<i>Phyllobacterium meliloti</i> sp. nov. a novel non-symbiotic bacterium isolated from root nodules of <i>Melilotus albus</i> (white sweet clover) grown in Canada
Bibliographic record
Abstract
Abstract Two novel bacterial strains isolated from root-nodules of white sweet clover ( Melilotus albus ) plants grown at a Canadian site were previously characterized and placed in the genus Phyllobacterium . Here we present phylogenomic and phenotypic data to support the description of strain T1293 T as representative of a novel species and present the first complete closed genome sequence of a bacterial strain (T1018) representing the species ‘ P. pellucidum’ . Phylogenetic analysis of genome sequences as well as analysis of 53 core genes placed novel strain T1293 T in a highly supported cluster of strains distinct from named Phyllobacterium species with P. myrsinacearum and P. calauticae as closest relatives. The highest average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values of genome sequences of T1293 T compared to closest species type strains (84.1% and 26.5%, respectively) are well below the threshold values for bacterial species circumscription. The genome of strain T1293 T has a size of 5074034 bp with a DNA G+C content of 55 mol% and possesses three plasmids with sizes of 397619 bp, 476847 bp and 519835 bp. Detected in the genome were Type III and Type VI secretion system genes, implicated in plant-microbe and microbe-microbe interactions, but key nodulation, nitrogen-fixation and photosystem genes were not detected. Further analysis revealed that T1293 T , like other Phyllobacterium species, possesses key genes encoding an enzyme complex implicated in the degradation of glyphosate, a widely used broad-spectrum herbicide that has negative consequences for many microorganisms including the human gut microbiome. A novel prophage (size ∼ 41.5 kb) was also detected in the genome of T1293 T . Data for multiple phenotypic tests complemented the sequence-based characterization of strain T1293 T . The data presented support the description of a new species and the name Phyllobacterium meliloti sp. nov. is proposed with T1293 T = LMG32641 T = HAMBI 3765 T as the species type strain.
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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) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.000 |
| Bibliometrics | 0.000 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| 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".