Metagenomics: A New Way to Illustrate the Crosstalk between Infectious Diseases and Host Microbiome

Gut microbiota diversity predicts immune status in HIV-1 infection

(2015) Piotr Nowak et al.   AIDS

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

(2015) James M. Beck et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

Humoral Immunity in the Gut Selectively Targets Phenotypically Virulent Attaching-and-Effacing Bacteria for Intraluminal Elimination

(2015) Nobuhiko Kamada et al.   Cell Host & Microbe

HIV and mucosal barrier interactions: consequences for transmission and pathogenesis

(2015) Adam Burgener et al.   CURRENT OPINION IN IMMUNOLOGY

Metagenomic Analysis of Microbiome in Colon Tissue from Subjects with Inflammatory Bowel Diseases Reveals Interplay of Viruses and Bacteria

(2015) Weiwei Wang et al.   INFLAMMATORY BOWEL DISEASES

Metagenomic Analysis of Crohnʼs Disease Patients Identifies Changes in the Virome and Microbiome Related to Disease Status and Therapy, and Detects Potential Interactions and Biomarkers

(2015) Vicente Pérez-Brocal et al.   INFLAMMATORY BOWEL DISEASES

The oral microbiome in human immunodeficiency virus (HIV)-positive individuals

(2015) James O. Kistler et al.   JOURNAL OF MEDICAL MICROBIOLOGY

Stability of the gorilla microbiome despite simian immunodeficiency virus infection

(2015) Andrew H. Moeller et al.   MOLECULAR ECOLOGY

Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples

(2015) T. Korem et al.   SCIENCE

HIV and the Gut Microbiota, Partners in Crime: Breaking the Vicious Cycle to Unearth New Therapeutic Targets

(2015) Kishanda Vyboh et al.   Journal of Immunology Research

The Vaginal Microbiota over an 8- to 10-Year Period in a Cohort of HIV-Infected and HIV-Uninfected Women

(2015) Supriya D. Mehta et al.   PLoS One

Salivary Microbiota and Metabolome Associated with Celiac Disease

(2014) Ruggiero Francavilla et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

An analysis of microbiota-targeted therapies in patients with avian influenza virus subtype H7N9 infection

(2014) Haifeng Lu et al.   BMC INFECTIOUS DISEASES

Profiling bacterial community in upper respiratory tracts

(2014) Hana Yi et al.   BMC INFECTIOUS DISEASES

Microbiome in Human Immunodeficiency Virus Infection

(2014) January T. Salas et al.   CLINICS IN LABORATORY MEDICINE

Vaginal Microbiota and Sexually Transmitted Infections That May Influence Transmission of Cell-Associated HIV

(2014) R. A. Cone   JOURNAL OF INFECTIOUS DISEASES

Intestinal Microbiota, Microbial Translocation, and Systemic Inflammation in Chronic HIV Infection

(2014) Duy M. Dinh et al.   JOURNAL OF INFECTIOUS DISEASES

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

Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile

(2014) Charlie G. Buffie et al.   NATURE

Stool Microbiota and Vaccine Responses of Infants

(2014) M. N. Huda et al.   PEDIATRICS

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

(2014) Kathryn Winglee et al.   PLoS One

Comparison of Lower Genital Tract Microbiota in HIV-Infected and Uninfected Women from Rwanda and the US

(2014) Lorie Benning et al.   PLoS One

The Lung Microbiome of Ugandan HIV-Infected Pneumonia Patients Is Compositionally and Functionally Distinct from That of San Franciscan Patients

(2014) Shoko Iwai et al.   PLoS One

Gut Microbiota in HIV Infection: Implication for Disease Progression and Management

(2014) Felix Chinweije Nwosu et al.   Gastroenterology Research and Practice

Comprehensive profiling of the vaginal microbiome in HIV positive women using massive parallel semiconductor sequencing

(2014) Adam Ameur et al.   Scientific Reports

The Semen Microbiome and Its Relationship with Local Immunology and Viral Load in HIV Infection

