Genomic Discovery of Robust Molecular Markers Differentiating Lactobacillaceae Genera and Providing Novel Tools for Functional Insights
Bibliographic record
Abstract
Background: Members of the family Lactobacillaceae, encompassing 23 distinct genera, play essential roles in food fermentation processes such as wine, yogurt, and cheese production and contribute significantly to human health through their probiotic properties. Despite their importance, accurately distinguishing between Lactobacillaceae genera has been challenging due to the absence of reliable biochemical or molecular markers. Currently, these genera are primarily differentiated based on phylogenetic relationships. Methods: To address this limitation, we have performed comprehensive phylogenomic and comparative analyses of protein sequences from 411 publicly available Lactobacillaceae genomes. Results: The results of these analyses have identified 171 novel conserved signature indels (CSIs), within proteins involved in diverse cellular functions, which are specific for the species from different Lactobacillaceae genera. The taxon-specificities of these CSIs make them robust molecular markers for differentiation of Lactobacillaceae genera and for functional insights. Using these taxon-specific CSIs and the AppIndels.com server, we were able to successfully predict the taxonomic affiliation of 112 uncharacterized genomes of Lactobacillus isolates, demonstrating the practical utility of these CSIs for genus-level identification and classification. Structural analyses on representative CSIs specific for Lactobacillaceae genera reported here show that all examined CSIs are located in surface-exposed loops of proteins, suggesting their potential roles in genus-specific functional traits, such as interaction with specific proteins and ligands, host interactions, or environmental adaptations. Conclusions: The CSIs identified here not only provide reliable tools for diagnostic and taxonomic studies but also open new avenues for exploring the functional diversity and biotechnological potential of species from different Lactobacillaceae genera.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
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 | 0.001 | 0.002 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.002 | 0.003 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.002 | 0.001 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.002 | 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".