Impact of investigational microbiota therapeutic RBX2660 on the gut microbiome and resistome revealed by a placebo-controlled clinical trial

Restoration of Bacterial Microbiome Composition and Diversity Among Treatment Responders in a Phase 2 Trial of Rbx2660—An Investigational Microbiome Restoration Therapeutic

(2019) Ken F Blount et al.   Open Forum Infectious Diseases

The incremental cost of infections associated with multidrug-resistant organisms in the inpatient hospital setting-A national estimate

(2019) Kenton J. Johnston et al.   HEALTH SERVICES RESEARCH

Interactive Tree Of Life (iTOL) v4: recent updates and new developments

(2019) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Meta-omics analysis of elite athletes identifies a performance-enhancing microbe that functions via lactate metabolism

(2019) Jonathan Scheiman et al.   NATURE MEDICINE

Fecal Microbial Transplantation and Its Potential Application in Cardiometabolic Syndrome

(2019) Avner Leshem et al.   Frontiers in Immunology

Drug-Resistant E. coli Bacteremia Transmitted by Fecal Microbiota Transplant

(2019) Zachariah DeFilipp et al.   NEW ENGLAND JOURNAL OF MEDICINE

Neuroinflammation and the Gut Microbiota: Possible Alternative Therapeutic Targets to Counteract Alzheimer’s Disease?

(2019) Milica Cerovic et al.   Frontiers in Aging Neuroscience

Corrigendum: The Role of Fecal Microbiota Transplantation in Reducing Intestinal Colonization With Antibiotic-Resistant Organisms: The Current Landscape and Future Directions

(2019) Michael H Woodworth et al.   Open Forum Infectious Diseases

Tapering Courses of Oral Vancomycin Induce Persistent Disruption of the Microbiota That Provide Colonization Resistance to Clostridium difficile and Vancomycin-Resistant Enterococci in Mice

(2018) Myreen E. Tomas et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Results From a Randomized, Placebo-Controlled Clinical Trial of a RBX2660—A Microbiota-Based Drug for the Prevention of Recurrent Clostridium difficile Infection

(2018) Erik R Dubberke et al.   CLINICAL INFECTIOUS DISEASES

Safety and efficacy of encapsulated fecal microbiota transplantation for recurrent Clostridium difficile infection

(2018) Umair Iqbal et al.   EUROPEAN JOURNAL OF GASTROENTEROLOGY & HEPATOLOGY

Clinical Application and Potential of Fecal Microbiota Transplantation

(2018) R.E. Ooijevaar et al.   Annual Review of Medicine

Genus-Wide Assessment of Antibiotic Resistance in Lactobacillus spp.

(2018) Ilenia Campedelli et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Recurrent Clostridium difficile Infection: Risk Factors, Treatment, and Prevention

(2018) Jung Hoon Song et al.   Gut and Liver

Fecal microbiota transplantation shortens the colonization period and allows the re-entry of patients carrying carbapenamase-producing bacteria into medical care facilities

(2018) Nadia SAÏDANI et al.   INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS

Species-level functional profiling of metagenomes and metatranscriptomes

(2018) Eric A. Franzosa et al.   NATURE METHODS

Effect of Fidaxomicin versus Vancomycin on Susceptibility to Intestinal Colonization with Vancomycin-Resistant Enterococci and Klebsiella pneumoniae in Mice

(2016) Abhishek Deshpande et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

A two-part mixed-effects model for analyzing longitudinal microbiome compositional data

(2016) Eric Z. Chen et al.   BIOINFORMATICS

Faecal carriage of antibiotic resistant Escherichia coli in asymptomatic children and associations with primary care antibiotic prescribing: a systematic review and meta-analysis

(2016) Ashley Bryce et al.   BMC INFECTIOUS DISEASES

Fecal Microbial Transplants Reduce Antibiotic-resistant Genes in Patients With RecurrentClostridium difficileInfection

(2016) Braden Millan et al.   CLINICAL INFECTIOUS DISEASES

Does the donor matter? Donor vs patient effects in the outcome of a next-generation microbiota-based drug trial for recurrent Clostridium difficile infection