(2014) Cindy M. Liu et al.   PLoS Pathogens

A Compositional Look at the Human Gastrointestinal Microbiome and Immune Activation Parameters in HIV Infected Subjects

(2014) Ece A. Mutlu et al.   PLoS Pathogens

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

(2014) Luz Botero et al.   Microbiome

Oral serum-derived bovine immunoglobulin improves duodenal immune reconstitution and absorption function in patients with HIV enteropathy

(2013) David M. Asmuth et al.   AIDS

Widespread Colonization of the Lung byTropheryma whippleiin HIV Infection

(2013) Catherine Lozupone et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

Abnormal fecal microbiota community and functions in patients with hepatitis B liver cirrhosis as revealed by a metagenomic approach

(2013) Xiao Wei et al.   BMC GASTROENTEROLOGY

Alterations in the Gut Microbiota Associated with HIV-1 Infection

(2013) Catherine A. Lozupone et al.   Cell Host & Microbe

The gut microbiota of a patient with resistant tuberculosis is more comprehensively studied by culturomics than by metagenomics

(2013) G. Dubourg et al.   EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES

Advances in inflammatory bowel disease pathogenesis: linking host genetics and the microbiome

(2013) Dan Knights et al.   GUT

Probiotic/prebiotic supplementation of antiretrovirals improves gastrointestinal immunity in SIV-infected macaques

(2013) Nichole R. Klatt et al.   JOURNAL OF CLINICAL INVESTIGATION

AIDS Alters the Commensal Plasma Virome

(2013) L. Li et al.   JOURNAL OF VIROLOGY

Dolutegravir versus raltegravir in antiretroviral-experienced, integrase-inhibitor-naive adults with HIV: week 48 results from the randomised, double-blind, non-inferiority SAILING study

(2013) Pedro Cahn et al.   LANCET

Mucosal immunity in human and simian immunodeficiency lentivirus infections

(2013) J M Brenchley   Mucosal Immunology

Control of pathogens and pathobionts by the gut microbiota

(2013) Nobuhiko Kamada et al.   NATURE IMMUNOLOGY

Sputum Microbiota in Tuberculosis as Revealed by 16S rRNA Pyrosequencing

(2013) Man Kit Cheung et al.   PLoS One

Brain Microbial Populations in HIV/AIDS: α-Proteobacteria Predominate Independent of Host Immune Status

(2013) William G. Branton et al.   PLoS One

Association of the Vaginal Microbiota with Human Papillomavirus Infection in a Korean Twin Cohort

(2013) Jung Eun Lee et al.   PLoS One

Life on Human Surfaces: Skin Metagenomics

(2013) Alban Mathieu et al.   PLoS One

Identification of Hepatotropic Viruses from Plasma Using Deep Sequencing: A Next Generation Diagnostic Tool

(2013) John Law et al.   PLoS One

A Multi-Omic View of Host-Pathogen-Commensal Interplay in Salmonella-Mediated Intestinal Infection

(2013) Brooke L. Deatherage Kaiser et al.   PLoS One

Characterization of the Upper Respiratory Tract Microbiomes of Patients with Pandemic H1N1 Influenza

(2013) Bonnie Chaban et al.   PLoS One

Sputum Microbiota Associated with New, Recurrent and Treatment Failure Tuberculosis

(2013) Jing Wu et al.   PLoS One

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

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

HIV Infection is associated with compositional and functional shifts in the rectal mucosal microbiota

(2013) Ian H McHardy et al.   Microbiome

Preclinical Evaluation of HIV Eradication Strategies in the Simian Immunodeficiency Virus-Infected Rhesus Macaque: A Pilot Study Testing Inhibition of Indoleamine 2,3-Dioxygenase

(2012) Richard M. Dunham et al.   AIDS RESEARCH AND HUMAN RETROVIRUSES

Randomized pilot trial of a synbiotic dietary supplement in chronic HIV-1 infection

(2012) Marco Schunter et al.   BMC Complementary and Alternative Medicine

Evidence of an increased pathogenic footprint in the lingual microbiome of untreated HIV infected patients

