Journal: Nature Communications

Article Title: Vancomycin-resistant enterococci utilise antibiotic-enriched nutrients for intestinal colonisation

doi: 10.1038/s41467-025-61731-z

Figure Lengend Snippet: a Heatmap illustrating the log2 fold change (antibiotic-treated relative to water-treated) in bacterial taxa that were significantly decreased (shown in blue) or increased (shown in red) in faecal cultures following treatment with antibiotics that promote VRE intestinal colonisation. Taxa not significantly changed with antibiotic treatment were not plotted (shown in white). n = 12 human faecal donors, Wilcoxon signed rank test (two-sided) of log-transformed abundances with Benjamini-Hochberg false discovery rate (FDR) correction, p < 0.05. b Heatmap illustrating the log2 fold change (antibiotic-treated relative to water-treated) in nutrients and metabolites that were significantly decreased (shown in blue) or increased (shown in red) in faecal cultures following treatment with antibiotics that promote VRE intestinal colonisation. Nutrients and metabolites not significantly changed with antibiotic treatment were not plotted (shown in white). n = 12 human faecal donors, Wilcoxon signed rank test (two-sided) with Benjamini-Hochberg FDR correction, p < 0.05. c , d Antibiotic treatment significantly promoted the growth of vancomycin-resistant E. faecium (NCTC 12202) and E. faecalis (NCTC 12201) in faecal microbiomes. E. faecium or E. faecalis were spiked into faecal cultures at 10 3 CFU/ml (horizontal dashed line). Number of human faecal donors used in ( c ): Faeces + H 2 O n = 8, Faeces + MTZ n = 5, Faeces + CLI n = 5, Faeces + VAN n = 6, Faeces + CRO n = 8, No faeces control n = 6. Number of human faecal donors used in ( d ): Faeces + H 2 O n = 8, Faeces + MTZ n = 5, Faeces + CLI n = 5, Faeces + VAN n = 7, Faeces + CRO n = 7, No faeces control n = 6. Antibiotic-treated faecal culture counts (shown in red) were compared to water-treated faecal culture counts (shown in blue) using a mixed effects model (one-way) of log transformed CFU/ml with Dunnett’s multiple comparison. No faeces counts (shown in grey) were compared to water-treated faecal culture counts (shown in blue) using an unpaired t-test (two-sided) of log transformed CFU/ml. Data shown as mean ± SD. ** = P ≤ 0.01, *** = P ≤ 0.001, **** = P ≤ 0.0001. MTZ metronidazole, CLI clindamycin, VAN vancomycin, CRO ceftriaxone, TZP piperacillin/tazobactam.

Article Snippet: Vancomycin-resistant E. faecium (DSM 25698) and vancomycin-resistant E. faecalis (DSM 116626) were purchased from the Leibniz Institute DSMZ.

Techniques: Transformation Assay, Control, Comparison

Journal: Nature Communications

Article Title: Vancomycin-resistant enterococci utilise antibiotic-enriched nutrients for intestinal colonisation

doi: 10.1038/s41467-025-61731-z

Figure Lengend Snippet: a Nutrients that were increased in the faeces of VAN-treated mice (shown in red) compared to H 2 O-treated mice (shown in blue). b Metabolites that were decreased in the faeces of VAN-treated mice (shown in red) compared to H 2 O-treated mice (shown in blue). a , b comparison of nutrients and metabolites in the VAN-treated faeces to the H 2 O-treated faeces used an unpaired t-test (two-sided) with Benjamini-Hochberg FDR, n = 5 mice per group from one independent experiment, with data shown as mean ± SD. c Vancomycin-resistant E. faecium (NCTC 12202) counts were high in the faeces from vancomycin-treated mice (shown in red) and nearly undetectable in the faeces of water-treated mice (shown in blue). Comparisons of the E. faecium plate counts were made using a Mann–Whitney U test (two-sided) of log10-transformed counts. n = 5 mice per group from one independent experiment, with data shown as medians ± IQR. * = P ≤ 0.05, ** = P ≤ 0.01, *** = P ≤ 0.001. VAN vancomycin, H 2 O water, LOD limit of detection.

Article Snippet: Vancomycin-resistant E. faecium (DSM 25698) and vancomycin-resistant E. faecalis (DSM 116626) were purchased from the Leibniz Institute DSMZ.

