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

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

PROVIDER: PRJNA688501 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13324423_1.fastq.gz	Fastqsanger.gz
	SRR13324423_2.fastq.gz	Fastqsanger.gz
	SRR13324424_1.fastq.gz	Fastqsanger.gz
	SRR13324424_2.fastq.gz	Fastqsanger.gz
	SRR13324425_1.fastq.gz	Fastqsanger.gz

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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

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

2015-10-28 | GSE58773 | GEO

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

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

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

Human Milk Oligosaccharide Utilization in Intestinal Bifidobacteria is Governed by Global Transcriptional Regulator NagR

Project description: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. A bioinformatic regulon reconstruction approach used in this study implicated NagR, a transcription factor from the ROK family, as a negative global regulator of genomic loci encoding lacto-N-biose/galacto-N-biose (LNB/GNB), lacto-N-tetraose (LNT), and lacto-N-neotetraose (LNnT) utilization pathways in B. infantis. This conjecture was corroborated by transcriptome profiling upon nagR genetic inactivation and experimental assessment of binding of recombinant NagR to predicted DNA operators. The latter approach also implicated N-acetylglucosamine (GlcNAc), a universal intermediate of LNT and LNnT catabolism, and its phosphorylated derivatives as plausible NagR effectors. Reconstruction of NagR regulons in various Bifidobacterium lineages revealed multiple regulon expansion events, suggesting evolution from a local regulator of GlcNAc catabolism in ancestral bifidobacteria to a global regulator controlling foraging of mixtures of GlcNAc-containing host-derived glycans in mammalian gut-colonizing B. infantis and Bifidobacterium bifidum.

2022-04-02 | GSE196064 | 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

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

Comparative genomic hybridization by array of Bifodobacterium longum strains exhibiting various human milk oligosaccharide utilization phenotypes and host associations

Project description:Whole genome microarray comparisons (comparative genomic hybridizations) were used to associate genotypic biomarkers among 15 Bifidobacterium longum strains exhibiting various Human Milk Oligosaccharide utilization phenotypes and host associations.

2010-10-21 | E-MEXP-2951 | biostudies-arrayexpress

RNA sequencing of CACO-2 cells incubated with bifidobacteria grown on human milk oligosaccharides.

Project description: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. The purpose of the current study was to investigate the effects of carbon source—glucose, lactose, or HMO—on the ability of B. breve and B. infantis to adhere to and affect the transcription of intestinal epithelial cells on a genome-wide basis. Results: HMO-grown B. infantis had higher percent binding to Caco-2 cell monolayers compared to B. infantis grown on glucose or lactose. B. breve had low adhesive ability regardless of carbon source. Despite differential binding ability, both HMO-grown strains significantly differentially affected the Caco-2 transcriptome compared to their glucose or lactose grown controls. HMO-grown B. breve and B. infantis both down-regulated genes in Caco-2 cells associated with chemokine activity. Conclusion: The choice of carbon source affects the interaction of bifidobacteria with intestinal epithelial cells. HMO-grown bifidobacteria reduce markers of inflammation, compared to glucose or lactose-grown bifidobacteria. In the future, the design of preventative or therapeutic probiotic supplements may need to include appropriately chosen prebiotics.

2017-02-10 | GSE63950 | GEO

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