BIOLOG phenotype microarrays: workflow and data analysis

The BIOLOG phenotype microarray experiments with PM1 carbon sources were performed following the manufacturer’s instruction with the following modification: the glycerol stocks of the strains were plated on Columbia Blood Agar (Oxoid). The growth kinetics measurements of the PM1 plates were done in a TECAN Infinite F200 instrument by determining the OD₅₉₅ every 15 min for 24 h at 37 °C without shaking. BIOLOG data was analyzed and visualized using the opm package v.1.3.77 for R [73]. Briefly, after importing of kinetic raw data and metadata integration, descriptive curve parameters (lag phase (λ), respiration rate (μ), maximum curve height (A) and Area Under the Curve (AUC)) were estimated using do_aggr function via spline-fitting. Statistical analysis of growth curves of the three strains (naive MG1655, MG1655::ϕO104 and MG1655::ϕPA8) in three independent repetitions was performed with opm_mcp method, which internally accounts for multiple comparisons.