Techniques: Comparison, MANN-WHITNEY, Transformation Assay

Journal: Nature Communications

Article Title: Vancomycin-resistant enterococci utilise antibiotic-enriched nutrients for intestinal colonisation

doi: 10.1038/s41467-025-61731-z

Figure Lengend Snippet: Vancomycin-resistant E. faecium and vancomycin-resistant E. faecalis strains were grown in tryptic soy broth (pH 6) supplemented with an individual metabolite at low, average or high concentrations measured in healthy human faeces, concentrations spanning a defined range (4–128 mM), or unsupplemented (no metabolite control). Cultures were incubated under anaerobic conditions overnight. Growth was measured in 14 replicates in two independent experiments for NCTC 12202 and NCTC 12201, and growth was measured in 10 replicates in two independent experiments for NCTC 12204, DSM 25698, NCTC 13779, and DSM 116626. Kruskal-Wallis test with Dunn’s multiple comparison test (each metabolite was compared to the no metabolite control). * = P ≤ 0.05, ** = P ≤ 0.01, *** = P ≤ 0.001, **** = P ≤ 0.0001. Data are presented as medians ± IQR. Growth of E. faecium or E. faecalis without metabolites shown in grey. Growth of E. faecium strains with supplemented metabolites shown in shades of blue. Growth of E. faecalis strains with supplemented metabolites shown in shades of green. Optical density at 600 nm, OD 600 .

Article Snippet: Vancomycin-resistant E. faecium (DSM 25698) and vancomycin-resistant E. faecalis (DSM 116626) were purchased from the Leibniz Institute DSMZ.

Techniques: Control, Incubation, Comparison

Journal: Nature Communications

Article Title: Vancomycin-resistant enterococci utilise antibiotic-enriched nutrients for intestinal colonisation

doi: 10.1038/s41467-025-61731-z

Figure Lengend Snippet: Vancomycin-resistant E. faecium and vancomycin-resistant E. faecalis strains were grown in tryptic soy broth supplemented with a mixture of propionate, butyrate, and valerate (PBV) or a mixture of acetate, propionate, butyrate, and valerate (APBV) at concentrations mimicking the high concentrations measured in human faeces, or unsupplemented (No metabolites control). Broth was adjusted to pH 6, 6.5, or 7 to mimic the pH of the healthy large intestine, and cultures were incubated under anaerobic conditions overnight. Data shown as medians ± IQR, with 12 replicates from 3 independent experiments. Kruskal-Wallis with Dunn’s multiple comparison test comparing the no metabolites control to each metabolite mixture at the same pH. * P ≤ 0.05, ** = P ≤ 0.01, *** = P ≤ 0.001, **** = P ≤ 0.0001. OD 600 optical density at 600 nm.

Article Snippet: Vancomycin-resistant E. faecium (DSM 25698) and vancomycin-resistant E. faecalis (DSM 116626) were purchased from the Leibniz Institute DSMZ.

Techniques: Control, Incubation, Comparison

Journal: Nature Communications

Article Title: Vancomycin-resistant enterococci utilise antibiotic-enriched nutrients for intestinal colonisation

doi: 10.1038/s41467-025-61731-z

Figure Lengend Snippet: AMiGA-predicted growth curves for vancomycin-resistant E. faecium and vancomycin-resistant E. faecalis strains cultured in minimal medium supplemented with a mixture of nutrients under anaerobic or aerobic conditions. The bold lines show the predicted mean of growth while the shaded bands show the predicted 95% credible intervals. n = 6 replicates in two independent experiments. OD optical density.

Article Snippet: Vancomycin-resistant E. faecium (DSM 25698) and vancomycin-resistant E. faecalis (DSM 116626) were purchased from the Leibniz Institute DSMZ.

Techniques: Cell Culture

Journal: Nature Communications

Article Title: Vancomycin-resistant enterococci utilise antibiotic-enriched nutrients for intestinal colonisation

doi: 10.1038/s41467-025-61731-z

Figure Lengend Snippet: Minimal medium was supplemented with a mixture of nutrients that were increased with antibiotics and inoculated with either fresh healthy human faeces ( n = 3 donors for 9 replicates from 3 independent experiments, shown in brown), a single VRE strain ( E. faecium NCTC 12202 shown in blue or E. faecalis NCTC 12201 shown in green; n = 9 replicates from 3 independent experiments), or left uninoculated (shown in grey, n = 9 replicates from 3 independent experiments). Spent supernatants were filter sterilised and then inoculated with ( a ) E. faecium NCTC 12202 or ( b ) E. faecalis NCTC 12201. As a control, spent supernatants were also supplemented with 0.5% glucose to confirm nutrient depletion. VRE growth was measured after overnight incubation using plate counts. a , b comparisons between growth in the spent supernatants and fresh medium were assessed using a Kruskal-Wallis with Dunn’s multiple comparison test, and comparisons of unsupplemented vs glucose-supplemented supernatants was assessed through a Wilcoxon signed rank test (two-sided). ** = P ≤ 0.01, *** = P ≤ 0.001, **** = P ≤ 0.0001. Data are presented as medians ± IQR.

Article Snippet: Vancomycin-resistant E. faecium (DSM 25698) and vancomycin-resistant E. faecalis (DSM 116626) were purchased from the Leibniz Institute DSMZ.

Techniques: Control, Incubation, Comparison

Journal: Nature Communications

Article Title: Vancomycin-resistant enterococci utilise antibiotic-enriched nutrients for intestinal colonisation

doi: 10.1038/s41467-025-61731-z

Figure Lengend Snippet: AMiGA-predicted growth curves for vancomycin-resistant E. faecium and vancomycin-resistant E. faecalis strains cultured in minimal medium supplemented with single carbon sources under anaerobic or aerobic conditions. The bold lines show the predicted mean of growth while the shaded bands show the predicted 95% credible intervals. n = 6 replicates in 2–3 independent experiments. OD optical density.

Article Snippet: Vancomycin-resistant E. faecium (DSM 25698) and vancomycin-resistant E. faecalis (DSM 116626) were purchased from the Leibniz Institute DSMZ.

Techniques: Cell Culture

Journal: Nature Communications

Article Title: Vancomycin-resistant enterococci utilise antibiotic-enriched nutrients for intestinal colonisation

doi: 10.1038/s41467-025-61731-z

Figure Lengend Snippet: AMiGA-predicted growth curves for vancomycin-resistant E. faecium and vancomycin-resistant E. faecalis strains cultured in minimal medium supplemented with a mixture of all nitrogen sources (all nitrogen sources), a leave-one-out mixture lacking a single nitrogen source, or lacking all nitrogen sources (no nitrogen sources) under anaerobic or aerobic conditions. The bold lines show the predicted mean of growth while the shaded bands show the predicted 95% credible intervals. n = 6 replicates in 2–3 independent experiments. OD optical density.

Article Snippet: Vancomycin-resistant E. faecium (DSM 25698) and vancomycin-resistant E. faecalis (DSM 116626) were purchased from the Leibniz Institute DSMZ.

Techniques: Cell Culture

Journal: Nature Communications

Article Title: Vancomycin-resistant enterococci utilise antibiotic-enriched nutrients for intestinal colonisation

doi: 10.1038/s41467-025-61731-z

Figure Lengend Snippet: Percentage of nutrients remaining in vancomycin-resistant E. faecium (NCTC 12202) and E. faecalis (NCTC 12201) cultures grown in a minimal medium supplemented with a mixture of nutrients, under aerobic or anaerobic conditions. 1 H-NMR spectroscopy peak integrations were used to measure nutrient concentrations. Comparisons were made using a two-way mixed ANOVA followed by pairwise comparisons with Bonferroni correction. n = 3 replicates per group, with data shown as mean ± SD. * = P ≤ 0.05, ** = P ≤ 0.01, *** = P ≤ 0.001, **** = P ≤ 0.0001.

Article Snippet: Vancomycin-resistant E. faecium (DSM 25698) and vancomycin-resistant E. faecalis (DSM 116626) were purchased from the Leibniz Institute DSMZ.

Techniques: Structural Proteomics

Journal: Nature Communications

Article Title: Vancomycin-resistant enterococci utilise antibiotic-enriched nutrients for intestinal colonisation

doi: 10.1038/s41467-025-61731-z

Figure Lengend Snippet: a E. faecium (NCTC 12202) and E. faecalis (NCTC 12201) were co-cultured in a minimal medium supplemented with a mixture of nutrients that were enriched in antibiotic-treated faecal microbiomes. Monoculture growth shown in grey. E. faecium growth when co-cultured with E. faecalis shown in green. E. faecalis growth when co-cultured with E. faecium shown in blue. b E. faecium (NCTC 12202) or E. faecalis (NCTC 12201) were co-cultured with K. pneumoniae , E. coli , or E. hormaechei in a minimal medium supplemented with a mixture of nutrients that were enriched in antibiotic-treated faecal microbiomes. Monoculture growth shown in grey. E. faecium or E. faecalis growth when co-cultured with K. pneumoniae shown in red, with E. coli shown in orange, and with E. hormaechei shown in yellow. K. pneumoniae , E. coli , or E. hormaechei growth when co-cultured with E. faecium shown in blue, and with E. faecalis shown in green. For panels a and b, each strain was inoculated into the minimal media at a concentration of 10 3 CFU/ml (represented as the grey dashed line) and the cultures were incubated for 24 h under anaerobic conditions. Samples were plated on Brilliance VRE plates to quantify E. faecium or E. faecalis growth and on Brilliance CRE plates to quantify K. pneumoniae , E. coli , or E. hormaechei growth. Growth of each isolate was measured with 6 replicates in two independent experiments. Comparison of E. faecium and E. faecalis monoculture growth to co-culture growth was made using an unpaired t-test (two-sided). Comparison of VRE strain and CRE strain monoculture growth to co-culture growth was made using a one-way ANOVA with Dunnett’s multiple comparison test. * = P ≤ 0.05, ** = P ≤ 0.01, *** = P ≤ 0.001, **** = P ≤ 0.0001. Data are presented as mean values ± SD.

Article Snippet: Vancomycin-resistant E. faecium (DSM 25698) and vancomycin-resistant E. faecalis (DSM 116626) were purchased from the Leibniz Institute DSMZ.

Techniques: Cell Culture, Concentration Assay, Incubation, Comparison, Co-Culture Assay