Myoviridae phage PDX kills enteroaggregative Escherichia coli without human microbiome dysbiosis

Efficacy of bacteriophage treatment against carbapenem-resistant Acinetobacter baumannii in Galleria mellonella larvae and a mouse model of acute pneumonia

(2019) Jongsoo Jeon et al.   BMC MICROBIOLOGY

Current State of Compassionate Phage Therapy

(2019) McCallin et al.   Viruses-Basel

Design of a Broad-Range Bacteriophage Cocktail That Reduces Pseudomonas aeruginosa Biofilms and Treats Acute Infections in Two Animal Models

(2018) Francesca Forti et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Isolation, characterization and in vivo efficacy of Escherichia phage myPSH1131

(2018) Prasanth Manohar et al.   PLoS One

AIEC infection triggers modification of gut microbiota composition in genetically predisposed mice, contributing to intestinal inflammation

(2018) Alexis Bretin et al.   Scientific Reports

Bacteriophage Therapy: Clinical Trials and Regulatory Hurdles

(2018) Lucy L. Furfaro et al.   Frontiers in Cellular and Infection Microbiology

Exact sequence variants should replace operational taxonomic units in marker-gene data analysis

(2017) Benjamin J Callahan et al.   ISME Journal

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Isolation of Polyvalent Bacteriophages by Sequential Multiple-Host Approaches

(2015) Pingfeng Yu et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Analysis of whole genome sequencing for the Escherichia coli O157:H7 typing phages

(2015) Lauren A Cowley et al.   BMC GENOMICS

Antibiotics, Pediatric Dysbiosis, and Disease

(2015) Pajau Vangay et al.   Cell Host & Microbe

Enteropathogenic and enteroaggregative E. coli in stools of children with acute gastroenteritis in Davidson County, Tennessee

(2015) Monique A. Foster et al.   DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE

Antibiotic Resistance of Bacteria

(2015) Madhab K. Chattopadhyay et al.   Biomed Research International

Bacteriophage Therapy: Advances in Formulation Strategies and Human Clinical Trials

(2015) Dieter Vandenheuvel et al.   Annual Review of Virology

Effects of Antibiotics on Human Microbiota and Subsequent Disease

(2014) Kristie M. Keeney et al.   Annual Review of Microbiology

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Core Lipopolysaccharide-Specific Phage SSU5 as an Auxiliary Component of a Phage Cocktail for Salmonella Biocontrol

(2013) Minsik Kim et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Recent Advances in Understanding Enteric Pathogenic Escherichia coli

(2013) M. A. Croxen et al.   CLINICAL MICROBIOLOGY REVIEWS

Phage cocktails and the future of phage therapy

(2013) Benjamin K Chan et al.   Future Microbiology

Effect of the Abortive Infection Mechanism and Type III Toxin/Antitoxin System AbiQ on the Lytic Cycle of Lactococcus lactis Phages

(2013) J. E. Samson et al.   JOURNAL OF BACTERIOLOGY

Burden and aetiology of diarrhoeal disease in infants and young children in developing countries (the Global Enteric Multicenter Study, GEMS): a prospective, case-control study

(2013) Karen L Kotloff et al.   LANCET

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

Safety analysis of a Russian phage cocktail: From MetaGenomic analysis to oral application in healthy human subjects

(2013) Shawna McCallin et al.   VIROLOGY

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

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

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Oral T4-like phage cocktail application to healthy adult volunteers from Bangladesh

(2012) Shafiqul Alam Sarker et al.   VIROLOGY

Characterization and Comparative Genomic Analysis of a Novel Bacteriophage, SFP10, Simultaneously Inhibiting both Salmonella enterica and Escherichia coli O157:H7

(2011) Minjung Park et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

Pediatric Diarrhea in Southern Ghana: Etiology and Association with Intestinal Inflammation and Malnutrition

(2010) Japheth A. Opintan et al.   AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE

UniFrac: an effective distance metric for microbial community comparison

(2010) Catherine Lozupone et al.   ISME Journal

Bacteriophage resistance mechanisms

(2010) Simon J. Labrie et al.   NATURE REVIEWS MICROBIOLOGY

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

A controlled clinical trial of a therapeutic bacteriophage preparation in chronic otitis due to antibiotic-resistantPseudomonas aeruginosa; a preliminary report of efficacy

(2009) A. Wright et al.   CLINICAL OTOLARYNGOLOGY

Reproducible Community Dynamics of the Gastrointestinal Microbiota following Antibiotic Perturbation

(2009) D. A. Antonopoulos et al.   INFECTION AND IMMUNITY

Quality-Controlled Small-Scale Production of a Well-Defined Bacteriophage Cocktail for Use in Human Clinical Trials

(2009) Maya Merabishvili et al.   PLoS One

Bacteriophage Therapy and the Mutant Selection Window

(2008) B. J. Cairns et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

The pst operon of enteropathogenic Escherichia coli enhances bacterial adherence to epithelial cells

(2008) G. M. Ferreira et al.   MICROBIOLOGY-SGM