GEO DataSets

(Submitter supplied) Extracellular vesicles (EVs) are released by most cell types and are implicated in several biological and pathological processes, including multiple sclerosis (MS). In this study we performed RNA sequencing to analyze the diversity of microorganisms by assignment of reads using different taxa profilers. To diminish the risk of false positive biases derived from sample handling, we performed a similar analysis on EVs derived from known cultured bacterial species, as well as artificially-generated samples. more...

Organism:

Lactobacillus acidophilus; Homo sapiens; synthetic construct; Bifidobacterium animalis subsp. lactis

Type:

Expression profiling by high throughput sequencing

4 related Platforms

15 Samples

Download data: CSV

(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 longum subsp. infantis (B. infantis) resides in the human infant gut and helps with the utilization of human milk-derived nutrient components. While its utilization of various carbohydrate sources has been studied extensively, mechanisms behind utilization of nitrogen components from human milk remain largely unknown. In this study, we present B. infantis growth profiles on the N-containing human milk oligosaccharides (HMO) as nitrogen sources, namely, lacto-N-tetraose (LNT) and lacto-N-neotetraose (LNnT). more...

Organism:

Bifidobacterium longum subsp. infantis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28926

14 Samples

Download data: CSV, TXT

(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) RNA-seq based transcriptome analysis was employed to understand the genome-wide expression patterns under cultivation with resistant starch (RS). To identify differentially expressed genes, we compared RS-induced transcriptome to non-RS transcriptome as sole carbon source.

Organism:

Bifidobacterium adolescentis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27584

8 Samples

Download data: TXT

(Submitter supplied) The purpose of this project was to determine the whole transcriptome response of Bifidobacterium longum subsp. infantis to human milk urea compared to complex nitrogen and L-cysteine.

Organism:

Bifidobacterium longum subsp. infantis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28926

18 Samples

Download data: TXT

(Submitter supplied) In order to understand gene expression profile of Bifidobacterium adolescentis ATCC 15703, it was grown in minimal media upto late log phase in the presence of β-mannooligosaccharide from copra till OD A600 = 0.800

Organism:

Bifidobacterium adolescentis; Bifidobacterium adolescentis ATCC 15703

Type:

Expression profiling by array

Platform:

GPL30400

8 Samples

Download data: TXT

(Submitter supplied) Bifidobacterium longum subsp. infantis (B. infantis) is a prevalent beneficial bacterium that colonizes the human neonatal gut and is uniquely adapted to efficiently use human milk oligosaccharides (HMOs) as a carbon and energy source. Multiple studies have focused on characterizing the elements of HMO utilization machinery in B. infantis; however, the regulatory mechanisms governing the expression of these catabolic pathways remain poorly understood. more...

Organism:

Bifidobacterium longum subsp. infantis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28926

12 Samples

Download data: TXT

(Submitter supplied) This study was aimed to further illustrate the expression files of BAA6 between the stationary phase and the exponential phase in MRSc broth, we combined the transcriptomic analysis with RNA sequencing and tandem mass tags (TMT) quantitative proteomic methods to quantitatively screen the differentially expressed genes and proteins. During the stationary phase, BAA6 expanded its carbon source utilizing profile and enhanced the transport of cellobiose, xylooligosaccharides (XOS), and raffinose to confront with glucose consumption. more...

Organism:

Bifidobacterium animalis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30086

7 Samples

Download data: XLS

(Submitter supplied) To explore the molecular mechanism of B. bifidum adhesion, we compared transcriptomes among WT and non-adhesive mutants cultured in MRS or m-ILS medium.

Organism:

Bifidobacterium bifidum

Type:

Expression profiling by array

Platform:

GPL30211

8 Samples

Download data: TXT

(Submitter supplied) RNA sequencing revolutionized the bacterial gene expression analysis. The objective of this study was to identify the genes involved in metabolism of 2'-FL and LNFP1 in Bifidobacterium pseudocatenulatum MP80. We have obtained a list of genes upregulated in Bifidobacterium pseudocatenulatum MP80 when it is grown in 2% 2'-FL and LNFP1. Lactose grown samples were used as the control.

Organism:

Bifidobacterium pseudocatenulatum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30210

12 Samples

Download data: TXT

(Submitter supplied) The purpose of this course is to study the relationship between the primary structure of exopolysaccharides and the gene expression level of Bifidobacterium longum W13 and W13R, and to better explain the differences between different strains from the level of gene transcription.

Organism:

Bifidobacterium longum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29554

6 Samples

Download data: TXT

(Submitter supplied) 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. more...

Organism:

Bifidobacterium animalis subsp. animalis; Bifidobacterium animalis

Type:

Expression profiling by array

Platform:

GPL24807

4 Samples

Download data: TXT

(Submitter supplied) Bifidobacterium longum subsp. infantis (B. infantis) colonizes the infant gut microbiome with a 43-kb gene cluster that enables human milk oligosaccharide (HMO) utilization. Although there is relative genomic homogeneity in this regard, previous observations suggest that B. infantis strains may differ in their utilization phenotype. To test this hypothesis, a panel of B. infantis strains were evaluated for their ability to utilize pooled HMOs to yield differential phenotypes including biomass accumulation, HMO consumption glycoprofile, end-product secretion, and global transcriptomes. more...

Organism:

Bifidobacterium longum subsp. infantis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28926

32 Samples

Download data: DAT, FASTA, MATRIX

(Submitter supplied) Human milk oligosaccharides (HMOs) enrich beneficial bifidobacteria in the infant gut microbiome which produce molecules that impact development and physiology. 2´fucosyllactose (2´FL) is a highly abundant fucosylated HMO which is utilized by Bifidobacterium longum subsp. infantis, despite limited scientific understanding of the underlying mechanism. Moreover, there is not a current consensus on whether free fucose could be metabolized when not incorporated in a larger oligosaccharide structure. more...

Organism:

Bifidobacterium longum subsp. infantis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28926

6 Samples

Download data: CSV, TXT

(Submitter supplied) Human milk oligosaccharides (HMOs) function as prebiotics for beneficial bacteria in the developing gut, often dominated by Bifidobacterium spp. To understand the relationship between Bifidobacterium utilizing HMOs and how the metabolites that are produced could affect the host, we analyzed the metabolism of HMO 2’-fucosyllactose (2’-FL), 3-fucosyllactose (3FL and difucosyllactose (DFL) in Bifidobacterium longum ssp. more...

Organism:

Bifidobacterium longum subsp. infantis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25787

41 Samples

Download data: TSV

(Submitter supplied) Bacterial promoters consist of core sequence motifs termed –35 and –10 boxes. The consensus motifs are TTGACA and TATAAT, respectively, which were identified from leading investigations on E. coli. However, the consensus sequences are not likely to fit genetically divergent bacteria. The sigma factor of the genus Bifidobacterium has a characteristic polar domain in the N-terminus, suggesting the possibility of specific promoter recognition. more...

Organism:

Bifidobacterium longum NCC2705

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27983

3 Samples

Download data: XLSX

(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