<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 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 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.001 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.001 | 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 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".