Fermentation Process Optimization

Enhancement of α-galactosidase production using novel Actinoplanes utahensis B1 strain: sequential optimization and purification of enzyme

α-Galactosidase is an important exoglycosidase belonging to the hydrolase class of enzymes, which has therapeutic and industrial potential. It plays a crucial role in hydrolyzing α-1,6 linked terminal galacto-oligosaccharide residues such as melibiose, raffinose, and branched polysaccharides such as galacto-glucomannans and galactomannans. In this study, Actinoplanes utahensis B1 was explored for α-galactosidase production, yield improvement, and activity enhancement by purification. Initially, nine media components were screened using the Plackett-Burman design (PBD). Among these components, sucrose, soya bean flour, and sodium glutamate were identified as the best-supporting nutrients for the highest enzyme secretion by A. Utahensis B1. Later, the Central Composite Design (CCD) was implemented to fine-tune the optimization of these components. Based on sequential statistical optimization methodologies, a significant, 3.64-fold increase in α-galactosidase production, from 16 to 58.37 U/mL was achieved. The enzyme was purified by ultrafiltration-I followed by multimode chromatography and ultrafiltration-II. The purity of the enzyme was confirmed by Sodium Dodecyl Sulphate-Polyacrylamide Agarose Gel Electrophoresis (SDS-PAGE) which revealed a single distinctive band with a molecular weight of approximately 72 kDa. Additionally, it was determined that this process resulted in a 2.03-fold increase in purity. The purified α-galactosidase showed an activity of 2304 U/mL with a specific activity of 288 U/mg. This study demonstrates the isolation of Actinoplanes utahensis B1 and optimization of the process for the α-galactosidase production as well as single-step purification.

Whole genome sequencing of a novel chitinolytic Streptomyces sp. RB7AG reveals it's chitosan production potential: optimization of the process through Taguchi experimental design

This study reports about the De novo whole genome sequencing and analysis of a bacterial isolate Streptomyces sp. Strain. RB7AG, isolated from the sediments of Chilika Lake, Odisha, India. The genome report in this paper highlights a size of 7,708,681 bp and a GC content of 72.3%. It also consists of 7274 coding sequence, 66 tRNA and 4 rRNA. Furthermore, carbohydrate active enzyme analysis revealed that the strain RB7AG has 127 glycoside hydrolase family genes, which is well known for hydrolysis of glycosidic bond in complex sugars. Thus, exploiting these microorganisms for the production of chitosan can be an appropriate waste disposal method of choice. Chitosan being an important biomolecule that has various industrial applications. Hence, the study also sought to improve the culture conditions for the Streptomyces sp. strain RB7AG for generation, recovery, and characterization of chitosan. Utilizing the isolate, various low-cost nitrogen sources, including peptone, yeast extract, ammonium chloride, urea along with pH, media, metal ions and surfactant were assessed for chitosan synthesis. In this context, traditional methods such as One Factor One Time are more time consuming and expensive too. The current work aims to establish a methodology to optimize the degradation of chitin by the chitinolytic Streptomyces sp. strain RB7AG, isolated from lake sediment for the production of chitosan. More than one factor was considered at the time of experiments, and the knowledge was integrated into Taguchi statistical design to determine the contribution of the most important factors required to achieve the desired end product i.e. chitosan. Highest chitosan production (2.188 µg/ml) was observed in MSM media, 1.0% NaCl (w/v), 0.5% Yeast extract, 1% Ca2+ and 0.1% Tween 80 at pH 9. The whole genome analysis of RB7AG would help in determining the mechanism involved in the breakdown activity.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03613-z.

Optimization of the growth conditions through response surface methodology and metabolomics for maximizing the auxin production by Pantoea agglomerans C1

Introduction

The fermentative production of auxin/indole 3-acetate (IAA) using selected Pantoea agglomerans strains can be a promising approach to developing novel plant biostimulants for agriculture use.

Methods

By integrating metabolomics and fermentation technologies, this study aimed to define the optimal culture conditions to obtain auxin/IAA-enriched plant postbiotics using P. agglomerans strain C1. Metabolomics analysis allowed us to demonstrate that the production of a selected.

