GEO DataSets

(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:

Bifidobacterium breve UCC2003; Mus musculus; Bifidobacterium breve

Type:

Expression profiling by array; Genome variation profiling by array

Platforms:

GPL13210 GPL8878

21 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) 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) 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) N4-methylcytosine is a major DNA modification integral to restriction-modification (R-M) systems in bacterial genomes. Here we describe 4mC-Tet-Assisted Bisulfite-sequencing (4mC-TAB-seq), a method that accurately and rapidly reveals the genome-wide locations of N4-methylcytosines at single-base resolution. By coupling Tet-mediated oxidation with a modified sodium bisulfite conversion reaction, unmodified cytosines and 5-methylcytosines are read out as thymines, whereas N4-methylcytosines are read out as cytosines revealing their positions throughout the genome.

Organism:

Caldicellulosiruptor acetigenus; synthetic construct

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL19424 GPL19423

7 Samples

Download data: TSV

(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) Six bacterial genomes, Geobacter metallireducens GS-15, Chromohalobacter salexigens, Vibrio breoganii 1C-10, Bacillus cereus ATCC 10987, Campylobacter jejuni subsp. jejuni 81-176 and Campylobacter jejuni NCTC 11168, all of which had previously been sequenced using other platforms were re-sequenced using single-molecule, real-time (SMRT) sequencing specifically to analyze their methylomes. In every case a number of new N6-methyladenine (m6A) and N4-methylcytosine (m4C) methylation patterns were discovered and the DNA methyltransferases (MTases) responsible for those methylation patterns were assigned. more...

Organism:

Bacillus cereus; Vibrio breoganii; Geobacter metallireducens; Chromohalobacter israelensis; Campylobacter jejuni

Type:

Methylation profiling by high throughput sequencing

5 related Platforms

6 Samples

Download data: CSV, GFF

(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