(2012) Angeline T Dang et al.   BMC MICROBIOLOGY

Complex sputum microbial composition in patients with pulmonary tuberculosis

(2012) Zelin Cui et al.   BMC MICROBIOLOGY

Indoleamine 2,3-dioxygenase inhibition attenuates lipopolysaccharide induced persistent microglial activation and depressive-like complications in fractalkine receptor (CX3CR1)-deficient mice

(2012) Angela W. Corona et al.   BRAIN BEHAVIOR AND IMMUNITY

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

(2012) Scott A. Handley et al.   CELL

The Impact of the Gut Microbiota on Human Health: An Integrative View

(2012) Jose C. Clemente et al.   CELL

Anti-infective properties of bacteriocins: an update

(2012) Riadh Hammami et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Modulation of potential respiratory pathogens by pH1N1 viral infection

(2012) R.K.-K. Leung et al.   CLINICAL MICROBIOLOGY AND INFECTION

Oral and Airway Microbiota in HIV-Infected Pneumonia Patients

(2012) S. Iwai et al.   JOURNAL OF CLINICAL MICROBIOLOGY

A framework for human microbiome research

(2012)   NATURE

A metagenome-wide association study of gut microbiota in type 2 diabetes

(2012) Junjie Qin et al.   NATURE

Human gut microbiome viewed across age and geography

(2012) Tanya Yatsunenko et al.   NATURE

Symptomatic atherosclerosis is associated with an altered gut metagenome

(2012) Fredrik H. Karlsson et al.   Nature Communications

Host–Pathogen Interaction in Invasive Salmonellosis

(2012) Hanna K. de Jong et al.   PLoS Pathogens

Bacterial vaginosis, HIV serostatus and T-cell subset distribution in a cohort of East African commercial sex workers

(2011) John J. Schellenberg et al.   AIDS

Detection and identification of plasma bacterial and viral elements in HIV/AIDS patients in comparison to healthy adults

(2011) S.-K. Li et al.   CLINICAL MICROBIOLOGY AND INFECTION

Gut Microbiota and Pediatric Disease

(2011) Valerio Iebba et al.   DIGESTIVE DISEASES

Characterization of fecal microbial communities in patients with liver cirrhosis

(2011) Yanfei Chen et al.   HEPATOLOGY

Differences of small intestinal bacteria populations in adults and children with/without celiac disease: Effect of age, gluten diet, and disease

(2011) Esther Nistal et al.   INFLAMMATORY BOWEL DISEASES

Specific prebiotics modulate gut microbiota and immune activation in HAART-naive HIV-infected adults: results of the “COPA” pilot randomized trial

(2011) A Gori et al.   Mucosal Immunology

Probiotic yogurt consumption may improve gastrointestinal symptoms, productivity, and nutritional intake of people living with human immunodeficiency virus in Mwanza, Tanzania

(2011) Stephanie L. Irvine et al.   NUTRITION RESEARCH

Evidence for Polymicrobic Flora Translocating in Peripheral Blood of HIV-Infected Patients with Poor Immune Response to Antiretroviral Therapy

(2011) Esther Merlini et al.   PLoS One

Resources and Costs for Microbial Sequence Analysis Evaluated Using Virtual Machines and Cloud Computing

(2011) Samuel V. Angiuoli et al.   PLoS One

Diet Drives Convergence in Gut Microbiome Functions Across Mammalian Phylogeny and Within Humans

(2011) B. D. Muegge et al.   SCIENCE

Effect of Probiotic Bacteria on Microbial Host Defense, Growth, and Immune Function in Human Immunodeficiency Virus Type-1 Infection

(2011) Susanna Cunningham-Rundles et al.   Nutrients

Causes of Death in HIV‐1–Infected Patients Treated with Antiretroviral Therapy, 1996–2006: Collaborative Analysis of 13 HIV Cohort Studies

(2010)   CLINICAL INFECTIOUS DISEASES

Correlation between gastrointestinal fungi and varying degrees of chronic hepatitis B virus infection

(2010) Yu Chen et al.   DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE

Role of the gut microbiota in defining human health

(2010) Kei E Fujimura et al.   Expert Review of Anti-Infective Therapy

The Sensing of Environmental Stimuli by Follicular Dendritic Cells Promotes Immunoglobulin A Generation in the Gut