Results and discussion

Array of compounds with plant growth-promoting- (IAA and hypoxanthine) and biocontrol activity (NS-5, cyclohexanone, homo-L-arginine, methyl hexadecenoic acid, and indole-3-carbinol) can be stimulated by cultivating this strain on minimal saline medium amended with sucrose as a carbon source. We applied a three-level-two-factor central composite design (CCD) based response surface methodology (RSM) to explore the impact of the independent variables (rotation speed and medium liquid-to-flask volume ratio) on the production of IAA and IAA precursors. The ANOVA component of the CCD indicated that all the process-independent variables investigated significantly impacted the auxin/IAA production by P. agglomerans strain C1. The optimum values of variables were a rotation speed of 180 rpm and a medium liquid-to-flask volume ratio of 1:10. Using the CCD-RSM method, we obtained a maximum indole auxin production of 208.3 ± 0.4  mg IAA_equ/L, which was a 40% increase compared to the growth conditions used in previous studies. Targeted metabolomics allowed us to demonstrate that the IAA product selectivity and the accumulation of the IAA precursor indole-3-pyruvic acid were significantly affected by the increase in the rotation speed and the aeration efficiency.

Evaluation of the Estimation Capability of Response Surface Methodology and Artificial Neural Network for the Optimization of Bacteriocin-Like Inhibitory Substances Production by Lactococcus lactis Gh1

Bacteriocin-like inhibitory substances (BLIS) produced by Lactococcus lactis Gh1 had shown antimicrobial activity against Listeria monocytogenes ATCC 15313. Brain Heart Infusion (BHI) broth is used for the cultivation and enumeration of lactic acid bacteria, but there is a need to improve the current medium composition for enhancement of BLIS production, and one of the approaches is to model the optimization process and identify the most appropriate medium formulation. Response surface methodology (RSM) and artificial neural network (ANN) models were employed in this study. In medium optimization, ANN (R² = 0.98) methodology provided better estimation point and data fitting as compared to RSM (R² = 0.79). In ANN, the optimal medium consisted of 35.38 g/L soytone, 16 g/L fructose, 3.25 g/L sodium chloride (NaCl) and 5.40 g/L disodium phosphate (Na₂HPO₄). BLIS production in optimal medium (717.13 ± 0.76 AU/mL) was about 1.40-fold higher than that obtained in nonoptimised (520.56 ± 3.37 AU/mL) medium. BLIS production was further improved by about 1.18 times higher in 2 L stirred tank bioreactor (787.40 ± 1.30 AU/mL) as compared to that obtained in 250 mL shake flask (665.28 ± 14.22 AU/mL) using the optimised medium.

New lipase-producing Streptomyces isolated from halo-alkaline habitat in Wadi El Natrun: polyphasic identification and statistical optimization of enzyme production

Background

Bioprospecting lipase producers in non-conventional habitats are the way to find special enzymes of diverse applications. Halo-alkaline marshes in Wadi El Natrun in Egypt are some of the most stable ecological systems in the world, and because of the double extremities of alkalinity and salinity, they harbor individual microbes capable of adapting stress conditions.

Results

Eight strains were recovered from the coastline soil of Al-Beida Lake in Wadi El Natrun and have been tested for lipase production. Among the eight isolates, the strain SBLWN_MH2 was the most active producer of lipase (7.5 U/ml). The crude SBLWN_MH2 lipase showed activity over a wide pH range (3.5 to 13) with an optimum pH at 10.5, and it was able to show more than 75% of its highest activity at pH elevated up to 13. The identification using phenotypic and genotypic methods strongly indicated that the strain SBLWN_MH2 belonged to the genus Streptomyces with a similarity of 99%. Thus, it has been given the suggested name Streptomyces sp. SBLWN_MH2 (MG593538). SBLWN_MH2 produced extracellular lipase in modified starch casein medium supplemented with different oils or Tween-80, and the potential production rate has been attained in the case of linseed oil after 3 days. Further experiments have been carried out to optimize medium composition through Box-Behnken design and response surface methodology, and it was possible to achieve more than 3.5-fold increase in lipase production.

Conclusions

The present study indicates that Streptomyces sp. SBLWN_MH2 is a potential lipase producer and could be fruitfully employed in the large-scale production of highly alkaline lipase.

Rapid Evaluation and Optimization of Medium Components Governing Tryptophan Production by Pediococcus acidilactici TP-6 Isolated from Malaysian Food via Statistical Approaches

Tryptophan is one of the most extensively used amino acids in livestock industry owing to its effectiveness in enhancing the growth performance of animals. Conventionally, the production of tryptophan relies heavily on genetically modified Escherichia coli but its pathogenicity is a great concern. Our recent study demonstrated that a lactic acid bacterium (LAB), Pediococcus acidilactici TP-6 that isolated from Malaysian food was a promising tryptophan producer. However, the tryptophan production must enhance further for viable industrial application. Hence, the current study evaluated the effects of medium components and optimized the medium composition for tryptophan production by P. acidilactici TP-6 statistically using Plackett-Burman Design, and Central Composite Design. The optimized medium containing molasses (14.06 g/L), meat extract (23.68 g/L), urea (5.56 g/L) and FeSO4 (0.024 g/L) significantly enhanced the tryptophan production by 150% as compared to the control de Man, Rogosa and Sharpe medium. The findings obtained in this study revealed that rapid evaluation and effective optimization of medium composition governing tryptophan production by P. acidilactici TP-6 were feasible via statistical approaches. Additionally, the current findings reveal the potential of utilizing LAB as a safer alternative tryptophan producer and provides insight for future exploitation of various amino acid productions by LAB.

Proline-Based Cyclic Dipeptides from Korean Fermented Vegetable Kimchi and from Leuconostoc mesenteroides LBP-K06 Have Activities against Multidrug-Resistant Bacteria

Lactobacillus plantarum and Leuconostoc mesenteroides play a prominent role as functional starters and predominant isolates in the production of various types of antimicrobial compound-containing fermented foods, especially including kimchi. In the case of the bioactive cyclic dipeptides, their racemic diastereomers inhibitory to bacteria and fungi have been suggested to come solely from Lactobacillus spp. of these strains. We previously demonstrated the antifungal and antiviral activities of proline-based cyclic dipeptides, which were fractionated from culture filtrates of Lb. plantarum LBP-K10 originated from kimchi. However, cyclic dipeptides have not been identified in the filtrates, either from cultures or fermented subject matter, driven by Ln. mesenteroides, which have been widely used as starter cultures for kimchi fermentation. Most importantly, the experimental verification of cyclic dipeptide-content changes during kimchi fermentation have also not been elucidated. Herein, the antibacterial fractions, including cyclo(Leu-Pro) and cyclo(Phe-Pro), from Ln. mesenteroides LBP-K06 culture filtrates, which exhibited a typical chromatographic retention behavior (t_R), were identified by using semi-preparative high-performance liquid chromatography and gas chromatography-mass spectrometry. Based on this finding, the proline-based cyclic dipeptides, including cyclo(Ser-Pro), cyclo(Tyr-Pro), and cyclo(Leu-Pro), were additionally identified in the filtrates only when fermenting Chinese cabbage produced with Ln. mesenteroides LBP-K06 starter cultures. The detection and isolation of cyclic dipeptides solely in controlled fermented cabbage were conducted under the control of fermentation-process parameters concomitantly with strong CDP selectivity by using a two-consecutive-purification strategy. Interestingly, cyclic dipeptides in the filtrates, when using this strain as a starter, increased with fermentation time. However, no cyclic dipeptides were observed in the filtrates of other fermented products, including other types of kimchi and fermented materials of plant and animal origin. This is the first report to conclusively demonstrate evidence for the existence of antimicrobial cyclic dipeptides produced by Ln. mesenteroides in kimchi. Through filtrates from lactic acid bacterial cultures and from fermented foods, we have also proved a method of combining chromatographic fractionation and mass spectrometry-based analysis for screening cyclic dipeptide profiling, which may allow evaluation of the fermented dairy foods from a new perspective.

Optimization of complex fermentation media for glucose oxidase production using statistical approach

Production cost of enzyme is largely determined by the type of the strain and raw material used to propagate the strain. Hence, selection of the strain and raw materials is crucial in enzyme production. For Glucose oxidase (GOx), previous studies showed Aspergillus terreus UniMAP AA-1 offers a better alternative to the existing sources. Thus, a lower production cost could be logically anticipated by growing the strain in a cheaper complex media such as molasses. In this work, sugar cane molasses, supplemented with urea and carbonate salt and a locally isolated strain Aspergillus terreus UniMAP AA-1 were used to produce a crude GOx enzyme in a small scale. A statistical optimization approach namely Response Surface Methodology (RSM) was used to optimize the media components for highest GOx activity. It was found that the highest GOx activity was achieved using a combination of molasses, carbonate salt and urea at concentration 32.51, 4.58 and 0.93% (w/v), respectively. This study provides an alternative optimized media conditions for GOx production using locally available raw materials.