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References from First report of food-associated Enterococcus bulliens CFF05 from Thai cooked fermented fish: Genomic insights and safety assessment. Local targets link to admitted publications; unresolved targets remain external evidence.
CARD 2023: Expanded curation, support for machine learning, and resistome prediction at the comprehensive antibiotic resistance database
10.1093/nar/gkac920 · 2022 · External reference
A natural ANI gap that can define intra-species units of bacteriophages and other viruses
10.1128/mbio.01536-24 · 2024 · External reference
A mechanistic understanding of the effect of Staphylococcus aureus VraS histidine kinase single-point mutation on antibiotic resistance
10.1128/spectrum.00095-25 · 2025 · External reference
Cellular functions of the ClpP protease impacting bacterial virulence
10.3389/fmolb.2022.1054408 · 2022 · External reference
Cell envelope and stress-responsive pathways underlie an evolved oleaginous Rhodotorula toruloides strain multi-stress tolerance
10.1186/s13068-024-02518-0 · 2024 · External reference
Multifunctional applications of lactic acid bacteria: Enhancing safety, quality, and nutritional value in foods and fermented beverages
2024 · External reference
Antimicrobial resistance, virulence factors, and genotypes of Enterococcus faecalis and Enterococcus faecium clinical isolates in Northern Japan: Identification of optrA in ST480 E. faecalis
10.3390/antibiotics12010108 · 2023 · External reference
The RAST server: Rapid annotations using subsystems technology
10.1186/1471-2164-9-75 · 2008 · External reference
JVENN: An interactive Venn diagram viewer
10.1186/1471-2105-15-293 · 2014 · External reference
Fermented fish and fermented fish-based products, an ever-growing source of microbial diversity: A literature review
10.1016/j.foodres.2023.113112 · 2023 · External reference
Integrons in the development of antimicrobial resistance: Critical review and perspectives
10.3389/fmicb.2023.1231938 · 2023 · External reference
Widespread phages of endosymbionts: Phage WO genomics and the proposed taxonomic classification of Symbioviridae
10.1371/journal.pgen.1010227 · 2022 · External reference
A negative feedback loop is critical for recovery of RpoS after stress in Escherichia coli
10.1371/journal.pgen.1011059 · 2024 · External reference
In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing
10.1128/aac.02412-14 · 2014 · External reference
From stress tolerance to virulence: Recognizing the roles of Csps in pathogenicity and food contamination
2024 · External reference
Antibiotic resistance in fermented foods chain: Evaluating the risks of emergence of enterococci as an emerging pathogen in raw milk cheese
10.1155/ijm/2409270 · 2024 · External reference
VFDB: A reference database for bacterial virulence factors
10.1093/nar/gki008 · 2005 · External reference
Effect of trehalose and lactose treatments on the freeze-drying resistance of lactic acid bacteria in high-density culture
10.3390/microorganisms11010048 · 2022 · External reference
The complete genome sequences of the two novel probiotics were isolated from the human gut microbiota: Pediococcus acidilactici WNYM01 and Pediococcus acidilactici WNYM02, vitamin B9, and B2-producers
10.4103/epj.epj_83_24 · 2024 · External reference
Antioxidant peptides produced by Pediococcus acidilactici YKP4 and Lacticaseibacillus rhamnosus BD2 in fermented soymilk made from germinated soybeans
10.1093/ijfood/vvae002 · 2025 · External reference
Whole-genome prediction of bacterial pathogenic capacity on novel bacteria using protein language models, with PathogenFinder2
2025 · External reference
ResFinder - an open online resource for identification of antimicrobial resistance genes in next-generation sequencing data and prediction of phenotypes from genotypes
10.1099/mgen.0.000748 · 2022 · External reference
Proksee: In-depth characterization and visualization of bacterial genomes
10.1093/nar/gkad326 · 2023 · External reference
Protein interaction network analysis to investigate stress response, virulence, and antibiotic resistance mechanisms in Listeria monocytogenes
10.3390/microorganisms11040930 · 2023 · External reference
Whole genome sequencing and extracellular metabolite profiling of Lactiplantibacillus plantarum FRT4: Insights into probiotic functionality
10.3390/biology14091167 · 2025 · External reference
Isolation and characterization of lactic acid bacteria with potential probiotic activity and further investigation of their activity by α-amylase and α-glucosidase inhibitions of fermented batters
10.3389/fmicb.2022.1042263 · 2023 · External reference
High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries
10.1038/s41467-018-07641-9 · 2018 · External reference
Detection of mobile genetic elements associated with antibiotic resistance in Salmonella enterica using a newly developed web tool: MobileElementFinder
10.1093/jac/dkaa390 · 2020 · External reference
Gene expression and metabolic activity of Streptococcus mutans during exposure to dietary carbohydrates glucose, sucrose, lactose, and xylitol
10.1111/omi.12428 · 2023 · External reference
Enterococcus bulliens sp. nov., a novel lactic acid bacterium isolated from camel milk
10.1007/s10482-015-0579-z · 2015 · External reference
The evolutionary genomics of adaptation to stress in wild rhizobium bacteria
10.1073/pnas.2311127121 · 2024 · External reference
Assembly of long, error-prone reads using repeat graphs
10.1038/s41587-019-0072-8 · 2019 · External reference
Prevalence of Enterococcus spp. And the whole-genome characteristics of Enterococcus faecium and Enterococcus faecalis strains isolated from free-living birds in Poland
2023 · External reference
Empowering bioinformatics communities with Nextflow and nf-core
10.1186/s13059-025-03673-9 · 2025 · External reference
Interactive Tree of Life (iTOL) v6: Recent updates to the phylogenetic tree display and annotation tool
10.1093/nar/gkae268 · 2024 · External reference
Vancomycin resistance in Enterococcus and Staphylococcus aureus
10.3390/microorganisms11010024 · 2022 · External reference
Commercial probiotic products in public health: Current status and potential limitations
10.1080/10408398.2023.2169858 · 2024 · External reference
Phenotypic and genotypic characterization of Enterococcus faecalis and Enterococcus faecium isolated from fish, vegetables, and humans
10.1038/s41598-024-71610-0 · 2024 · External reference
Distribution of bacterial DNA repair proteins and their co-occurrence with immune systems
10.1016/j.celrep.2024.115110 · 2025 · External reference
Genomic characterization of Bacillus sp. THPS1: A hot spring-derived species with functional features and biotechnological potential
10.3390/microorganisms12122476 · 2024 · External reference
Roary: Rapid large-scale prokaryote pan genome analysis
2015 · External reference
Antimicrobial resistance in veterinary medicine: An overview
10.3390/ijms21061914 · 2020 · External reference
Review and comparison of antimicrobial resistance gene databases
10.3390/antibiotics11030339 · 2022 · External reference
GTDB: An ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy
10.1093/nar/gkab776 · 2021 · External reference
The emergence of antimicrobial resistance and virulence characteristics in Enterococcus species isolated from bovine milk
10.3390/antibiotics12081243 · 2023 · External reference
Unraveling Enterococcus susceptibility to quaternary ammonium compounds: Genes, phenotypes, and the impact of environmental conditions
10.1128/spectrum.02324-23 · 2023 · External reference
Strain-level identification of bacteria persisting in food and in food processing facilities: When do two isolates represent the same strain and which tools identify a strain?
10.1016/j.cofs.2024.101245 · 2025 · External reference
Understanding functional redundancy and promiscuity of multidrug transporters in E. coli under lipophilic cation stress
10.3390/membranes12121264 · 2022 · External reference
Mycobacterium tuberculosis TlyA protein negatively regulates T helper (Th) 1 and Th17 differentiation and promotes tuberculosis pathogenesis
10.1074/jbc.m115.653600 · 2015 · External reference
An ANI gap within bacterial species that advances the definitions of intra-species units
10.1128/mbio.02696-23 · 2024 · External reference
Functional genomic insights into Floricoccus penangensis ML061-4 isolated from leaf surface of Assam tea
10.1038/s41598-025-86602-x · 2025 · External reference
Linear dicentric chromosomes in bacterial natural isolates reveal common constraints for replicon fusion
10.1128/mbio.01046-25 · 2025 · External reference
Hidden diversity of double-stranded DNA phages in symbiotic Rhizobium species
10.1098/rstb.2020.0468 · 2022 · External reference
Exploring bekasam, an indigenous fermented fish product of Indonesia: Original South Sumatra region
10.1186/s42779-024-00230-w · 2024 · External reference
Whole genome sequencing provides evidence for Bacillus velezensis SH-1471 as a beneficial rhizosphere bacterium in plants
10.1038/s41598-023-48171-9 · 2023 · External reference
Intestinal phages interact with bacteria and are involved in human diseases
10.1080/19490976.2022.2113717 · 2022 · External reference
Heat shock response and heat shock proteins: Current understanding and future opportunities in human diseases
10.3390/ijms25084209 · 2024 · External reference
Diverse and specialized metabolic capabilities of microbes in oligotrophic built environments
10.1186/s40168-024-01926-6 · 2024 · External reference
Probiotic potential of traditional and emerging microbial strains in functional foods: From characterization to applications and health benefits
10.3390/microorganisms13112521 · 2025 · External reference
Genomic insights into the genetic diversity, resistance determinants, and plasmid content of carbapenem-resistant Acinetobacter baumannii clinical isolates
10.1007/s00203-026-04736-6 · 2026 · External reference
Prokaryotic transposable elements
10.1002/9781394312467.ch2 · 2024 · External reference
Metabolic and transcriptomic-based characterization of Streptococcus salivarius ssp. Thermophilus snew fermentation in milk
2025 · External reference
Insights into ecology, pathogenesis, and biofilm formation of Enterococcus faecalis from functional genomics
10.1128/mmbr.00081-23 · 2025 · External reference
Global genomic landscapes of Lactiplantibacillus plantarum: Universal GABA biosynthetic capacity with strain-level functional diversity
2025 · External reference
Pan-genome analysis of Delftia tsuruhatensis reveals important traits concerning the genetic diversity, pathogenicity, and biotechnological properties of the species
10.1128/spectrum.02072-21 · 2022 · External reference
A large-scale comparative genomics study reveals niche-driven and within-sample intra-species functional diversification in Lacticaseibacillus rhamnosus
10.1016/j.foodres.2023.113446 · 2023 · External reference
Molecular and regulatory mechanisms of oxidative stress adaptation in Streptococcus mutans
10.1111/omi.12388 · 2023 · External reference
Role of lactic acid bacteria in food preservation and safety
2022 · External reference
Resilience mechanisms of rhizosphere microorganisms in lead-zinc tailings: Metagenomic insights into heavy metal resistance
10.1016/j.ecoenv.2025.117956 · 2025 · External reference
Foodborne microbial communities as potential reservoirs of antimicrobial resistance genes for pathogens: A critical review of the recent literature
10.3390/microorganisms11071696 · 2023 · External reference
