TEM Experiment and Complete Genome Sequencing with Comparative Genomic Analysis to Uncover Potential Probiotic Features of Isolated <i>Lactobacillus delbrueckii</i> subsp. <i>indicus</i> TY-11
Bibliographic record
Abstract
Abstract Background Probiotics refer to living microorganisms that exerts a variety of beneficial effects on human health. On the contrary, they also can cause infection, produce toxins within the body, and transfer antibiotic resistant genes to the other microorganisms in the digestive tract necessitating a comprehensive safety assessment. This study aimed to conduct functional genomic analysis to uncover the probiotic potential of Lactobacillus delbrueckii subsp. indicus TY-11 isolated from native yogurt in Bangladesh. We also performed Transmission Electron Microscopic (TEM) analysis, comparative genomic study as well as phylogenetic tree construction with 332 core genes from 262 genomes. These experiments on subspecies indicus were not studied previously. Results The strain TY-11 was identified as Lactobacillus delbrueckii subsp. indicus, whose genome (1916674bp) contained genes to adapt to diverse and stressful environments of the human gut, and no gene was identified for either antibiotic resistance or toxic metabolites. It embraced genes for the degradation of toxic metabolites, treatment of lactose intolerance, toll-like receptor 2-dependent innate immune response, heat and cold shock, bile salts tolerance in the gut, and acidic pH tolerance in the stomach. Genes were annotated for inhibiting pathogenic bacteria in the gut by inhibitory substances, (bacteriocin: Helveticin-J (331bp) and Enterolysin-A (275bp), hydrogen peroxide, and acid); blockage of adhesion sites; and competition for nutrients. Its metabolic pathway helped the human gut to recover the digestive disorders and digest indigestible nutrients. The TY-11 genome possessed additional 37 core genes of subspecies indicus which were deficient in the core genome of the most popular subspecies bularicus . Conclusions This is the first study to explore the molecular insights into intestinal residence and probiotic roles including antimicrobial activities of a representative strain (TY-11) of Lactobacillus delbrueckii subsp. indicus .
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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 | 0.001 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.001 | 0.002 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.001 |
| Insufficient payload (model declined to judge) | 0.003 | 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".