Computational protocol: Rhizobium leguminosarum bv. viciae 3841 Adapts to 2,4-Dichlorophenoxyacetic Acid with “Auxin-Like” Morphological Changes, Cell Envelope Remodeling and Upregulation of Central Metabolic Pathways

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Protocol publication

[…] GC-MS spectra were converted to net-CDF files, peaks detected and compounds identified (Metabolite detector software tool []). Retention indices were calibrated using alkane standards (C10-C30), and identified metabolites were batch quantified and exported. Metabolites found in at least 60% of the replicates were subsequently analyzed, with remaining missing values imputed by k-means nearest neighbor (KNN) []. Data were normalized by median fold change, centered and unit-variance scaled for multivariate statistical analysis (Simca-P 12, Umetrics). General clustering trends and metabolite differences were assessed with unsupervised principal component analysis (PCA). Metabolite variations and good models (R 2 Y and Q 2 ~ 1) were confirmed with supervised orthogonal partial least square discriminant analysis (OPLS-DA) []. Reliability and significance (p < 0.05) of the OPLS models were tested with seven-fold Cross Validation Analysis Of Variance (CV-ANOVA). Shared and unique structures plots (SUS-plots) of variable influence on projection (VIP) and correlation coefficient (p(corr)) values were generated (GraphPad Prism), and metabolic pathways most representative of detected metabolites determined (MBrole pathway enrichment analysis) []. […]

Pipeline specifications

Software tools Metabolite Detector, MBRole
Application MS-based untargeted metabolomics
Organisms Rhizobium leguminosarum, Homo sapiens
Chemicals Nitrogen, 2,4-Dichlorophenoxyacetic Acid