Influence of extracellular pH on growth, viability, cell size, acidification activity, and intracellular pH of Lactococcus lactis in batch fermentations

Integration Approaches to Model Bioreactor Hydrodynamics and Cellular Kinetics for Advancing Bioprocess Optimisation

Large-scale bioprocesses are increasing globally to cater to the larger market demands for biological products. As fermenter volumes increase, the efficiency of mixing decreases, and environmental gradients become more pronounced compared to smaller scales. Consequently, the cells experience gradients in process parameters, which in turn affects the efficiency and profitability of the process. Computational fluid dynamics (CFD) simulations are being widely embraced for their ability to simulate bioprocess performance, facilitate bioprocess upscaling, downsizing, and process optimisation. Recently, CFD approaches have been integrated with dynamic Cell reaction kinetic (CRK) modelling to generate valuable information about the cellular response to fluctuating hydrodynamic parameters inside large production processes. Such coupled approaches have the potential to facilitate informed decision-making in intelligent biomanufacturing, aligning with the principles of "Industry 4.0" concerning digitalisation and automation. In this review, we discuss the benefits of utilising integrated CFD-CRK models and the different approaches to integrating CFD-based bioreactor hydrodynamic models with cellular kinetic models. We also highlight the suitability of different coupling approaches for bioprocess modelling in the purview of associated computational loads.

bglG Regulates the Heterogeneity Driven by the Acid Tolerance Response in Lacticaseibacillus paracasei L9

The acid tolerance of lactic acid bacteria is crucial for their fermentation and probiotic functions. Acid adaption significantly enhances the acid tolerance of strains, and the phenotypic heterogeneity driven by the acid tolerance response (ATR) contributes to this process by providing a selective advantage in harsh environments. The mechanism of heterogeneity under the ATR is not yet clear, but individual gene expression differences are recognized as the cause. In this study, we observed four heterogeneous subpopulations (viable, injured, dead, and unstained) of Lacticaseibacillus paracasei L9 (L9) induced by acid adaption (pH 5.0, 40 min) using flow cytometry. The viable subpopulation represented a significantly superior acid tolerance to the injured subpopulation or total population. Different subpopulations were sorted and transcriptomic analysis was performed. Five genes were found to be upregulated in the viable subpopulation and downregulated in the injured subpopulation, and bglG (LPL9_RS14735) was identified as having a key role in this process. Using salicin (glucoside)-inducing gene expression and gene insertion mutagenesis, we verified that bglG regulated the heterogeneity of the acid stress response and that the relevant mechanisms might be related to activating hsp20. This study provides new evidence for the mechanism of the ATR and may contribute to the theoretical basis of improving the acid tolerance of Lacticaseibacillus paracasei L9.

Microfluidic single-cell scale-down bioreactors: A proof-of-concept for the growth of Corynebacterium glutamicum at oscillating pH values

In large-scale bioreactors, gradients in cultivation parameter such as oxygen, substrate and pH result in fluctuating cell environments. pH fluctuations were identified as a critical parameter for bioprocess performance. Traditionally, scale-down systems at the laboratory scale are used to analyze the effects of fluctuating pH values on strain and thus process performance. Here, we demonstrate the application of dynamic microfluidic single-cell cultivation (dMSCC) as a novel scale-down system for the characterization of Corynebacterium glutamicum growth using oscillating pH conditions as a model stress-factor. A detailed comparison between two-compartment reactor (two-CR) scale-down experiments and dMSCC was performed for one specific pH oscillation between reference pH 7 (~ 8 min) and disturbed pH 6 (~2 min). Similar reductions in growth rates were observed in both systems (dMSCC 21% and two-CR 27%) compared to undisturbed cultivation at pH 7. Afterwards, systematic experiments at symmetric and asymmetric pH oscillations between pH ranges of 4-6 and 8-11 and different intervals from 1 minute to 20 minutes, were performed to demonstrate the unique application range and throughput of the dMSCC system. Finally, the strength of the dMSCC application was demonstrated by mimicking fluctuating environmental conditions of a putative large-scale bioprocesse, which is difficult to conduct using two-CRs. This article is protected by copyright. All rights reserved.

Digital models in biotechnology: Towards multi-scale integration and implementation

Industrial biotechnology encompasses a large area of multi-scale and multi-disciplinary research activities. With the recent megatrend of digitalization sweeping across all industries, there is an increased focus in the biotechnology industry on developing, integrating and applying digital models to improve all aspects of industrial biotechnology. Given the rapid development of this field, we systematically classify the state-of-art modelling concepts applied at different scales in industrial biotechnology and critically discuss their current usage, advantages and limitations. Further, we critically analyzed current strategies to couple cell models with computational fluid dynamics to study the performance of industrial microorganisms in large-scale bioprocesses, which is of crucial importance for the bio-based production industries. One of the most challenging aspects in this context is gathering intracellular data under industrially relevant conditions. Towards comprehensive models, we discuss how different scale-down concepts combined with appropriate analytical tools can capture intracellular states of single cells. We finally illustrated how the efforts could be used to develop digitals models suitable for both cell factory design and process optimization at industrial scales in the future.

Use of qPCR for the analysis of population heterogeneity and dynamics during Lactobacillus delbrueckii spp. bulgaricus batch fculture

Direct molecular methods such as real-time polymerase chain reaction (qPCR) and propidium monoazide (PMA)-qPCR have been successfully used for quantifying viable microorganisms in the food industry. This study attempted to use qPCR and PMA-qPCR for quantifying Lactobacillus delbrueckii spp. bulgaricus sp1.1 physiological states. The qPCR standards of the 16S rRNA gene were employed to calibrate the qPCR assay, which contributed to an amplification efficiency of 98.42%. The number of copies of the 16S rRNA gene was linearly related to cell density, and this linear relationship was used to construct a quantitative curve (R² =0.9981) with a detection limit of 15.1 colony-forming units mL^-1·reaction^-1. qPCR in combination with an optimal PMA concentration (60 μM) helped in discriminating and quantifying the viable cells, without any interference by heat-killed cells. Compared with the conventional methods, the population heterogeneity of viable, culturable, dormant-like and membrane-permeabilized cells were well identified and quantified using qPCR during L. delbrueckii spp. bulgaricus sp1.1 batch culture. Despite the restriction in the enumeration of lysed cells, qPCR-based methods facilitated reliable identification and quantification of bacterial physiological states and provided additional knowledge on the dynamics of L. delbrueckii spp. bulgaricus sp1.1 physiological states.

L-Lactic acid production from fructose by chitosan film-coated sodium alginate-polyvinyl alcohol immobilized Lactobacillus pentosus cells and its kinetic analysis

Under the optimal conditions of immobilization and fermentation, the highest LA yield of 0.966 ± 0.006 g/g fructose and production rate of 2.426 ± 0.018 g/(L × h) with an error of -0.5% and -0.2% to the predicted results were obtained from batch fermentation by the CS film-coated SA-PVA immobilized L. pentosus cells. The LA yield and production rate of these immobilized cells were 2.7% and 10.1% higher than that of normal SA-PVA immobilized cells respectively, and they were 5.7% and 48.4% higher than that of free cells, respectively. The effect of temperature on different types of immobilized cells and free cells was significantly different, but the effect of pH on different types of cells was not much different. The kinetic models could effectively describe the different fermentation performances of three types of cells. The immobilized cells have excellent reusability to conduct 9 runs of repeated batch fermentation.

Influence of Lactic Acid on Cell Cycle Progressions in Lactobacillus bulgaricus During Batch Culture

Lactic acid has been proved to inhibit the proliferation of lactic acid bacteria in the fermentation process. To shed light on the cell cycle alterations in acidic conditions, the cell division of Lactobacillus bulgaricus sp1.1 in batch culture was analyzed directly by implementing of the intracellular fluorescent tracking assay in different pH adjusted by lactic acid. Cell proliferation and cell division were investigated to be negatively controlled by the decrease of pH, and pH 4.1 was the critical condition of downregulating cell division but retains cell culturability. The cell area and cell length in pH 4.1 were examined by using fluorescent labeling, and they reduced to about 29.18-34.89% and 32.67-40% of cells cultured in the unacidified medium, respectively. The DNA replication initiation was undergoing prompted by the low extent of DNA condensation and higher expression of the dnaA gene in this critical pH. The results indicated that the cell cycle progressions of Lactobacillus bulgaricus sp1.1 in acidic conditions were arrested at intracellular biomass accumulation and cell division stage. These findings provide fundamental insight into cell cycle control of the acidic environment in Lactobacillus bulgaricus sp1.1.

Genome Analysis and Physiological Characterization of Four Streptococcus thermophilus Strains Isolated From Chinese Traditional Fermented Milk

Streptococcus thermophilus plays important roles in the dairy industry and is widely used as a dairy starter in the production of fermented dairy products. The genomes of S. thermophilus strains CS5, CS9, CS18, and CS20 from fermented milk in China were sequenced and used for biodiversity analysis. In the present study, the phylogenetic analysis of all 34 S. thermophilus genomes publicly available including these four strains reveals that the phylogenetic reconstruction does not match geographic distribution as strains isolated from the same continent are not even clustered on the nearby branches. The core and variable genes were also identified, which vary among strains from 0 to 202. CS9 strain contained 127 unique genes from a variety of distantly related species. It was speculated that CS9 had undergone horizontal gene transfer (HGT) during the long evolutionary process. The safety evaluation of these four strains indicated that none of them contains antibiotic resistance genes and that they are all sensitive to multiple antibiotics. In addition, the strains do not contain any pathogenic virulence factors or plasmids and thus can be considered safe. Furthermore, these strains were investigated in terms of their technological properties including milk acidification, exopolysaccharide (EPS) and γ-aminobutyric acid (GABA) production, and in vitro survival capacity in the gastrointestinal tract. CS9 possesses a special eps gene cluster containing significant traces of HGT, while the eps gene clusters of CS5, CS18, and CS20 are almost the same. The monosaccharide compositional analysis indicated that crude EPS-CS5, EPS-CS9, EPS-CS18, and EPS-CS20 contain similar monosaccharide compositions with different ratios. Furthermore, CS9 was one of a few GABA-producing strains that could ferment glutamate to produce GABA, which is beneficial for improving the acid tolerance of the strain. CS18 has the most potential for the production of fermented food among these four strains because of its fast growth rate, rapid acidifying capacity, and stronger acid and bile salt resistance capacity. This study focused on the genome analysis of the four new S. thermophilus strains to investigate the diversity of strains and provides a reference for selecting excellent strains by use of the genome data.

Role of major facilitator superfamily transporter Qdr2p in biofilm formation by Candida glabrata

Candida glabrata represents the second-most frequent cause of candidiasis infections of the mucosa, bloodstream and genito-urinary tract in immunocompromised individuals. The incidence of C glabrata infection has increased significantly in the last two decades, mainly due to this species' abilities to resist various antifungal drugs and to form biofilms. We focused on the relationship between biofilm formation and the product of QDR2, a C glabrata member of the major facilitator superfamily (MFS) gene family, given that fungal biofilm formation limits drug penetration and is associated with persistent infection. The fungal cells in biofilms were compared between a C glabrata ∆qdr2 mutant and its wild-type strain. Cells were analysed for metabolism activity and drug susceptibility (using tetrazolium assay), adhesion activity, growth assay and intracellular pH (using flow cytometry). Compared to the wild type, the C glabrata ∆qdr2 showed lower adhesion activity and higher fluconazole susceptibility when assessed as a biofilm. The mutant also showed decreased metabolic activity during biofilm formation. Furthermore, the mutant grew more slowly under neutral-basic pH conditions. The qdr2 deletion in C glabrata resulted in an impaired ability to maintain pH homeostasis, which led in turn to a reduction of cell growth and of adherence to an artificial matrix. These results suggested that the Qdr2p function is needed for proper biofilm formation and biofilm maintenance in C glabrata as well as biofilm drug resistance towards fluconazole. Qdr2p may play an important role in C glabrata's ability to form biofilms on implanted medical devices in human bodies.

High-throughput extracellular pH monitoring and antibiotics screening by polymeric fluorescent sensor with LCST property

Monitoring extracellular pH (pHe) is important for biology understanding, since pHe and its homeostasis are closely relevant to cellular metabolism. Hydrogel-based pHe sensors have attracted significant attention and showed wide application, while they are tedious with significant time-cost operation and reproducibility variations for high-throughput application. Herein, we synthesized two polymers for pHe monitoring which are soluble in water at room temperature with easy operations and high reproducibility among various micro-plate wells for high-throughput analysis. P1 (P(OEGMA-co-MEO₂MA-co-pHS)) and P2 (P(OEGMA-co-pHS)) were synthesized via the Reversible Addition Fragmentation Chain Transfer (RAFT) copolymerization of oligo(ethylene glycol) methacrylate (OEGMA), 2-(2'-methoxyethoxy) ethyl methacrylate (MEO₂MA) and the pH sensitive fluorescence moiety N-fluoresceinyl methacrylamide (pHS). P1 is soluble in water at room temperature (25 °C) while insoluble at the temperature above 33 °C, indicating its feature of lower critical solution temperature (LCST) at 33 °C. Further P1 showed higher pH sensitivity and photostability than P2 (without LCST property) when used at physiological temperature (37 °C). Thus, P1 was chosen to in-situ monitor the micro-environmental acidification of E. coli, Hela and Ramos cells during their growth, and the metabolism inhibiting activity of a representative antibiotic, ampicillin. Cell concentration-dependent cellular acidification and drug concentration-dependent inhibition of cellular acidification were observed, demonstrating that the LCST polymer (P1) is suitable for real-time cellular acidification monitoring as well as for high-throughput drug screening. This study firstly demonstrated the use of a LCST polymeric sensor for high-throughput screening of antibiotics and investigation of cell metabolism.

Ion-selective electrode integrated in small-scale bioreactor for continuous intracellular pH determination in Lactobacillus plantarum

The aim of the present study was to develop an ion-selective electrode method for the continuous determination of the intracellular pH in Lactobacillus plantarum using a small-scale bioreactor. This method employed a salicylate-selective electrode basing on the distribution of salicylic acid across the cytoplasmic membrane. This developed electrode responded to salicylate concentrations above 20 μmol/L with a Nernstian sensitivity. The energized and concentrated cells were added into a thermostated small-scale bioreactor that contained the salicylate anions dissolved in a 100 mmol/L potassium phosphate buffer at different pH values. The changes in salicylate concentration that occurred in the medium containing bacterial suspension were measured as a voltage change. The cells of Lactobacillus plantarum showed maintenance of pH homeostasis at the studied pH ranging from 4.0 to 7.0, and they kept a neutral intracellular pH up to 5.8. The simplicity of the measuring preparation and the relatively low cellular concentration, as well as the advantages of the small-scale bioreactor, lead us to believe that the described method can facilitate the study of the physicochemical factors on the intracellular pH of lactic acid bacteria using a single pH probe in one method.

Influence of culture conditions on the technological properties of Carnobacterium maltaromaticum CNCM I-3298 starters

AIM

The aim of this study is to investigate the effect of a broad spectrum of culture conditions on the acidification activity and viability of Carnobacterium maltaromaticum CNCM I-3298, the main technological properties that determine the shelf-life of biological time-temperature integrator (TTI) labels.

METHODS AND RESULTS

Cells were cultivated at different temperatures (20-37°C) and pH (6-9·5) according to a modified central composite design and harvested at increasing times up to 10 h of stationary phase. Acidification activity and viability of freeze-thawed concentrates were assessed in medium mimicking the biological label. Acidification activity was influenced by all three culture conditions, but pH and harvest time were the most influential. Viability was not significantly affected by the tested range of culture conditions.

CONCLUSIONS

Carnobacterium maltaromaticum CNCM I-3298 must be cultivated at 20°C, pH 6 and harvested at the beginning of stationary phase to exhibit fastest acidification activities. However, if slower acidification activities are pursued, the recommended culture conditions are 30°C, pH 9·5 and a harvest time between 4-6 h of stationary phase.

SIGNIFICANCE AND IMPACT OF THE STUDY

Quantifying the impact of fermentation temperature, pH and harvest time has led to a predictive model for the production of biological TTI covering a broad range of shelf-lives.

Electrooptical Determination of Polarizability for On-Line Viability and Vitality Quantification of Lactobacillus plantarum Cultures

The rapid assessment of cell viability is crucial for process optimization, e.g., during media selection, determination of optimal environmental growth conditions and for quality control. In the present study, the cells' electric anisotropy of polarizability (AP) as well as the mean cell length in Lactobacillus plantarum batch and fed-batch fermentations were monitored with electrooptical measurements coupled to fully automated sample preparation. It was examined, whether this measurement can be related to the cells' metabolic activity, and thus represents a suitable process analytical technology. It is demonstrated that the AP is an early indicator to distinguish between suitable and unsuitable growth conditions in case of a poor energy regeneration or cell membrane defects in L. plantarum batch and fed-batch cultivations. It was shown that the applied method allowed the monitoring of physiological and morphological changes of cells in various growth phases in response to a low pH-value, substrate concentration changes, temperature alterations, exposure to air and nutrient limitation. An optimal range for growth in batch mode was achieved, if the AP remained above 25·10⁻²⁸ F·m² and the mean cell length at ~2.5 μm. It was further investigated, in which way the AP develops after freeze-drying of samples, which were taken in different cultivation phases. It was found that the AP increased most rapidly in resuspended samples from the retardation and late stationary phases, while samples from the early stationary phase recovered slowly. Electrooptical measurements provide valuable information about the physiologic and morphologic state of L. plantarum cells, e.g., when applied as starter cultures or as probiotic compounds.

Hydrogel-Based Fluorescent Dual pH and Oxygen Sensors Loaded in 96-Well Plates for High-Throughput Cell Metabolism Studies

In this study, we developed fluorescent dual pH and oxygen sensors loaded in multi-well plates for in-situ and high-throughput monitoring of oxygen respiration and extracellular acidification during microbial cell growth for understanding metabolism. Biocompatible PHEMA-co-PAM materials were used as the hydrogel matrix. A polymerizable oxygen probe (OS2) derived from PtTFPP and a polymerizable pH probe (S2) derived from fluorescein were chemically conjugated into the matrix to solve the problem of the probe leaching from the matrix. Gels were allowed to cure directly on the bottom of 96-well plates at room-temperature via redox polymerization. The influence of matrix’s composition on the sensing behaviors was investigated to optimize hydrogels with enough robustness for repeatable use with good sensitivity. Responses of the dual sensing hydrogels to dissolved oxygen (DO) and pH were studied. These dual oxygen-pH sensing plates were successfully used for microbial cell-based screening assays, which are based on the measurement of fluorescence intensity changes induced by cellular oxygen consumption and pH changes during microbial growth. This method may provide a real-time monitoring of cellular respiration, acidification, and a rapid kinetic assessment of multiple samples for cell viability as well as high-throughput drug screening. All of these assays can be carried out by a conventional plate reader.

Shear treatment of starter culture medium improves separation behavior of Streptococcus thermophilus cells

A central step in the production of starter cultures is the separation of the cells from the fermentation medium, which is usually achieved by disk centrifuges. In case of microorganisms which produce exopolysaccharides (e.g., various strains of lactic acid bacteria), the properties of the respective exopolysaccharides may interfere with this separation step. By using six strains of Streptococcus thermophilus the hypothesis was tested that a shear treatment of the fermented culture medium improves subsequent cell separation markedly. Depending on the type of exopolysaccharides (freely present in the medium, or as capsules around the cells) an energy input of up to 2.5 kJ/mL generated with an Ultra-Turrax affected cell chain length of the strains and viscosity of fermentation medium differently. For bacteria producing capsular exopolysaccharides, space- and time-resolved centrifugation experiments revealed an increase of sedimentation velocity after shear treatment. In general, viability of the microorganisms, detected by flow cytometry measurements and fermentation experiments, was not affected by the shearing procedure. The results therefore indicate that strain-targeted shearing is helpful to improve the separability of cells from the fermented media.

Promoting acid resistance and nisin yield of Lactococcus lactis F44 by genetically increasing D-Asp amidation level inside cell wall

Nisin fermentation by Lactococcus lactis requires a low pH to maintain a relatively higher nisin activity. However, the acidic environment will result in cell arrest, and eventually decrease the relative nisin production. Hence, constructing an acid-resistant L. lactis is crucial for nisin harvest in acidic nisin fermentation. In this paper, the first discovery of the relationship between D-Asp amidation-associated gene (asnH) and acid resistance was reported. Overexpression of asnH in L. lactis F44 (F44A) resulted in a sevenfold increase in survival capacity during acid shift (pH 3) and enhanced nisin desorption capacity compared to F44 (wild type), which subsequently contributed to higher nisin production, reaching 5346 IU/mL, 57.0% more than that of F44 in the fed-batch fermentation. Furthermore, the engineered F44A showed a moderate increase in D-Asp amidation level (from 82 to 92%) compared to F44. The concomitant decrease of the negative charge inside the cell wall was detected by a newly developed method based on the nisin adsorption amount onto cell surface. Meanwhile, peptidoglycan cross-linkage increased from 36.8% (F44) to 41.9% (F44A), and intracellular pH can be better maintained by blocking extracellular H⁺ due to the maintenance of peptidoglycan integrity, which probably resulted from the action of inhibiting hydrolases activity. The inference was further supported by the acmC-overexpression strain F44C, which was characterized by uncontrolled peptidoglycan hydrolase activity. Our results provided a novel strategy for enhancing nisin yield through cell wall remodeling, which contributed to both continuous nisin synthesis and less nisin adsorption in acidic fermentation (dual enhancement).

Common Distribution of gad Operon in Lactobacillus brevis and its GadA Contributes to Efficient GABA Synthesis toward Cytosolic Near-Neutral pH

Many strains of lactic acid bacteria (LAB) and bifidobacteria have exhibited strain-specific capacity to produce γ-aminobutyric acid (GABA) via their glutamic acid decarboxylase (GAD) system, which is one of amino acid-dependent acid resistance (AR) systems in bacteria. However, the linkage between bacterial AR and GABA production capacity has not been well established. Meanwhile, limited evidence has been provided to the global diversity of GABA-producing LAB and bifidobacteria, and their mechanisms of efficient GABA synthesis. In this study, genomic survey identified common distribution of gad operon-encoded GAD system in Lactobacillus brevis for its GABA production among varying species of LAB and bifidobacteria. Importantly, among four commonly distributed amino acid-dependent AR systems in Lb. brevis, its GAD system was a major contributor to maintain cytosolic pH homeostasis by consuming protons via GABA synthesis. This highlights that Lb. brevis applies GAD system as the main strategy against extracellular and intracellular acidification demonstrating its high capacity of GABA production. In addition, the abundant GadA retained its activity toward near-neutral pH (pH 5.5–6.5) of cytosolic acidity thus contributing to efficient GABA synthesis in Lb. brevis. This is the first global report illustrating species-specific characteristic and mechanism of efficient GABA synthesis in Lb. brevis.