The scale-up of microbial batch and fed-batch fermentation processes

Enhanced high β-carotene yeast cell production by Rhodotorula paludigena CM33 and in vitro digestibility in aquatic animals

This study assessed Rhodotorula paludigena CM33's growth and β-carotene production in a 22-L bioreactor for potential use as an aquatic animal feed supplement. Optimizing the feed medium's micronutrient concentration for high-cell-density fed-batch cultivation using glucose as the carbon source yielded biomass of 89.84 g/L and β-carotene concentration of 251.64 mg/L. Notably, using sucrose as the carbon source in feed medium outperforms glucose feeds, resulting in a β-carotene concentration of 285.00 mg/L with a similar biomass of 87.78 g/L. In the fed-batch fermentation using Sucrose Feed Medium, R. paludigena CM33 exhibited high biomass production rates (Qx) of 0.91 g/L.h and remarkable β-carotene production rates (Qp) of 2.97 mg/L.h. In vitro digestibility assays showed that R. paludigena CM33, especially when cultivated using sucrose, enhances protein digestibility affirming its suitability as an aquatic feed supplement. Furthermore, R. paludigena CM33's nutrient-rich profile and probiotic potential make it an attractive option for aquatic nutrition. This research highlights the importance of cost-effective carbon sources in large-scale β-carotene production for aquatic animal nutrition.

Adapted feeding strategies in fed-batch fermentation improve sugar delivery and ethanol productivity

Bioethanol is a renewable fuel widely used in road transportation and is generally regarded as a clean energy source. Although fermentation is one of the major processes in bioethanol production, studies on improving its efficiency through operational design are limited, especially compared to other steps (pretreatment and hydrolysis/saccharification). In this study, two adapted feeding strategies, in which feed medium addition (sugar delivery) was adjusted to increase the supply of fermentable sugar, were developed to improve ethanol productivity in 5-L fed-batch fermentation by Saccharomyces cerevisiae. Specifically, a linear adapted feeding strategy was established based on changes in cell biomass, and an exponential adapted feeding strategy was developed based on cell biomass accumulation. By implementing these two feeding strategies, the overall ethanol productivity reached 0.88± 0.04 and 0.87± 0.06 g/L/h, respectively. This corresponded to ~20% increases in ethanol productivity compared to fixed pulsed feeding operations. Additionally, there was no residual glucose at the end of fermentation, and final ethanol content reached 95± 3 g/L under the linear adapted operation and 104± 3 g/L under the exponential adapted feeding strategy. No statistical difference was observed in the overall ethanol yield (ethanol-to-sugar ratio) between fixed and adapted feeding strategies (~91%). These results demonstrate that sugar delivery controlled by adapted feeding strategies was more efficient than fixed feeding operations, leading to higher ethanol productivity. Overall, this study provides novel adapted feeding strategies to improve sugar delivery and ethanol productivity. Integration into the current practices of the ethanol industry could improve productivity and reduce production costs of fermentation processes.

Beyond rational-biosensor-guided isolation of 100 independently evolved bacterial strain variants and comparative analysis of their genomes

BACKGROUND

In contrast to modern rational metabolic engineering, classical strain development strongly relies on random mutagenesis and screening for the desired production phenotype. Nowadays, with the availability of biosensor-based FACS screening strategies, these random approaches are coming back into fashion. In this study, we employ this technology in combination with comparative genome analyses to identify novel mutations contributing to product formation in the genome of a Corynebacterium glutamicum L-histidine producer. Since all known genetic targets contributing to L-histidine production have been already rationally engineered in this strain, identification of novel beneficial mutations can be regarded as challenging, as they might not be intuitively linkable to L-histidine biosynthesis.

RESULTS

In order to identify 100 improved strain variants that had each arisen independently, we performed > 600 chemical mutagenesis experiments, > 200 biosensor-based FACS screenings, isolated > 50,000 variants with increased fluorescence, and characterized > 4500 variants with regard to biomass formation and L-histidine production. Based on comparative genome analyses of these 100 variants accumulating 10-80% more L-histidine, we discovered several beneficial mutations. Combination of selected genetic modifications allowed for the construction of a strain variant characterized by a doubled L-histidine titer (29 mM) and product yield (0.13 C-mol C-mol-1) in comparison to the starting variant.

CONCLUSIONS

This study may serve as a blueprint for the identification of novel beneficial mutations in microbial producers in a more systematic manner. This way, also previously unexplored genes or genes with previously unknown contribution to the respective production phenotype can be identified. We believe that this technology has a great potential to push industrial production strains towards maximum performance.

Effects of the fermentation process on the selenite metabolism and selenium incorporation and speciation in a probiotic Bifidobacterium longum

The influence of the fermentation process on selenite metabolism by a probiotic Bifidobacterium longum DD98 and its consequent enrichment in selenium (Se) were studied. The effects of sodium selenite (Na2SeO3) concentration (18-400 μg/ml), feeding time (12, 16, and 24 h), and fermentation stage (secondary and tertiary fermentation) were evaluated by measuring (i) the total Se content and its distribution between the water-soluble metabolome fraction and the water-insoluble fraction; (ii) the total concentrations of the two principal Se compounds produced: selenomethionine (SeMet) and γ-glutamyl-selenomethionine (γ-Glu-SeMet), and (iii) the speciation of Se in the metabolite fraction. The results revealed that the fermentation process notably changed the Se incorporation into metabolites (γ-Glu-SeMet and free SeMet) and proteins (bound-SeMet) in B. longum DD98. In particular, the production of SeMet was negatively correlated to that of γ-Glu-SeMet when no red precipitate was seen in the bacteria. The study offers a tool for the control of the optimization of the fermentation process towards the desired molecular speciation of the incorporated Se and hence contributes to the production of Se-enriched probiotics with good qualities and bioactivities.

Optimization and Scale-Up of Fermentation Processes Driven by Models

In the era of sustainable development, the use of cell factories to produce various compounds by fermentation has attracted extensive attention; however, industrial fermentation requires not only efficient production strains, but also suitable extracellular conditions and medium components, as well as scaling-up. In this regard, the use of biological models has received much attention, and this review will provide guidance for the rapid selection of biological models. This paper first introduces two mechanistic modeling methods, kinetic modeling and constraint-based modeling (CBM), and generalizes their applications in practice. Next, we review data-driven modeling based on machine learning (ML), and highlight the application scope of different learning algorithms. The combined use of ML and CBM for constructing hybrid models is further discussed. At the end, we also discuss the recent strategies for predicting bioreactor scale-up and culture behavior through a combination of biological models and computational fluid dynamics (CFD) models.

Efficient biosynthesis of exopolysaccharide in Candida glabrata by a fed-batch culture

Polysaccharides are important natural biomacromolecules. In particular, microbial exopolysaccharides have received much attention. They are produced by a variety of microorganisms, and they are widely used in the food, pharmaceutical, and chemical industries. The Candida glabrata mutant 4-C10, which has the capacity to produce exopolysaccharide, was previously obtained by random mutagenesis. In this study we aimed to further enhance exopolysaccharide production by systemic fermentation optimization. By single factor optimization and orthogonal design optimization in shaking flasks, an optimal fermentation medium composition was obtained. By optimizing agitation speed, aeration rate, and fed-batch fermentation mode, 118.6 g L⁻¹ of exopolysaccharide was obtained by a constant rate feeding fermentation mode, with a glucose yield of 0.62 g g⁻¹ and a productivity of 1.24 g L⁻¹ h⁻¹. Scaling up the established fermentation mode to a 15-L fermenter led to an exopolysaccharide yield of 113.8 g L⁻¹, with a glucose yield of 0.60 g g⁻¹ and a productivity of 1.29 g L⁻¹ h⁻¹.

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.

Assessing the growth kinetics and stoichiometry of Escherichia coli at the single-cell level

Microfluidic cultivation and single-cell analysis are inherent parts of modern microbial biotechnology and microbiology. However, implementing biochemical engineering principles based on the kinetics and stoichiometry of growth in microscopic spaces remained unattained. We here present a novel integrated framework that utilizes distinct microfluidic cultivation technologies and single-cell analytics to make the fundamental math of process-oriented biochemical engineering applicable at the single-cell level. A combination of non-invasive optical cell mass determination with sub-pg sensitivity, microfluidic perfusion cultivations for establishing physiological steady-states, and picoliter batch reactors, enabled the quantification of all physiological parameters relevant to approximate a material balance in microfluidic reaction environments. We determined state variables (biomass concentration based on single-cell dry weight and mass density), biomass synthesis rates, and substrate affinities of cells grown in microfluidic environments. Based on this data, we mathematically derived the specific kinetics of substrate uptake and growth stoichiometry in glucose-grown Escherichia coli with single-cell resolution. This framework may initiate microscale material balancing beyond the averaged values obtained from populations as a basis for integrating heterogeneous kinetic and stoichiometric single-cell data into generalized bioprocess models and descriptions.

Bioengineering Outlook on Cultivated Meat Production

Cultured meat (also referred to as cultivated meat or cell-based meat)—CM—is fabricated through the process of cellular agriculture (CA), which entails application of bioengineering, i.e., tissue engineering (TE) principles to the production of food. The main TE principles include usage of cells, grown in a controlled environment provided by bioreactors and cultivation media supplemented with growth factors and other needed nutrients and signaling molecules, and seeded onto the immobilization elements—microcarriers and scaffolds that provide the adhesion surfaces necessary for anchor-dependent cells and offer 3D organization for multiple cell types. Theoretically, many solutions from regenerative medicine and biomedical engineering can be applied in CM-TE, i.e., CA. However, in practice, there are a number of specificities regarding fabrication of a CM product that needs to fulfill not only the majority of functional criteria of muscle and fat TE, but also has to possess the sensory and nutritional qualities of a traditional food component, i.e., the meat it aims to replace. This is the reason that bioengineering aimed at CM production needs to be regarded as a specific scientific discipline of a multidisciplinary nature, integrating principles from biomedical engineering as well as from food manufacturing, design and development, i.e., food engineering. An important requirement is also the need to use as little as possible of animal-derived components in the whole CM bioprocess. In this review, we aim to present the current knowledge on different bioengineering aspects, pertinent to different current scientific disciplines but all relevant for CM engineering, relevant for muscle TE, including different cell sources, bioreactor types, media requirements, bioprocess monitoring and kinetics and their modifications for use in CA, all in view of their potential for efficient CM bioprocess scale-up. We believe such a review will offer a good overview of different bioengineering strategies for CM production and will be useful to a range of interested stakeholders, from students just entering the CA field to experienced researchers looking for the latest innovations in the field.

