Bifidobacterium sp.
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1040429 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR30481589_1.fastq.gz | Fastqsanger.gz | |||
| SRR30481590_1.fastq.gz | Fastqsanger.gz | |||
| SRR30481591_1.fastq.gz | Fastqsanger.gz | |||
| SRR30481592_1.fastq.gz | Fastqsanger.gz |
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Project description:Development of the human gut microbiota commences at birth with bifidobacteria being among the first colonizers of the sterile newborn gastrointestinal tract. To date the genetic basis of bifidobacterial colonization and persistence remains poorly understood. Transcriptomic analysis of the 2,422,684 bp genome of Bifidobacterium breve UCC2003, a strain isolated from a nursling stool, during colonization of a mouse model revealed the differential expression of a type IVb or so-called Tad pilus-encoding cluster. Mutational analysis coupled with colonization experiments demonstrated that the UCC2003 tad gene cluster is essential for colonization. Immunogold transmission electron microscopy confirmed the presence of the Tad pili at the cell poles of B. breve UCC2003. Conservation of the Tad pilus-encoding locus among sequenced bifidobacterial genomes supports the notion of a ubiquitous and novel host colonization and persistence mechanism for bifidobacteria.
2011-07-01 | GSE27491 | GEO
Project description:B. kashiwanohense PV20-2 and B. pseudolongum PV8-2 are strains isolated from breast fed iron deficient Kenyan infants, selected for their high iron sequestration mechanisms and their genome was completely sequenced. Based on their high iron sequestration features we hypothesized that B. kashiwanohense PV20-2 and B. pseudolongum PV8-2, possess iron related genes and excrete iron binding proteins in the culture media under iron limited conditions. Thus, the complete genomes of B. kashiwanohense PV20-2 and B. pseudolongum PV8-2 were compared to other bifidobacterial genomes to identify genes potentially involved in iron metabolism and the coding sequences from the genome were used as a scaffold to identify the extracellular proteome of both strains grown under low iron conditions using a gel-based shotgun proteomic approach.
2015-12-14 | PXD001451 | Pride
Project description:B. kashiwanohense PV20-2 and B. pseudolongum PV8-2 are strains isolated from breast fed iron deficient Kenyan infants, selected for their high iron sequestration mechanisms and their genome was completely sequenced. Based on their high iron sequestration features we hypothesized that B. kashiwanohense PV20-2 and B. pseudolongum PV8-2, possess iron related genes and excrete iron binding proteins in the culture media under iron limited conditions. Thus, the complete genomes of B. kashiwanohense PV20-2 and B. pseudolongum PV8-2 were compared to other bifidobacterial genomes to identify genes potentially involved in iron metabolism and the coding sequences from the genome were used as a scaffold to identify the extracellular proteome of both strains grown under low iron conditions using a gel-based shotgun proteomic approach.
2015-12-14 | PXD001452 | Pride
Project description:This work aimed to investigate the ability of two human-derived bifidobacterial strains, i.e. Bifidobacterium breve UCC2003 and Bifidobacterium longum NCIMB 8809, to utilize various oligosaccharides (i.e., 4-galactosyl-kojibiose, lactulosucrose, lactosyl-oligofructosides, raffinosyl-oligofructosides and lactulose-derived galacto-oligosaccharides) synthesized by means of microbial glycoside hydrolases. With the exception of raffinosyl-oligofructosides, these biosynthetic oligosaccharides were shown to support growth of at least one of the two studied strains. Short-chain fatty acid (SCFA) analysis by HPLC corroborated the suitability of most of the studied novel oligosaccharides as growth substrates for the two bifidobacterial strains, showing that acetate is the main metabolic end product followed by lactic and formic acids. Transcriptomic and functional genomic approaches carried out for B. breve UCC2003 allowed the identification of key genes encoding glycoside hydrolases and protein transport systems involved in the metabolism of 4-galactosyl-kojibiose and lactulosucrose. In particular, the role of β-galactosidases in the hydrolysis of these particular trisaccharides was demonstrated, highlighting their importance in oligosaccharide metabolism by human bifidobacterial strains.
2019-06-18 | GSE132879 | GEO
Project description:Bifidobacteria are among the earliest colonizers of the human gut, conferring multiple health benefits. While multiple Bifidobacterium strains are used as probiotics, accumulating evidence suggests that the individual responses to probiotic supplementation may vary, likely due to a variety of factors, including strain type(s), gut community composition, dietary habits of the consumer, and other health/lifestyle conditions. Given the saccharolytic nature of bifidobacteria, the carbohydrate composition of the diet is one of the primary factors dictating the colonization efficiency of Bifidobacterium strains. Therefore, a comprehensive understanding of bifidobacterial glycan metabolism at the strain level is necessary to rationally design probiotic or synbiotic formulations that combine bacterial strains with glycans that match their nutrient preferences. In this study, we systematically reconstructed 66 pathways involved in the utilization of mono-, di-, oligo-, and polysaccharides by analyzing the representation of 565 curated functional roles (catabolic enzymes, transporters, transcriptional regulators) in 2973 non-redundant cultured Bifidobacterium isolates and metagenome-assembled genomes (MAGs). Our analysis uncovered substantial heterogeneity in the predicted glycan utilization capabilities at the species and strain level and revealed the presence of a yet undescribed phenotypically distinct clade within the Bifidobacterium longum species. We also identified Bangladeshi isolates harboring unique gene clusters tentatively implicated in the breakdown of xyloglucan and human milk oligosaccharides. Predicted carbohydrate utilization phenotypes were experimentally characterized and validated. Our large-scale genomic analysis expands the knowledge of carbohydrate metabolism in bifidobacteria and provides a foundation for rationally designing single- or multi-strain probiotic formulations of a given bifidobacterial species as well as synbiotic combinations of bifidobacterial strains matched with their preferred carbohydrate substrates.
2024-08-08 | GSE239955 | GEO
Project description:Multiple bifidobacterial species RnaSeq transcriptome
| PRJNA289955 | ENA
Project description:Bifidobacterial species Genome sequencing and assembly
| PRJNA379831 | ENA
Project description:Bifidobacterial novel species Genome sequencing and assembly
| PRJNA394715 | ENA
Project description:Modulation of gut microbiota through probiotic supplementation is an interesting strategy to prevent obesity We use microarrays to study the global genome expression of C. elegans fed with the probiotic strain Bifidobacterium animalis sbsp. lactis CECT 8145 Wild type strain N2 of C. elegans was cutured in Nematode Growth medium (NGM, control fed) or NGM with a bacterial lawn fed of the strain B. animalis subsp. lactis CECT 8145, until reach young adult stage. Worm population were age-synchronized. RNA was isolated from each populations (control and treated) using RNAasy Kit (Qiagen) and hybridizated on Affymetrix microarrays.
2015-11-22 | E-GEOD-63531 | biostudies-arrayexpress