A promising novel strain of L. reuteri DSM20016 as a chassis for synthetic biology applications
Bibliographic record
Abstract
Limosilactobacillus reuteri strain DSM 20016 is specialised to colonize the human gut for much longer than other L. reuteri strains and most other Lactobacillaceae family members. These adaptations, along with its safe-to-consume food status and public acceptance as a probiotic, make it an attractive chassis for synthetic biology endeavours aimed at introducing novel functions into the gut microbiome, including feedback systems for sensing disease state and therapeutic applications for remedying chronic disorders. Here, we perform whole-genome sequencing and present a novel variant of L. reuteri DSM 20016 (now denoted “LAD4” in this work; DSMZ repository number 116333) with mutations that disrupt DNA restriction-modification and cell wall regulation; these appear to enable increased uptake of the PAMβ1-origin low copy-number plasmid pTRKH3. Additional mutations include genes involved in protein degradation ability, alkaline shock responses, and a mobile genetic element transfer. One of these mutations, or some combination of them, enables stable, consistent production and detection, without the need to buffer media, of the acid-resistant reporter protein mCherry2. This novel variant, in combination with the pTRKH3 plasmid backbone, will enable researchers to more easily utilize this uniquely positioned microbe, which was previously limited by inconsistent reporter protein production and unreliable growth characteristics.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
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 teacher head, 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".