Discovery and assembly of plasmids in the fish pathogen Tenacibaculum
Bibliographic record
Abstract
Members of the marine bacterial genus Tenacibaculum cause disease in finfish and outbreaks result in significant animal harm and losses in aquaculture around the globe. Plasmids have not been previously identified in Tenacibaculum , but long-read DNA sequencing of genomes from disease-associated Tenacibaculum isolates collected between 2017 and 2020 in British Columbia, Canada, revealed circular putative plasmids in three Tenacibaculum species. In addition to high-quality circular assembly, the putative plasmids contained genes encoding plasmid replication, mobility, and partitioning proteins. Genes for type B conjugation machinery and type 6 iii secretion system components were also identified on each of the two largest plasmid sequences. Several protocols were tested to visualize and enrich Tenacibaculum plasmid DNA. Rolling-circle replication with Phi29 DNA polymerase amplified putative plasmids smaller than 100 kb. Alkaline lysis extraction provided weak enrichment of putative plasmid DNA, and plasmids could not be confidently resolved by Eckhardt extraction and electrophoresis in agarose gels. The newly assembled plasmids matched previously sequenced Tenacibaculum contigs, highlighting that publicly available Tenacibaculum genomes contain unrecognized plasmids. The discovery of putative plasmids in Tenacibaculum is significant because plasmids often confer important functions to host cells and serve as vehicles for horizontal gene transfer within and beyond the host species.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.002 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.000 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.001 | 0.001 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".