Dataset Information

Genome-wide identification of small RNAs in Bifidobacterium animalis subsp. lactis KLDS 2.0603 and their regulation role in the adaption to gastrointestinal environment.

ABSTRACT: OBJECTIVE:Bifidobacteria are one of the predominant bacterial species in the human gastrointestinal tract (GIT) and play a vital role in the host's health by acting as probiotics. However, how they regulate themselves to adapt to GIT of their host remains unknown. METHODS:Eighteen bifidobacterial strains were used to analyze their adaptive capacities towards simulated GIT environment. The strain with highest survival rate and adhesion ability was selected for comparative genome as well as transcriptomic analysis. RESULTS:The Bifidobacterium animalis subsp. lactis KLDS 2.0603 strain was demonstrated to have the highest survival rate and adhesion ability in simulated GIT treatments. The comparative genome analysis revealed that the KLDS 2.0603 has most similar whole genome sequence compared with BB-12 strain. Eleven intergenic sRNAs were identified after genomes prediction and transcriptomic analysis of KLDS 2.0603. Transcriptomic analysis also showed that genes (mainly sRNAs targeted genes) and sRNAs were differentially expressed in different stress conditions, suggesting that sRNAs might play a crucial role in regulating genes involved in the stress resistance of this strain towards environmental changes. CONCLUSIONS:This study first provided deep and comprehensive insights into the regulation of KLDS 2.0603 strain at transcription and post-transcription level towards environmental.

SUBMITTER: Zhu DQ

PROVIDER: S-EPMC4338058 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Genome-wide identification of small RNAs in Bifidobacterium animalis subsp. lactis KLDS 2.0603 and their regulation role in the adaption to gastrointestinal environment.

Zhu De-Quan DQ Liu Fei F Sun Yu Y Yang Li-Mei LM Xin Li L Meng Xiang-Chen XC

PloS one 20150223 2

<h4>Objective</h4>Bifidobacteria are one of the predominant bacterial species in the human gastrointestinal tract (GIT) and play a vital role in the host's health by acting as probiotics. However, how they regulate themselves to adapt to GIT of their host remains unknown.<h4>Methods</h4>Eighteen bifidobacterial strains were used to analyze their adaptive capacities towards simulated GIT environment. The strain with highest survival rate and adhesion ability was selected for comparative genome as ...[more]

PMID: 25706951

Similar Datasets

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 sequencing to assess the transcriptional differences related to genomic polymorphisms. We detected specific stress responses to the antibiotic by correlating ATP concentration to number of 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 multidrug 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 upregulated only during subinhibitory tetracycline concentrations, while two novel tetracycline resistance genes were upregulated at high concentrations. Furthermore, many genes involved in amino acid metabolism and transporter function were upregulated, while genes for complex carbohydrate utilization, protein metabolism, and clustered regularly interspaced short palindromic repeat(s) (CRISPR)-Cas systems were downregulated. These results provide high-throughput means for assessing antibiotic resistances of two highly related probiotic strains and determine the genetic network that contributes to the global tetracycline response.IMPORTANCEBifidobacterium animalis subsp. lactis is widely used in human food and dietary supplements. Although well documented to be safe, B. animalis subsp. lactis strains must not contain transferable antibiotic resistance elements. Many B. animalis subsp. lactis strains have different resistance measurements despite being genetically similar, and the reasons for this are not well understood. In the current study, we sought to examine how genomic differences between two closely related industrial B. animalis subsp. lactis strains contribute to different resistance levels. This will lead to a better understanding of resistance, identify future targets for analysis of transferability, and expand our understanding of tetracycline resistance in bacteria.

Dataset Information

Genome-wide identification of small RNAs in Bifidobacterium animalis subsp. lactis KLDS 2.0603 and their regulation role in the adaption to gastrointestinal environment.

Publications

Genome-wide identification of small RNAs in Bifidobacterium animalis subsp. lactis KLDS 2.0603 and their regulation role in the adaption to gastrointestinal environment.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets