Antibiotic-induced microbiome perturbations are associated with significant alterations to colonic mucosal immunity in rhesus macaques

Intestinal damage precedes mucosal immune dysfunction in SIV infection

(2018) Tiffany Hensley-McBain et al.   Mucosal Immunology

A Gut Commensal-Produced Metabolite Mediates Colonization Resistance to Salmonella Infection

(2018) Amanda Jacobson et al.   Cell Host & Microbe

Nonhuman Primate Models and Understanding the Pathogenesis of HIV Infection and AIDS

(2017) Ronald S Veazey et al.   ILAR JOURNAL

Nontargeted Metabolomics Reveals the Multilevel Response to Antibiotic Perturbations

(2017) Mattia Zampieri et al.   Cell Reports

SIV Infection-Mediated Changes in Gastrointestinal Bacterial Microbiome and Virome Are Associated with Immunodeficiency and Prevented by Vaccination

(2016) Scott A. Handley et al.   Cell Host & Microbe

Effects of Fecal Microbial Transplantation on Microbiome and Immunity in Simian Immunodeficiency Virus-Infected Macaques

(2016) Tiffany Hensley-McBain et al.   JOURNAL OF VIROLOGY

Host-mediated sugar oxidation promotes post-antibiotic pathogen expansion

(2016) Franziska Faber et al.   NATURE

Intestinal microbiome is related to lifetime antibiotic use in Finnish pre-school children

(2016) Katri Korpela et al.   Nature Communications

Microbial Translocation and Inflammation Occur in Hyperacute Immunodeficiency Virus Infection and Compromise Host Control of Virus Replication

(2016) Adam J. Ericsen et al.   PLoS Pathogens

The Dual Role of Neutrophils in Inflammatory Bowel Diseases

(2016) Odile Wéra et al.   Journal of Clinical Medicine

Soluble CD14 is a nonspecific marker of monocyte activation

(2015) Carey L. Shive et al.   AIDS

Biogeography of the Intestinal Mucosal and Lumenal Microbiome in the Rhesus Macaque

(2015) Koji Yasuda et al.   Cell Host & Microbe

Antibiotics promote inflammation through the translocation of native commensal colonic bacteria

(2015) Kathryn A Knoop et al.   GUT

SIV-induced Translocation of Bacterial Products in the Liver Mobilizes Myeloid Dendritic and Natural Killer Cells Associated With Liver Damage

(2015) Tristan I. Evans et al.   JOURNAL OF INFECTIOUS DISEASES

Dysbiotic bacteria translocate in progressive SIV infection

(2015) Z Klase et al.   Mucosal Immunology

Gut dendritic cell activation links an altered colonic microbiome to mucosal and systemic T-cell activation in untreated HIV-1 infection

(2015) S M Dillon et al.   Mucosal Immunology

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Bactericidal Antibiotics Induce Toxic Metabolic Perturbations that Lead to Cellular Damage

(2015) Peter Belenky et al.   Cell Reports

Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys

(2015) William Walters et al.   mSystems

Antibiotics in Early Life Alter the Gut Microbiome and Increase Disease Incidence in a Spontaneous Mouse Model of Autoimmune Insulin-Dependent Diabetes

(2015) Sophie Candon et al.   PLoS One

Diet, the Gut Microbiome, and Epigenetics

(2014) Meredith A. J. Hullar et al.   CANCER JOURNAL

Early Divergence in Neutrophil Apoptosis between Pathogenic and Nonpathogenic Simian Immunodeficiency Virus Infections of Nonhuman Primates

(2014) C. Elbim et al.   JOURNAL OF IMMUNOLOGY

An altered intestinal mucosal microbiome in HIV-1 infection is associated with mucosal and systemic immune activation and endotoxemia

(2014) S M Dillon et al.   Mucosal Immunology

Regulatory T cells promote a protective Th17-associated immune response to intestinal bacterial infection with C. rodentium

(2014) Z Wang et al.   Mucosal Immunology

Short-chain fatty acids induce both effector and regulatory T cells by suppression of histone deacetylases and regulation of the mTOR–S6K pathway

(2014) J Park et al.   Mucosal Immunology

Swarm: robust and fast clustering method for amplicon-based studies

(2014) Frédéric Mahé et al.   PeerJ

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

(2013) Y. Liao et al.   BIOINFORMATICS

GSVA: gene set variation analysis for microarray and RNA-Seq data

(2013) Sonja Hänzelmann et al.   BMC BIOINFORMATICS

SIV-Induced Instability of the Chimpanzee Gut Microbiome

(2013) Andrew H. Moeller et al.   Cell Host & Microbe

The interplay between the innate immune system and the microbiota

(2013) Christoph A Thaiss et al.   CURRENT OPINION IN IMMUNOLOGY

Macaque Models of Human Infectious Disease

(2013) M. B. Gardner et al.   ILAR JOURNAL

High-level colonisation of the human gut by Verrucomicrobia following broad-spectrum antibiotic treatment

(2013) Grégory Dubourg et al.   INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS

Mucosal immunity in human and simian immunodeficiency lentivirus infections

(2013) J M Brenchley   Mucosal Immunology

Microbiota-liberated host sugars facilitate post-antibiotic expansion of enteric pathogens

(2013) Katharine M. Ng et al.   NATURE

Dysbiosis of the Gut Microbiota Is Associated with HIV Disease Progression and Tryptophan Catabolism

(2013) Ivan Vujkovic-Cvijin et al.   Science Translational Medicine

Pathogenic Simian Immunodeficiency Virus Infection Is Associated with Expansion of the Enteric Virome

(2012) Scott A. Handley et al.   CELL

A call for action

(2012) Patrice Savard et al.   CURRENT OPINION IN INFECTIOUS DISEASES

Th22 Cells Are an Important Source of IL-22 for Host Protection against Enteropathogenic Bacteria

(2012) Rajatava Basu et al.   IMMUNITY

A role for mucosal IL-22 production and Th22 cells in HIV-associated mucosal immunopathogenesis

(2012) C J Kim et al.   Mucosal Immunology

Animal models for HIV/AIDS research

(2012) Theodora Hatziioannou et al.   NATURE REVIEWS MICROBIOLOGY

Plasma Levels of Soluble CD14 Independently Predict Mortality in HIV Infection

(2011) Netanya G. Sandler et al.   JOURNAL OF INFECTIOUS DISEASES

The Genome of Akkermansia muciniphila, a Dedicated Intestinal Mucin Degrader, and Its Use in Exploring Intestinal Metagenomes

(2011) Mark W. J. van Passel et al.   PLoS One

Nonhuman Primate Models of Human Immunology

(2010) Ilhem Messaoudi et al.   ANTIOXIDANTS & REDOX SIGNALING

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Evidence for a cross-talk between human neutrophils and Th17 cells

(2009) M. Pelletier et al.   BLOOD

Plasma Levels of Bacterial DNA Correlate with Immune Activation and the Magnitude of Immune Restoration in Persons with Antiretroviral‐Treated HIV Infection

(2009) Wei Jiang et al.   JOURNAL OF INFECTIOUS DISEASES