Global Gene Expression in Bifidobacterium breve

Global gene expression was determined during log-phase growth of B. breve UCC2003 in mMRS supplemented with either LNT, LNnT, LNB, lactosamine-HCl or lactose. The obtained transcriptome was compared to that determined for log-phase B. breve UCC2003 cells when grown in mMRS supplemented with ribose. DNA microarrays containing oligonucleotide primers representing each of the 1864 identified open reading frames on the genome of B. breve UCC2003 were designed and obtained from Agilent Technologies (Palo Alto, Ca., USA). Methods for cell disruption, RNA isolation, RNA quality control, complementary DNA synthesis and labelling were performed as described previously68 (link). Labelled cDNA was hybridized using the Agilent Gene Expression hybridization kit (part number 5188-5242) as described in the Agilent Two-Colour Microarray-Based Gene Expression Analysis v4.0 manual (publication number G4140-90050). Following hybridization, microarrays were washed in accordance with Agilent’s standard procedures and scanned using an Agilent DNA microarray scanner (model G2565A). Generated scans were converted to data files with Agilent’s Feature Extraction software (Version 9.5). DNA-microarray data were processed as previously described69 (link)70 (link)71 (link). Differential expression tests were performed with the Cyber-T implementation of a variant of the t-test72 (link).