despite within-host variability in bacterial killing

(2013) Philana Ling Lin et al.   NATURE MEDICINE

Tuberculosis

(2013) Alimuddin Zumla et al.   NEW ENGLAND JOURNAL OF MEDICINE

Sputum Microbiota in Tuberculosis as Revealed by 16S rRNA Pyrosequencing

(2013) Man Kit Cheung et al.   PLoS One

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(2013) Paul J. McMurdie et al.   PLoS One

Sputum Microbiota Associated with New, Recurrent and Treatment Failure Tuberculosis

(2013) Jing Wu et al.   PLoS One

UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota

(2013) J. H. Campbell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Use of bronchoalveolar lavage to assess the respiratory microbiome: signal in the noise

(2013) Homer L Twigg et al.   Lancet Respiratory Medicine

The Microbiome in Infectious Disease and Inflammation

(2012) Kenya Honda et al.   Annual Review of Immunology

Complex sputum microbial composition in patients with pulmonary tuberculosis

(2012) Zelin Cui et al.   BMC MICROBIOLOGY

Genome Sequence of Aggregatibacter actinomycetemcomitans RHAA1, Isolated from a Rhesus Macaque, an Old World Primate

(2012) M. Karched et al.   JOURNAL OF BACTERIOLOGY

Antibiotics in early life alter the murine colonic microbiome and adiposity

(2012) Ilseung Cho et al.   NATURE

The human microbiome: at the interface of health and disease

(2012) Ilseung Cho et al.   NATURE REVIEWS GENETICS

Dirichlet Multinomial Mixtures: Generative Models for Microbial Metagenomics

(2012) Ian Holmes et al.   PLoS One

Discrimination of the oral microbiota associated with high hydrogen sulfide and methyl mercaptan production

(2012) Toru Takeshita et al.   Scientific Reports

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

(2012) Xochitl C Morgan et al.   GENOME BIOLOGY

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons

(2011) B. J. Haas et al.   GENOME RESEARCH

Human nutrition, the gut microbiome and the immune system

(2011) Andrew L. Kau et al.   NATURE

Use of whole genome sequencing to estimate the mutation rate of Mycobacterium tuberculosis during latent infection

(2011) Christopher B Ford et al.   NATURE GENETICS

Microbial Genomics and Infectious Diseases

(2011) David A. Relman   NEW ENGLAND JOURNAL OF MEDICINE

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

Successful Transmission of a Retrovirus Depends on the Commensal Microbiota

(2011) M. Kane et al.   SCIENCE

Intestinal Microbiota Promote Enteric Virus Replication and Systemic Pathogenesis

(2011) S. K. Kuss et al.   SCIENCE

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

Phylogeny of Gammaproteobacteria

(2010) K. P. Williams et al.   JOURNAL OF BACTERIOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

(2010) J. G. Caporaso et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

PyNAST: a flexible tool for aligning sequences to a template alignment

(2009) J. G. Caporaso et al.   BIOINFORMATICS

Quantitative Comparison of Active and Latent Tuberculosis in the Cynomolgus Macaque Model

(2009) P. L. Lin et al.   INFECTION AND IMMUNITY

The spectrum of latent tuberculosis: rethinking the biology and intervention strategies

(2009) Clifton E. Barry et al.   NATURE REVIEWS MICROBIOLOGY

The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

(2008) J. R. Cole et al.   NUCLEIC ACIDS RESEARCH