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A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Microbial Biotechnology".

Deadline for manuscript submissions: closed (31 July 2021) | Viewed by 33182

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Prof. Dr. Dietmar Haltrich

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Department of Food Sciences and Technology, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Wien, Austria
Interests: microbial biotechnology; enzyme-based processes; biocatalysis; (carbohydrate) oxidoreductases; glycoside hydrolases; oligosaccharides; lactic acid bacteria; recombinant proteins
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Dr. Daniel Kracher

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Institute of Molecular Biotechnology, Graz University of Technology, 8010 Graz, Austria
Interests: biomass degradation; second-generation biofuels; cellulases; redox enzymes; biocatalysis
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Microbial enzymes play an integral and important role in a number of different biotechnological applications, ranging from analytics and medicine to industry. In addition to their well-established applications in these areas, recent developments in the fields of molecular biology, protein chemistry, and enzyme engineering have significantly increased the use of enzymes as biocatalysts in biotechnology. Microbial enzymes and, especially, biocatalysis have developed enormously in the last decade and now offer solutions for the sustainable production of chiral and highly functionalized molecules. Recent advances in oxidative enzymes have furthermore boosted research towards biorefineries and biofuels. This enormous progress is based on new approaches for the screening and identification of novel microbial enzymes, various methods to efficiently (over)produce enzymes in an economic way, various techniques to tailor enzymes with respect to desired or novel properties, as well as a wealth of structural data on enzymes. The successful use of enzymes in industry and biocatalysis requires a transdisciplinary expertise, ranging from biochemistry, to biotechnology, micromolecular and structural biology, process engineering/enzyme reactors, and thus provides a dynamic environment, which will fuel new applications and future innovations. This dynamic interplay between different scientific areas will also be reflected in this Special Issue on the structure, function, and discovery of microbial enzymes, both in traditional fields and in novel industrial applications.

Prof. Dr. Dietmar Haltrich
Dr. Daniel Kracher
Guest Editors

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Keywords

microbial enzymes
biocatalysis
enzyme engineering
structure/function relationships of enzymes
production of recombinant enzymes

Published Papers (11 papers)

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Research

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16 pages, 6173 KiB

Open AccessArticle

Coconut Mesocarp-Based Lignocellulosic Waste as a Substrate for Cellulase Production from High Promising Multienzyme-Producing Bacillus amyloliquefaciens FW2 without Pretreatments

by Van Hong Thi Pham, Jaisoo Kim, Jeahong Shim, Soonwoong Chang and Woojin Chung

Microorganisms 2022, 10(2), 327; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10020327 - 31 Jan 2022

Cited by 21 | Viewed by 3056

Abstract

Facing the crucial issue of high cost in cellulase production from commercial celluloses, inexpensive lignocellulosic materials from agricultural wastes have been attractive. Therefore, several studies have focused on increasing the efficiency of cellulase production by potential microorganisms capable of secreting a high and diversified amount of enzymes using agricultural waste as valuable substrates. Especially, extremophilic bacteria play an important role in biorefinery due to their high value catalytic enzymes that are active even under harsh environmental conditions. Therefore, in this study, we aim to investigate the ability to produce cellulase from coconut-mesocarp of the potential bacterial strain FW2 that was isolated from kitchen food waste in South Korea. This strain was tolerant in a wide range of temperature (−6–75 °C, pH range (4.5–12)) and at high salt concentration up to 35% NaCl. The molecular weight of the purified cellulase produced from strain FW2 was estimated to be 55 kDa. Optimal conditions for the enzyme activity using commercial substrates were found to be 40–50 °C, pH 7.0–7.5, and 0–10% NaCl observed in 920 U/mL of CMCase, 1300 U/mL of Avicelase, and 150 U/mL of FPase. It was achieved in 650 U/mL, 720 U/mL, and 140 U/mL of CMCase, Avicelase, and FPase using coconut-mesocarp, respectively. The results revealed that enzyme production by strain FW2 may have significant commercial values for industry, argo-waste treatment, and other potential applications. Full article

(This article belongs to the Special Issue Advanced Biotechnology of Microbial Enzymes)

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14 pages, 4436 KiB

Open AccessArticle

Gene Analysis, Cloning, and Heterologous Expression of Protease from a Micromycete Aspergillus ochraceus Capable of Activating Protein C of Blood Plasma

by Sergei K. Komarevtsev, Peter V. Evseev, Mikhail M. Shneider, Elizaveta A. Popova, Alexey E. Tupikin, Vasiliy N. Stepanenko, Marsel R. Kabilov, Sergei V. Shabunin, Alexander A. Osmolovskiy and Konstantin A. Miroshnikov

Microorganisms 2021, 9(9), 1936; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9091936 - 11 Sep 2021

Cited by 5 | Viewed by 2353

Abstract

Micromycetes are known to secrete numerous enzymes of biotechnological and medical potential. Fibrinolytic protease-activator of protein C (PAPC) of blood plasma from micromycete Aspergillus ochraceus VKM-F4104D was obtained in recombinant form utilising the bacterial expression system. This enzyme, which belongs to the proteinase-K-like proteases, is similar to the proteases encoded in the genomes of Aspergillus fumigatus ATCC MYA-4609, A. oryzae ATCC 42149 and A. flavus 28. Mature PAPC-4104 is 282 amino acids long, preceded by the 101-amino acid propeptide necessary for proper folding and maturation. The recombinant protease was identical to the native enzyme from micromycete in terms of its biological properties, including an ability to hydrolyse substrates of activated protein C (pGlu-Pro-Arg-pNA) and factor Xa (Z-D-Arg-Gly-Arg-pNA) in conjugant reactions with human blood plasma. Therefore, recombinant PAPC-4104 can potentially be used in medicine, veterinary science, diagnostics, and other applications. Full article

(This article belongs to the Special Issue Advanced Biotechnology of Microbial Enzymes)

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18 pages, 3729 KiB

Open AccessArticle

Polyphenol-Hydroxylating Tyrosinase Activity under Acidic pH Enables Efficient Synthesis of Plant Catechols and Gallols

by Hanbit Song, Pyung-Gang Lee, Hyun Kim, Uk-Jae Lee, Sang-Hyuk Lee, Joonwon Kim and Byung-Gee Kim

Microorganisms 2021, 9(9), 1866; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9091866 - 02 Sep 2021

Cited by 5 | Viewed by 2560

Abstract

Tyrosinase is generally known as a melanin-forming enzyme, facilitating monooxygenation of phenols, oxidation of catechols into quinones, and finally generating biological melanin. As a homologous form of tyrosinase in plants, plant polyphenol oxidases perform the same oxidation reactions specifically toward plant polyphenols. Recent studies reported synthetic strategies for large scale preparation of hydroxylated plant polyphenols, using bacterial tyrosinases rather than plant polyphenol oxidase or other monooxygenases, by leveraging its robust monophenolase activity and broad substrate specificity. Herein, we report a novel synthesis of functional plant polyphenols, especially quercetin and myricetin from kaempferol, using screened bacterial tyrosinases. The critical bottleneck of the biocatalysis was identified as instability of the catechol and gallol under neutral and basic conditions. To overcome such instability of the products, the tyrosinase reaction proceeded under acidic conditions. Under mild acidic conditions supplemented with reducing agents, a bacterial tyrosinase from Bacillus megaterium (BmTy) displayed efficient consecutive two-step monophenolase activities producing quercetin and myricetin from kaempferol. Furthermore, the broad substrate specificity of BmTy toward diverse polyphenols enabled us to achieve the first biosynthesis of tricetin and 3′-hydroxyeriodictyol from apigenin and naringenin, respectively. These results suggest that microbial tyrosinase is a useful biocatalyst to prepare plant polyphenolic catechols and gallols with high productivity, which were hardly achieved by using other monooxygenases such as cytochrome P450s. Full article

(This article belongs to the Special Issue Advanced Biotechnology of Microbial Enzymes)

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9 pages, 777 KiB

Open AccessArticle

Rational Design for Enhanced Acyltransferase Activity in Water Catalyzed by the Pyrobaculum calidifontis VA1 Esterase

by Amanda Staudt, Henrik Terholsen, Jasmin Kaur, Henrik Müller, Simon P. Godehard, Ivaldo Itabaiana, Jr., Ivana C. R. Leal and Uwe T. Bornscheuer

Microorganisms 2021, 9(8), 1790; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9081790 - 23 Aug 2021

Cited by 8 | Viewed by 3003

Abstract

Biocatalytic transesterification is commonly carried out employing lipases in anhydrous organic solvents since hydrolases usually prefer hydrolysis over acyl transfer in bulk water. However, some promiscuous acyltransferases can catalyze acylation in an aqueous solution. In this study, a rational design was performed to enhance the acyltransferase selectivity and substrate scope of the Pyrobaculum calidifontis VA1 esterase (PestE). PestE wild type and variants were applied for the acylation of monoterpene alcohols. The mutant PestE_I208A is selective for (–)-menthyl acetate (E-Value = 55). Highly active acyltransferases were designed, allowing for complete conversion of (–)-citronellol to citronellyl acetate. Additionally, carvacrol was acetylated but with lower conversions. To the best of our knowledge, this is the first example of the biocatalytic acylation of a phenolic alcohol in bulk water. In addition, a high citronellol conversion of 92% was achieved with the more environmentally friendly and inexpensive acyl donor ethyl acetate using PestE_N288F as a catalyst. PestE_N288F exhibits good acyl transfer activity in an aqueous medium and low hydrolysis activity at the same time. Thus, our study demonstrates an alternative synthetic strategy for acylation of compounds without organic solvents. Full article

(This article belongs to the Special Issue Advanced Biotechnology of Microbial Enzymes)

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19 pages, 4206 KiB

Open AccessArticle

Molecular Characterization of Novel Family IV and VIII Esterases from a Compost Metagenomic Library

by Jong-Eun Park, Geum-Seok Jeong, Hyun-Woo Lee and Hoon Kim

Microorganisms 2021, 9(8), 1614; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9081614 - 29 Jul 2021

Cited by 7 | Viewed by 2305

Abstract

Two novel esterase genes, est8L and est13L, were isolated and identified from a compost metagenomic library. The encoded Est8L and Est13L had molecular masses of 33,181 and 44,913 Da consisting of 314 and 411 amino acids, respectively, without signal peptides. Est8L showed the highest identity (32.9%) to a hyper-thermophilic carboxylesterase AFEST from Archaeoglobus fulgidus compared to other esterases reported and was classified to be a novel member of family IV esterases with conserved regions such as HGGG, DY, GXSXG, DPL, and GXIH. Est13L showed the highest identity (98.5%) to the family VIII esterase Est7K from the metagenome library. Est8L and Est13L had the highest activities for p-nitrophenyl butyrate (C4) and p-nitrophenyl caproate (C6), respectively, and Est13L showed a broad substrate specificity for p-nitrophenyl substrates. Est8L and Est13L effectively hydrolyzed glyceryl tributyrate. The optimum temperatures for activities of Est8L and Est13L were identical (40 °C), and the optimum pH values were 9.0 and 10.0, respectively. Est13L showed higher thermostability than Est8L. Sephacryl S-200 HR chromatography showed that the native form of Est8L was a dimer. Interestingly, Est13L was found to be a tetramer, contrary to other family VIII esterases reported. Est8L was inhibited by 30% isopropanol, methanol, and acetonitrile; however, Est13L was activated to 182.9% and 356.1%, respectively, by 30% isopropanol and methanol. Est8L showed enantioselectivity for the S-form, but Est13L showed no enantioselectivity. These results show that intracellular Est8L and/or Est13L are oligomeric in terms of native forms and can be used for pharmaceutical and industrial applications with organic solvents under alkaline conditions. Full article