(2016) Arnab Ray et al.   Future Microbiology

Short- and long-term effects of oral vancomycin on the human intestinal microbiota

(2016) Sandrine Isaac et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Interconnected microbiomes and resistomes in low-income human habitats

(2016) Erica C. Pehrsson et al.   NATURE

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

(2016) Baofeng Jia et al.   NUCLEIC ACIDS RESEARCH

Clinical epidemiology of vancomycin-resistant Enterococcus gallinarum and Enterococcus casseliflavus bloodstream infections

(2016) Nicholas S. Britt et al.   Journal of Global Antimicrobial Resistance

Fecal Microbiota Transplantation and Its Usage in Neuropsychiatric Disorders

(2016) Alper Evrensel et al.   Clinical Psychopharmacology and Neuroscience

Clostridium difficile infection

(2016) Wiep Klaas Smits et al.   Nature Reviews Disease Primers

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

Safety and Durability of RBX2660 (Microbiota Suspension) for RecurrentClostridium difficileInfection: Results of the PUNCH CD Study

(2015) Robert Orenstein et al.   CLINICAL INFECTIOUS DISEASES

Assessment of Reproducibility of Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry for Bacterial and Yeast Identification

(2015) Lars F. Westblade et al.   JOURNAL OF CLINICAL MICROBIOLOGY

High-Specificity Targeted Functional Profiling in Microbial Communities with ShortBRED

(2015) James Kaminski et al.   PLoS Computational Biology

Inexpensive Multiplexed Library Preparation for Megabase-Sized Genomes

(2015) Michael Baym et al.   PLoS One

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Fecal Microbiota Transplant for Relapsing Clostridium difficile Infection Using a Frozen Inoculum From Unrelated Donors: A Randomized, Open-Label, Controlled Pilot Study

(2014) Ilan Youngster et al.   CLINICAL INFECTIOUS DISEASES

Evaluation of the Bruker Biotyper and VITEK MS MALDI-TOF MS systems for the identification of unusual and/or difficult-to-identify microorganisms isolated from clinical specimens

(2014) E. McElvania TeKippe et al.   EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES

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

(2014) Molly K Gibson et al.   ISME Journal

Fecal microbiota transplantation as therapy for inflammatory bowel disease: A systematic review and meta-analysis

(2014) Ruben J. Colman et al.   Journal of Crohns & Colitis

Is fecal microbiota transplantation (FMT) an effective treatment for patients with functional gastrointestinal disorders (FGID)?

(2014) D. M. Pinn et al.   NEUROGASTROENTEROLOGY AND MOTILITY

The Comprehensive Antibiotic Resistance Database

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

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

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

(2013) Carles Ubeda et al.   INFECTION AND IMMUNITY

Impact of oral vancomycin on gut microbiota, bile acid metabolism, and insulin sensitivity

(2013) Anne Vrieze et al.   JOURNAL OF HEPATOLOGY

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Diversity, stability and resilience of the human gut microbiota

(2012) Catherine A. Lozupone et al.   NATURE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Metagenomic microbial community profiling using unique clade-specific marker genes

(2012) Nicola Segata et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Fast Identification and Removal of Sequence Contamination from Genomic and Metagenomic Datasets

(2011) Robert Schmieder et al.   PLoS One

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

Commensal Escherichia coli of healthy humans: a reservoir for antibiotic-resistance determinants

(2010) J. K. Bailey et al.   JOURNAL OF MEDICAL MICROBIOLOGY

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Interspecies Signaling between Veillonella atypica and Streptococcus gordonii Requires the Transcription Factor CcpA

(2009) B. P. Johnson et al.   JOURNAL OF BACTERIOLOGY

Both Oral Metronidazole and Oral Vancomycin Promote Persistent Overgrowth of Vancomycin-Resistant Enterococci during Treatment of Clostridium difficile-Associated Disease

(2008) W. N. Al-Nassir et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY