At least three different biological replicates were performed for each condition. Variations in the level of cytoplasmic protein concentrations of B. longum cells grown in the presence of mucus were analysed by a 2DE study. We used a pI range between 4 and 7, which theoretically allows the separation of about c-Met inhibitor two-thirds of the total proteome of B. longum (Sánchez et al., 2008). In all the experiments, cells were collected in the early stationary phase of growth (OD600 nm 0.5–0.9). Cell-free protein extracts were obtained as
described previously (Ruiz et al., 2009a). For 2DE analysis, 500 μg of protein from B. longum NCIMB8809 extracts were loaded onto a strip with an immobilized pH range of 4 to 7 (GE Healthcare) and focused at 65 000 V h−1. Separation in the second dimension was carried out in 12.5% polyacrylamide-sodium dodecyl sulphate gels and protein spots were visualized with colloidal Coomassie staining. Proteins PLX3397 cell line were identified by peptide mass fingerprinting and matrix-assisted laser desorption ionization/time of flight/MS at the Proteomics Unit of
the Parque Científico de Madrid (Cantoblanco, Madrid, Spain). Protein identification was achieved by combining MS data to search a nonredundant protein database (NR; 4.106 entries; National Center for Biotechnology Information) using the mascot software (Matrix Science). Spot detection, volume quantification and statistical analysis were performed using imagemaster platinum software (version 5.00, GE Healthcare). Three protein extracts, coming from three independent GNAT2 cultures, were obtained
for each condition (mucus absence or mucus presence), and at least three independent gels (technical replicates) were performed for each extract. Enzymatic activities were measured for the cytoplasmic fraction and for the secreted fraction. Cell-free protein extracts from the cytoplasmic fraction were obtained as described above. The supernatants were collected by centrifugation from cells grown to the early stationary phase, concentrated 10 times using VivaSpin Columns (cutoff 3000 kDa, Sartorius), and filtered through 0.22-μm sterile filters. Glycosidase activities were measured spectrophotometrically from the release of p-nitrophenol (pNP) produced by the enzymatic hydrolysis of the corresponding pNP-glycoside substrates (Sigma), as described previously (Ruiz et al., 2009b). One unit of enzymatic activity was defined as the amount of protein that releases 1 nmol pNP min−1. Specific activities were determined in duplicate for each culture, and expressed as units per milligram protein. For organic acid determination, Bifidobacterium cultures, grown in the absence or presence of mucus, were collected by centrifugation.