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| Status |
Public on Sep 27, 2018 |
| Title |
Transcriptional and functional analysis of Bifidobacterium animalis subsp. lactis exposure to tetracycline |
| Organism |
Bifidobacterium animalis subsp. lactis |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
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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| Overall design |
Two bacterial strains, B. lactis Bl-04 and B. lactis HN019. Control (ISO_0): colonies picked into MRS broth to O.D. 0.16-2.0, diluted 1:500, and grown to O.D. 0.14-0.30 (early log phase; three treatments: 1) (ISO_4) as control, but exposed to 4 µg/mL tetracycline, 2) (LOG_8) as control, but not diluted 1:500 and exposed to 8 µg/mL tetracycline, 3) (LOG_32) as control, but not diluted 1:500 and exposed to 32 µg/mL tetracycline. Two replicates of each.
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| Contributor(s) |
Morovic W, Roos P, Zabel B, Hidalgo-Cantabrana C, Kiefer A, Barrangou R |
| Citation(s) |
30266728 |
| BioProject |
PRJNA481603 |
| Submission date |
Jul 30, 2018 |
| Last update date |
Apr 27, 2022 |
| Contact name |
Wesley w. Morovic |
| E-mail(s) |
wesley.morovic@dupont.com
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| Phone |
608-395-2819
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| Organization name |
DuPont Nutrition & Health
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| Department |
Genomics & Microbiome Science
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| Street address |
3329 Agriculture Dr.
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| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53716 |
| Country |
USA |
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| Platforms (1) |
| GPL25402 |
Illumina HiSeq 2500 (Bifidobacterium animalis subsp. lactis) |
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| Samples (16)
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| Relations |
| SRA |
SRP155754 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE117878_RNAseq_Bl-04_alignment.gff.gz |
1.3 Mb |
(ftp)(http) |
GFF |
| GSE117878_raw_seq_counts.tsv.gz |
510.8 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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