GEO DataSets

(Submitter supplied) In this paper, two predicted lac I type transcription factors (TFs) were characterised and shown to be involved in the regulation of the central metabolic pathways of B. breve UCC2003. Although, genetically different, these TF were functionally very similar. When first identified these TFs were named AraQ and MalR1, due to their predicted associations with arabinose and maltose metabolism, respectively. more...

Organism:

Bifidobacterium breve UCC2003

Type:

Expression profiling by array

Platform:

GPL13210

4 Samples

Download data: TXT

(Submitter supplied) A bacterial nursling stool isolate, Bifidobacterium breve UCC2003, encodes two putative sulfatases. The sulfated monosaccharide N-acetylglucosamine-6-sulfate (GlcNAc-6-S) was shown to support growth of B. breve UCC2003, while three other tested sulfated monosaccharides, N-acetylglucosamine-3-sulfate, N-acetylgalactosamine-3-sulfate and N-acetylgalactosamine-6-sulfate, did not. Using a combination of transcriptomic and functional genomic approaches, a gene cluster, designated ats2, was shown to be specifically required for GlcNAc-6-S metabolism. more...

Organism:

Bifidobacterium breve UCC2003

Type:

Expression profiling by array

Platform:

GPL8878

4 Samples

Download data: TXT

(Submitter supplied) Regulation of carbohydrate metabolism in Bifidobacterium breve has been studied in detail for a variety of both plant and human-derived glycans, particularly in the model strain UCC2003. We have recently comprehensively elucidated the precise metabolic pathways by which the human milk oligosaccharide (HMO) components LNT, LNnT and LNB are utilized by B. breve UCC2003. However, no work has been carried out to date in identifying and understanding the regulatory mechanisms that control transcription of the genetic loci involved in these metabolic pathways. more...

Organism:

Bifidobacterium breve UCC2003

Type:

Expression profiling by array

Platforms:

GPL24137 GPL24138

8 Samples

Download data: TXT

(Submitter supplied) To extend our understanding of bifidobacterial mutualism and carbohydrate syntrophy in the gut we adopted advanced functional genomics to create single- and double-deletion isogenic strains of the NagA encoding genes of B. breve UCC2003. The resulting strains were examined, as compared to the parent strain, for their ability to metabolise particular host derived carbohydrates. In addition, the B. breve strains were examined for their crossfeeding capability and ability to establish, in the presence of B. more...

Organism:

Bifidobacterium breve UCC2003

Type:

Expression profiling by array

Platform:

GPL8878

2 Samples

Download data: TXT

(Submitter supplied) The recognition specificity and associated affinity of the RNA polymerase sigma subunit towards its cognate promoter sequence is one of the elements contributing to the modulation of gene expression in bacteria. In the present study we identified and assessed vegetative promoters of the bifidobacterial prototype Bifidobacterium breve UCC2003 employing a combination of tiling array analysis and RNA sequencing. more...

Organism:

Bifidobacterium breve UCC2003

Type:

Expression profiling by genome tiling array

Platform:

GPL23645

2 Samples

Download data: TXT

(Submitter supplied) Members of the genus Bifidobacterium are Gram-positive bacteria which are commonly found in the gastrointestinal tract (GIT) of mammals, including humans. Growth of bifidobacteria has been shown to be selectively stimulated by various carbohydrates found in the human diet. To extend our understanding of the regulation of bifidobacterial carbohydrate utilization systems, we investigated the regulation of two carbohydrate utilisation clusters dedicated to the metabolism of raffinose type sugars and melezitose. more...

Organism:

Bifidobacterium breve UCC2003

Type:

Expression profiling by array

Platform:

GPL8878

6 Samples

Download data: TXT

(Submitter supplied) Recent studies have begun to elucidate the mechanisms of utilisation of some human milk oligosaccharides (HMO) components by Bifidobacterium breve. However, this phenomenon is still relatively poorly understood, with little to no work to date in understanding a number of specific structures common to HMO.   In this study, we demonstrate that the prototype B. breve strain UCC2003 possesses specific metabolic pathways for the utilisation of Lacto-N-Tetraose and Lacto-N-neoTetraose, which represent the central moieties of Type I and Type II HMOs, respectively. more...

Organism:

Bifidobacterium breve UCC2003

Type:

Expression profiling by array

Platform:

GPL13210

10 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Cereibacter sphaeroides; Cereibacter sphaeroides 2.4.1

Type:

Expression profiling by array; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL18841 GPL162 GPL18840

13 Samples

Download data: CEL, WIG

(Submitter supplied) To gain a better understanding of the transcription factors that regulate central carbon metabolism in Rhodobacter sphaeroides ChIP-seq was used to determine the genome-wide binding locations of 2 transcription factors: CceR (RSP_1663) and AkgR (RSP_0981) both predicted to be involved in the regulation of of central carbon and energy metabolism.

Organism:

Cereibacter sphaeroides

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL18841 GPL18840

4 Samples

Download data: WIG

(Submitter supplied) To gain a better understanding of the transcription factors that regulate central carbon metabolism in Rhodobacter sphaeroides global gene expression analysis was used to determine genes under the regulatory influence of 2 transcription factors: CcmR (RSP_1663) and AkgR (RSP_0981) both predicted to be involved in the regulation of central carbon and energy metabolism.

Organism:

Cereibacter sphaeroides; Cereibacter sphaeroides 2.4.1

Type:

Expression profiling by array

Platform:

GPL162

12 Samples

Download data: CEL

(Submitter supplied) Members of the genus Bifidobacterium are typically found in the gastrointestinal tract (GIT) of humans and other mammals. Bifidobacterium breve strains are numerically prevalent among the gut microbiota of healthy, breast-fed infants. The metabolism of sialic acid, a ubiquitous monosaccharide in the infant and adult gut, by B. breve UCC2003 is dependent on a large gene cluster, designated the nan/nag cluster. more...

Organism:

Bifidobacterium breve UCC2003

Type:

Expression profiling by array

Platform:

GPL8878

2 Samples

Download data: TXT

(Submitter supplied) Bifidobacterium breve represents one of the most abundant (bifido)bacterial species in the gastro-intestinal tract of (breast-fed) infants, where their presence is believed to be beneficial. In the present study whole genome sequencing, employing PacBio’s Single Molecule, Real-Time (SMRT) sequencing platform, combined with comparative genome analysis allowed the most extensive genetic investigation of this taxon. more...

Organism:

Bifidobacterium breve UCC2003; Bifidobacterium breve

Type:

Genome variation profiling by array

Platforms:

GPL8878 GPL13210

66 Samples

Download data: TXT

(Submitter supplied) Development of the human gut microbiota commences at birth with bifidobacteria being among the first colonizers of the sterile newborn gastrointestinal tract. To date the genetic basis of bifidobacterial colonization and persistence remains poorly understood. Transcriptomic analysis of the 2,422,684 bp genome of Bifidobacterium breve UCC2003, a strain isolated from a nursling stool, during colonization of a mouse model revealed the differential expression of a type IVb or so-called Tad pilus-encoding cluster. more...

Organism:

Mus musculus; Bifidobacterium breve; Bifidobacterium breve UCC2003

Type:

Expression profiling by array; Genome variation profiling by array

Platforms:

GPL13210 GPL8878

21 Samples

Download data: TXT