Rapid gastrointestinal loss of Clostridial Clusters IV and XIVa in the ICU associates with an expansion of gut pathogens

Protective Factors in the Intestinal Microbiome Against Clostridium difficile Infection in Recipients of Allogeneic Hematopoietic Stem Cell Transplantation

(2017) Yeon Joo Lee et al.   JOURNAL OF INFECTIOUS DISEASES

Microbiota-activated PPAR-γ signaling inhibits dysbiotic Enterobacteriaceae expansion

(2017) Mariana X. Byndloss et al.   SCIENCE

Neonatal acquisition of Clostridia species protects against colonization by bacterial pathogens

(2017) Yun-Gi Kim et al.   SCIENCE

Comparative gut microbiota and resistome profiling of intensive care patients receiving selective digestive tract decontamination and healthy subjects

(2017) Elena Buelow et al.   Microbiome

A Dietary Fiber-Deprived Gut Microbiota Degrades the Colonic Mucus Barrier and Enhances Pathogen Susceptibility

(2016) Mahesh S. Desai et al.   CELL

The Gut as the Motor of Multiple Organ Dysfunction in Critical Illness

(2016) Nathan J. Klingensmith et al.   CRITICAL CARE CLINICS

Role of the microbiome, probiotics, and ‘dysbiosis therapy’ in critical illness

(2016) Paul E. Wischmeyer et al.   Current Opinion in Critical Care

Critically ill patients demonstrate large interpersonal variation in intestinal microbiota dysregulation: a pilot study

(2016) Jacqueline M. Lankelma et al.   INTENSIVE CARE MEDICINE

The evolution of cooperation within the gut microbiota

(2016) Seth Rakoff-Nahoum et al.   NATURE

Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity

(2016) Alexandra Zhernakova et al.   SCIENCE

Population-level analysis of gut microbiome variation

(2016) Gwen Falony et al.   SCIENCE

The Shift of an Intestinal “Microbiome” to a “Pathobiome” Governs the Course and Outcome of Sepsis Following Surgical Injury

(2016) Monika A. Krezalek et al.   SHOCK

Dysbiosis Across Multiple Body Sites in Critically Ill Adult Surgical Patients

(2016) Andrew Yeh et al.   SHOCK

The microbiome and critical illness

(2016) Robert P Dickson   Lancet Respiratory Medicine

Extreme Dysbiosis of the Microbiome in Critical Illness

(2016) Daniel McDonald et al.   mSphere

Fat, fibre and cancer risk in African Americans and rural Africans

(2015) Stephen J. D. O’Keefe et al.   Nature Communications

The effects of intestinal tract bacterial diversity on mortality following allogeneic hematopoietic stem cell transplantation

(2014) Y. Taur et al.   BLOOD

Microbiota-Generated Metabolites Promote Metabolic Benefits via Gut-Brain Neural Circuits

(2014) Filipe De Vadder et al.   CELL

Starving our Microbial Self: The Deleterious Consequences of a Diet Deficient in Microbiota-Accessible Carbohydrates

(2014) Erica D. Sonnenburg et al.   Cell Metabolism

Rapid and Sustained Long-Term Decrease of Fecal Short-Chain Fatty Acids in Critically Ill Patients With Systemic Inflammatory Response Syndrome

(2014) Tomoki Yamada et al.   JOURNAL OF PARENTERAL AND ENTERAL NUTRITION

Rectal Swabs for Analysis of the Intestinal Microbiota

(2014) Andries E. Budding et al.   PLoS One

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

Intestinal Microbiota Containing Barnesiella Species Cures Vancomycin-Resistant Enterococcus faecium Colonization

(2013) Carles Ubeda et al.   INFECTION AND IMMUNITY

Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota

(2013) Koji Atarashi et al.   NATURE

Commensal Clostridia: leading players in the maintenance of gut homeostasis

(2013) Loris R Lopetuso et al.   Gut Pathogens

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

(2012) Ying Taur et al.   CLINICAL INFECTIOUS DISEASES

Probiotics in the critically ill

(2012) Elaine O. Petrof et al.   CRITICAL CARE MEDICINE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Dramatic Changes of the Gut Flora Immediately After Severe and Sudden Insults

(2011) Mineji Hayakawa et al.   DIGESTIVE DISEASES AND SCIENCES

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

(2011) Daniel McDonald et al.   ISME Journal

Experimental and analytical tools for studying the human microbiome

(2011) Justin Kuczynski et al.   NATURE REVIEWS GENETICS

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Altered Gut Flora Are Associated with Septic Complications and Death in Critically Ill Patients with Systemic Inflammatory Response Syndrome

(2010) Kentaro Shimizu et al.   DIGESTIVE DISEASES AND SCIENCES

Vancomycin-resistant Enterococcus domination of intestinal microbiota is enabled by antibiotic treatment in mice and precedes bloodstream invasion in humans

(2010) Carles Ubeda et al.   JOURNAL OF CLINICAL INVESTIGATION

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

International Study of the Prevalence and Outcomes of Infection in Intensive Care Units

(2009) Jean-Louis Vincent   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Effect of synbiotic therapy on the incidence of ventilator associated pneumonia in critically ill patients: a randomised, double-blind, placebo-controlled trial

(2008) David J. W. Knight et al.   INTENSIVE CARE MEDICINE

Probiotic prophylaxis in predicted severe acute pancreatitis: a randomised, double-blind, placebo-controlled trial

(2008) Marc GH Besselink et al.   LANCET