Genomic Insights Into the Pathogenicity of a Novel Biofilm-Forming Enterococcus sp. Bacteria (Enterococcus lacertideformus) Identified in Reptiles

Challenges of unculturable bacteria: environmental perspectives

(2020) Attila Bodor et al.   REVIEWS IN ENVIRONMENTAL SCIENCE AND BIO-TECHNOLOGY

Complete genome sequences of two Enterococcus faecium strains and comparative genomic analysis

(2020) Yong‑Qi Gan et al.   Experimental and Therapeutic Medicine

antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline

(2019) Kai Blin et al.   NUCLEIC ACIDS RESEARCH

Validating the NCBI AMRFinder Tool and Resistance Gene Database Using Antimicrobial Resistance Genotype-Phenotype Correlations in a Collection of NARMS Isolates

(2019) Michael Feldgarden et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Exploiting biofilm phenotypes for functional characterization of hypothetical genes in Enterococcus faecalis

(2019) Julia L. E. Willett et al.   npj Biofilms and Microbiomes

CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database

(2019) Brian P Alcock et al.   NUCLEIC ACIDS RESEARCH

Sugar-mediated regulation of a c-di-GMP phosphodiesterase in Vibrio cholerae

(2019) Kyoo Heo et al.   Nature Communications

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms

(2018) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

BAGEL4: a user-friendly web server to thoroughly mine RiPPs and bacteriocins

(2018) Auke J van Heel et al.   NUCLEIC ACIDS RESEARCH

Biofilm-associated infection by enterococci

(2018) Jun-Hong Ch’ng et al.   NATURE REVIEWS MICROBIOLOGY

ICEberg 2.0: an updated database of bacterial integrative and conjugative elements

(2018) Meng Liu et al.   NUCLEIC ACIDS RESEARCH

PointFinder: a novel web tool for WGS-based detection of antimicrobial resistance associated with chromosomal point mutations in bacterial pathogens

(2017) Ea Zankari et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Comparative genomic analysis of the genus Enterococcus

(2017) Zhi Zhong et al.   MICROBIOLOGICAL RESEARCH

IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets

(2017) Claire Bertelli et al.   NUCLEIC ACIDS RESEARCH

Emergent multisystemic Enterococcus infection threatens endangered Christmas Island reptile populations

(2017) Karrie Rose et al.   PLoS One

Biofilm formation in enterococci: genotype-phenotype correlations and inhibition by vancomycin

(2017) Yomna A. Hashem et al.   Scientific Reports

Combination Susceptibility Testing of Common Antimicrobials in Vitro and the Effects of Sub-MIC of Antimicrobials on Staphylococcus aureus Biofilm Formation

(2017) Bing Yang et al.   Frontiers in Microbiology

Genomic insights into the pathogenicity and environmental adaptability of Enterococcus hirae R17 isolated from pork offered for retail sale

(2017) Zixin Peng et al.   MicrobiologyOpen

The stereospecificity of glycerol-phosphate cytidylyltransferase is key to understanding the distinct stereochemical composition of glycerophosphoinositol in Bacteria and Archaea

(2016) Marta V. Rodrigues et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

PHASTER: a better, faster version of the PHAST phage search tool

(2016) David Arndt et al.   NUCLEIC ACIDS RESEARCH

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

(2016) Baofeng Jia et al.   NUCLEIC ACIDS RESEARCH

Discovery and Partial Genomic Characterisation of a Novel Nidovirus Associated with Respiratory Disease in Wild Shingleback Lizards (Tiliqua rugosa)

(2016) Mark A. O’Dea et al.   PLoS One

Sugar Allocation to Metabolic Pathways is Tightly Regulated and Affects the Virulence of Streptococcus mutans

(2016) Miki Kawada-Matsuo et al.   Genes

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

VFDB 2016: hierarchical and refined dataset for big data analysis—10 years on

(2015) Lihong Chen et al.   NUCLEIC ACIDS RESEARCH

Evaluation of the Enterococcus faecalis Biofilm-Associated Virulence Factors AhrC and Eep in Rat Foreign Body Osteomyelitis and In Vitro Biofilm-Associated Antimicrobial Resistance

(2015) Kristi L. Frank et al.   PLoS One

In SilicoDetection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing

(2014) Alessandra Carattoli et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

The long goodbye: the rise and fall of flavodoxin during plant evolution

(2014) J. J. Pierella Karlusich et al.   JOURNAL OF EXPERIMENTAL BOTANY

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Classification and evolution of type II CRISPR-Cas systems

(2014) Krzysztof Chylinski et al.   NUCLEIC ACIDS RESEARCH

Mycoplasmosis and upper respiratory tract disease of tortoises: A review and update

(2014) Elliott R. Jacobson et al.   VETERINARY JOURNAL

Chrysosporium-Related Fungi and Reptiles: A Fatal Attraction

(2014) F. Javier Cabañes et al.   PLoS Pathogens

ARG-ANNOT, a New Bioinformatic Tool To Discover Antibiotic Resistance Genes in Bacterial Genomes

(2013) Sushim Kumar Gupta et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Diverse Functions of Restriction-Modification Systems in Addition to Cellular Defense

(2013) K. Vasu et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

BacMet: antibacterial biocide and metal resistance genes database

(2013) Chandan Pal et al.   NUCLEIC ACIDS RESEARCH

Contribution of Individual Ebp Pilus Subunits of Enterococcus faecalis OG1RF to Pilus Biogenesis, Biofilm Formation and Urinary Tract Infection

(2013) Jouko Sillanpää et al.   PLoS One

Biofilm-specific antibiotic resistance

(2012) Thien-Fah Mah   Future Microbiology

Identification of acquired antimicrobial resistance genes

(2012) E. Zankari et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

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

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

Proteins and DNA elements essential for the CRISPR adaptation process in Escherichia coli

(2012) Ido Yosef et al.   NUCLEIC ACIDS RESEARCH

Evolution and classification of the CRISPR–Cas systems

(2011) Kira S. Makarova et al.   NATURE REVIEWS MICROBIOLOGY

Domain Movement within a Gene: A Novel Evolutionary Mechanism for Protein Diversification

(2011) Yoshikazu Furuta et al.   PLoS One

Strategies for culture of ‘unculturable’ bacteria

(2010) Sonia R. Vartoukian et al.   FEMS MICROBIOLOGY LETTERS

The Phosphoenolpyruvate Phosphotransferase System: as Important for Biofilm Formation by Vibrio cholerae as It Is for Metabolism in Escherichia coli

(2010) B. A. Lazazzera   JOURNAL OF BACTERIOLOGY

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

(2010) Aaron E. Darling et al.   PLoS One

Reordering contigs of draft genomes using the Mauve Aligner

(2009) Anna I. Rissman et al.   BIOINFORMATICS

CRISPI: a CRISPR interactive database

(2009) C. Rousseau et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Functional Genomics of Enterococcus faecalis: Multiple Novel Genetic Determinants for Biofilm Formation in the Core Genome

(2009) K. S. Ballering et al.   JOURNAL OF BACTERIOLOGY

A family of fibrinogen-binding MSCRAMMs from Enterococcus faecalis

(2009) J. Sillanpaa et al.   MICROBIOLOGY-SGM

Glycolipids are involved in biofilm accumulation and prolonged bacteraemia inEnterococcus faecalis

(2009) Christian Theilacker et al.   MOLECULAR MICROBIOLOGY

Flavodoxin-Mediated Electron Transfer from Photosystem I to Ferredoxin-NADP+Reductase inAnabaena:  Role of Flavodoxin Hydrophobic Residues in Protein−Protein Interactions†

(2008) Guillermina Goñi et al.   BIOCHEMISTRY

Identification and phenotypic characterization of a second collagen adhesin, Scm, and genome-based identification and analysis of 13 other predicted MSCRAMMs, including four distinct pilus loci, in Enterococcus faecium

(2008) J. Sillanpaa et al.   MICROBIOLOGY-SGM

Antibiotics and Antibiotic Resistance Genes in Natural Environments

(2008) J. L. Martinez   SCIENCE