Whole genome sequencing of S. Infantis
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB35626 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR3697220_1.fastq.gz | Fastqsanger.gz | |||
| ERR3697220_2.fastq.gz | Fastqsanger.gz | |||
| ERR3697230_1.fastq.gz | Fastqsanger.gz | |||
| ERR3697230_2.fastq.gz | Fastqsanger.gz | |||
| ERR3697240_1.fastq.gz | Fastqsanger.gz |
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Project description:The deposited microarray data were generated in a study that integrated the gene expression profiles and metabolic responses of Caco2 cells incubated with Bifidobacterium infantis subsp. infantis and Salmonella enterica subsp. enterica sv. Typhimurium. The aim of this study was to investigate the interaction of B. infantis, S. Typhimurium, and host cells (Caco2) in the course of infection to understand the molecular mechanics of probiotic-pathogen-host interactions.
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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
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
Project description:To validate the use of chicken array for turkey, the ability of species-specific hybridization (SSH, chicken samples-chicken arrays) and cross-species hybridization (CSH, turkey samples-chicken arrays) were compared in the same biological conditions. Reproductively active laying chickens and reproductively inactive non-laying pullets were used to generate the results for SSH. Similarly, reproductively active laying turkeys and reproductively inactive non-laying photorefractory turkeys were used to generate the results for CSH.
2015-03-11 | GSE66704 | GEO
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.
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Project description:Salmonella Infantis NRL-AR Italy
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Project description:15N-labeled N-acetylglucosamine (NAG) fed to B. infantis cells are incorporated into its proteome. This indicates that NAG, an amino sugar residue of human milk oligosaccharides (HMO) and other biopolymers, is used as a nitrogen source. Transcriptomics while subsisting on NAG nitrogen are consistent with the proteomics results. This further indicates that B. infantis utilizes NAG nitrogen in and shunts it towards a fundamental cellular processes.
2023-05-18 | PXD035809 | Pride
Project description:The success of turkey breeding for rapid growth rate and larger breast size has coincided with an increasing incidence of a meat quality defect described as pale, soft and exudative (PSE). We hypothesized that this defect, which is associated with an abnormally rapid rate of postmortem metabolism, derives from altered expression of genes involved in metabolic regulation. Our objective was to use deep transcriptome RNA sequence analysis (RNAseq) to identify differentially expressed genes between normal and PSE turkey breasts. Following harvest of turkey breasts (n = 43), the pH at 15 min post-slaughter and percent marinade uptake at 24h post-slaughter were determined. Breast samples were classified as normal or PSE based on marinade uptake (high = normal; low = PSE). Total RNA from samples with the highest (n=4) and lowest (n=4) marinade uptake were isolated and sequenced using the Illumina GAIIX platform. Of 21,340 gene loci discovered by RNAseq, 8480 loci completely matched the turkey reference genome, and 480 genes were differentially expressed (false discovery rate, FDR<0.05) between normal and PSE samples. Two highlights were the genes nephroblastoma overexpressed (NOV), upregulated about 38-fold and pyruvate dehydrogenase kinase isoform 4 (PDK4), downregulated 14-fold in PSE samples. Pathway analysis suggested that several biological functions, including carbohydrate metabolism and energy production, were affected by meat quality. Because PDK4 regulates conversion of pyruvate to acetyl CoA, differences in regulation of oxidative metabolism may exist among turkeys. Accelerated early postmortem metabolism would result in faster pH decline in PSE meat. This hypothesis was supported by the fact that decreased expression of PDK4 was associated with lower pH in PSE samples (pH[PSE] = 5.59±0.09, pH[normal] = 5.77±0.17). The RNAseq results provided a greater molecular mechanistic understanding of development of PSE turkey, which will be a foundation for new intervention strategies to prevent development of this defect.
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