GEO DataSets

(Submitter supplied) The purpose of this project was to determine the whole transcriptome response of Bifidobacterium longum subsp. longum SC596 to pooled and individual human milk oligosaccharides (HMO) relative to lactose

Organism:

Bifidobacterium longum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22529

18 Samples

Download data: TXT

(Submitter supplied) The purpose of this project was to determine the whole transcriptome response of Bifidobacterium bifidum SC555 to pooled and individual human milk oligosaccharides (HMO) relative to lactose

Organism:

Bifidobacterium bifidum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18891

20 Samples

Download data: TXT

(Submitter supplied) The purpose of this project was to determine the whole transcriptome response of Bifidobacterium longum subsp. Infantis to pooled and individual human milk oligosaccharides (HMO) relative to lactose

Organism:

Bifidobacterium longum subsp. infantis ATCC 15697 = JCM 1222 = DSM 20088

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18859

18 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) 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) Background: Breastfed human infants are predominantly colonized by bifidobacteria that thrive on human milk oligosaccharides (HMO). The two most predominant species of bifidobacteria in infant feces are Bifidobacterium breve (B. breve) and Bifidobacterium longum subsp. infantis (B. infantis), both avid HMO-consumer strains. Our laboratory has previously shown that B. infantis, when grown on HMO, increase adhesion to intestinal cells and increase the expression of the anti-inflammatory cytokine interleukin-10. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

9 Samples

Download data: XLSX

(Submitter supplied) Background: Breastfed human infants are predominantly colonized by bifidobacteria that thrive on human milk oligosaccharides (HMO). The two most predominant species of bifidobacteria in infant feces are Bifidobacterium breve (B. breve) and Bifidobacterium longum subsp. infantis (B. infantis), both avid HMO-consumer strains. Our laboratory has previously shown that B. infantis, when grown on HMO, increase adhesion to intestinal cells and increase the expression of the anti-inflammatory cytokine interleukin-10. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

9 Samples

Download data: XLSX

(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) in Bifidobacterium longum ssp. infantis Bi-26. RNA-seq and metabolite analysis (NMR/GCMS) was performed on samples at early (A600=0.25), mid-log (0.5-0.7) and late-log phases (1.0-2.0) of growth. more...

Organism:

Bifidobacterium longum subsp. infantis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25787

12 Samples

Download data: GFF, TSV

(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) 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) 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) 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) The factors that govern the retention and abundance of specific microbial lineages within a developing intestinal microbiota remain poorly defined. Human milk oligosaccharides consumed by nursing infnats pass undigested to the distal gut where they may be consumed by microbes. We investigated the transcriptional response of Bacterides fragilis, a prominent gut resident, to the presence of HMOs.

Organism:

Bacteroides fragilis NCTC 9343

Type:

Expression profiling by array

Platform:

GPL14584

4 Samples

Download data: CEL

(Submitter supplied) Investigation of the overall in vitro response of Bacteroides thetaiotaomicron to human milk oligosaccharides. Comparison with response to MM-lactose and MM-galactose (Analysis performed using as a baseline datasets GSM301635 and GSM301637 corresponding to Bacteroides thetaiotaomicron response in MM-Glucose)

Organism:

Bacteroides thetaiotaomicron; Bifidobacterium longum

Type:

Expression profiling by array; Third-party reanalysis

Platform:

GPL1821

8 Samples

Download data: CEL, 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) Bifidobacterium longum strain BBMN68 is resistant to low concentrations of oxygen. In this study, a transcriptomic study was performed to detail the cellular response of B. longum strain BBMN68 to oxidative stress. Oxygen and its intermediate metabolites, reactive oxygen species (ROS), induced abundant changes in gene expression at the mRNA level. Increased expression was found for genes involved in ROS detoxification and the redox homeostasis system, protein and DNA synthesis and repair, the Fe–S cluster assembly system, and biosynthesis of branched-chain amino acids and tetrahydrofolate. more...

Organism:

Bifidobacterium longum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17084

3 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 breve UCC2003; Bifidobacterium catenulatum subsp. kashiwanohense

Type:

Expression profiling by array

Platforms:

GPL24138 GPL24316

10 Samples

Download data: TXT