Journal:

Article Title: Importance of the Endocarditis and Biofilm-associated Pilus ( ebp ) Locus in the Pathogenesis of Enterococcus faecalis Ascending Urinary Tract Infection

doi: 10.1086/517524

Figure Lengend Snippet: Mixed infection (competition assay) by w.t. E. faecalis OG1RF and nonpiliated TX5475 in the kidneys and urinary bladder of mice (n=16). Data are expressed as log10CFU of w.t. E. faecalis OG1RF or TX5475. The log10CFU/gm from both kidneys were combined and averaged. Solid diamonds and triangles represent w.t. E. faecalis OG1RF and TX5475, respectively, from kidney homogenates and empty diamonds and triangles represent w.t. E. faecalis OG1RF and TX5475, respectively, from urinary bladder homogenates. Horizontal bars represent geometric mean titer. Mean fold difference in CFU are given. Log10 CFU were compared for statistical significance using a paired t test.

Article Snippet: Bacterial strains and growth conditions Bacteria used in the study include wild type OG1RF (resistant to rifampicin 100 μg/ml, fusidic acid 25 μg/ml) (ATCC 47077), a well-known plasmid-free isolate used in many laboratories [ 13 ]; OG1RF is a medium biofilm producer [ 7 ] and has been shown to be pathogenic in various animal models [ 12 , 14 - 17 ].

Techniques: Infection, Competitive Binding Assay

Journal:

Article Title: Importance of the Endocarditis and Biofilm-associated Pilus ( ebp ) Locus in the Pathogenesis of Enterococcus faecalis Ascending Urinary Tract Infection

doi: 10.1086/517524

Figure Lengend Snippet: Tropism for the kidneys by E. faecalis strains OG1RF and its isogenic nonpiliated Δ ebpA (TX5475) mutant in a murine model of ascending urinary tract infection

Article Snippet: Bacterial strains and growth conditions Bacteria used in the study include wild type OG1RF (resistant to rifampicin 100 μg/ml, fusidic acid 25 μg/ml) (ATCC 47077), a well-known plasmid-free isolate used in many laboratories [ 13 ]; OG1RF is a medium biofilm producer [ 7 ] and has been shown to be pathogenic in various animal models [ 12 , 14 - 17 ].

Techniques: Mutagenesis, Infection

Journal:

Article Title: Importance of the Endocarditis and Biofilm-associated Pilus ( ebp ) Locus in the Pathogenesis of Enterococcus faecalis Ascending Urinary Tract Infection

doi: 10.1086/517524

Figure Lengend Snippet: Monoinfection (106, 105, 104, and 103 inocula) using w.t. E. faecalis OG1RF or nonpiliated TX5475 in the kidneys of mice (n=10). Data are expressed as log10CFU/gm of w.t. E. faecalis OG1RF or TX5475 recovered from kidney homogenates 48 hrs after transurethral challenge. The log10CFU from both kidneys were combined and averaged. Solid and empty triangles represent w.t. E. faecalis OG1RF and TX5475, respectively. Horizontal bars represent geometric mean titer. Mean difference in CFU is given as log10 ± standard deviation (SD) for the respective inocula. TX5475 CFUs (recovered from kidneys) were significantly reduced versus OG1RF with all four inocula using unpaired t test.

Article Snippet: Bacterial strains and growth conditions Bacteria used in the study include wild type OG1RF (resistant to rifampicin 100 μg/ml, fusidic acid 25 μg/ml) (ATCC 47077), a well-known plasmid-free isolate used in many laboratories [ 13 ]; OG1RF is a medium biofilm producer [ 7 ] and has been shown to be pathogenic in various animal models [ 12 , 14 - 17 ].

