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

ABSTRACT: 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.

ORGANISM(S): Bifidobacterium animalis subsp. lactis

SUBMITTER: Todd Klaenhammer

PROVIDER: E-GEOD-41906 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Transcriptional analysis of oligosaccharide utilization by Bifidobacterium lactis Bl-04.

Andersen Joakim M JM Barrangou Rodolphe R Abou Hachem Maher M Lahtinen Sampo J SJ Goh Yong Jun YJ Svensson Birte B Klaenhammer Todd R TR

BMC genomics 20130510

<h4>Background</h4>Probiotic bifidobacteria in combination with prebiotic carbohydrates have documented positive effects on human health regarding gastrointestinal disorders and improved immunity, however the selective routes of uptake remain unknown for most candidate prebiotics. The differential transcriptomes of Bifidobacterium animalis subsp. lactis Bl-04, induced by 11 potential prebiotic oligosaccharides were analyzed to identify the genetic loci involved in the uptake and catabolism of α- ...[more]

PMID: 23663691

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

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2013-10-23 | GSE41906 | GEO

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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.

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

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

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

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