A phylogenetic perspective on the performance of Lactococcus lactis as starter culture in milk and plant milks
Bibliographic record
Abstract
Lactococcus lactis is used as a starter culture in dairy fermentations but also occurs in spontaneous plant fermentations. Phylogenetic analyses have differentiated Lc. lactis into distinct clades. One clade consists exclusively of dairy isolates, which evolved from a more ancestral clade comprising both plant and dairy isolates. However, it remains unclear whether strains from these clades differ in their ability to ferment milk and plant-based milk. This study aimed to compare the fermentative properties of Lc. lactis from a phylogenetic perspective. A core genome phylogenetic tree based on high-quality Lc. lactis genomes revealed distinct ancestral, plant, and dairy lineages which were not congruent with the current subspecies classification. The phylogeny of the dairy lineage and the geographic origin of the isolates supported domestication of the dairy lineage. A phenotypic analysis of 12 representative strains from the lineages (ancestral, plant and dairy) demonstrated that sugar metabolism and acidification profiles aligned with genotypic differences. Dairy-lineage strains acidified bovine milk more effectively and produced higher levels of lactic acid. In contrast, most strains of the plant-lineage were unable to acidify bovine milk below pH 5.4, or to produce lactic acid in milk. These strains, however, exhibited efficient metabolism of raffinose family oligosaccharides and rapidly acidified lupin milk. Lc. lactis FUA3579, classified within the ancestral lineage, effectively acidified both plant-based and dairy matrices and metabolized sugars in both. This study highlights the metabolic divergence among Lc. lactis lineages and provides insights for selection of starter cultures tailored for milk or plant-based dairy alternatives. • Lactococcus lactis includes a domesticated and ancestral phylogenetic clades. • The domesticated clade lost genes coding for metabolism of sugars other than lactose. • The domesticated clade metabolises lactose with the tagatose phosphate pathway. • The domesticated clade efficiently acidifies milk. • The ancestral clades efficiently acidify plant milk.
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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".