Techniques: Standard Deviation

Journal: Journal of Bacteriology

Article Title: Genome-wide analysis of Enterococcus faecalis genes that facilitate interspecies competition with Lactobacillus crispatus

doi: 10.1128/jb.00438-24

Figure Lengend Snippet: L. crispatus antagonizes the growth of enterococci. ( A ) Representative image of macro-colony biofilms on an MRS agar plate. ( B ) CFU recovered from E. faecalis OG1RF and L. crispatus VPI 3199 grown, respectively, either as single-species macro-colony biofilm or as dual-species ( E. faecalis + L. crispatus ) macro-colony biofilm for 24 h, 72 h, and 120 h post-incubation. ( C ) CFU recovered from selected E. faecalis and E. faecium strains, respectively, grown either as single-species macro-colony biofilm, or grown as dual-species macro-colony biofilms after 72 h incubation. ( D ) CFU recovered from E. faecalis OG1RF grown either as single-species macro-colony biofilm or grown respectively with selected L. crispatus strains as dual-species macro-colony biofilm after 72 h incubation. For B–D, data points represent 9–12 biological replicates, collated from at least three repeated experiments. Statistical analysis was performed using the Brown-Forsythe ANOVA test with Welch’s correction. Error bars represent standard error of the mean. * P ≤ 0.05, ** P ≤ 0.01, *** P ≤ 0.001, **** P ≤ 0.0001.

Article Snippet: E. faecalis strains , OG1RF parent strain (ATCC 47077) , Laboratory strain, Rif R , Fus R , ( ) .

Techniques: Incubation

Journal: Journal of Bacteriology

Article Title: Genome-wide analysis of Enterococcus faecalis genes that facilitate interspecies competition with Lactobacillus crispatus

doi: 10.1128/jb.00438-24

Figure Lengend Snippet: L. crispatus antagonism of E. faecalis is facilitated in a contact-independent manner. ( A ) CFU recovered from E. faecalis OG1RF and L. crispatus VPI 3199 grown statically for 72 h in MRS media as single-species biofilm, either in separate wells or in the same well separated by a Transwell membrane insert that prevents physical contact between cells. L. crispatus biofilm is grown on the flat surface of the well in the tissue culture plate, whereas E. faecalis biofilm is seeded on the surface of the Transwell membrane insert. The dotted line indicates the limit of detection (LOD), CFU < 42.5. ( B ) Representative images of spot antagonism assay showing growth inhibition of E. faecalis when L. crispatus macrocolony biofilms were established at the same time (T0), 24 h, 48 h, or 72 h before inoculating E. faecalis . CFU recovered from E. faecalis OG1RF growth after 24 h in MRS media mixed with 72 h cell-free biofilm supernatant isolated from single-species and dual-species biofilms at an equal ratio, either ( C ) pH-unadjusted or ( D ) adjusted to pH 6.5 to mirror the MRS media. For A, C, and D, data points represent 9–12 biological replicates, collated from at least three repeated experiments. Statistical analysis was performed using the Brown-Forsythe ANOVA test with Welch’s correction. Error bars represent the standard error of the mean. ** P ≤ 0.01, **** P ≤ 0.0001.

Article Snippet: E. faecalis strains , OG1RF parent strain (ATCC 47077) , Laboratory strain, Rif R , Fus R , ( ) .

Techniques: Membrane, Inhibition, Isolation

Journal: Journal of Bacteriology

Article Title: Genome-wide analysis of Enterococcus faecalis genes that facilitate interspecies competition with Lactobacillus crispatus

doi: 10.1128/jb.00438-24

Figure Lengend Snippet: L. crispatus antagonistic activity is enhanced in an aciduric environment. pH measurements from E. faecalis OG1RF and L. crispatus VPI 3199 grown statically between 24 and 120 h either as single-species biofilm or as dual-species ( E. faecalis + L. crispatus ) biofilm in MRS ( A ) or MRS supplemented with 300 mM MOPS buffer ( B ). Corresponding growth dynamics of E. faecalis ( C ) and L. crispatus ( D ) in MRS or MRS supplemented with 300 mM MOPS buffer. ( E ) CFU recovered from E. faecalis OG1RF and L. crispatus VPI 3199 grown, respectively, either as single-species macro-colony biofilm or as dual-species ( E. faecalis + L. crispatus ) macro-colony biofilm for 24 h, 72 h, and 120 h post-incubation in MRS agar supplemented with 300 mM MOPS. For A–D, data points represent 9–12 biological replicates, collated from at least three repeated experiments. For A and B, statistical analysis was performed using two-way ANOVA. For C and D, linear regression of the slope of the exponential growth phase was performed. For E, statistical analysis was performed using the Brown-Forsythe ANOVA test with Welch’s correction. Error bars represent the standard error of the mean. * P ≤ 0.05, ** P ≤ 0.01, *** P ≤ 0.001, **** P ≤ 0.0001.

Article Snippet: E. faecalis strains , OG1RF parent strain (ATCC 47077) , Laboratory strain, Rif R , Fus R , ( ) .

Techniques: Activity Assay, Incubation

Journal: Journal of Bacteriology

Article Title: Genome-wide analysis of Enterococcus faecalis genes that facilitate interspecies competition with Lactobacillus crispatus

doi: 10.1128/jb.00438-24

Figure Lengend Snippet: Select list of the most differentially expressed genes during co-culture with L. crispatus relative to E. faecalis single-species control

Article Snippet: E. faecalis strains , OG1RF parent strain (ATCC 47077) , Laboratory strain, Rif R , Fus R , ( ) .

Techniques: Binding Assay, Modification

Journal: Journal of Bacteriology

Article Title: Genome-wide analysis of Enterococcus faecalis genes that facilitate interspecies competition with Lactobacillus crispatus

doi: 10.1128/jb.00438-24

Figure Lengend Snippet: Selected list of differentially abundant E. faecalis transposon mutants during co-culture with L. crispatus relative to E. faecalis single-species counterpart

Article Snippet: E. faecalis strains , OG1RF parent strain (ATCC 47077) , Laboratory strain, Rif R , Fus R , ( ) .

Techniques:

Journal: Journal of Bacteriology

Article Title: Genome-wide analysis of Enterococcus faecalis genes that facilitate interspecies competition with Lactobacillus crispatus

doi: 10.1128/jb.00438-24

Figure Lengend Snippet: E. faecalis genes contribute to tolerance against L. crispatus antagonism. CFU recovered from E. faecalis OG1RF, its isogenic transposon mutants, and L. crispatus VPI 3199 grown, respectively, either as single-species macro-colony biofilm or as dual-species ( E. faecalis +L. crispatus ) macro-colony biofilm ( A and B ) for 72 h. CFU recovered from E. faecalis OG1RF, its isogenic LDH deletion, and complementation mutants, as well as L. crispatus VPI 3199 grown respectively either as single-species macro-colony biofilm or as dual-species ( E. faecalis +L. crispatus ) macro-colony biofilm ( C and D ) for 72 h. Data points represent 9–12 biological replicates, collated from at least three repeated experiments. Statistical analysis was performed using the Brown-Forsythe ANOVA test with Welch’s correction. Error bars represent the standard error of the mean. * P ≤ 0.05, ** P ≤ 0.01, *** P ≤ 0.001, **** P ≤ 0.0001.

Article Snippet: E. faecalis strains , OG1RF parent strain (ATCC 47077) , Laboratory strain, Rif R , Fus R , ( ) .

Techniques:

Journal: Journal of Bacteriology

Article Title: Genome-wide analysis of Enterococcus faecalis genes that facilitate interspecies competition with Lactobacillus crispatus

doi: 10.1128/jb.00438-24

Figure Lengend Snippet: Loss of ldh1 restores virulence of E. faecalis in a co-infection model of Galleria larvae. Percentage survival of G. mellonella larvae 72 h post-injection with either single-species controls; E. faecalis OG1RF or L. crispatus, and their heat-killed counterparts ( A ), or co-injected with both ( B ). Percentage survival of G. mellonella larvae 72 h post-injection with E. faecalis OG1RF parent strain and its isogenic LDH deletion and complementation strains alone ( C ), or their corresponding co-injected counterparts ( D ). In each Galleria infection experiment, 20 larvae were infected with one biological replicate of E. faecalis inoculant, with a total of three replicates per experiment. Data points represent 9 biological replicates of E. faecalis inoculum, repeated thrice ( n = 3) on non-consecutive days. Each curve represents a group of 180 larvae, individually injected with 10 5 CFUs of E. faecalis suspended in PBS at a final volume of 5 µL. Statistical analysis was performed using the log-rank (Mantel-Cox) test. **** P ≤ 0.0001.

