Stress and stability: applying the Anna Karenina principle to animal microbiomes

Normalization and microbial differential abundance strategies depend upon data characteristics

(2017) Sophie Weiss et al.   Microbiome

Dynamics of the human gut microbiome in inflammatory bowel disease

(2017) Jonas Halfvarson et al.   Nature Microbiology

Effect of Advanced HIV Infection on the Respiratory Microbiome

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

Microbiome alterations in HIV infection a review

(2016) Brett Williams et al.   CELLULAR MICROBIOLOGY

How stable is the human gut microbiota? And why this question matters

(2016) Harald Brüssow   ENVIRONMENTAL MICROBIOLOGY

Cigarette smoking and the oral microbiome in a large study of American adults

(2016) Jing Wu et al.   ISME Journal

Skin bacterial diversity of Panamanian frogs is associated with host susceptibility and presence of Batrachochytrium dendrobatidis

(2016) Eria A Rebollar et al.   ISME Journal

Climate change stressors destabilize the microbiome of the Caribbean barrel sponge, Xestospongia muta

(2016) Michael P. Lesser et al.   JOURNAL OF EXPERIMENTAL MARINE BIOLOGY AND ECOLOGY

Diet-induced extinctions in the gut microbiota compound over generations

(2016) Erica D. Sonnenburg et al.   NATURE

Disturbance Regimes Predictably Alter Diversity in an Ecologically Complex Bacterial System

(2016) Sean M. Gibbons et al.   mBio

Overfishing and nutrient pollution interact with temperature to disrupt coral reefs down to microbial scales

(2016) Jesse R. Zaneveld et al.   Nature Communications

Diversity, structure and convergent evolution of the global sponge microbiome

(2016) Torsten Thomas et al.   Nature Communications

Fecal bacterial microbiome diversity in chronic HIV-infected patients in China

(2016) Yang Sun et al.   Emerging Microbes & Infections

A new view of the tree of life

(2016) Laura A. Hug et al.   Nature Microbiology

Extreme Dysbiosis of the Microbiome in Critical Illness

(2016) Daniel McDonald et al.   mSphere

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

Hospitalization Type and Subsequent Severe Sepsis

(2015) Hallie C. Prescott et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

Metagenomics meets time series analysis: unraveling microbial community dynamics

(2015) Karoline Faust et al.   CURRENT OPINION IN MICROBIOLOGY

Gut dysbiosis in acute-on-chronic liver failure and its predictive value for mortality

(2015) Yanfei Chen et al.   JOURNAL OF GASTROENTEROLOGY AND HEPATOLOGY

Stability of the gorilla microbiome despite simian immunodeficiency virus infection

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

Defensive symbioses of animals with prokaryotic and eukaryotic microorganisms

(2015) Laura V. Flórez et al.   NATURAL PRODUCT REPORTS

Coral transplantation triggers shift in microbiome and promotion of coral disease associated potential pathogens

(2015) Jordan M. Casey et al.   Scientific Reports

Local bacteria affect the efficacy of chemotherapeutic drugs

(2015) Panos Lehouritis et al.   Scientific Reports

Expression of the Blood-Group-Related Gene B4galnt2 Alters Susceptibility to Salmonella Infection

(2015) Philipp Rausch et al.   PLoS Pathogens

Intestinal Microbiota Signatures Associated with Inflammation History in Mice Experiencing Recurring Colitis

(2015) David Berry et al.   Frontiers in Microbiology

Chronic Trichuris muris Infection in C57BL/6 Mice Causes Significant Changes in Host Microbiota and Metabolome: Effects Reversed by Pathogen Clearance

(2015) Ashley Houlden et al.   PLoS One

Microbiome Profiles in Periodontitis in Relation to Host and Disease Characteristics

(2015) Bo-Young Hong et al.   PLoS One

Chronic Trichuris muris Infection Decreases Diversity of the Intestinal Microbiota and Concomitantly Increases the Abundance of Lactobacilli

(2015) Jacob Bak Holm et al.   PLoS One

Burn Injury Alters the Intestinal Microbiome and Increases Gut Permeability and Bacterial Translocation

(2015) Zachary M. Earley et al.   PLoS One

Community Structure and Function of Amphibian Skin Microbes: An Experiment with Bullfrogs Exposed to a Chytrid Fungus

(2015) Jenifer B. Walke et al.   PLoS One

Dysbiosis and Alterations in Predicted Functions of the Subgingival Microbiome in Chronic Periodontitis

(2014) Mariana E. Kirst et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Immunoglobulin A Coating Identifies Colitogenic Bacteria in Inflammatory Bowel Disease

(2014) Noah W. Palm et al.   CELL

Prevention and Treatment of Opportunistic Infections in HIV-Infected Adults and Adolescents: Updated Guidelines From the Centers for Disease Control and Prevention, National Institutes of Health, and HIV Medicine Association of the Infectious Diseases Society of America

(2014) H. Masur et al.   CLINICAL INFECTIOUS DISEASES

Gut microbes of mammalian herbivores facilitate intake of plant toxins

(2014) Kevin D. Kohl et al.   ECOLOGY LETTERS

Host adaptive immunity alters gut microbiota

(2014) Husen Zhang et al.   ISME Journal

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

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

The pathogenBatrachochytrium dendrobatidisdisturbs the frog skin microbiome during a natural epidemic and experimental infection

(2014) Andrea J. Jani et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dietary iron depletion at weaning imprints low microbiome diversity and this is not recovered with oral nano Fe(III)

(2014) Dora I. A. Pereira et al.   MicrobiologyOpen

Association of gut microbiota with post-operative clinical course in Crohn’s disease

(2013) Neelendu Dey et al.   BMC GASTROENTEROLOGY

Microbiota Modulate Behavioral and Physiological Abnormalities Associated with Neurodevelopmental Disorders

(2013) Elaine Y. Hsiao et al.   CELL

SIV-Induced Instability of the Chimpanzee Gut Microbiome

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

The Gut Microbiome: Insights for Personalized Medicine

(2013) David Gurwitz   DRUG DEVELOPMENT RESEARCH

Assessment of Microbiome Variation During the Perioperative Period in Liver Transplant Patients: a Retrospective Analysis

(2013) Haifeng Lu et al.   MICROBIAL ECOLOGY

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

Diet rapidly and reproducibly alters the human gut microbiome

(2013) Lawrence A. David et al.   NATURE

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

(2013) Morgan G I Langille et al.   NATURE BIOTECHNOLOGY

Animals in a bacterial world, a new imperative for the life sciences

(2013) Margaret McFall-Ngai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bacteriophage adhering to mucus provide a non-host-derived immunity

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

Predicting and Manipulating Cardiac Drug Inactivation by the Human Gut Bacterium Eggerthella lenta

(2013) H. J. Haiser et al.   SCIENCE

Significant changes in the skin microbiome mediated by the sport of roller derby

(2013) James F. Meadow et al.   PeerJ

Study of the Viral and Microbial Communities Associated With Crohn’s Disease: A Metagenomic Approach

(2013) Vicente Pérez-Brocal et al.   Clinical and Translational Gastroenterology

Colonic microbiome is altered in alcoholism

(2012) Ece A. Mutlu et al.   AMERICAN JOURNAL OF PHYSIOLOGY-GASTROINTESTINAL AND LIVER PHYSIOLOGY

Lung-enriched Organisms and Aberrant Bacterial and Fungal Respiratory Microbiota after Lung Transplant

(2012) Emily S. Charlson et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

How to assemble a beneficial microbiome in three easy steps

(2012) István Scheuring et al.   ECOLOGY LETTERS

Temporal shifts in the skin microbiome associated with disease flares and treatment in children with atopic dermatitis

(2012) H. H. Kong et al.   GENOME RESEARCH

Dirichlet Multinomial Mixtures: Generative Models for Microbial Metagenomics

(2012) Ian Holmes et al.   PLoS One

Macroalgae Decrease Growth and Alter Microbial Community Structure of the Reef-Building Coral, Porites astreoides

(2012) Rebecca Vega Thurber et al.   PLoS One

Chytrid fungus Batrachochytrium dendrobatidis has nonamphibian hosts and releases chemicals that cause pathology in the absence of infection

(2012) T. A. McMahon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Therapeutic Modulation of Microbiota-Host Metabolic Interactions

(2012) E. Holmes et al.   Science Translational Medicine

The Evolution of Mutualism in Gut Microbiota Via Host Epithelial Selection

(2012) Jonas Schluter et al.   PLOS BIOLOGY

Characterization of fecal microbial communities in patients with liver cirrhosis

(2011) Yanfei Chen et al.   HEPATOLOGY

Evolutionary transitions in bacterial symbiosis

(2011) J. L. Sachs et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A global network of coexisting microbes from environmental and whole-genome sequence data

(2010) S. Chaffron et al.   GENOME RESEARCH

Toward defining the autoimmune microbiome for type 1 diabetes

(2010) Adriana Giongo et al.   ISME Journal

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Ribosomal RNA diversity predicts genome diversity in gut bacteria and their relatives

(2010) Jesse R. Zaneveld et al.   NUCLEIC ACIDS RESEARCH

Disordered Microbial Communities in the Upper Respiratory Tract of Cigarette Smokers

(2010) Emily S. Charlson et al.   PLoS One

Commensal bacteria play a role in mating preference of Drosophila melanogaster

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

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

Has the Microbiota Played a Critical Role in the Evolution of the Adaptive Immune System?

(2010) Y. K. Lee et al.   SCIENCE

Pharmacometabonomic identification of a significant host-microbiome metabolic interaction affecting human drug metabolism

(2009) T. A. Clayton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Unstable Composition of the Fecal Microbiota in Ulcerative Colitis During Clinical Remission

(2008) Cristina Martinez et al.   AMERICAN JOURNAL OF GASTROENTEROLOGY

A core gut microbiome in obese and lean twins

(2008) Peter J. Turnbaugh et al.   NATURE