GEO DataSets

(Submitter supplied) The bacterial world offers diverse strains for understanding medical and environmental processes and for engineering synthetic-biology chasses. However, genetically manipulating these strains has faced a long-standing bottleneck: how to efficiently transform DNA. Here we report IMPRINT, a generalized, rapid and scalable approach to overcome DNA restriction, a prominent barrier to transformation. IMPRINT utilizes cell-free systems to express DNA methyltransferases from the bacterial host’s restriction-modification systems. more...

Organism:

Escherichia coli; Bifidobacterium breve

Type:

Other

Platforms:

GPL25368 GPL33564

7 Samples

Download data: TSV

(Submitter supplied) We report a method for bypassing restriction modification systems to increase DNA transformation in batceria and develop a high-throughput way to determine the optimal methylation pattern for DNA transformation.

Organism:

Bifidobacterium breve

Type:

Other

Platform:

GPL31014

8 Samples

Download data: XLSX

(Submitter supplied) Bifidobacterium species in the infant gut can metabolize intact human milk oligosaccrides. There is species varation in the types of the olgosaccharides that can bedigested by Bifidobacterium species. B. breve strains have shown digestion of LNT and LNnT oligoscchrides. The objective of te current study was idetification of B. breve strains that can digest sialylated oligosacchrides. The currnet study was designed to idetify the genes that show upregulation when grown in lactose, 3'-siallylactose and Bovine Milk Oligosaccharides

Organism:

Bifidobacterium breve

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33564

9 Samples

Download data: TXT

(Submitter supplied) Bifidobacteria dominate the composition of the neonatal gut microbiota in the first number of weeks following birth. A number of species in particular are found with a significantly higher frequency in the microbiome of breastfed infants, owing to their ability to rely on Human Milk Oligosacchraides (HMOs) as their sole carbohydrate substrate; namely B. bifidum, B. longum spp. infantis and B. breve. more...

Organism:

Bifidobacterium catenulatum subsp. kashiwanohense; Bifidobacterium breve UCC2003

Type:

Expression profiling by array

Platforms:

GPL24138 GPL24316

10 Samples

Download data: TXT

(Submitter supplied) we investigated the effect of linoleic acid on the metabolism Bifidobacterium breve DSM 20213 by means of transcriptomic approach

Organism:

Bifidobacterium breve DSM 20213 = JCM 1192

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27650

6 Samples

Download data: TXT

(Submitter supplied) This work aimed to investigate the ability of two human-derived bifidobacterial strains, i.e. Bifidobacterium breve UCC2003 and Bifidobacterium longum NCIMB 8809, to utilize various oligosaccharides (i.e., 4-galactosyl-kojibiose, lactulosucrose, lactosyl-oligofructosides, raffinosyl-oligofructosides and lactulose-derived galacto-oligosaccharides) synthesized by means of microbial glycoside hydrolases. more...

Organism:

Bifidobacterium breve UCC2003

Type:

Expression profiling by array

Platform:

GPL24138

8 Samples

Download data: TXT, XLSX

(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) Bifidobacterium are considered to be beneficial for human health and are classified as probiotic bacterium. They must resist many environmental stress factors in order to survive in the gastrointestinal environment including; pH, oxygen availability, bile and nutrient starvation (eg: iron or carbon). This study investigates Bifidobacterium breve UCC2003 global genome response to growth under ferrous and/or ferric iron limiting conditions. more...

Organism:

Bifidobacterium breve UCC2003

Type:

Expression profiling by array

Platforms:

GPL13210 GPL24137

5 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) Bifidobacteria resident in the gastrointestinal tract are subject to many stresses such as bile stress, osmotic stress and starvation. Adaption to these stresses requires a high amount of energy and rapid changes in gene transcription. Four Bifidobacterium breve UCC2003-encoded Lac I type transcriptional regulators had been proposed to be involved in the utilisation of maltose, maltodextrins and related polymers such as starch, amylopectin, amylose, glycogen and pullulan. more...

Organism:

Bifidobacterium breve UCC2003

Type:

Expression profiling by array

Platform:

GPL13210

8 Samples

Download data: TXT

(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) 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; Bifidobacterium breve UCC2003

Type:

Genome variation profiling by array

Platforms:

GPL8878 GPL13210

66 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) This SuperSeries is composed of the SubSeries listed below.

Organism:

Bifidobacterium adolescentis; Bifidobacterium breve 12L; Bifidobacterium bifidum PRL2010; Bifidobacterium longum subsp. infantis ATCC 15697 = JCM 1222 = DSM 20088

Type:

Expression profiling by array

Platform:

GPL19766

20 Samples

Download data: TXT

(Submitter supplied) We describe the molecular cross talk established under in vivo conditions between a set of human gut bifidobacterial commensals. Eleven groups of five conventional female 8-wk-old BALB/c mice taking a standard polysaccharide-rich Chow diet were administered a single daily dose of 109 CFU of either B. bifidum PRL2010, B. breve 12L , B. adolescentis 22L , B. longum subsp. infantis ATCC15697, or bifidobacterial couples, i.e., PRL2010-12L, PRL2010-22L, PRL2010-ATCC15696, 12L-22L, 12L-ATCC15697, 22L-ATCC15697, or a combination of all bifidobacterial strains. more...

Organism:

Bifidobacterium adolescentis; Bifidobacterium longum subsp. infantis ATCC 15697 = JCM 1222 = DSM 20088; Bifidobacterium bifidum PRL2010; Bifidobacterium breve 12L

Type:

Expression profiling by array

Platform:

GPL19766

5 Samples

Download data: TXT

(Submitter supplied) We describe the molecular cross talk established under in vivo conditions between a set of human gut bifidobacterial commensals. Eleven groups of five conventional female 8-wk-old BALB/c mice taking a standard polysaccharide-rich Chow diet were administered a single daily dose of 109 CFU of either B. bifidum PRL2010, B. breve 12L , B. adolescentis 22L , B. longum subsp. infantis ATCC15697, or bifidobacterial couples, i.e., PRL2010-12L, PRL2010-22L, PRL2010-ATCC15696, 12L-22L, 12L-ATCC15697, 22L-ATCC15697, or a combination of all bifidobacterial strains. more...

Organism:

Bifidobacterium breve 12L; Bifidobacterium bifidum PRL2010; Bifidobacterium longum subsp. infantis ATCC 15697 = JCM 1222 = DSM 20088; Bifidobacterium adolescentis

Type:

Expression profiling by array

Platform:

GPL19766

5 Samples

Download data: TXT

(Submitter supplied) We describe the molecular cross talk established under in vivo conditions between a set of human gut bifidobacterial commensals. Eleven groups of five conventional female 8-wk-old BALB/c mice taking a standard polysaccharide-rich Chow diet were administered a single daily dose of 109 CFU of either B. bifidum PRL2010, B. breve 12L , B. adolescentis 22L , B. longum subsp. infantis ATCC15697, or bifidobacterial couples, i.e., PRL2010-12L, PRL2010-22L, PRL2010-ATCC15696, 12L-22L, 12L-ATCC15697, 22L-ATCC15697, or a combination of all bifidobacterial strains. more...

Organism:

Bifidobacterium breve 12L; Bifidobacterium adolescentis; Bifidobacterium longum subsp. infantis ATCC 15697 = JCM 1222 = DSM 20088; Bifidobacterium bifidum PRL2010

Type:

Expression profiling by array

Platform:

GPL19766

5 Samples

Download data: TXT

(Submitter supplied) We describe the molecular cross talk established under in vivo conditions between a set of human gut bifidobacterial commensals. Eleven groups of five conventional female 8-wk-old BALB/c mice taking a standard polysaccharide-rich Chow diet were administered a single daily dose of 109 CFU of either B. bifidum PRL2010, B. breve 12L , B. adolescentis 22L , B. longum subsp. infantis ATCC15697, or bifidobacterial couples, i.e., PRL2010-12L, PRL2010-22L, PRL2010-ATCC15696, 12L-22L, 12L-ATCC15697, 22L-ATCC15697, or a combination of all bifidobacterial strains. more...

Organism:

Bifidobacterium bifidum PRL2010; Bifidobacterium breve 12L; Bifidobacterium adolescentis; Bifidobacterium longum subsp. infantis ATCC 15697 = JCM 1222 = DSM 20088

Type:

Expression profiling by array

Platform:

GPL19766

5 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) Phenotypic screening of a random mutant library combined with microarray analysis of the transcriptional response of B. breve UCC2003 to iron limitation, allowed the identification of a number of genes implicated in the survival of Bifidbacterium breve UCC2003 under iron-limiting conditions. Of the identified genes, two putative iron-uptake systems, were further characterised: (i) a presumed ferrous iron uptake system, designated here as bfeUO, and (ii) a predicted ferric iron/siderophore uptake system, designated sifABCDE. more...

Organism:

Bifidobacterium breve UCC2003

Type:

Expression profiling by array

Platform:

GPL13210

2 Samples

Download data: TXT