This study was conducted to evaluate the bioactive (antioxidant and antimicrobial) properties of essential oils (EOs) from seven genotypes of Lippia gracilis Schauer (LGRA106, LGRA107, LGRA108, LGRA109, LGRA110, LGRA201, and LGRA202). In addition, predictive models of bacterial growth under different pH conditions (5.0, 6.0, and 9.0), in the presence and absence of LGRA 109 EO (1.32, 2.64, or 5.29 mg/mL), were obtained. The LGRA106 and LGRA109 EOs exhibited strong antioxidant (2652.2 μmol Trolox/L via the FRAP method) and antimicrobial (minimum inhibitory and minimum bactericidal concentrations of 1.32-2.64 mg/mL) activities, respectively. The Baranyi and Roberts model showed good agreement with the experimental data, with coefficients of determination ranging from 0.84 to 0.99 and adequate representation of the growth curves. The model was validated using Bias and accuracy factor values of 1, and root mean square error values ranging from 0.02 to 0.14. The model was applied to predict bacterial growth under the tested conditions. Lag phase time and maximum specific growth rate parameters were determined for all the tested bacteria. The combination of pH and EO was effective in inhibiting the growth of Staphylococcus aureus, Escherichia coli, and Salmonella Typhimurium. These results demonstrate that L. gracilis EOs are potent natural antioxidants and antimicrobials that may be further explored for applications in the pharmaceutical, food, and cosmetic industries.

Outbreaks involving Salmonella in mangoes from Brazil have been reported in importing countries, causing social and economic losses, especially to consumers. This study aimed to develop predictive models for the growth kinetics of Salmonella enterica serovar Typhi in the peel and pulp of Tommy Atkins mangoes as a function of temperature, as well as to evaluate the transfer of S. enterica serovar Typhimurium from contaminated to non-contaminated fruits. No significant differences in kinetic parameters were observed between peel and pulp. At lower temperatures (7, 10, and 15 °C), significant differences (p ≤ 0.05) were found in lag phase (λ), whereas at higher temperatures (25, 30, and 35 °C), significant differences were observed in the maximum specific growth rate (µ). The secondary models developed (R² > 0.88) adequately described the effect of temperature on λ and µ in both peel and pulp. In the transfer assay, the passage of S. Typhimurium from the surface of inoculated mangoes to non-inoculated fruits was low. The hydrothermal treatment with chlorine was more effective in reducing S. Typhimurium transfer rates compared with hydrothermal treatment without sanitizer. The results demonstrate that both the peel and pulp of mangoes support Salmonella growth over a wide temperature range and indicate that exposure of Tommy Atkins mango surfaces to chlorinated solution during hydrothermal treatment may reduce the risk of salmonellosis.

With the advance of gene sequencing technology, genome-scale metabolic models have become favored tools for systematically analyzing microbial metabolic networks. In this study, a genome-scale metabolic model of Bifidobacterium animalis subsp. lactis BLa80 was constructed via a semi-automated modeling approach and subsequently validated, providing a tool for subsequent research into its metabolic mechanisms and probiotic functions. In terms of structural quality, the model achieved a Memote score of 82%. For wet-lab validation, the model's simulations of growth on fourteen single carbon sources and amino acid requirements were fully consistent with experimental findings. The maximum specific growth rate and the corresponding specific production rates of two major organic acids predicted by the model based on the existing synthetic medium and modified MRS medium showed errors within 5% and 10%, respectively, compared to the experimental results. The final model, designated iMJ519, comprises 1 005 reactions, 1 047 metabolites, and 519 genes, providing a powerful tool for in-depth research on the growth and metabolic regulation of B. lactis BLa80.

The industrial application of starter cultures requires stable physiological and genetic performance. In this study, Streptococcus salivarius subsp. thermophilus and Lactobacillus delbrueckii subsp. bulgaricus were continuously subcultured. Physiological stability was assessed through colony morphology, fermentation activity, and growth profiling. Genetic stability was evaluated through comparative genomics of carbohydrate metabolism networks and single-nucleotide polymorphism (SNP) analysis. The results showed that after 2000 generations, the cellular morphology of the strains remained intact. Additionally, the strains exhibited enhanced growth performance and fermentation capability. The Gompertz model revealed that adapted S. thermophilus A37 and L. bulgaricus B29 exhibited shortened lag phases, increased maximum specific growth rates, and high stationary-phase cell densities. Phenotypic microarray and comparative genomics revealed that S. thermophilus mainly used mono- and disaccharides, with impaired ribose metabolism due to the absence of the rbsk gene in the pentose phosphate pathway. In contrast, L. bulgaricus metabolized diverse oligosaccharides, sugar alcohols, and plant-derived substrates. Additionally, it effectively catabolized ribose through the phosphoketolase pathway and possessed a trehalose degradation cluster. All strains exhibited genomic stability, with SNPs revealing fewer than 21 variations per isolate. This study provides an important theoretical foundation for evaluating the stability of fermentation starter cultures.

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−1 and a glucose uptake rate of 11.75 mmol gDCW−1 h−1, 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.

The application of Genome-Scale Metabolic Network Models (GSMM) in fermentation optimization is hampered by challenges in differentiating viable from dead cells and parameter distortion induced by conventional detection methods. Using E. coli BL21(DE3) as the model organism, this study developed a flux analysis strategy that couples cell kinetics with GSMM. Key parameters were estimated using the gradient descent algorithm, thereby enabling precise prediction of viable cell concentration and glucose consumption dynamics. Integrating this with the Quadratic Programming-based parsimonious Flux Balance Analysis (QP-pFBA) algorithm, intracellular metabolic reaction fluxes were quantified. Results demonstrated that the model can effectively differentiate viable from dead cells; Batch D, adopting the gradient-increasing feeding strategy, achieved the maximum specific growth rate (μmax) of 0.6457, the highest among the four batches. Moreover, key metabolic reaction fluxes were highly correlated with the feeding strategy. This framework forgoes specialized, high-cost equipment and offers robust cross-strain/process adaptability, thereby greatly advancing GSMM utility. It provides a powerful tool for precise fermentation control and accelerates the shift toward data-driven biomanufacturing.

Xylaria karsticola NBIMCC 9097 is a recently described and rare fungicolous species originating from Bulgaria. Understanding its growth behavior and bioactive potential is essential for evaluating its biotechnological and pharmaceutical relevance. In the presented study, we model the in vitro growth kinetics of X. karsticola mycelium under submerged cultivation and assess its antimicrobial activity. Optimization of MCM and MYB media markedly increased biomass yields to 20.11 and 23.25 g/dm3, respectively, compared with non-optimized media (9.9 ± 0.21 and 10.8 ± 0.28 g/dm3). The maximum specific growth rate was higher in the MCM (0.803 ± 0.004 h-1) in comparison with the MYB medium (0.711 ± 0.003 h-1); however, the MYB medium supported greater biomass accumulation and more efficient substrate utilization, reflected by a higher utilization coefficient (0.9900 ± 0.001 versus 0.9644 ± 0.005). The antimicrobial activity was evaluated using agar disk diffusion and minimum inhibitory concentration assays against Gram-positive and Gram-negative bacteria and yeasts. Hexane and ethyl acetate extracts were most effective against Pseudomonas aeruginosa ATCC 9027 (MIC 0.067 and 0.059 mg/cm3), while notable anti-yeast activity was observed, particularly against Wickerhamomyces anomalus, Saccharomycodes ludwigii, and Pichia membranifaciens. The lowest MIC (0.02 mg/cm3) was recorded for the water biomass extract against S. ludwigii indicating potent antimicrobial activity against the tested microorganism. These findings identify X. karsticola as a potential source of antimicrobial metabolites and provide a strong motivation for comprehensive metabolomic profiling and systematic optimization of its cultivation.

Synthetic autotrophs are a promising platform for sustainable bioproduction using CO2 as substrate. The methylotrophic yeast Komagataella phaffii has been engineered to use CO2 as the sole carbon source by integration of the Calvin-Benson-Bassham (CBB) cycle, based on its native methanol assimilating xylulose monophosphate (XuMP) cycle. Initial growth rates were low, but could be doubled by adaptive laboratory evolution (ALE). Beneficial mutations led to a decrease of CBB cycle reactions, indicating further limitations. During this study, temperature was identified as one of the key process parameters to improve autotrophic growth. For this reason, a new round of adaptive laboratory evolution was performed at the identified optimal cultivation temperature of 25°C, resulting in clones growing up to 50 % faster compared to the control strain. Whole genome re-resequencing followed by reverse engineering helped to identify first key mutations of the evolved strains. In addition, targeted engineering was performed by increasing the copy number of the key gene of the CBB cycle, RuBisCO, which is the bottleneck for carbon fixation. Combining this strategy together with optimal temperature conditions for cultivation, boosted maximum specific growth rates of the autotrophic K. phaffii strain. In comparison to ALE, the targeted engineering still is lagging behind a bit. Starting from the initial condition, growth was improved more than 2.5-fold in this study reaching a maximum of 0.025 h-1.

Micro-nano bubbles enhanced biodegradation of n-hexane by a new isolated Pseudomonas sp. ZZH-1.

Valorization of biomaterial side Streams: Kinetics of cassava pulp and its components degradation by Clostridium manihotivorum CT4T

Dual effect of seawater as a chemical and solvent in the pretreatment, saccharification and fermentation of corn cobs for lactic acid production

Vibrio parahaemolyticus is a foodborne pathogen that can cause severe gastroenteritis. After entering the human intestine through contaminated seafood (1.00% NaCl) V. parahaemolyticus will encounter a physiologically related dual pressure environment: low salinity and elevated bile salts (0.03%-0.30%). Although bile salts can affect V. parahaemolyticus under optimal salinity conditions (3.00% NaCl), little is known about their effects on paralysis under low salt conditions (0.90% NaCl) in the intestinal stress environment. This research uniquely simulated this intestinal niche using 0.90% NaCl-0.10% bile salts, revealing its effects on growth kinetics, motility, biofilm formation, and transcriptome responses. The main findings include: significant inhibition of growth (prolonged the lag time (LT)), decreased the maximum specific growth rate (µmax)), swimming ability, and biofilm formation; But it enhances the ability to swarming; And unique transcriptome reprogramming. In addition, transcriptome sequencing revealed that swarming related genes, biofilm related genes, and T3SS virulence genes were significantly down regulated, while iron metabolism and swimming related genes were significantly up-regulated. It is crucial that KEGG enrichment indicates that the ribosomal pathway may be the central regulatory hub for observed biofilm and motility inhibition. This research provides the first comprehensive analysis of the effects of bile salts on intestinal related low salinity, providing important insights into the intestinal adaptation and pathogenic mechanisms of V. parahaemolyticus.

ABSTRACT The accumulation of carbon monoxide (CO) in goafs is a key challenge in preventing and controlling mining disasters, as it can easily trigger violent explosions. Therefore, Pseudomonas (M1), Chryseobacterium (M3), and Comamonas (M13) were extracted from the mine environment for cocultivation. They were used to study their metabolism of goaf CO under different temperatures, microbial inoculation levels and ventilation conditions. The results showed that the synergistic effect of enzyme catalysis kinetics and mass transfer efficiency is the key mechanism regulating bacterial metabolism. The optimal inoculation amount of microorganisms is 10%. Ventilated conditions enhanced the CO metabolic rate, with the M13 strain showing a more robust metabolic response to environmental disturbances. During the coal oxidation stage, the three strains exhibited high CO metabolic activity at 35–60°C. The peak CO concentration was 6.183 ppm, significantly lower than the 55.14 ppm detected in the raw coal group. When the temperature rose to 60–100°C, high temperature caused irreversible enzyme inactivation, reducing CO metabolic rate. Additionally, neither air leakage nor inoculation amount significantly affected strain metabolism. The growth curves of M1, M3 and M13 all conform to the logistic model. Their maximum specific growth rates were 0.995d−1, 1.558d−1 and 1.154d−1, and decay coefficients were −0.497d−1, −0.22d−1 and −0.613d−1. Based on the CO metabolic reaction equation and gas-liquid mass transfer analysis, the CO biochemical degradation rates were 7.83%% d−1, 2.3%% d−1 and 9.49% d−1. The M13 exhibited the best metabolic CO performance. This study has important theoretical and practical significance for the prevention and control of coal mine CO and safe mining.

The escalating global demand for large-scale, cost-effective, and sustainable high-quality protein has positioned single-cell protein (SCP) production from one-carbon (C1) gases as a highly promising solution. In this study, eight chemolithoautotrophic hydrogen-oxidizing bacteria (HOB) were isolated from mangrove sediments. Based on the 16S rRNA gene sequence analysis, they belonged to genera Sulfurimonas, Sulfurovum, Thiomicrolovo, and Marinobacterium. Among these, Thiomicrolovo sp. ZZH C-3 was identified as the most promising candidate for SCP production based on the highest biomass and protein content, and was selected for further characterization. Strain ZZH C-3 is a Gram-negative, short rod-shaped bacterium with multiple flagella. It can grow chemolithoautotrophically by using molecular hydrogen as an energy source and molecular oxygen as an electron acceptor. Genomic analysis further confirmed that ZZH C-3 harbors a complete reverse tricarboxylic acid (rTCA) cycle gene set for carbon fixation, and diverse hydrogenases (Group I, II, IV) for hydrogen oxidation. Subsequently, its cultivation conditions and medium composition for SCP production were systematically optimized using single-factor experiments and response surface methodology (RSM). Results showed that the optimal growth conditions were 28 °C, pH 7.0, and with 1 g/L (NH4)2SO4 as the nitrogen source, 5-10% oxygen concentration, 9.70 mg/L FeSO4·7H2O, 0.17 g/L CaCl2·2H2O, and 1.90 mg/L MnSO4·H2O. Under the optimized conditions, strain ZZH C-3 achieved a maximum specific growth rate of 0.46 h-1. After 28 h of cultivation, the optical density at 600 nm (OD600) reached 0.94, corresponding to a biomass concentration of 0.60 g/L, and the protein content ranked at 73.56%. The biomass yield on hydrogen (YH2) was approximately 3.01 g/g H2, with an average H2-to-CO2 consumption molar ratio of about 3.78. Compared to the model HOB Cupriavidus necator, strain ZZH C-3 exhibited a lower H2/CO2 consumption ratio, superior substrate conversion efficiency, and high protein content. Overall, this study not only validated the potential of mangrove HOB for SCP production but also offers new insights for future metabolic engineering strategies designed to enhance CO2-to-biomass conversion efficiency.

The production of a functional ingredient (FI) containing Lactobacillus acidophilus (ATCC 4356) immobilised in oat bran was designed and optimised. The effects of the independent variables, incubation time and hydration level, were analysed and optimised to simultaneously maximise the cell count and growth, as well as the yield of the obtained FI and the resistance of the probiotic to simulated gastric conditions after 7 days of storage at 25°C, minimising pH and nutrient loss (proteins and carbohydrates) in the washing water. The optimal design conditions found were 60h of incubation and 13 mL of water/g oat bran. The growth kinetics of L. acidophilus was determined for the optimal system, showing no lag phase and the maximum specific growth rate (µmax) of 1.1 ± 0.1h- 1. The system with an optimal hydration level (13 mL/g oat bran) and 36h of fermentation was selected for being scaled-up in one order of magnitude. A reduction in cell growth, in the FI yield, and an increase in the value of the titratable acidity of the recovered supernatants were observed. During the fermentation, the acids produced were mainly lactic acid followed by acetic acid. It must be highlighted that the fermentation process proposed, reduced the initial oxalic acid content in oat bran. The production of FI based on oat bran containing L. acidophilus represented a sustainable process that also improved the nutritional aspects of the raw material. Oat bran could be by itself an adequate support for L. acidophilus storage stabilisation.

Elucidating the characteristic pleasant aroma profile and underlying molecular sensory mechanisms in vine tea (Ampelopsis grossedentata) cells: a novel supplementary resource for substitute tea.

This study investigated the growth dynamics of Salmonella spp. on parsley under three storage temperatures (15°C, 25°C, and 35°C) using the Baranyi primary model and relevant secondary models. Growth parameters, including maximum specific growth rate (μmax), lag time (tlag), and maximum population density (ymax), were significantly influenced by temperature. At 35°C, Salmonella exhibited rapid proliferation (μmax =1.40 h⁻¹), minimal lag (tlag =1.79 h), and high population density (ymax =7.05 log CFU/g), reaching hazardous levels in less than 24 hours. These findings highlight the critical importance of maintaining cold chain integrity to limit Salmonella growth on parsley. The application of predictive models provides a valuable tool for microbial risk assessment and can inform food safety management strategies, particularly in settings with inadequate refrigeration.

Chitin valorization through microbial bioprocessing relies on efficient utilization of its monomeric units as fermentation substrates. In this study, the effects of salt concentration and the mixing ratio of N-acetylglucosamine (GlcNAc) to glucosamine hydrochloride (GlcN·HCl) on the specific growth rate of our previously isolated V. natriegens N5.3 was investigated in the shake-flask. Batch and fed-batch fermentations using chitin-derived amino sugars were further performed to assess high-cell-density cultivation potential.Although the maximum specific growth rate ( ) at 60 g/L NaCl was nearly two-fold lower than that at the optimal concentration of 15 g/L, strain N5.3 retained robust growth with values of 0.37 h-1 on GlcN·HCl and 0.66 h-1 on GlcNAc. Fed-batch cultivation yielded a maximum cell dry weight (CDW) of 42.3 g/L within 9 h on GlcNAc, with of 0.53 h-1, but with a low biomass yield ( = 0.16 g/g). In contrast, a substrate mixture containing 5% (w/w) GlcNAc and 95% (w/w) GlcN·HCl maintained a high (0.49 h-1) while substantially improving (0.29 g/g), resulting in a CDW of 35.5 g/L after 9 h. Due to low solubility of both amino sugars, exponential feeding with non-sterilized powders was successfully applied. The absence of contamination demonstrate the feasibility of this approach. These results demonstrate that the mixture of GlcNAc:GlcN·HCl (1:19 ratio) is effective substrate for cultivation of V. natriegens N5.3. This provides a promising foundation for the microbial conversion of chitin-derived feedstocks into high-value products.

We demonstrate that the commonly assumed matrix-independence of the cardinal (minimum, optimum and maximum) temperatures for bacterial growth is not necessarily valid for Bacillus licheniformis growing in plant-based milk. If confirmed, a consequence is that the ratio (called correction factor) between the maximum specific growth rate in a specific food matrix and in culture medium is not temperature-independent for every food matrix, opposed to general expectations. We found that, while the cardinal temperatures of B. licheniformis growing in either white almond or coconut beverages did not significantly differ from those in culture medium, this was not the case for another almond-based beverage, where we observed a smaller growth range and lower optimum temperature. A possible reason for this is that the food composition affects the cardinal temperatures. Our investigation is an example of "tertiary modelling" inasmuch it studies the effect of food matrix (a category variable) on the parameters of secondary models.

Harmful algal blooms (HABs) threaten ecosystems, aquaculture, and public health worldwide. However, current monitoring tools are limited to satellite imaging, which is too slow and spatially coarse, or chlorophyll assays which lack specificity for species and sensitivity to early physiological shifts. Anticipating bloom onset requires real-time, species-specific probes that can reproduce how environmental drivers shape algal growth. Here, we introduce uncoated FEP microcapillary strips as an advanced cultivation platform that enables cell-level tracking of microalgal growth under controlled nutrient and light conditions. Using Parachlorella kessleri as a model, we systematically tested the effects of light intensity, gas permeability, and nitrogen-to‑phosphorus (N:P) stoichiometry on growth dynamics. As expected, light availability governed both growth rates and exponential onset of growth, with cultivation in dark conditions fully suppressing cell proliferation. Gas-permeable uncoated FEP strips supported higher densities than encapsulated or PVOH-coated strips, highlighting the critical role of O₂/CO₂ exchange. Nutrient stoichiometry further modulated the kinetics of exponential growth for cultures under balanced conditions. A nitrogen to phosphorous, N:P ratio of 11:1 yielded a high cell density of 4.1×107±5.6×106 cells/mL, whereas excess nitrogen, corresponding to a N:P ratio of 47:1, suppressed expansion by nearly 50%. Although maximum specific growth rates were found stable across the range of conditions tested, the timing of exponential initiation and the final yields were strongly dependent on the microenvironment. This positions uncoated FEP microcapillary strips as a sensitive probe for analysis of environmental drivers of HAB dynamics, enabling early, high-resolution detection of bloom-favouring conditions and advancing predictive bloom surveillance.