Triacyl Glycerols from Yeast-Catalyzed Batch and Fed-Batch Bioconversion of Hydrolyzed Lignocellulose from Cardoon Stalks

The lipogenic ability of the yeast Solicoccozyma terricola DBVPG 5870 grown on hydrolyzed lignocellulose obtained from cardoon stalks was evaluated. Data on cell biomass, lipid production, and fatty acid profiles of triacylglycerols obtained in batch and fed-batch experiments were carried out at the laboratory scale in a 5L fermenter, and at two different temperatures (20 and 25 °C) were reported. The higher production of total intracellular lipids (13.81 g/L) was found in the fed-batch experiments carried out at 20 °C. S. terricola exhibited the ability to produce high amounts of triacylglycerol (TAGs) with a characteristic fatty acids profile close to that of palm oil. The TAGs obtained from S. terricola grown on pre-treated lignocellulose could be proposed as a supplementary source of oleochemicals. Indeed, due to the rising prices of fossil fuels and because of the environmental-related issues linked to their employment, the use of TAGs produced by S. terricola grown on lignocellulose could represent a promising option as a supplementary oleochemical, especially for biodiesel production.

Glucose-Limited Fed-Batch Cultivation Strategy to Mimic Large-Scale Effects in Escherichia coli Linked to Accumulation of Non-Canonical Branched-Chain Amino Acids by Combination of Pyruvate Pulses and Dissolved Oxygen Limitation

Insufficient mixing in large-scale bioreactors provokes gradient zones of substrate, dissolved oxygen (DO), pH, and other parameters. E. coli responds to a high glucose, low oxygen feeding zone with the accumulation of mixed acid fermentation products, especially formate, but also with the synthesis of non-canonical amino acids, such as norvaline, norleucine and β-methylnorleucine. These amino acids can be mis-incorporated into recombinant products, which causes a problem for pharmaceutical production whose solution is not trivial. While these effects can also be observed in scale down bioreactor systems, these are challenging to operate. Especially the high-throughput screening of clone libraries is not easy, as fed-batch cultivations would need to be controlled via repeated glucose pulses with simultaneous oxygen limitation, as has been demonstrated in well controlled robotic systems. Here we show that not only glucose pulses in combination with oxygen limitation can provoke the synthesis of these non-canonical branched-chain amino acids (ncBCAA), but also that pyruvate pulses produce the same effect. Therefore, we combined the enzyme-based glucose delivery method Enbase^® in a PALL24 mini-bioreactor system and combined repeated pyruvate pulses with simultaneous reduction of the aeration rate. These cultivation conditions produced an increase in the non-canonical branched chain amino acids norvaline and norleucine in both the intracellular soluble protein and inclusion body fractions with mini-proinsulin as an example product, and this effect was verified in a 15 L stirred tank bioreactor (STR). To our opinion this cultivation strategy is easy to apply for the screening of strain libraries under standard laboratory conditions if no complex robotic and well controlled parallel cultivation devices are available.

Alginate-chitosan core-shell microcapsule cultures of hepatic cells in a small scale stirred bioreactor: impact of shear forces and microcapsule core composition

A small scale stirred bioreactor was designed and the effect of different agitation rates (30, 60 and 100 rpm) was investigated on HepG2 cells cultured in alginate-chitosan (AC) core-shell microcapsule in terms of the cell proliferation and liver-specific function. The microencapsulated hepatic cells could proliferate well when they were cultured for 10 days at 30 rpm while the cell-laden microcapsules showed no cell proliferation at 100 rpm in the bioreactor system. Albumin production rate, as an important liver function, increased also 1.8- and 1.5- fold under stirring rate of 30 rpm compared to the static culture and 60 rpm of agitation, respectively. Moreover, In comparison with the static culture, about 1.5-fold increment in urea production was observed at 30 rpm. Similarly, the highest expressions of albumin and P450 genes were found at 30 rpm stirring rate, which were 4.9- and 19.2-fold of the static culture. Addition of collagen to the microcapsule core composition (ACol/C) could improve the cell proliferation and functionality at 60 rpm in comparison with the cell-laden microcapsules without collagen. The study demonstrated the hepatic cell-laden ACol/C microcapsule hydrogel cultured in the small scale stirred bioreactor at low mixing rate has a great potential for mass production of the hepatic cells while maintaining liver-specific functions.

Use of glycerol for the production of actinobacteria with well-known bioremediation abilities

In recent years, there has been an increasing interest in the remediation of contaminated environments, and a suitable solution is in situ bioremediation. To achieve this, large-scale bacterial biomass production should be sustainable, using economic culture media. The main aim of this study was to optimize the physicochemical conditions for the biomass production of an actinobacterium with well-known bioremediation ability using inexpensive substrates and to scale-up its production in a bioreactor. For this, the growth of four strains of actinobacteria were evaluated in minimal medium with glucose and glycerol as carbon and energy sources. In addition, l-asparagine and ammonium sulfate were assayed as alternative nitrogen sources. The strain Streptomyces sp. A5 showed the highest biomass production in shake-flasks culture using glycerol and ammonium sulfate as carbon and nitrogen sources, respectively. Factorial designs with five factors (glycerol concentration, inoculum size, pH, temperature, and agitation) were employed to optimize the biomass production of Streptomyces sp. A5. The maximum biomass production was obtained using 5 g L^-1 of glycerol, 0.25 µL of inoculum, pH 7, 30 °C and 200 rpm. Finally, the production was successfully scaled to a 2 L stirred tank bioreactor.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-020-02588-5.

