The effect of antibiotics on the gut microbiome: a metagenomics analysis of microbial shift and gut antibiotic resistance in antibiotic treated mice

Pharmacokinetics and Pharmacodynamics of Fosfomycin and Its Activity against Extended-Spectrum-β-Lactamase-, Plasmid-Mediated AmpC-, and Carbapenemase-Producing Escherichia coli in a Murine Urinary Tract Infection Model

(2018) Ilya Nikolaevich Zykov et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Strategies to prevent the occurrence of resistance against antibiotics by using advanced materials

(2018) Arnau Bassegoda et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Metaxa2 Database Builder: enabling taxonomic identification from metagenomic or metabarcoding data using any genetic marker

(2018) Johan Bengtsson-Palme et al.   BIOINFORMATICS

Antibiotic-induced microbiota perturbation causes gut endocannabinoidome changes, hippocampal neuroglial reorganization and depression in mice

(2018) F. Guida et al.   BRAIN BEHAVIOR AND IMMUNITY

The Local Defender and Functional Mediator: Gut Microbiome

(2018) Hang Yang et al.   DIGESTION

Developmental validation of a Nextera XT mitogenome Illumina MiSeq sequencing method for high-quality samples

(2018) Michelle A. Peck et al.   Forensic Science International-Genetics

Catheter-associated urinary tract infections in persons with neurogenic bladders

(2018) Todd A. Linsenmeyer   JOURNAL OF SPINAL CORD MEDICINE

When drugs unintentionally affect gut bugs

(2018) Cassandra Willyard   NATURE REVIEWS DRUG DISCOVERY

Preliminary Comparison of Oral and Intestinal Human Microbiota in Patients with Colorectal Cancer: A Pilot Study

(2018) Edda Russo et al.   Frontiers in Microbiology

Gut Microbiota Dysfunction as Reliable Non-invasive Early Diagnostic Biomarkers in the Pathophysiology of Parkinson's Disease: A Critical Review

(2018) Arun T Nair et al.   Journal of Neurogastroenterology and Motility

Mobile Genetic Elements Associated with Antimicrobial Resistance

(2018) Sally R. Partridge et al.   CLINICAL MICROBIOLOGY REVIEWS

Transposons: the agents of antibiotic resistance in bacteria

(2018) Sajad Babakhani et al.   JOURNAL OF BASIC MICROBIOLOGY

Maternal gut and breast milk microbiota affect infant gut antibiotic resistome and mobile genetic elements

(2018) Katariina Pärnänen et al.   Nature Communications

Choosing an appropriate probiotic product for your patient: An evidence-based practical guide

(2018) Jason C. Sniffen et al.   PLoS One

Efflux drug transporters at the forefront of antimicrobial resistance

(2017) Tahmina Rahman et al.   EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS

The Brain-Gut Axis and Stress in Inflammatory Bowel Disease

(2017) Charles N. Bernstein   GASTROENTEROLOGY CLINICS OF NORTH AMERICA

Antibiotic Resistance among Urinary Isolates from Female Outpatients in the United States in 2003 and 2012

(2016) Guillermo V. Sanchez et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson’s Disease

(2016) Timothy R. Sampson et al.   CELL

Metaxa2 Diversity Tools: Easing microbial community analysis with Metaxa2

(2016) Johan Bengtsson-Palme et al.   Ecological Informatics

Antibiotic-Induced Changes in the Intestinal Microbiota and Disease

(2016) Simone Becattini et al.   TRENDS IN MOLECULAR MEDICINE

Emergence of a Potent Multidrug Efflux Pump Variant That Enhances Campylobacter Resistance to Multiple Antibiotics

(2016) Hong Yao et al.   mBio

The gut microbiome in health and in disease

(2015) Andrew B. Shreiner et al.   CURRENT OPINION IN GASTROENTEROLOGY

Functional genomic and metagenomic approaches to understanding gut microbiota–animal mutualism

(2015) Sang Sun Yoon et al.   CURRENT OPINION IN MICROBIOLOGY

Antibiotics and the developing infant gut microbiota and resistome

(2015) Molly K Gibson et al.   CURRENT OPINION IN MICROBIOLOGY

New insights in antibiotic resistance of Lactobacillus species from fermented foods

(2015) Hikmate Abriouel et al.   FOOD RESEARCH INTERNATIONAL

metaxa2: improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data

(2015) Johan Bengtsson-Palme et al.   Molecular Ecology Resources

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Genome-wide analysis captures the determinants of the antibiotic cross-resistance interaction network

(2014) Viktória Lázár et al.   Nature Communications

Antibiotic Administration Routes Significantly Influence the Levels of Antibiotic Resistance in Gut Microbiota

(2013) Lu Zhang et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

The Comprehensive Antibiotic Resistance Database

(2013) Andrew G. McArthur et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Differential abundance analysis for microbial marker-gene surveys

(2013) Joseph N Paulson et al.   NATURE METHODS

Metagenome-wide analysis of antibiotic resistance genes in a large cohort of human gut microbiota

(2013) Yongfei Hu et al.   Nature Communications

Efficacy of Ceftobiprole Medocaril against Enterococcus faecalis in a Murine Urinary Tract Infection Model

(2012) Kavindra V. Singh et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Defining a Healthy Human Gut Microbiome: Current Concepts, Future Directions, and Clinical Applications

(2012) Fredrik Bäckhed et al.   Cell Host & Microbe

A comparison of the microbiome and the metabolome of different regions of the equine hindgut

(2012) Kirsty Dougal et al.   FEMS MICROBIOLOGY ECOLOGY

Antibiotics in early life alter the murine colonic microbiome and adiposity

(2012) Ilseung Cho et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

International Clinical Practice Guidelines for the Treatment of Acute Uncomplicated Cystitis and Pyelonephritis in Women: A 2010 Update by the Infectious Diseases Society of America and the European Society for Microbiology and Infectious Diseases

(2011) Kalpana Gupta et al.   CLINICAL INFECTIOUS DISEASES

Long-term impacts of antibiotic exposure on the human intestinal microbiota

(2010) C. Jernberg et al.   MICROBIOLOGY-SGM

Transurethral Induction of Mouse Urinary Tract Infection

(2010) Kim H. Thai et al.   Jove-Journal of Visualized Experiments

Fast and accurate short read alignment with Burrows-Wheeler transform

(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

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Antibiotic resistance of Gardnerella vaginalis in recurrent bacterial vaginosis

(2009) P Nagaraja   Indian Journal of Medical Microbiology