 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Mar 03, 2021 |
| Title |
Comprehensive genomic, phenotypic and transcriptomic approaches to enhance Bifidobacterium animalis subsp. animalis growth and survival in milk |
| Platform organism |
Bifidobacterium animalis |
| Sample organism |
Bifidobacterium animalis subsp. animalis |
| Experiment type |
Expression profiling by array
|
| Summary |
Bifidobacterium animalis subsp. animalis CNCM I-4602 was tested for its ability to grow in reconstituted skimmed milk (RSM). Strain CNCM I-4602 grows and survives poorly in reconstituted skimmed milk (RSM), although this was partially countered by the addition of certain compounds, including yeast extract, uric acid, glutathione, cysteine, ferrous sulfate and a combination of magnesium sulfate and manganese sulfate. Microarray analysis of the strain grown in RSM revealed a number of up-regulated amino acid biosynthetic pathways, as well as stress-related genes.
Expression profiling by array
|
| |
|
| Overall design |
Bifidobacterial cells were isolated from milk-based medium (RSM) according to a previously described method (de Jong et al., 2013). In brief, a 15 ml sample of a bifidobacterial culture in RSM was harvested by centrifugation at 6,000 x g for 10 mins at 4°C. Following centrifugation, the pellet was resuspended in 1-4 ml of 3 M guanidium chloride (depending on the level of coagulation of the milk), and then solubilized by 5 cycles of vortex mixing and chilling on ice, each for one minute. Cells were collected from the solution by centrifugation at 3,500 x g for 15 mins at 4°C, then washed twice with 0.9 % (wt/vol) saline solution, after which cells were frozen at -80°C or used directly for RNA extraction. RNA was extracted using a combination of the Macaloid method and the Roche High Pure RNA isolation kit (Zomer et al. 2009). RNA quality control, complementary DNA synthesis and labelling were performed as described previously (Zomer et al., 2009). DNA microarrays containing oligonucleotide primers representing each of the identified open reading frames on the genome of B. animalis subsp. animalis CNCM I-4602 were designed and obtained from Agilent Technologies (Palo Alto, Ca., USA). Two separate microarray experiments were performed. The first compared gene expression of B. animalis subsp. animalis CNCM I-4602 in mMRS supplemented with glucose (used as the reference condition) to the strain in gRSM (test condition). The second microarray experiment compared the strain in mMRS with glucose (reference condition) compared to gRSM supplemented with cysteine (test condition). Each transcriptome experiment was performed as a dye swap so as to account for any dye bias. Hybridization, washing of the slides and processing of the DNA microarray data was performed as previously described (Pokusaeva et al., 2010).
|
| |
|
| Contributor(s) |
Egan M, Bottacini F |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| |
| Submission date |
Apr 03, 2018 |
| Last update date |
Mar 05, 2021 |
| Contact name |
Francesca Bottacini |
| Organization name |
University College Cork
|
| Department |
APC Microbiome Institute & School of Microbiology
|
| Street address |
Western Road
|
| City |
Cork |
| ZIP/Postal code |
ND |
| Country |
Ireland |
| |
|
| Platforms (1) |
| GPL24807 |
Agilent-075649 B. animalis 14602 |
|
| Samples (4)
|
| GSM3074523 |
B. animalis subsp. animalis CNCM I-4602 grown in modified MRS with glucose vs. grown in RSM |
| GSM3074524 |
B. animalis subsp. animalis CNCM I-4602 grown in RSM vs. grown in modified MRS with glucose |
| GSM3074525 |
B. animalis subsp. animalis CNCM I-4602 grown in modified MRS with glucose vs. grown in RSM with cysteine |
| GSM3074526 |
B. animalis subsp. animalis CNCM I-4602 grown in RSM with cysteine vs. grown in modified MRS with glucose |
|
| Relations |
| BioProject |
PRJNA448570 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE112626_RAW.tar |
52.4 Mb |
(http)(custom) |
TAR (of TXT) |
| Processed data included within Sample table |
| Processed data provided as supplementary file |
|
|
|
|
 |
Less...
More...