Article Snippet: E. faecalis strains , OG1RF parent strain (ATCC 47077) , Laboratory strain, Rif R , Fus R , ( ) .

Techniques: Infection, Injection

Journal: Journal of Bacteriology

Article Title: Genome-wide analysis of Enterococcus faecalis genes that facilitate interspecies competition with Lactobacillus crispatus

doi: 10.1128/jb.00438-24

Figure Lengend Snippet: Strains used in this study

Article Snippet: E. faecalis strains , OG1RF parent strain (ATCC 47077) , Laboratory strain, Rif R , Fus R , ( ) .

Techniques: Isolation

Journal: BMC Microbiology

Article Title: Comparative genomics of Enterococcus spp. isolated from bovine feces

doi: 10.1186/s12866-017-0962-1

Figure Lengend Snippet: Genome characteristics of Enterococcus spp. isolated from bovine feces

Article Snippet: The 27 compete genomes from NCBI included: E. hirae (2 strains; ATCC 9790, R17), E. faecium (13 strains; Aus0004, Aus0085, T110, 6E6, VRE001, E1, E745, E39, UW8175, NRRL B2354, ATCC 700221, EFE10021), E. faecalis (9 strains; LD33, L12, KB1, 62, D32, V583, DENG1, OG1RF, ATCC 29212), E. durans (1 strain; KLDS6_0933), E. gallinarum (1 strain; FDAARGOS163), and E. casseliflavus (1 strain; EC20).

Techniques: Isolation

Journal: BMC Microbiology

Article Title: Comparative genomics of Enterococcus spp. isolated from bovine feces

doi: 10.1186/s12866-017-0962-1

Figure Lengend Snippet: Phylogenetic tree constructed based on analysis of single-nucleotide polymorphisms (SNPs) of the core genes of 48 entercocci genomes, including the 21 isolates obtained from bovine feces in the present study. Entercoccus faecalis , Entercoccus faecium , Enterococcus hirae , Entercoccus durans , Entercoccus casseliflavus and Entercoccus gallinarum were compared using E. faecium strain T110 as a reference

Article Snippet: The 27 compete genomes from NCBI included: E. hirae (2 strains; ATCC 9790, R17), E. faecium (13 strains; Aus0004, Aus0085, T110, 6E6, VRE001, E1, E745, E39, UW8175, NRRL B2354, ATCC 700221, EFE10021), E. faecalis (9 strains; LD33, L12, KB1, 62, D32, V583, DENG1, OG1RF, ATCC 29212), E. durans (1 strain; KLDS6_0933), E. gallinarum (1 strain; FDAARGOS163), and E. casseliflavus (1 strain; EC20).

Techniques: Construct

Journal: BMC Microbiology

Article Title: Comparative genomics of Enterococcus spp. isolated from bovine feces

doi: 10.1186/s12866-017-0962-1

Figure Lengend Snippet: Antibiotic resistance gene profile of Enterococcus spp. isolated from bovine feces. Values represent % pairwise identity

Article Snippet: The 27 compete genomes from NCBI included: E. hirae (2 strains; ATCC 9790, R17), E. faecium (13 strains; Aus0004, Aus0085, T110, 6E6, VRE001, E1, E745, E39, UW8175, NRRL B2354, ATCC 700221, EFE10021), E. faecalis (9 strains; LD33, L12, KB1, 62, D32, V583, DENG1, OG1RF, ATCC 29212), E. durans (1 strain; KLDS6_0933), E. gallinarum (1 strain; FDAARGOS163), and E. casseliflavus (1 strain; EC20).