(2010) Keiichiro Suzuki et al.   IMMUNITY

Rectal Gonorrhea and Chlamydia Reinfection Is Associated With Increased Risk of HIV Seroconversion

(2010) Kyle T Bernstein et al.   JAIDS-JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES

Changes in the Composition of the Human Fecal Microbiome After Bacteriotherapy for Recurrent Clostridium Difficile-associated Diarrhea

(2010) Alexander Khoruts et al.   JOURNAL OF CLINICAL GASTROENTEROLOGY

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

The role of secretory antibodies in infection immunity

(2010) Richard A. Strugnell et al.   NATURE REVIEWS MICROBIOLOGY

Gut Flora and Hepatic Encephalopathy in Patients with Cirrhosis

(2010) Stephen M. Riordan et al.   NEW ENGLAND JOURNAL OF MEDICINE

Short-Term Antibiotic Treatment Has Differing Long-Term Impacts on the Human Throat and Gut Microbiome

(2010) Hedvig E. Jakobsson et al.   PLoS One

Infection with Helicobacter pylori Is Associated with Protection against Tuberculosis

(2010) Sharon Perry et al.   PLoS One

Deep Sequencing of the Vaginal Microbiota of Women with HIV

(2010) Ruben Hummelen et al.   PLoS One

A Metagenomic Analysis of Pandemic Influenza A (2009 H1N1) Infection in Patients from North America

(2010) Alexander L. Greninger et al.   PLoS One

A Catalog of Reference Genomes from the Human Microbiome

(2010) et al.   SCIENCE

Bacterial Vaginosis, Not HIV, Is Primarily Responsible for Increased Vaginal Concentrations of Proinflammatory Cytokines

(2009) Caroline M. Mitchell et al.   AIDS RESEARCH AND HUMAN RETROVIRUSES

Defining the healthy "core microbiome" of oral microbial communities

(2009) Egija Zaura et al.   BMC MICROBIOLOGY

Gastrointestinal tract in liver disease: which organ is sick?

(2009) Kristina Norman et al.   CURRENT OPINION IN CLINICAL NUTRITION AND METABOLIC CARE

Community-Wide Response of the Gut Microbiota to Enteropathogenic Citrobacter rodentium Infection Revealed by Deep Sequencing

(2009) C. Hoffmann et al.   INFECTION AND IMMUNITY

Precolonized Human Commensal Escherichia coli Strains Serve as a Barrier to E. coli O157:H7 Growth in the Streptomycin-Treated Mouse Intestine

(2009) M. P. Leatham et al.   INFECTION AND IMMUNITY

Concentrated and linked epidemics of both HSV-2 and HIV-1/HIV-2 infections in Senegal: public health impacts of the spread of HIV

(2009) C Toure Kane et al.   INTERNATIONAL JOURNAL OF STD & AIDS

Streptococcus pneumoniae Coinfection Is Correlated with the Severity of H1N1 Pandemic Influenza

(2009) Gustavo Palacios et al.   PLoS One

Microbial translocation is associated with sustained failure in CD4+ T-cell reconstitution in HIV-infected patients on long-term highly active antiretroviral therapy

(2008) Giulia Marchetti et al.   AIDS

New subgroup of Bacteroidetes and diverse microorganisms in Tibetan plateau glacial ice provide a biological record of environmental conditions

(2008) Xiaojun Zhang et al.   FEMS MICROBIOLOGY ECOLOGY

Predominant Role of Bacterial Pneumonia as a Cause of Death in Pandemic Influenza: Implications for Pandemic Influenza Preparedness

(2008) David M. Morens et al.   JOURNAL OF INFECTIOUS DISEASES

The Macaque Gut Microbiome in Health, Lentiviral Infection, and Chronic Enterocolitis

(2008) Philip McKenna et al.   PLoS Pathogens

Paneth cells directly sense gut commensals and maintain homeostasis at the intestinal host-microbial interface

(2008) S. Vaishnava et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA