Safety assessment of Enterococcus lactis strains complemented with comparative genomics analysis reveals probiotic and safety characteristics of the entire species

CRISPR-Cas system as a promising player against bacterial infection and antibiotic resistance

(2023) Mohammad Abavisani et al.   DRUG RESISTANCE UPDATES

antiSMASH 7.0: new and improved predictions for detection, regulation, chemical structures and visualisation

(2023) Kai Blin et al.   NUCLEIC ACIDS RESEARCH

Controlling the Evolution of Selective Vancomycin Resistance through Successful Ophthalmic Eye-Drop Preparation of Vancomycin-Loaded Nanoliposomes Using the Active-Loading Method

(2023) El Tahra M. Ahmed et al.   Pharmaceutics

Enterococcal biofilm—A nidus for antibiotic resistance transfer?

(2022) Michael Conwell et al.   JOURNAL OF APPLIED MICROBIOLOGY

Alternative functions of CRISPR–Cas systems in the evolutionary arms race

(2022) Prarthana Mohanraju et al.   NATURE REVIEWS MICROBIOLOGY

Enterocin: Promising Biopreservative Produced by Enterococcus sp.

(2022) Melisa Elsie Kasimin et al.   Microorganisms

Anti-Helicobacter pylori activity of potential probiotic Lactiplantibacillus pentosus SLC13

(2022) Tran Thi Dieu Thuy et al.   BMC MICROBIOLOGY

Probiotic capability of novel lactic acid bacteria isolated from worker honey bees gut microbiota

(2021) Hoda Mahmoud Elzeini et al.   FEMS MICROBIOLOGY LETTERS

Mechanisms of Action of Ribosomally Synthesized and Posttranslationally Modified Peptides (RiPPs)

(2021) Li Cao et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Comparison of MiSeq, MinION, and hybrid genome sequencing for analysis of Campylobacter jejuni

(2021) Jason M. Neal-McKinney et al.   Scientific Reports

Whole-genome analysis of probiotic product isolates reveals the presence of genes related to antimicrobial resistance, virulence factors, and toxic metabolites, posing potential health risks

(2021) Ying Wang et al.   BMC GENOMICS

Probiotics in the dairy industry—Advances and opportunities

(2021) Jie Gao et al.   COMPREHENSIVE REVIEWS IN FOOD SCIENCE AND FOOD SAFETY

dbAMP 2.0: updated resource for antimicrobial peptides with an enhanced scanning method for genomic and proteomic data

(2021) Jhih-Hua Jhong et al.   NUCLEIC ACIDS RESEARCH

CRISPR-Cas is associated with fewer antibiotic resistance genes in bacterial pathogens

(2021) Elizabeth Pursey et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Probiotic biomarkers and models upside down: From humans to animals

(2021) Vladimir I. Trukhachev et al.   VETERINARY MICROBIOLOGY

Safety, beneficial and technological properties of enterococci for use in functional food applications – a review

(2020) Ken Graham et al.   CRITICAL REVIEWS IN FOOD SCIENCE AND NUTRITION

What Is Wrong with Enterococcal Probiotics?

(2020) Alexander Suvorov   Probiotics and Antimicrobial Proteins

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0

(2020) Francesco Asnicar et al.   Nature Communications

Bacteria producing antimicrobials against Clostridium difficile isolated from human stool

(2020) Rania Abdelmonem Khattab et al.   ANAEROBE

Safety Assessment of a Nham Starter Culture Lactobacillus plantarum BCC9546 via Whole-genome Analysis

(2020) Nipa Chokesajjawatee et al.   Scientific Reports

Probiotic Properties of New Lactobacillus Strains Intended to Be Used as Feed Additives for Monogastric Animals

(2020) Katarzyna Śliżewska et al.   Probiotics and Antimicrobial Proteins

Evolutionary Ecology and Interplay of Prokaryotic Innate and Adaptive Immune Systems

(2020) Tatiana Dimitriu et al.   CURRENT BIOLOGY

CRISPR-Cas systems restrict horizontal gene transfer in Pseudomonas aeruginosa

(2020) Rachel M. Wheatley et al.   ISME Journal

Genome-wide correlation analysis suggests different roles of CRISPR-Cas systems in the acquisition of antibiotic resistance genes in diverse species

(2019) Saadlee Shehreen et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy

(2019) Jan P. Meier-Kolthoff et al.   Nature Communications

Biomonitoring detoxification efficiency of an algal-bacterial microcosm system for treatment of coking wastewater: Harmonization between Chlorella vulgaris microalgae and wastewater microbiome

(2019) Mariam Hassan et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Comprehensive approaches for assessing the safety of probiotic bacteria

(2019) Diwas Pradhan et al.   FOOD CONTROL

Risks associated with enterococci as probiotics

(2019) Xingmin Wang et al.   FOOD RESEARCH INTERNATIONAL

Illumina sequencing and assessment of new cost-efficient protocol for metagenomic-DNA extraction from environmental water samples

(2018) Mariam Hassan et al.   BRAZILIAN JOURNAL OF MICROBIOLOGY

Cyclic Peptides that Govern Signal Transduction Pathways: From Prokaryotes to Multi-Cellular Organisms

(2018) Ryan W. Mull et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Using average nucleotide identity to improve taxonomic assignments in prokaryotic genomes at the NCBI

(2018) Stacy Ciufo et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins

(2018) David Couvin et al.   NUCLEIC ACIDS RESEARCH

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update

(2018) Enis Afgan et al.   NUCLEIC ACIDS RESEARCH

Enterococcus faecium SF68 as a model for efficacy and safety evaluation of pharmaceutical probiotics

(2018) W. Holzapfel et al.   Beneficial Microbes

Comparative genome analysis reveals key genetic factors associated with probiotic property in Enterococcus faecium strains

(2018) Vikas C. Ghattargi et al.   BMC GENOMICS

The Genus Enterococcus: Between Probiotic Potential and Safety Concerns—An Update

(2018) Hasna Hanchi et al.   Frontiers in Microbiology

VFDB 2019: a comparative pathogenomic platform with an interactive web interface

(2018) Bo Liu et al.   NUCLEIC ACIDS RESEARCH

dbAMP: an integrated resource for exploring antimicrobial peptides with functional activities and physicochemical properties on transcriptome and proteome data

(2018) Jhih-Hua Jhong et al.   NUCLEIC ACIDS RESEARCH

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses

(2018) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries

(2018) Chirag Jain et al.   Nature Communications

Identical bacterial populations colonize premature infant gut, skin, and oral microbiomes and exhibit different in situ growth rates

(2017) Matthew R. Olm et al.   GENOME RESEARCH

Probiotics: From Isolation to Application

(2017) Parisa Shokryazdan et al.   JOURNAL OF THE AMERICAN COLLEGE OF NUTRITION

Probiotics History

(2016) Giovanni Gasbarrini et al.   JOURNAL OF CLINICAL GASTROENTEROLOGY

BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences

(2016) Minoru Kanehisa et al.   JOURNAL OF MOLECULAR BIOLOGY

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

NCBI prokaryotic genome annotation pipeline

(2016) Tatiana Tatusova et al.   NUCLEIC ACIDS RESEARCH

CRISPR-Cas and Restriction-Modification Act Additively against Conjugative Antibiotic Resistance Plasmid Transfer in Enterococcus faecalis

(2016) Valerie J. Price et al.   mSphere

High level aminoglycoside resistance in Enterococcus, Pediococcus and Lactobacillus species from farm animals and commercial meat products

(2015) George Jaimee et al.   ANNALS OF MICROBIOLOGY

Emerging resistance to aminoglycosides in lactic acid bacteria of food origin—an impending menace

(2015) G. Jaimee et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Discovering probiotic microorganisms: in vitro, in vivo, genetic and omics approaches

(2015) Konstantinos Papadimitriou et al.   Frontiers in Microbiology

Friend Turned Foe: Evolution of Enterococcal Virulence and Antibiotic Resistance

(2014) Daria Van Tyne et al.   Annual Review of Microbiology

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

The International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic

(2014) Colin Hill et al.   Nature Reviews Gastroenterology & Hepatology

To acquire or resist: the complex biological effects of CRISPR–Cas systems

(2014) Joseph Bondy-Denomy et al.   TRENDS IN MICROBIOLOGY

Nonclinical and Clinical Enterococcus faecium Strains, but Not Enterococcus faecalis Strains, Have Distinct Structural and Functional Genomic Features

(2013) Eun Bae Kim et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

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

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

Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain

(2012) K. A. Jolley et al.   MICROBIOLOGY-SGM

IS element IS16 as a molecular screening tool to identify hospital-associated strains of Enterococcus faecium

(2011) Guido Werner et al.   BMC INFECTIOUS DISEASES

Thuricin CD, a posttranslationally modified bacteriocin with a narrow spectrum of activity against Clostridium difficile

(2010) M. C. Rea et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Probiotics: Definition, Sources, Selection, and Uses

(2008) Mary Ellen Sanders   CLINICAL INFECTIOUS DISEASES

Genes and Molecules of Lactobacilli Supporting Probiotic Action

(2008) S. Lebeer et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS