Recovery of gut microbiota of healthy adults following antibiotic exposure

Extensive impact of non-antibiotic drugs on human gut bacteria

(2018) Lisa Maier et al.   NATURE

Precision editing of the gut microbiota ameliorates colitis

(2018) Wenhan Zhu et al.   NATURE

Normalization and microbial differential abundance strategies depend upon data characteristics

(2017) Sophie Weiss et al.   Microbiome

Consensus report: faecal microbiota transfer - clinical applications and procedures

(2016) J. König et al.   ALIMENTARY PHARMACOLOGY & THERAPEUTICS

MOCAT2: a metagenomic assembly, annotation and profiling framework

(2016) Jens Roat Kultima et al.   BIOINFORMATICS

Effect of antibiotics on gut microbiota, glucose metabolism and body weight regulation: a review of the literature

(2016) K. H. Mikkelsen et al.   DIABETES OBESITY & METABOLISM

The Human Intestinal Microbiome in Health and Disease

(2016) Susan V. Lynch et al.   NEW ENGLAND JOURNAL OF MEDICINE

CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database

(2016) Baofeng Jia et al.   NUCLEIC ACIDS RESEARCH

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

(2016) Katri Korpela et al.   Nature Communications

Roux-en-Y gastric bypass surgery of morbidly obese patients induces swift and persistent changes of the individual gut microbiota

(2016) Albert Palleja et al.   Genome Medicine

Microbial diversity in individuals and their household contacts following typical antibiotic courses

(2016) Shira R. Abeles et al.   Microbiome

Determining the Long-term Effect of Antibiotic Administration on the Human Normal Intestinal Microbiota Using Culture and Pyrosequencing Methods

(2015) Mamun-Ur Rashid et al.   CLINICAL INFECTIOUS DISEASES

The initial state of the human gut microbiome determines its reshaping by antibiotics

(2015) Frédéric Raymond et al.   ISME Journal

Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota

(2015) Kristoffer Forslund et al.   NATURE

Antibiotic Exposure in Infancy and Risk of Being Overweight in the First 24 Months of Life

(2015) A. Saari et al.   PEDIATRICS

The human gut resistome

(2015) W. van Schaik   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Updates on the sporulation process in Clostridium species

(2015) Prabhat K. Talukdar et al.   RESEARCH IN MICROBIOLOGY

Same Exposure but Two Radically Different Responses to Antibiotics: Resilience of the Salivary Microbiome versus Long-Term Microbial Shifts in Feces

(2015) E. Zaura et al.   mBio

Metabolic and metagenomic outcomes from early-life pulsed antibiotic treatment

(2015) Yael R. Nobel et al.   Nature Communications

Proportionality: A Valid Alternative to Correlation for Relative Data

(2015) David Lovell et al.   PLoS Computational Biology

Temporal and technical variability of human gut metagenomes

(2015) Anita Y Voigt et al.   GENOME BIOLOGY

Effect of Antibiotics on Gut Microbiota, Gut Hormones and Glucose Metabolism

(2015) Kristian H. Mikkelsen et al.   PLoS One

Improved annotation of antibiotic resistance determinants reveals microbial resistomes cluster by ecology

(2014) Molly K Gibson et al.   ISME Journal

An integrated catalog of reference genes in the human gut microbiome

(2014) Junhua Li et al.   NATURE BIOTECHNOLOGY

Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes

(2014) H Bjørn Nielsen et al.   NATURE BIOTECHNOLOGY

Intestinal Microbial Variation May Predict Early Acute Rejection after Liver Transplantation in Rats

(2014) Zhigang Ren et al.   TRANSPLANTATION

Country-specific antibiotic use practices impact the human gut resistome

(2013) K. Forslund et al.   GENOME RESEARCH

Selective decontamination of the oropharynx and the digestive tract, and antimicrobial resistance: a 4 year ecological study in 38 intensive care units in the Netherlands

(2013) A. J. M. Houben et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Richness of human gut microbiome correlates with metabolic markers

(2013) Emmanuelle Le Chatelier et al.   NATURE

Gut metagenome in European women with normal, impaired and diabetic glucose control

(2013) Fredrik H. Karlsson et al.   NATURE

Metagenomic species profiling using universal phylogenetic marker genes

(2013) Shinichi Sunagawa et al.   NATURE METHODS

Preserving Antibiotics, Rationally

(2013) Aidan Hollis et al.   NEW ENGLAND JOURNAL OF MEDICINE

Data, information, knowledge and principle: back to metabolism in KEGG

(2013) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Host-Derived Nitrate Boosts Growth of E. coli in the Inflamed Gut

(2013) S. E. Winter et al.   SCIENCE

Bacterial Quorum Sensing: Its Role in Virulence and Possibilities for Its Control

(2013) S. T. Rutherford et al.   Cold Spring Harbor Perspectives in Medicine

Study of the Correlation of Imipenem Resistance with Efflux Pumps AdeABC, AdeIJK, AdeDE and AbeM in Clinical Isolates of Acinetobacter baumannii

(2012) Pan Fei Hou et al.   CHEMOTHERAPY

Infant antibiotic exposures and early-life body mass

(2012) L Trasande et al.   INTERNATIONAL JOURNAL OF OBESITY

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

(2012) Junjie Qin et al.   NATURE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

The human microbiome: at the interface of health and disease

(2012) Ilseung Cho et al.   NATURE REVIEWS GENETICS

Inflammation Drives Dysbiosis and Bacterial Invasion in Murine Models of Ileal Crohn’s Disease

(2012) Melanie Craven et al.   PLoS One

MOCAT: A Metagenomics Assembly and Gene Prediction Toolkit

(2012) Jens Roat Kultima et al.   PLoS One

Integration and visualization of host–pathogen data related to infectious diseases

(2011) Timothy Driscoll et al.   BIOINFORMATICS

Systemic absorption of oral vancomycin in patients with Clostridium difficile infection

(2011) Sriharsha Rao et al.   SCANDINAVIAN JOURNAL OF INFECTIOUS DISEASES

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Comparative Metagenomic Study of Alterations to the Intestinal Microbiota and Risk of NosocomialClostridum difficile–Associated Disease

(2010) Amee R. Manges et al.   JOURNAL OF INFECTIOUS DISEASES

Gut inflammation provides a respiratory electron acceptor for Salmonella

(2010) Sebastian E. Winter et al.   NATURE

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Acquired vancomycin resistance in clinically relevant pathogens

(2008) Guido Werner et al.   Future Microbiology

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(2008) B. Liu et al.   NUCLEIC ACIDS RESEARCH