Integrated Growth Physiology and Transcriptome Profiling Uncover Probiotic Adaptability of Limosilactobacillus fermentum KUB-D18
Issued Date
2026-03-01
Resource Type
eISSN
23115637
Scopus ID
2-s2.0-105034010175
Journal Title
Fermentation
Volume
12
Issue
3
Rights Holder(s)
SCOPUS
Bibliographic Citation
Fermentation Vol.12 No.3 (2026)
Suggested Citation
He Y., Junyakul S., Raethong N., Nakphaichit M., Mussatto S.I., Vongsangnak W. Integrated Growth Physiology and Transcriptome Profiling Uncover Probiotic Adaptability of Limosilactobacillus fermentum KUB-D18. Fermentation Vol.12 No.3 (2026). doi:10.3390/fermentation12030168 Retrieved from: https://repository.li.mahidol.ac.th/handle/123456789/115982
Title
Integrated Growth Physiology and Transcriptome Profiling Uncover Probiotic Adaptability of Limosilactobacillus fermentum KUB-D18
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Abstract
Limosilactobacillus fermentum KUB-D18 is a probiotic strain with significant potential in food fermentation and health promotion, yet the systems-level mechanisms underlying its physiological robustness remain elusive. To elucidate the metabolic remodeling strategies operating across growth phases, we developed an integrated framework combining genome-scale metabolic modeling (GSMM) with transcriptomics. A high-quality metabolic model for L. fermentum KUB-D18, designated iYH640 and comprising 640 genes, 1530 metabolites, and 1922 reactions, was constructed and validated against experimental growth data. Specifically, in vitro assays measuring biomass and glucose concentrations showed a maximum specific growth rate of 0.2696 h<sup>−1</sup> and a glucose uptake rate of 11.75 mmol gDCW<sup>−1</sup> h<sup>−1</sup>, providing physiological constraints for the model. Using transcriptome-regulated flux balance analysis (TR-FBA), gene expression profiles from the logarithmic phase (L-phase) and stationary phase (S-phase) were integrated to quantify growth phase-specific metabolic flux distributions. These simulations revealed a distinct transcription-driven metabolic shift, in which the organism moves from a proliferation-oriented metabolic state with active central carbon metabolism and macromolecule synthesis to a maintenance-oriented state. This S-phase is characterized by reduced flux through anabolic pathways together with the selective preservation of redox balance and nucleotide homeostasis. Collectively, these results provide a quantitative explanation of how L. fermentum KUB-D18 balances growth and maintenance, offering a mechanistic basis for improving its stability and functional performance in industrial probiotic applications.