Techniques: Isolation

Journal: Cell reports

Article Title: The Toll Signaling Pathway Targets the Insulin-like Peptide Dilp6 to Inhibit Growth in Drosophila.

doi: 10.1016/j.celrep.2019.07.015

Figure Lengend Snippet: Figure 2. Toll Signaling in Fat Body Reduces Dilp6 Transcripts and Larval Body Weight in Parallel (A) Drs, IM2, and Dilp6 transcripts in control and Enterococcus faecalis-infected late third-instar Dilp6HF larvae. n = 7–8 larvae/group. ***p % 0.0004, ****p < 0.0001 versus uninfected. (B–D) Dilp6 transcripts in wandering third-instar fat bodies expressing (B) Toll10b, (C) Dif, or (D) dorsal using r4-GAL4; n = 7–8 samples per genotype. **p % 0.0044, ***p = 0.0007 versus GFP. (E) Dilp6 mRNA measured in whole larvae or white prepupae (WPP) expressing GFP (black) or Toll10b

Article Snippet: Larvae were infected with the Gram-positive bacteria Enterococcus faecalis (strain OG1RF, ATCC 47077), grown in brain heart infusion media with rifampicin, and concentrated to OD600 10.0 in PBS, a dose shown to strongly activate Toll signaling in adult flies (Issa et al., 2018).

Techniques: Control, Infection, Expressing

Journal: bioRxiv

Article Title: Hidden Diversity in Enterococcus faecalis Revealed by CRISPR2 Screening: Eco-evolutionary Insights into a Novel Subspecies

doi: 10.1101/2025.05.05.652174

Figure Lengend Snippet: Phylogenetic trees were inferred using FastME 2.1.6.1 from GBDP distances calculated from genome sequences. Branch lengths are scaled according to the GBDP distance formula d5. The numbers above branches represent GBDP pseudo-bootstrap support values > 60% from 100 replications. The trees were midpoint-rooted. The taxonomic classifications at the species and subspecies levels are represented by color codes on the right side of each tree, based on the dDDH values obtained and the established thresholds (≥70% dDDH for species and ≥79% dDDH for subspecies) ( A ) Whole-genome sequence-based phylogeny of Enterococcus faecalis 209EA1 (representative strain of the genetically related group of E. faecalis lacking CRISPR2) and its closest related type-strains, as determined by TYGS by default. ( B ) Phylogeny focused exclusively on query genomes, encompassing all 16 E. faecalis strains lacking CRISPR2 along with E. faecalis reference strains, including the type strain ATCC 19433. Sequence types (STs) of each strain are shown in parentheses. * Type strain of a proposed species with nomenclatural status not yet validly published.

Article Snippet: This dataset included 55 E. faecalis genomes representing the species’ genetic diversity within the scope of this study, four well-characterized E. faecalis reference genomes (OG1RF, V583, T5), including the type strain (ATCC 19433 = NBRC 100480), 58 genomes representing other validly published Enterococcus species (as of June 13, 2024), and the Vagococcus fluvialis DSM 5731 genome as an outgroup.

Techniques: Sequencing

Journal: bioRxiv

Article Title: Hidden Diversity in Enterococcus faecalis Revealed by CRISPR2 Screening: Eco-evolutionary Insights into a Novel Subspecies

doi: 10.1101/2025.05.05.652174

Figure Lengend Snippet: The tree was estimated using IQ-TREE under the LG+F+I+R9 substitution model with 1,000 bootstrap replicates, based on the concatenation and alignment of 751 protein sequences corresponding to single-copy orthologs present in 95.8% of the 117 sampled enterococci and the outgroup strain Vagococcus fluvialis DSM 5731. The tree is presented at different scales. The global phylogeny on the left shows relationships between taxonomic species, with E. faecalis strains collapsed into their respective subspecies clades, which are highlighted by colored regions enclosed in a dashed rectangle. On the right, the E. faecalis clade is detailed at a fine scale, highlighting subspecies clusters (subspecies A in light orange and subspecies B in light teal). Red dots represent type strains; blue dots indicate E. faecalis model strains V583 and OG1RF; the black dot marks the E. faecalis reference genome from the NCBI datasets. Stars denote nodes with bootstrap support < 95%.

Article Snippet: This dataset included 55 E. faecalis genomes representing the species’ genetic diversity within the scope of this study, four well-characterized E. faecalis reference genomes (OG1RF, V583, T5), including the type strain (ATCC 19433 = NBRC 100480), 58 genomes representing other validly published Enterococcus species (as of June 13, 2024), and the Vagococcus fluvialis DSM 5731 genome as an outgroup.

Techniques: