Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Bifidobacterium animalis subsp. lactis strain:Bl-04 or HN019

ABSTRACT: Transcriptional responses to tetracycline differ in highly syntenous strains of probiotic Bifidobacterium animalis subsp. lactis.

PROVIDER: PRJNA481603 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other
	SRR7622860.fastq.gz	Fastqsanger.gz
	SRR7622870.fastq.gz	Fastqsanger.gz
	SRR7622861.fastq.gz	Fastqsanger.gz
	SRR7622871.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 17

Similar Datasets

Transcriptional and functional analysis of Bifidobacterium animalis subsp. lactis exposure to tetracycline

Project description:Commercial probiotic bacteria must be tested for acquired antibiotic resistance elements to avoid potential transfer to pathogens. The European Food Safety Authority recommends testing resistance using microdilution culture techniques previously used to establish inhibitory thresholds for the Bifidobacterium genus. Many Bifidobacterium animalis subsp. lactis strains exhibit increased resistance to tetracycline, historically attributed to the ribosomal protection gene tet(W). However, some strains that harbor genetically identical tet(W) genes show various inhibition levels suggesting that other genetic elements also contribute to observed differences. Here, we adapted several molecular assays to confirm the inhibition of B. animalis subsp. lactis strains Bl-04 and HN019, and employed RNA-seq to assess the transcriptional differences related to genomic polymorphisms. We detected specific stress responses to the antibiotic by correlating ATP concentration to viable genome copies from droplet digital PCR, and found that the bacteria were still metabolically active in high drug concentrations. Transcriptional analyses revealed that several polymorphic regions, particularly a novel multi-drug efflux transporter, were differentially expressed between the strains in each experimental condition, likely having phenotypic effects. We also found that the tet(W) gene was up-regulated only during sub-inhibitory tetracycline concentrations, while two novel tetracycline resistance genes were up-regulated at high concentrations. Furthermore, many genes involved in amino acid metabolism and transporter function were up-regulated while genes for complex carbohydrate utilization, protein metabolism, and CRISPR-Cas systems were down-regulated. These results provide high-throughput means for assessing antibiotic resistance and determine the genetic network that contributes to the global tetracycline response between two highly related probiotic strains.

2018-09-27 | GSE117878 | GEO

Expression data from Caenorhabditis elegans fed with the bacterial strain Bifidobacterium animalis sbsp. lactis CECT 8145

2015-11-22 | GSE63531 | GEO

Expression data from Caenorhabditis elegans fed with the bacterial strain Bifidobacterium animalis sbsp. lactis CECT 8145

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

Expression data from Caco-2 cells co-cultivated with B. animalis subsp. lactis BB-12

2010-07-01 | GSE21930 | GEO

Analysis of prebiotic carbohydrate utilization by Bifidobacterium lactis Bl-04 using differential transcriptomics

2013-10-23 | GSE41906 | GEO

Bifidobacterium animalis subsp. lactis Bl-04

Project description:Bifidobacterium animalis subsp. lactis Bl-04 genome sequencing project

| PRJNA32897 | ENA

Expression data from Caco-2 cells co-cultivated with B. animalis subsp. lactis BB-12

Project description:Although intestinal microbiota play a pivotal role in the development of host immune system this biological issue was not so far studied in great detail. In this study we examined immune response of Caco-2 enterocytes after incubation with common probiotic Bifidobacterium animalis subsp. lactis BB-12 for 4 hours. We used microarrays to inspect the global gene expression of Caco-2 cells upon co-culturing with B. animalis subsp. lactis BB-12 and several distinct immune-related genes up-regulated during this process. One time point (T4) and two controls (T0) were analysed. T0 represent differentiated Caco-2 cells cultivated for 3 weeks. T4 represents differentiated Caco-2 cells cultivated for 3 weeks plus consequent 4 hours of co-cultivation with B. animalis subsp. lactis BB-12. 3 technical replicates for T0-1, T0-2 or T4 were pooled to a single sample, RNA extracted and further used in gene expression experiments.

2010-07-30 | E-GEOD-21930 | biostudies-arrayexpress

Analysis of prebiotic carbohydrate utilization by Bifidobacterium lactis Bl-04 using differential transcriptomics

Project description:The global transcriptome of the Bifidobacterium animalis subsp. lactis Bl-04 was analyzed during exponential growth on 11 prebiotic carbohydrates and glucose to identify the specific gene cluster differentially upregulated in response to each carbohydrate. Affymetrix hybridization experiments were performed to compare the differential transcriptional profiles of the B. lactis Bl-04 at the early-log (OD600nm 0.3-0.5) phase. 12 carbohydrates were tested with two technical replicates to each condition for a total of 24 hybridizations.

2013-10-23 | E-GEOD-41906 | biostudies-arrayexpress

miRNAs expression in swine monocytes stimulated with Bifidobacterium animalis ssp. lactis Bb12

Project description:Bifidobacterium animalis ssp. lactis Bb12 (Bb12) is a probiotic bacteria with several reported benefits, including immunomodulatory capacity. This is due to the bacteria recognition by receptors such as TLR2, which in turn affects the miRNA transcriptome of immune system cells. We aimed to analyze miRNA expression in swine monocytes stimulated with Bb12, and their expression when TLR2 receptor is blocked. A microarray containing 407 porcine unique miRNA probes was employed to identify differences in the miRNA expression pattern in swine monocytes in response to Bb12. A total of 143 were differentially expressed miRNAs (p<0.05); out of which, 87 miRNAs are statistically significant but have lower signals (signal <500).

2019-06-30 | GSE132995 | GEO

Transcriptome analysis of Bifidobacterium animalis subsp. lactis BB12 grown on xylo-oligosaccharides

Project description:Comparison of the growth of Bifidobacterium animalis subsp. lactis BB12 in MRS (without carbon source) with either 2% XOS (xylo-oligosaccharides) or 2% glucose using whole-genome transcriptome analysis.

2010-09-10 | GSE20322 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data