Antibiotic treatment for Tuberculosis induces a profound dysbiosis of the microbiome that persists long after therapy is completed

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

(2017) Sivaranjani Namasivayam et al.   Microbiome

Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity

(2016) Melanie Schirmer et al.   CELL

The microbiota in adaptive immune homeostasis and disease

(2016) Kenya Honda et al.   NATURE

Identifying species of symbiont bacteria from the human gut that, alone, can induce intestinal Th17 cells in mice

(2016) Tze Guan Tan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Functional Redundancy-Induced Stability of Gut Microbiota Subjected to Disturbance

(2016) Andrés Moya et al.   TRENDS IN MICROBIOLOGY

Antibiotic-Induced Changes in the Intestinal Microbiota and Disease

(2016) Simone Becattini et al.   TRENDS IN MOLECULAR MEDICINE

What can immunology contribute to the control of the world's leading cause of death from bacterial infection?

(2015) Carl Nathan   IMMUNOLOGICAL REVIEWS

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

Early infancy microbial and metabolic alterations affect risk of childhood asthma

(2015) Marie-Claire Arrieta et al.   Science Translational Medicine

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Gut microbiota metabolism of dietary fiber influences allergic airway disease and hematopoiesis

(2014) Aurélien Trompette et al.   NATURE MEDICINE

Harnessing Microbiota to Kill a Pathogen: Fixing the microbiota to treat Clostridium difficile infections

(2014) Ying Taur et al.   NATURE MEDICINE

Human genetics of tuberculosis: a long and winding road

(2014) L. Abel et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Membership and Behavior of Ultra-Low-Diversity Pathogen Communities Present in the Gut of Humans during Prolonged Critical Illness

(2014) A. Zaborin et al.   mBio

Antibiotic-induced shifts in the mouse gut microbiome and metabolome increase susceptibility to Clostridium difficile infection

(2014) Casey M. Theriot et al.   Nature Communications

Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells

(2013) Yukihiro Furusawa et al.   NATURE

Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation

(2013) Nicholas Arpaia et al.   NATURE

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

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

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

Outer Membrane Vesicles of a Human Commensal Mediate Immune Regulation and Disease Protection

(2012) Yue Shen et al.   Cell Host & Microbe

Intestinal Domination and the Risk of Bacteremia in Patients Undergoing Allogeneic Hematopoietic Stem Cell Transplantation

(2012) Ying Taur et al.   CLINICAL INFECTIOUS DISEASES

Human gut microbiome viewed across age and geography

(2012) Tanya Yatsunenko et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome

(2012) Sahar Abubucker et al.   PLoS Computational Biology

The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome

(2012) Daniel McDonald et al.   GigaScience

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

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

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

High Rates of Recurrence in HIV‐Infected and HIV‐Uninfected Patients with Tuberculosis

(2010) Judith R. Glynn et al.   JOURNAL OF INFECTIOUS DISEASES

Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation

(2010) L. Dethlefsen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

The NCBI BioSystems database

(2009) Lewis Y. Geer et al.   NUCLEIC ACIDS RESEARCH

Research electronic data capture (REDCap)—A metadata-driven methodology and workflow process for providing translational research informatics support

(2008) Paul A. Harris et al.   JOURNAL OF BIOMEDICAL INFORMATICS

The Pervasive Effects of an Antibiotic on the Human Gut Microbiota, as Revealed by Deep 16S rRNA Sequencing

(2008) Les Dethlefsen et al.   PLOS BIOLOGY