Uncoupling growth and succinic acid production in an industrial Saccharomyces cerevisiae strain

This study explores the relation between biomass‐specific succinic acid (SA) production rate and specific growth rate of an engineered industrial strain of Saccharomyces cerevisiae, with the aim to investigate the extent to which growth and product formation can be uncoupled. Ammonium‐limited aerobic chemostat and retentostat cultures were grown at different specific growth rates under industrially relevant conditions, that is, at a culture pH of 3 and with sparging of a 1:1 CO₂–air mixture. Biomass‐specific SA production rates decreased asymptotically with decreasing growth rate. At near‐zero growth rates, the engineered strain maintained a stable biomass‐specific SA production rate for over 500 h, with a SA yield on glucose of 0.61 mol mol⁻¹. These results demonstrate that uncoupling of growth and SA production could indeed be achieved. A linear relation between the biomass‐specific SA production rate and glucose consumption rate indicated the coupling of SA production rate and the flux through primary metabolism. The low culture pH resulted in an increased death rate, which was lowest at near‐zero growth rates. Nevertheless, a significant amount of non‐viable biomass accumulated in the retentostat cultures, thus underlining the importance of improving low‐pH tolerance in further strain development for industrial SA production with S. cerevisiae.

Response surface methodology-mediated improvement of the irradiated endophytic fungal strain, Alternaria brassicae AGF041 for Huperzine A-hyperproduction

Huperzine A (HupA) is an anti-Alzheimer's therapeutic and a dietary supplement for memory boosting that is extracted mainly from Huperziacae plants. Endophytes represent the upcoming refuge to protect the plant resource from distinction but their HupA yield is still far from commercialization. In this context, UV and gamma radiation mutagenesis of the newly isolated HupA-producing Alternaria brassicae AGF041 would be applied in this study for improving the endophytic HupA yield. Compared to non-irradiated cultures, UV (30-40 min, exposure) and γ (0·5 KGy, dose) irradiated cultures, each separately, showed a significant higher HupA yield (17·2 and 30·3%, respectively). While, application of a statistically optimized compound irradiation (0·70 KGy of γ treatment and 42·49 min of UV exposure, sequentially) via Response Surface Methodology (RSM) resulted in 53·1% production increase. Moreover, a stable selected mutant strain CM003 underwent batch cultivation using a 6·6 l bioreactor for the first time and was successful for scaling up the HupA production to 261·6 µg l^-1 . Findings of this research are demonstrated to be valuable as the employed batch fermentation represents a successful starting step towards the promising endophytic HupA production at an industrial scale.

Process optimization and scale-up production of fungal aryl alcohol oxidase from genetically modified Aspergillus nidulans in stirred-tank bioreactor

Microbial production of aryl alcohol oxidase (AAO) has attracted increasing attention due to the central role of AAO in enzymatic lignin depolymerization. However, large-scale production of AAO has not been reached because of the low yield and inefficient fermentation process. This study aims to optimize the process parameters and scale-up production of AAO using Aspergillus nidulans in a stirred-tank bioreactor. Effects of pH and dissolved oxygen on AAO production at bioreactor scale were particularly investigated. Results revealed that pH control significantly affected protein production and increasing dissolved oxygen level stimulated AAO production. The greatest AAO activity (1906 U/L) and protein concentration (1.19 g/L) were achieved in 48 h at 60% dissolved oxygen with pH controlled at 6.0. The yield and productivity (in 48 h) were 31.2 U/g maltose and 39.7 U/L/h, respectively. In addition, crude AAO was concentrated and partially purified by ultrafiltration and verified by protein identification.

Expression, purification, and characterization of pneumococcal PsaA-PspA fusion protein

Streptococcus pneumoniae is a gram-positive bacterial pathogen causing invasive pneumonia, meningitis, otitis media, and bacteremia. Owing to the current pitfalls of polysaccharide and polysaccharide-conjugate vaccines, protein vaccines are considered promising candidates against pneumonia. Pneumococcal surface protein A (PspA) and pneumococcal surface adhesin A (PsaA) are virulence proteins showing good immunogenicity and protective effects against S. pneumoniae strains in mice. In this study, we expressed the fusion protein PsaA-PspA, which consists of PsaA and the N-terminal region of PspA family 1 and 2, in Escherichia coli. We describe a novel and effective method to purify PsaA-PspA using hydroxyapatite and two-step chromatography. After determining the optimal induction conditions and a series of purification steps, we obtained PsaA-PspA fusion protein with over 95% purity at a final yield of 22.44% from the starting cell lysate. The molecular weight of PsaA-PspA was approximately 83.6 kDa and its secondary structure was evaluated by circular dichroism. Immunization with the purified protein induced high levels of IgG antibodies in mice. Collectively, these results demonstrate that our purification method can effectively produce high-purity PsaA-PspA fusion protein with biological activity and chemical integrity, which can be widely applied to the purification of other PspA subclass proteins.

Effect of by-products from the dairy industry as alternative inducers of recombinant β-galactosidase expression

OBJECTIVE

The aim of the present study was to evaluate the efficiency of lactose derived from cheese whey and cheese whey permeate as inducer of recombinant Kluyveromyces sp. β-galactosidase enzyme produced in Escherichia coli. Two E. coli strains, BL21(DE3) and Rosetta (DE3), were used in order to produce the recombinant enzyme. Samples were evaluated for enzyme activity, total protein content, and sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis after induction with isopropyl-β-D-1-thiogalactoside (IPTG) (0.05 and 1 mM) and lactose, cheese whey, and cheese whey permeate solutions (1, 10, and 20 g/L lactose) at shake-flask cultivation, and whey permeate solution (10 g/L lactose) at bioreactor scale.

RESULTS

The highest specific activities obtained with IPTG as inducer (0.05 mM) after 9 h of induction, were 23 and 33 U/mg_protein with BL21(DE3) and Rosetta(DE3) strains, respectively. Inductions performed with lactose and cheese whey permeate (10 and 20 g/L lactose) showed the highest specific activities at the evaluated hours, exhibiting better results than those obtained with IPTG. Specific activity of recombinant β-galactosidase using whey permeate (10 g/L lactose) showed values of approximately 46 U/mg_protein after 24-h induction at shake-flask study, and approximately 26 U/mg_protein after 16-h induction at bench bioreactor.

CONCLUSIONS

The induction with cheese whey permeate was more efficient for recombinant β-galactosidase expression than the other inducers tested, and thus, represents an alternative form to reduce costs in recombinant protein production.

Escherichia coli metabolism under short-term repetitive substrate dynamics: adaptation and trade-offs

Background

Microbial metabolism is highly dependent on the environmental conditions. Especially, the substrate concentration, as well as oxygen availability, determine the metabolic rates. In large-scale bioreactors, microorganisms encounter dynamic conditions in substrate and oxygen availability (mixing limitations), which influence their metabolism and subsequently their physiology. Earlier, single substrate pulse experiments were not able to explain the observed physiological changes generated under large-scale industrial fermentation conditions.

Results

In this study we applied a repetitive feast–famine regime in an aerobic Escherichia coli culture in a time-scale of seconds. The regime was applied for several generations, allowing cells to adapt to the (repetitive) dynamic environment. The observed response was highly reproducible over the cycles, indicating that cells were indeed fully adapted to the regime. We observed an increase of the specific substrate and oxygen consumption (average) rates during the feast–famine regime, compared to a steady-state (chemostat) reference environment. The increased rates at same (average) growth rate led to a reduced biomass yield (30% lower). Interestingly, this drop was not followed by increased by-product formation, pointing to the existence of energy-spilling reactions. During the feast–famine cycle, the cells rapidly increased their uptake rate. Within 10 s after the beginning of the feeding, the substrate uptake rate was higher (4.68 μmol/g_CDW/s) than reported during batch growth (3.3 μmol/g_CDW/s). The high uptake led to an accumulation of several intracellular metabolites, during the feast phase, accounting for up to 34% of the carbon supplied. Although the metabolite concentrations changed rapidly, the cellular energy charge remained unaffected, suggesting well-controlled balance between ATP producing and ATP consuming reactions.

Conclusions

The adaptation of the physiology and metabolism of E. coli under substrate dynamics, representative for large-scale fermenters, revealed the existence of several cellular mechanisms coping with stress. Changes in the substrate uptake system, storage potential and energy-spilling processes resulted to be of great importance. These metabolic strategies consist a meaningful step to further tackle reduced microbial performance, observed under large-scale cultivations.

Scale-down studies for the scale-up of a recombinant Corynebacterium glutamicum fed-batch fermentation: loss of homogeneity leads to lower levels of cadaverine production

BACKGROUND

The loss of efficiency and performance of bioprocesses on scale-up is well known, but not fully understood. This work addresses this problem, by studying the effect of some fermentation gradients (pH, glucose and oxygen) that occur at the larger scale in a bench-scale two-compartment reactor [plug flow reactor (PFR) + stirred tank reactor (STR)] using the cadaverine-producing recombinant Corynebacterium glutamicum DM1945 Δact3 Ptuf-ldcC_OPT. The new scale-down strategy developed here studied the effect of increasing the magnitude of fermentation gradients by considering not only the average cell residence time in the PFR (τ _PFR), but also the mean frequency at which the bacterial cells entered the PFR (f _m) section of the two-compartment reactor.

RESULTS

On implementing this strategy the cadaverine production decreased on average by 26%, 49% and 59% when the τ _PFR was increased from 1 to 2 min and then 5 min respectively compared to the control fermentation. The carbon dioxide productivity was highest (3.1-fold that of the control) at a τ _PFR of 5 min, but no losses were observed in biomass production. However, the population of viable but non-culturable cells increased as the magnitude of fermentation gradients was increased. The new scale-down approach was also shown to have a bigger impact on fermentation performance than the traditional one.

CONCLUSION

This study demonstrated that C. glutamicum DM1945 Δact3 Ptuf-ldcC_OPT physiological response was a function of the magnitude of fermentation gradients simulated. The adaptations of a bacterial cell within a heterogeneous environment ultimately result in losses in fermentation productivity as observed here. © 2019 The Authors. Journal of Chemical Technology & Biotechnology published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Oil crop wastes as substrate candidates for enhancing erythritol production by modified Yarrowia lipolytica via one-step solid state fermentation

Oil crop wastes are attractive feedstocks in microbial processes due to their low cost. However, the product yields can be limited by their undesirable nitrogen surplus. Present study proposed a one-step solid state fermentation (SSF) method for producing erythritol from unrefined oil crop wastes using a modified strain Y. lipolytica M53-S. Enhanced erythritol production (185.4 mg/gds) was obtained from peanut press cake mixed with 40% sesame meal and 10% waste cooking oil. The process was performed at pH 4.0 in 5 L flasks, with initial moisture content, NaCl addition, and inoculum size of 70%, 0.02 g/gds, and 7.5 × 10⁴ cells/gds, respectively. This procedure showed advantages in terms of lower material cost than that of submerged fermentation and shorter culture cycle (96 h) than other SSF processes. In repeated-batch fermentation, erythritol was continuously produced for seven cycles. This study presents a feasible approach in developing an efficient erythritol cultivation from nitrogen-rich wastes.

The impact of technical failures during cultivation of an inclusion body process

In biotechnological processes, technical failures in the upstream process often lead to batch loss. It is of great interest to investigate the empirical impact of technical failures to understand and mitigate their impact accurately and reduce economic damage. We investigated the impact in the upstream and downstream of a recombinant antibody fragment inclusion body production process chain to provide integrated empirical data and knowledge. First, we provided a reproducible process chain that yielded high inclusion body content, high specific product titer, and a refolding yield of 30%. The inclusion body downstream proved to be of high reproducibility. Through the intended introduction of technical failures, we were not only able to shed more light on the empirical responses in the upstream and downstream, but also on process-boosting parameters that would have been neglected. Herein, a short increase in temperature during the cultivation clearly increased the refolding yield.

Assessment of upstream bioprocessing

Depending on the purpose and use, bioprocesses are carried out in order to reduce, maintain or increase the molar O/C ratio of biomass as the initial substrate. Cascade use considers the holistic and efficient use of biomass. In the current debate of biomass use, however, one may admit that an efficient use of biomass can further be based on the maintenance of initially present molar O/C ratio and functionality. In this regard, what compound should be formed that possesses highest functionality and similar molar O/C ratio as the substrate? How much energy should be spent on bioprocesses for the conversion of biomass under aerobic or anaerobic conditions? This study discusses and contributes to the efficiency assessment of aerobic and anaerobic bioprocesses based on chemical functionality and molar O/C ratio and their scale-depended energy need for creating appropriate environmental conditions for biological agents.

Protein engineering to enhance keratinolytic protease activity and excretion in Escherichia coli and its scale-up fermentation for high extracellular yield

Escherichia coli is one kind of the simple and excellent biosystem to overexpress heterologous enzymes, such as keratinolytic protease, an excellent enzyme to hydrolyze keratin substrate for broad industrial application. However, protein expression in E. coli frequently faces some problems such as inactive and inclusion body formation. This work described a series of protein engineering strategies of N-terminal propeptide replacement and site-directed mutagenesis to modify this enzyme activity and production. Site-directed mutagenesis (S180G/Y215S) on N-terminal propeptide altered mutant contributed to the highest specific activity (4725 ± 65 U/mg, more than 1300 U/mg improvement than wild-type enzyme). This comprehensive mutation also achieved 2.5-fold improvement of extracellular enzyme yield in shake-flask level. The fermentation strategies about optimizing glycerol feeding and inducing point in scale-up bioreactor resulted in tremendous leakage of keratinolytic protease (954 mg/L extracellular yield within 48 h, about 9.26-fold higher than the original shake-flask level) as well as cell lysis. Although this proposed strategy faces a major challenge to maintain cell integrity or viability, it still exists the opportunity to realize other enzymes extracellular expression in E. coli system and simplify downstream processing to meet the industrial application.

Importance of the cultivation history for the response of Escherichia coli to oscillations in scale-down experiments

Large-scale bioreactors are inhomogeneous systems, in which the fluid phase expresses concentration gradients. They depend on the mass transfer and fluid dynamics in the reactor, the feeding strategy, the cell-specific substrate uptake parameters, and the cell density. As high cell densities are only obtained at low specific growth rates, it is necessary to investigate the cellular responses to oscillations in particular under such conditions, an issue which is mostly neglected. Instead, the feed oscillations are often started directly after the batch phase, when the specific growth rate is close to the maximum. We show here that the cultivation mode before oscillations are started has a tremendous effect on the metabolic responses. In difference to cells, which were pre-grown under batch conditions at a high growth rate, Escherichia coli cells that were pre-grown under glucose limitation at a low growth rate accumulate short-chain fatty acids (acetate, lactate, succinate) and glycolysis-related amino acids to a higher extent in a two-compartment scale-down bioreactor. Thus, cells which enter oscillations from a lower specific growth rate seem to react more sensitive to oscillations than cells that are subjected to oscillations directly after a batch phase. These results are interesting in designing reliable scale-down systems, which better reflect large-scale bioprocesses.

