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Series GSE56291 Query DataSets for GSE56291
Status Public on May 29, 2014
Title Metabolism of sialic acid by Bifidobacterium breve UCC2003
Organism Bifidobacterium breve UCC2003
Experiment type Expression profiling by array
Summary Bifidobacteria constitute a specific group of commensal bacteria which inhabit the gastrointestinal tract of humans and other mammals. Bifidobacterium breve UCC2003 has previously been shown to utilise several plant-derived carbohydrates that include cellodextrins, starch and galactan. In the current study, we investigate the ability of this strain to utilise the mucin- and human milk oligosaccharide (HMO)-derived carbohydrate, sialic acid. Using a combination of transcriptomic and functional genomic approaches, we identified a gene cluster dedicated to the uptake and metabolism of sialic acid. Furthermore, we demonstrate that B. breve UCC2003 can cross feed on sialic acid derived from the metabolism of 3’ sialyllactose, a HMO, by Bifidobacterium bifidum PRL2010.
 
Overall design DNA-microarrays containing oligonucleotide primers representing each of the 1864 annotated genes on the genome of B. breve UCC2003 (O'Connell Motherway et al., 2011) were designed by and obtained from Agilent Technologies (Palo Alto, Ca., USA). Methods for cell disruption, RNA isolation, RNA quality control, complementary DNA synthesis and labeling were performed as described previously (Pokusaeva et al., 2009). Labeled cDNA was hybridized using the Agilent Gene Expression hybridization kit (part number 5188-5242) as described in the Agilent Two-Color Microarray-Based Gene Expression Analysis v4.0 manual (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 described (Garcia De La Nava et al., 2003). Differential expression tests were performed with the Cyber-T implementation of a variant of the t-test (Long et al., 2001). A gene was considered differentially expressed when p < 0.001 and an expression ratio of >3 or <0.33 relative to the control.
 
Contributor(s) Egan M
Citation(s) 24814790
Submission date Mar 27, 2014
Last update date Aug 04, 2014
Contact name Mary O'Connell Motherway
E-mail(s) m.oconnellmotherway@ucc.ie
Phone 00 353 21 490 1364
Organization name University College Cork
Department Department of Microbiology and Alimentary Pharmabiotic Centre
Street address Western Road
City Cork
ZIP/Postal code na
Country Ireland
 
Platforms (1)
GPL8878 Bifidobacterium breve UCC2003 Agilent 2x11K format
Samples (2)
GSM1358430 UCC2003 grown on ribose v. UCC2003 grown on sialic acid
GSM1358431 UCC2003 grown on sialic acid v. UCC2003 grown on ribose
Relations
BioProject PRJNA242858

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE56291_RAW.tar 6.1 Mb (http)(custom) TAR (of TXT)
Raw data provided as supplementary file
Processed data included within Sample table

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