Journal: PLoS Pathogens

Article Title: Enhanced in planta Fitness through Adaptive Mutations in EfpR, a Dual Regulator of Virulence and Metabolic Functions in the Plant Pathogen Ralstonia solanacearum

doi: 10.1371/journal.ppat.1006044

Figure Lengend Snippet: Phenotype Microarray data were collected over 82.5 hours at a temperature of 28°C on the Biolog plates PM01, PM02 and PM03. The respective curves from all six strains are superimposed. The x-axes show the measurement times in hours, the y-axes the curve heights in OmniLog units. In the caption of each panel the corresponding coordinate of the well is shown followed by the (A) carbon or (B) nitrogen source tested. Three replicates were performed. Data were treated with the R package opm.

Article Snippet: The environmental conditions tested correspond to the Biolog phenotype microarray environments PM01 and PM02.

Techniques: Microarray

Journal: Frontiers in Microbiology

Article Title: Levilactobacillus brevis , autochthonous to cucumber fermentation, is unable to utilize citric acid and encodes for a putative 1,2-propanediol utilization microcompartment

doi: 10.3389/fmicb.2023.1210190

Figure Lengend Snippet: Commonly used substrates by Lvb. brevis isolates. Carbohydrates utilized by all four Levilactobacillus brevis isolates included in the comparative genomic analysis, including 7.8.43 ( ), 14.2.10 ( ), 30.2.29 ( ), and 3.2.41 ( ), as determined by the PM01 (A) and PM02 (B) plates of the Omnilog for phenotype microarray.

Article Snippet: Four autochthonous Lvb. brevis (14.2.10, 30.2.29, 7.8.43, and 3.2.41) and two allochthonous isolates, ATCC14869 (type strain) and ATCC367, were used for phenotype microarray (PM) analysis using the PM01 and PM02 plates of the Omnilog system (Biolog, Hayward, CA) following the manufacturer's instructions.

Techniques: Microarray

Journal: Frontiers in Microbiology

Article Title: Levilactobacillus brevis , autochthonous to cucumber fermentation, is unable to utilize citric acid and encodes for a putative 1,2-propanediol utilization microcompartment

doi: 10.3389/fmicb.2023.1210190

Figure Lengend Snippet: Substrates utilized by selected Lvb. brevis . Carbohydrates utilized by 2 or 3 Levilactobacillus brevis isolates included in the comparative genomic analysis, including 7.8.43 ( ), 14.2.10 ( ), 30.2.29 ( ), and 3.2.41 ( ), as determined by the PM01 and PM02 plates of the Omnilog for phenotype microarray.

Article Snippet: Four autochthonous Lvb. brevis (14.2.10, 30.2.29, 7.8.43, and 3.2.41) and two allochthonous isolates, ATCC14869 (type strain) and ATCC367, were used for phenotype microarray (PM) analysis using the PM01 and PM02 plates of the Omnilog system (Biolog, Hayward, CA) following the manufacturer's instructions.

Techniques: Microarray

Journal: Frontiers in Microbiology

Article Title: Levilactobacillus brevis , autochthonous to cucumber fermentation, is unable to utilize citric acid and encodes for a putative 1,2-propanediol utilization microcompartment

doi: 10.3389/fmicb.2023.1210190

Figure Lengend Snippet: Carbon sources utilized by single Levilactobacillus brevis as determined by the PM01 and P02 plates of the Omnilog.

Article Snippet: Four autochthonous Lvb. brevis (14.2.10, 30.2.29, 7.8.43, and 3.2.41) and two allochthonous isolates, ATCC14869 (type strain) and ATCC367, were used for phenotype microarray (PM) analysis using the PM01 and PM02 plates of the Omnilog system (Biolog, Hayward, CA) following the manufacturer's instructions.

Techniques: Standard Deviation, Negative Control

Journal: Nature Communications

Article Title: Cross-protection and cross-feeding between Klebsiella pneumoniae and Acinetobacter baumannii promotes their co-existence

doi: 10.1038/s41467-023-36252-2

Figure Lengend Snippet: a Carbon-source utilisation activity calculated by AUC of AB6870155 (inner ring) and KP6870155 (outer ring) based on PM01-02 Biolog Phenotype Microarrays. b Venn diagram of C-source utilisation from phenome data showing overlap between AB6870155 and KP6870155. c Schematic of cross-feeding experiment utilising Millicell culture inserts (Merck). d Growth of AB6870155 in Millicell plates with minimal media and select compounds (glycerol, mannose, galactose, serine, maltose, sucrose) provided as the sole carbon source in the presence (denoted as AB + KP) and absence of KP6870155 (denoted as AB) ( n = 3 independent bacterial cultures). Data are presented as mean values + /− SD. Source data are provided as a Source Data file.

Article Snippet: Fig. 3 Carbon source utilisation and cross-feeding between A. baumannii AB6870155 and K. pneumoniae KP6870155. a Carbon-source utilisation activity calculated by AUC of AB6870155 (inner ring) and KP6870155 (outer ring) based on PM01-02 Biolog Phenotype Microarrays. b Venn diagram of C-source utilisation from phenome data showing overlap between AB6870155 and KP6870155. c Schematic of cross-feeding experiment utilising Millicell culture inserts (Merck). d Growth of AB6870155 in Millicell plates with minimal media and select compounds (glycerol, mannose, galactose, serine, maltose, sucrose) provided as the sole carbon source in the presence (denoted as AB + KP) and absence of KP6870155 (denoted as AB) ( n = 3 independent bacterial cultures).

Techniques: Activity Assay

Journal: Nature Communications

Article Title: Cross-protection and cross-feeding between Klebsiella pneumoniae and Acinetobacter baumannii promotes their co-existence

doi: 10.1038/s41467-023-36252-2

Figure Lengend Snippet: a Antibiotic cross-protection assay in 512 μg/mL cefotaxime. A + K denotes AB6870155 and KP6870155 co-cultures at a 30:70 ratio respectively. Inset of MacConkey agar plate shows KP (KP6870155) colonies appearing red due to K. pneumoniae β-galactosidase activity; AB (AB6870155) lacks this enzyme and appears as white colonies. b Growth of K. pneumoniae KP6870155 in cefotaxime only (+ CEF) and cefotaxime + sulbactam (+ CEF:SUL at 2:1) as measured by optical density (OD 600 ). “KP only” represents K. pneumoniae KP6870155 grown in wells without sharing media with A. baumannii AB6870155 while “KP ( + AB insert)” represents KP6870155 physically separated from AB6870155 via a Millicell hanging insert and able to share media ( n = 3). Data are presented as mean values + /− SEM. Significance was measured by paired Student’s t -test (two-tailed) where *represents a p < 0.05 ( p = 0.03) and ns (not significant) represents a p > 0.05. c Kaplan–Meier curves of single injected AB6870155 (AB) and KP6870155 (KP) and co-injected (A + K) at a 1:1 ratio in G. mellonella ( p -value based on log-rank test); PBS only controls had 100% survival (overlap with AB curve). d schematic representation created with BioRender and ChemDraw (v22.0.0) of A. baumannii AB6870155 and K. pneumoniae KP6870155 interactions. Source data are provided as a Source Data file.

Article Snippet: Fig. 3 Carbon source utilisation and cross-feeding between A. baumannii AB6870155 and K. pneumoniae KP6870155. a Carbon-source utilisation activity calculated by AUC of AB6870155 (inner ring) and KP6870155 (outer ring) based on PM01-02 Biolog Phenotype Microarrays. b Venn diagram of C-source utilisation from phenome data showing overlap between AB6870155 and KP6870155. c Schematic of cross-feeding experiment utilising Millicell culture inserts (Merck). d Growth of AB6870155 in Millicell plates with minimal media and select compounds (glycerol, mannose, galactose, serine, maltose, sucrose) provided as the sole carbon source in the presence (denoted as AB + KP) and absence of KP6870155 (denoted as AB) ( n = 3 independent bacterial cultures).

Techniques: Activity Assay, Two Tailed Test, Injection