Influence of Scale on Biomass Growth and Nutrient Removal in an Algal-Bacterial Leachate Treatment System

Data collected from experiments conducted at a flask scale are regularly used as input data for life cycle assessments and techno-economic analyses for predicting the potential productivities of large-scale commercial facilities. This study measures and compares nitrogen removal and biomass growth rates in treatment systems that utilize an algae-bacteria consortium to remediate landfill leachate at three scales: small (0.25 L), medium (100 L), and large (1000 L). The medium- and large-scale vessels were run for 52 consecutive weeks as semibatch reactors under variable environmental conditions. The small-scale experiments were conducted in flasks as batch experiments under controlled environmental conditions. Kolomogov-Smirnov statistical tests, which compare the distributions of entire data sets, were used to determine if the ammonia removal, total nitrogen removal, and biomass growth rates at each scale were statistically different. Results from the Kolmogov-Smirnov comparison indicate that there is a significant difference between all rates determined in the large-scale vessels compared to those in the small-scale vessels. These results suggest that small-scale experiments may not be appropriate as input data in predictive analyses of full scale algal processes. The accumulation of nitrite and nitrate within the reactor, observed midway through the experimental process, is attributed to high relative abundances of ammonia- and nitrite-oxidizing bacteria, identified via metagenomic analysis.

Focused Review: Cytotoxic and Antioxidant Potentials of Mangrove-Derived Streptomyces

Human life expectancy is rapidly increasing with an associated increasing burden of chronic diseases, such as neurodegenerative diseases and cancer. However, there is limited progress in finding effective treatment for these conditions. For this reason, members of the genus Streptomyces have been explored extensively over the past decades as these filamentous bacteria are highly efficient in producing bioactive compounds with human health benefits. Being ubiquitous in nature, streptomycetes can be found in both terrestrial and marine environments. Previously, two Streptomyces strains (MUSC 137T and MUM 256) isolated from mangrove sediments in Peninsular Malaysia demonstrated potent antioxidant and cytotoxic activities against several human cancer cell lines on bioactivity screening. These results illustrate the importance of streptomycetes from underexplored regions aside from the terrestrial ecosystem. Here we provide the insights and significance of Streptomyces species in the search of anticancer and/or chemopreventive agents and highlight the impact of next generation sequencing on drug discovery from the Streptomyces arsenal.

Valorization of Proteins from Co- and By-Products from the Fish and Meat Industry

Large volumes of protein-rich residual raw materials, such as heads, bones, carcasses, blood, skin, viscera, hooves and feathers, are created as a result of processing of animals from fisheries, aquaculture, livestock and poultry sectors. These residuals contain proteins and other essential nutrients with potentially bioactive properties, eligible for recycling and upgrading for higher-value products, e.g. for human, pet food and feed purposes. Here, we aim to cover all the important aspects of achieving optimal utilization of proteins in such residual raw materials, identifying those eligible for human consumption as co-products and for feed applications as by-products. Strict legislation regulates the utilization of various animal-based co- and by-products, representing a major hurdle if not addressed properly. Thorough understanding and optimization of all parts of the production chain, including conservation and processing, are important prerequisites for successful upgrading and industrial implementation of such products. This review includes industrially applied technologies such as freezing/cooling, acid preservation, salting, rendering and protein hydrolysis. In this regard, it is important to achieve stable production and quality through all the steps in the manufacturing chain, preferably supported by at- or online quality control points in the actual processing step. If aiming for the human market, knowledge of consumer trends and awareness are important for production and successful introduction of new products and ingredients.

Comparison of Scale in a Photosynthetic Reactor System for Algal Remediation of Wastewater

An experimental methodology is presented to compare the performance of two different sized reactors designed for wastewater treatment. In this study, ammonia removal, nitrogen removal and algal growth are compared over an 8-week period in paired sets of small (100 L) and large (1,000 L) reactors designed for algal remediation of landfill wastewater. Contents of the small and large scale reactors were mixed before the beginning of each weekly testing interval to maintain equivalent initial conditions across the two scales. System characteristics, including surface area to volume ratio, retention time, biomass density, and wastewater feed concentrations, can be adjusted to better equalize conditions occurring at both scales. During the short 8-week representative time period, starting ammonia and total nitrogen concentrations ranged from 3.1-14 mg NH3-N/L, and 8.1-20.1 mg N/L, respectively. The performance of the treatment system was evaluated based on its ability to remove ammonia and total nitrogen and to produce algal biomass. Mean ± standard deviation of ammonia removal, total nitrogen removal and biomass growth rates were 0.95±0.3 mg NH3-N/L/day, 0.89±0.3 mg N/L/day, and 0.02±0.03 g biomass/L/day, respectively. All vessels showed a positive relationship between the initial ammonia concentration and ammonia removal rate (R²=0.76). Comparison of process efficiencies and production values measured in reactors of different scale may be useful in determining if lab-scale experimental data is appropriate for prediction of commercial-scale production values.

The fed-batch principle for the molecular biology lab: controlled nutrient diets in ready-made media improve production of recombinant proteins in Escherichia coli

While the nutrient limited fed-batch technology is the standard of the cultivation of microorganisms and production of heterologous proteins in industry, despite its advantages in view of metabolic control and high cell density growth, shaken batch cultures are still the standard for protein production and expression screening in molecular biology and biochemistry laboratories. This is due to the difficulty and expenses to apply a controlled continuous glucose feed to shaken cultures. New ready-made growth media, e.g. by biocatalytic release of glucose from a polymer, offer a simple solution for the application of the fed-batch principle in shaken plate and flask cultures. Their wider use has shown that the controlled diet not only provides a solution to obtain significantly higher cell yields, but also in many cases folding of the target protein is improved by the applied lower growth rates; i.e. final volumetric yields for the active protein can be a multiple of what is obtained in complex medium cultures. The combination of the conventional optimization approaches with new and easy applicable growth systems has revolutionized recombinant protein production in Escherichia coli in view of product yield, culture robustness as well as significantly increased cell densities. This technical development establishes the basis for successful miniaturization and parallelization which is now an important tool for synthetic biology and protein engineering approaches. This review provides an overview of the recent developments, results and applications of advanced growth systems which use a controlled glucose release as substrate supply.

Fermentation Conditions that Affect Clavulanic Acid Production in Streptomyces clavuligerus: A Systematic Review

The β-lactamase inhibitor, clavulanic acid is frequently used in combination with β-lactam antibiotics to treat a wide spectrum of infectious diseases. Clavulanic acid prevents drug resistance by pathogens against these β-lactam antibiotics by preventing the degradation of the β-lactam ring, thus ensuring eradication of these harmful microorganisms from the host. This systematic review provides an overview on the fermentation conditions that affect the production of clavulanic acid in the firstly described producer, Streptomyces clavuligerus. A thorough search was conducted using predefined terms in several electronic databases (PubMed, Medline, ScienceDirect, EBSCO), from database inception to June 30th 2015. Studies must involve wild-type Streptomyces clavuligerus, and full texts needed to be available. A total of 29 eligible articles were identified. Based on the literature, several factors were identified that could affect the production of clavulanic acid in S. clavuligerus. The addition of glycerol or other vegetable oils (e.g., olive oil, corn oil) could potentially affect clavulanic acid production. Furthermore, some amino acids such as arginine and ornithine, could serve as potential precursors to increase clavulanic acid yield. The comparison of different fermentation systems revealed that fed-batch fermentation yields higher amounts of clavulanic acid as compared to batch fermentation, probably due to the maintenance of substrates and constant monitoring of certain entities (such as pH, oxygen availability, etc.). Overall, these findings provide vital knowledge and insight that could assist media optimization and fermentation design for clavulanic acid production in S. clavuligerus.

Evaluation of options for harvest of a recombinant E. Coli fermentation producing a domain antibody using ultra scale-down techniques and pilot-scale verification

Ultra scale‐down (USD) methods operating at the millilitre scale were used to characterise full‐scale processing of E. coli fermentation broths autolysed to different extents for release of a domain antibody. The focus was on the primary clarification stages involving continuous centrifugation followed by depth filtration. The performance of this sequence was predicted by USD studies to decrease significantly with increased extents of cell lysis. The use of polyethyleneimine reagent was studied to treat the lysed cell broth by precipitation of soluble contaminants such as DNA and flocculation of cell debris material. The USD studies were used to predict the impact of this treatment on the performance and here it was found that the fermentation could be run to maximum productivity using an acceptable clarification process (e.g., a centrifugation stage operating at 0.11 L/m² equivalent gravity settling area per hour followed by a resultant required depth filter area of 0.07 m²/L supernatant). A range of USD predictions was verified at the pilot scale for centrifugation followed by depth filtration. © 2016 The Authors Biotechnology Progress published by Wiley Periodicals, Inc. on behalf of American Institute of Chemical Engineers Biotechnol. Prog., 32:382–392, 2016

Lactic acid production from potato peel waste by anaerobic sequencing batch fermentation using undefined mixed culture

Lactic acid (LA) is a necessary industrial feedstock for producing the bioplastic, polylactic acid (PLA), which is currently produced by pure culture fermentation of food carbohydrates. This work presents an alternative to produce LA from potato peel waste (PPW) by anaerobic fermentation in a sequencing batch reactor (SBR) inoculated with undefined mixed culture from a municipal wastewater treatment plant. A statistical design of experiments approach was employed using set of 0.8L SBRs using gelatinized PPW at a solids content range from 30 to 50 g L(-1), solids retention time of 2-4 days for yield and productivity optimization. The maximum LA production yield of 0.25 g g(-1) PPW and highest productivity of 125 mg g(-1) d(-1) were achieved. A scale-up SBR trial using neat gelatinized PPW (at 80 g L(-1) solids content) at the 3 L scale was employed and the highest LA yield of 0.14 g g(-1) PPW and a productivity of 138 mg g(-1) d(-1) were achieved with a 1 d SRT.

Synbiotic functional drink from Jerusalem artichoke juice fermented by probiotic Lactobacillus plantarum PCS26

A probiotic strain Lactobacillus plantarum PCS26 was used to ferment Jerusalem artichoke juice. Growth kinetics of the bacterial strain was followed during juice fermentation both in flask and in laboratory fermentor. Jerusalem artichoke showed to be an excellent source of nutrients for L. plantarum PCS26 growth. The culture grew very well reaching more than 10(10) cfu/ml in just 12 h. The pH changed from the initial 6.5 to 4.6 at the end of fermentation. The culture hydrolyzed fructooligosaccharides present in the Jerusalem artichoke juice, yielding fructose which was presumably consumed along with the malic acid as energy and carbon source. Lactic acid was the main metabolite produced in concentration of 4.6 g/L. Acetic and succinic acid were also identified. Sensory evaluation of the fermented Jerusalem artichoke juice and its mixtures with blueberry juice showed that the 50/50 % v/v mixture would be very well accepted by the consumers. Above 80 % of the panelists would buy this drink, and over 60 % were willing to pay more for it. Culture survivability in the fermented juices during storage at 4-7 °C was assayed by the Weibullian model. The product shelf-life was extended from 19.70 ± 0.50 days of pure Jerusalem artichoke juice to 35.7 ± 6.4 days of the mixture containing 30 % blueberry juice.