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RNA sequencing of Bifidobacterium longum subsp. infantis in response to various substrates

ABSTRACT: 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(S): Bifidobacterium longum subsp. infantis ATCC 15697 = JCM 1222 = DSM 20088

PROVIDER: GSE58773 | GEO | 2015/10/28

SECONDARY ACCESSION(S): PRJNA253467

REPOSITORIES: GEO

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RNA sequencing of Bifidobacterium longum subsp. infantis in response to various substrates

Project description: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 Bacterial isolates grown on lactose, pooled human milk oligosaccharides (HMO), lacto-N-tetraose (LNT), lacto-N-neotetraose (LNnT), 2âfucosyllactose (2âFL), 3-fucosyllactose (3FL), and 6âsialyllactose (6âSL). RNA was extracted and sequenced, in duplicate, on an Illumina HiSeq. Early, mid, and late timepoints in response to pooled HMO were additionally sequenced in duplicate.

2015-10-28 | E-GEOD-58773 | biostudies-arrayexpress

RNA sequencing of Bifidobacterium longum subsp. longum SC596 in response to various substrates

Project description: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

2016-10-08 | GSE87697 | GEO

Bifidobacterium longum subsp. infantis (B. infantis) strain dependent utilization of human milk oligosaccharides

Project description: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. Two strains (ATCC 15697 and UMA301) efficiently consumed several HMO isomers/anomers that exhibit degrees of polymerization (DP) ³ 4. These same strains partially consumed the smaller DP HMOs including fucosyllactose and lactodifucotetraose isomers/anomers. In contrast, UMA299 efficiently utilized fucosylated small molecular weight HMOs (DP<4), and accumulated greater biomass on purified 2´FL with significantly higher 1,2-propanediol production. This study identifies several strain-dependent features in HMO utilization phenotypes that are consistent with metabolic variation within a bifidobacterial-dominated infant-gut microbiome.

2020-12-30 | GSE164005 | GEO

Strain-specific strategies of 2′-fucosyllactose, 3-fucosyllactose, and difucosyllactose assimilation by Bifidobacterium longum subsp. infantis Bi-26 and ATCC 15697

2020-06-07 | GSE151933 | GEO

Bifidobacterium longum subsp. infantis transcriptomes in response to various nitrogen sources

Project description: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.

2022-09-30 | GSE155078 | GEO

Bifidobacterium longum subsp. infantis utilizes urea as a nitrogen source

Project description:Bifidobacterium longum subsp. infantis is a bacterial commensal that colonizes the breast-fed infant gut where it utilizes indigestible components delivered in human milk. Accordingly, human milk contains several non-protein nitrogenous molecules, including urea at high abundance. This project investigates the degree to which urea is utilized as a primary nitrogen source by Bifidobacterium longum subsp. infantis and incorporation of hydrolysis products into the expressed proteome.

2023-03-22 | PXD019401 | Pride

Novel Genes and Metabolite Trends in Bifidobacterium longum ssp. infantis Bi-26 Involved in Metabolism of Human Milk Oligosaccharide 2’-fucosyllactose

Project description: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. Transcriptomic analysis revealed many gene clusters including three novel ABC-type sugar transport clusters to be upregulated in Bi-26 involved in processing of 2’-FL along with metabolism of its monomers glucose, fucose and galactose. Metabolite data confirmed the production of formate, acetate, 1,2-propanediol, lactate and cleaving of fucose from 2’-FL. The formation of acetate, formate, and lactate showed how the cell uses metabolites during fermentation to produce higher levels of ATP (mid-log compared to other stages) or generate cofactors to balance redox. We concluded 2’-FL metabolism is a complex process involving gene clusters throughout the genome producing more metabolites compared to lactose. These results provide valuable insight on the mode-of-action of 2’-FL utilization by Bifidobacterium longum ssp. infantis Bi-26.

2019-04-23 | GSE122350 | GEO

Bifidobacterium infantis intracellular 2-oxogluturate concentration is inversely related to nitrogen accessibility

Project description: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). Dietary 2-Oxoglutarate (2-OG) in known in mice model for its protective effects against intestinal inflammation and colitis development. In this study, we have shown that B. infantis had increased 2-OG concentration when utilizes LNT or LNnT as a primary nitrogen source. As LNT and LNnT are the isomers of HMO core structures, N-acetyl glucosamine (NAG), the N-containing monosaccharide, was regarded as the nitrogen provider of the HMO core structures. Differentially expressed gene patterns in B. infantis were analyzed under the less efficient nitrogen conditions (HMOs and NAG) relative to the complex nitrogen controls. Proteomics analysis of B. infantis using 15N-labeled NAG revealed that NAG nitrogen was incorporated into B. infantis metabolism. Transcriptomics results of B. infantis in LNT, LNnT and NAG nitrogen were consistent with the proteomics results. This further indicated that B. infantis metabolism was affected by NAG nitrogen in nitrogen assimilation, HMO catabolism, NAD cofactor biosynthesis and regeneration, and peptidoglycan biosynthesis pathways. In summary, B. infantis can use NAG-containing HMO as a nitrogen source and incorporate NAG nitrogen into metabolism pathways.

2023-09-14 | GSE209665 | GEO

Bifidobacterium infantis metabolizes 2´fucosyllactose-derived and free fucose through a common catabolic pathway resulting in 1,2-propanediol secretion

Project description: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. Based on metabolic and genomic analyses, we hypothesize that B. infantis catabolizes both free fucose and fucosyl oligosaccharide residues to produce 1,2-propanediol (1,2-PD). Accordingly, systems-level approaches including transcriptomics and proteomics support this metabolic path. Co-fermentation of fucose and limiting lactose or glucose was found to promote significantly higher biomass and 1,2-PD concentrations than individual substrates, suggesting a synergistic effect. In addition, and during growth on 2´FL, B. infantis achieves significantly higher biomass corresponding to increased 1,2-PD. These findings support a singular fucose catabolic pathway in B. infantis that is active on both free and HMO-derived fucose and intimately linked with central metabolism. The impact of fucose and 2´FL metabolism on B. infantis physiology provides insight into the role of fucosylated HMOs in influencing host- and microbe-microbe interactions within the infant gut microbiome.

2020-10-08 | GSE159189 | GEO

RNA sequencing of Bifidobacterium bifidum SC555 in response to various substrates

Project description: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 Bacterial isolates grown on lactose, pooled human milk oligosaccharides (HMO), lacto-N-tetraose (LNT), lacto-N-neotetraose (LNnT), 2âfucosyllactose (2âFL), 3-fucosyllactose (3FL), 6âsialyllactose (6âSL) and porcine mucin (MUC). RNA was extracted and sequenced, in duplicate, on an Illumina HiSeq. Early, mid, and late timepoints in response to pooled HMO were additionally sequenced in duplicate.

2015-10-28 | E-GEOD-59053 | biostudies-arrayexpress

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