The profiling of bacterial fatty acids is a well-established technique in identifying and classifying bacteria. Cultivation conditions may affect the biosynthesis, thereby, changing the fatty acid profile in bacteria. The effect of the culture conditions on the fatty acid components of Pseudomonas aeruginosa PAO1, Pseudomonas aeruginosa ATCC 27853, Pseudomonas aeruginosa polyresistant and Pseudomonas putida all are aligned to the genus Pseudomonas. The fatty acids in the lipopolysaccharides of Pseudomonas aeruginosa PAO1 were also examined. The effects of the cultivation conditions were followed by using agar and blood agar media at the characteristic temperatures, 25 °C, 37 °C and 42 °C, respectively, and an analysis was made during the 1st, 3rd and 5th day following inoculation. In addition to quantitative differences, we also experienced qualitative differences in the fatty acid profiles which detect newly appearing fatty acids, due to changes in environmental factors. The application of ionic liquid-based column unveils new possibilities for the analyses of fatty acids in GC-MS experiments for bacterial fatty acid profiling. The validation results (response linearity, limit of detection, limit of quantification, system suitability, intraday and interday repeatability and accuracy) show the high separation efficiency of the ionic liquid-based column in the analyses.

Knowledge of the type and level of saturated and unsaturated fatty acids in food and clinical matrices is of practical importance, but the wide variety of fatty acids makes analyses very complex. The discrimination of the geometric isomers of fatty acid needs proper and effective separation conditions. The efficiency of three different stationary phases was evaluated by GC–MS methods in the separation of fatty acids in their methyl ester forms. Significant differences were observed in the efficiencies of polysiloxane-based (non-polar HP-5MS and medium/high polarity DB-225MS) and ionic liquid-based (SLB-IL111) columns. Baseline separation of the geometric isomers of linoleic acid methyl ester was obtained by the extremely polar SLB-IL111 column, showing a preference over the other two columns. The optimization of the experimental conditions (response linearity, limit of detection, limit of quantification, system suitability, intraday and interday repeatability and accuracy) showed the separation power of the ionic liquid interaction in the analyses by using short (25–30 m long) columns. By deducting the general principles of the interaction, predictions can be made for the separation of other isomers. The results facilitate the precise identification of various types of fatty acids in real samples for nutritional information.