biolog phenotypic microarrays  (Biolog Inc)

Journal: Nature Communications

Article Title: Suppression of gut colonization by multidrug-resistant Escherichia coli clinical isolates through cooperative niche exclusion

doi: 10.1038/s41467-025-61327-7

Figure Lengend Snippet: A Results of competition assay in Biolog® Phenotypic microarray competitive index (CFU/ml E. coli MDR1/ CFU/ml E. coli MR102) and OD 600 of the respective strains of all carbon sources that both strains could utilize. One dot represents data from three independent experiments. B Results of competition assay in Biolog® Phenotypic microarray competitive index ( E. coli MDR1/ E. coli MR102) of all carbon sources that could be utilized by at least one of the strains. One dot represents data from three independent experiments. C Competition assay in MM9 supplemented with 5 g/L of the respective carbon source under aerobic and anaerobic conditions. P values indicate a nonparametric Kruskal-Wallis test * p < 0.05. Mean and SD with one dot representing data from one experiment performed in duplicates or triplicates. D Resulting fecal burden of E. coli MDR1 after different time points of colonization. Geometric mean and SD of two independent experiments with n = 8 (PBS), n = 9 (WT) and n = 10 ( ΔmanA and manA : :manA ) mice per group. E Commensal E. coli MR102 colonization levels at different time points. Geometric mean and SD of two independent experiments withof two independent experiments with n = 8 (PBS), n = 9 (WT) and n = 10 ( ΔmanA and manA : :manA ). F Clearance kinetics of E. coli MDR1 after different time points of colonization (clearance = CFU/g below the detection limit in feces). P -values represent the Log-rank (Mantel-Cox) test with 0.05, ** p < 0.01, *** p < 0.001, **** p < 0.0001.

Article Snippet: B Results of competition assay in Biolog® Phenotypic microarray competitive index ( E. coli MDR1/ E. coli MR102) of all carbon sources that could be utilized by at least one of the strains.

Techniques: Competitive Binding Assay, Microarray

Journal: mBio

Article Title: Physiological roles of an Acinetobacter -specific σ factor

doi: 10.1128/mbio.00968-25

Figure Lengend Snippet: SigAb mitigates and responds to copper stress. (A) Heatmap of heavy metal resistance genes significantly upregulated (log 2 FC > 1, FDR < 0.05, T = 10 min) in RNA-seq time course experiment of sigAb overexpression strain compared to empty vector control. Operons are denoted to the right, with arrows indicating the direction of transcription. (B) Growth curves plotted as OD 600 over time (h) of CRISPRi sigAb knockdown (KD) strain and non-targeting (NT) control in rich defined medium with 250 µg/mL CuSO 4 stress ( n = 3). Data are represented as mean ± s.d. for NT control with no stress (red), sigAb KD with no stress (blue), NT control with copper stress (green), and sigAb KD with copper stress (purple). (C) sigAb KD growth defects in metal stresses graphed as area under the curve normalized to NT control ( n = 2–9). Data are represented as the mean ± s.d., and significance was calculated with a two-tailed Student’s t -test ( P < 0.05). Bars without asterisks are not significantly different from the control. (D) SigAb induction curves plotted as P sigAb activity (mRFP fluorescence) versus cell density (OD 600 ) for metal and antibiotic stress conditions using Biolog Phenotype Microarray PM13.

Article Snippet: To expand our phenotyping to additional conditions (e.g., manganese, cobalt), we tested the growth of the sigAb knockdown in Biolog Phenotype Microarray (PM) plates ( ; ).

Techniques: RNA Sequencing, Over Expression, Plasmid Preparation, Control, Knockdown, Two Tailed Test, Activity Assay, Fluorescence, Microarray

Journal: Nature Communications

Article Title: Dietary carbohydrates alter immune-modulatory functionalities and DNA inversions in Bacteroides thetaiotaomicron

doi: 10.1038/s41467-025-60202-9

Figure Lengend Snippet: a Experimental design, conditioned media from carbon sources in which B. theta grew after 24 h was sterile filtered and introduced to SPF mice splenocytes. Five days later, cell population percentages were evaluated by flow cytometry analysis and IL-10 and IL-17 cytokine concentrations in the media were measured using ELISA. b , c Log2 fold change (compared to control, cells exposed to M9 minimal media and the relevant carbon source without any bacteria growing in it) of CD8 + Ki67 + PD1+ cell percentages of splenocytes exposed to conditioned media of B. theta grown on carbon sources from PM1 plate ( b ) and carbon sources from PM2A plate ( c ). d , e Log2 fold change (compared to control, cells exposed to M9 minimal media and the relevant carbon source without any bacteria growing in it) of IL-10 concentration in the media of splenocytes exposed to conditioned media of B. theta grown on carbon sources from PM1 plate ( d ) and carbon sources from PM2A plate ( e ). f , g Log2 fold change (compared to control, cells exposed to M9 minimal media and the relevant carbon source without any bacteria growing in it) of IL-17 concentration in the media of splenocytes exposed to conditioned media of B. theta grown on carbon sources from PM1 plate ( f ) and carbon sources from PM2A plate ( g ). h Heatmap representing the average log2 fold change value for each of the immune parameters examined (CD8 + Ki67 + PD1+ cell percentages, IL-10 and IL-17 concentrations). Z-score was calculated for each carbon source in each parameter. Carbon sources with |Z-score| ≥ 2 in each immune parameter were marked with #. b-g Each dot represents a biological repeat 3 ≤ n ≤ 10. b , c Kruskal–Wallis ANOVA, using Dunn’s multiple comparisons test, d , f , g Ordinary one-way ANOVA, using Tukey’s multiple comparisons test, e Brown-Forsythe and Welch ANOVA, using Dunnett’s T3 multiple comparisons test. Bars represent the mean. Error bars represent s.d. * P < 0.05 and ** P < 0.01, *** P < 0.001, **** P < 0.0001, all exact p -values are listed under “P-values” sheet in the Source Data file. Source data are provided as a Source Data file. Figure was created in BioRender. Geva-Zatorsky, N. (2025) https://BioRender.com/82criwi .

Article Snippet: To examine the suspected effects, B. theta was grown in M9 minimal media with 190 distinct carbon sources using PM1 and PM2A Biolog Phenotype MicroArraysTM plates for 24 h. Bacterial growth was assessed by both OD 600 measurements and colony-forming unit (CFU) counts (Supplementary Fig. ).

Techniques: Sterility, Flow Cytometry, Enzyme-linked Immunosorbent Assay, Control, Bacteria, Concentration Assay

Journal: Nature Communications

Article Title: Dietary carbohydrates alter immune-modulatory functionalities and DNA inversions in Bacteroides thetaiotaomicron

doi: 10.1038/s41467-025-60202-9

Figure Lengend Snippet: a , b Log2 fold change (compared to control, cells exposed to M9 minimal media and the relevant carbon source, boiled or not boiled, without any bacteria growing in it) of CD8 + Ki67 + PD1+ cell percentages of splenocytes exposed to conditioned media of B. theta grown on carbon sources from PM1 plate ( a ) and carbon sources from PM2A plate ( b ). Darker colors represent not boiled media, lighter colors represent boiled media. c , d Log2 fold change (compared to control, cells exposed to M9 minimal media and the relevant carbon source, boiled or not boiled, without any bacteria growing in it) of IL-10 concentrations in the media of splenocytes exposed to conditioned media of B. theta grown on carbon sources from PM1 plate ( c ) and carbon sources from PM2A plate ( d ). Darker colors represent not boiled media, lighter colors represent boiled media. Log2 fold change (compared to control, cells exposed to M9 minimal media and the relevant carbon source, boiled or not boiled, without any bacteria growing in it) of IL-17 concentrations in the media of splenocytes exposed to conditioned media of B. theta grown on carbon sources from PM1 plate ( e ) and carbon sources from PM2A plate ( f ). Darker colors represent not boiled media, lighter colors represent boiled media. a – f Each dot represents a biological repeat 6 ≤ n ≤ 9. Paired, tow tailed, t test for each couple of not boiled and boiled conditioned media. Bars represent the mean. Error bars represent s.d. * P < 0.05 and ** P < 0.01, *** P < 0.001, **** P < 0.0001, all exact p -values are listed under “P- values” sheet in the Source Data file. Source data are provided as a Source Data file.

Article Snippet: To examine the suspected effects, B. theta was grown in M9 minimal media with 190 distinct carbon sources using PM1 and PM2A Biolog Phenotype MicroArraysTM plates for 24 h. Bacterial growth was assessed by both OD 600 measurements and colony-forming unit (CFU) counts (Supplementary Fig. ).

Techniques: Control, Bacteria