(This article belongs to the Special Issue Advanced Biotechnology of Microbial Enzymes)

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16 pages, 2268 KiB

Open AccessArticle

Screening New Xylanase Biocatalysts from the Mangrove Soil Diversity

by Corinne Ivaldi, Mariane Daou, Laurent Vallon, Alexandra Bisotto, Mireille Haon, Sona Garajova, Emmanuel Bertrand, Craig B. Faulds, Giuliano Sciara, Adrien Jacotot, Cyril Marchand, Mylène Hugoni, Harivony Rakotoarivonina, Marie-Noëlle Rosso, Caroline Rémond, Patricia Luis and Eric Record

Microorganisms 2021, 9(7), 1484; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9071484 - 12 Jul 2021

Cited by 4 | Viewed by 2214

Abstract

Mangrove sediments from New Caledonia were screened for xylanase sequences. One enzyme was selected and characterized both biochemically and for its industrial potential. Using a specific cDNA amplification method coupled with a MiSeq sequencing approach, the diversity of expressed genes encoding GH11 xylanases was investigated beneath Avicenia marina and Rhizophora stylosa trees during the wet and dry seasons and at two different sediment depths. GH11 xylanase diversity varied more according to tree species and season, than with respect to depth. One complete cDNA was selected (OFU29) and expressed in Pichia pastoris. The corresponding enzyme (called Xyn11-29) was biochemically characterized, revealing an optimal activity at 40–50 °C and at a pH of 5.5. Xyn11-29 was stable for 48 h at 35 °C, with a half-life of 1 h at 40 °C and in the pH range of 5.5–6. Xyn11-29 exhibited a high hydrolysis capacity on destarched wheat bran, with 40% and 16% of xylose and arabinose released after 24 h hydrolysis. Its activity on wheat straw was lower, with a release of 2.8% and 6.9% of xylose and arabinose, respectively. As the protein was isolated from mangrove sediments, the effect of sea salt on its activity was studied and discussed. Full article

(This article belongs to the Special Issue Advanced Biotechnology of Microbial Enzymes)

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14 pages, 1309 KiB

Open AccessArticle

Acid Stable Yeast Cell-Associated Tannase with High Capability in Gallated Catechin Biotransformation

by Nalapat Leangnim, Jakkrit Aisara, Kridsada Unban, Chartchai Khanongnuch and Apinun Kanpiengjai

Microorganisms 2021, 9(7), 1418; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9071418 - 30 Jun 2021

Cited by 6 | Viewed by 2768

Abstract

Previously, nine tannin-tolerant and tannase-producing yeasts were isolated from Miang; all produced cell-associated tannase (CAT) during growth in tannin substrate. Among which, only CAT from Sporidiobolus ruineniae showed better stability than its purified form. Yet, it is of particular interest to directly characterize CATs from the latter yeasts. In this study, four CATs from yeasts, namely Cyberlindnera rhodanensis A22.3, Candida sp. A39.3, Debaryomyces hansenii A45.1, and Cy. rhodanensis A45.3 were characterized. The results indicate that all CATs were produced within the same production yield (11 mU/mL). Most CATs exhibited similar pH and temperature optima and stabilities, except for CAT from Cy. rhodanensis A22.3. This CAT was assigned as acid-stable tannase due to its unusual optimum pH of 2.0 with pH stability and half-life thermostability in the range of pH 2.0–4.0, and 70 °C, respectively. All CATs demonstrated high substrate specificity toward epigallocatechin gallate and epicatechin gallate, thus forming epigallocatechin and epicatechin, respectively. Moreover, they showed operational stability to repeated use for up to five cycles without loss of the initial activity. Therefore, CATs from these yeasts could be useful for the extraction and biotransformation of tea catechins and related applications. Full article

(This article belongs to the Special Issue Advanced Biotechnology of Microbial Enzymes)

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16 pages, 2147 KiB

Open AccessArticle

Prospection of Fungal Lignocellulolytic Enzymes Produced from Jatoba (Hymenaea courbaril) and Tamarind (Tamarindus indica) Seeds: Scaling for Bioreactor and Saccharification Profile of Sugarcane Bagasse

by Alex Graça Contato, Tássio Brito de Oliveira, Guilherme Mauro Aranha, Emanuelle Neiverth de Freitas, Ana Claudia Vici, Karoline Maria Vieira Nogueira, Rosymar Coutinho de Lucas, Ana Sílvia de Almeida Scarcella, Marcos Silveira Buckeridge, Roberto Nascimento Silva and Maria de Lourdes Teixeira de Moraes Polizeli

Microorganisms 2021, 9(3), 533; https://doi.org/10.3390/microorganisms9030533 - 05 Mar 2021

Cited by 16 | Viewed by 2658

Abstract

The lignocellulosic biomass comprises three main components: cellulose, hemicellulose, and lignin. Degradation and conversion of these three components are attractive to biotechnology. This study aimed to prospect fungal lignocellulolytic enzymes with potential industrial applications, produced through a temporal analysis using Hymenaea courbaril and Tamarindus indica seeds as carbon sources. α-L-arabinofuranosidase, acetyl xylan esterase, endo-1,5-α-L-arabinanase, β-D-galactosidase, β-D-glucosidase, β-glucanase, β-D-xylosidase, cellobiohydrolase, endoglucanase, lichenase, mannanase, polygalacturonase, endo-1,4-β-xylanase, and xyloglucanase activities were determined. The enzymes were produced for eight filamentous fungi: Aspergillus fumigatus, Trametes hirsuta, Lasiodiplodia sp., two strains of Trichoderma longibrachiatum, Neocosmospora perseae, Fusarium sp. and Thermothelomyces thermophilus. The best producers concerning enzymatic activity were T. thermophilus and T. longibrachiatum. The optimal conditions for enzyme production were the media supplemented with tamarind seeds, under agitation, for 72 h. This analysis was essential to demonstrate that cultivation conditions, static and under agitation, exert strong influences on the production of several enzymes produced by different fungi. The kind of sugarcane, pretreatment used, microorganisms, and carbon sources proved limiting sugar profile factors. Full article

(This article belongs to the Special Issue Advanced Biotechnology of Microbial Enzymes)

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17 pages, 3703 KiB

Open AccessArticle

From Data Mining of Chitinophaga sp. Genome to Enzyme Discovery of a Hyperthermophilic Metallocarboxypeptidase

by Gabriela Cabral Fernandes, Elwi Guillermo Machado Sierra, Paul Brear, Mariana Rangel Pereira and Eliana G. M. Lemos

Microorganisms 2021, 9(2), 393; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9020393 - 14 Feb 2021

Cited by 5 | Viewed by 2451

Abstract

For several centuries, microorganisms and enzymes have been used for many different applications. Although many enzymes with industrial applications have already been reported, different screening technologies, methods and approaches are constantly being developed in order to allow the identification of enzymes with even more interesting applications. In our work, we have performed data mining on the Chitinophaga sp. genome, a gram-negative bacterium isolated from a bacterial consortium of sugarcane bagasse isolated from an ethanol plant. The analysis of 8 Mb allowed the identification of the chtcp gene, previously annotated as putative Cht4039. The corresponding codified enzyme, denominated as ChtCP, showed the HEXXH conserved motif of family M32 from thermostable carboxypeptidases. After expression in E. coli, the recombinant enzyme was characterized biochemically. ChtCP showed the highest activity versus benziloxicarbonil Ala-Trp at pH 7.5, suggesting a preference for hydrophobic substrates. Surprisingly, the highest activity of ChtCP observed was between 55 °C and 75 °C, and 62% activity was still displayed at 100 °C. We observed that Ca²⁺, Ba²⁺, Mn²⁺ and Mg²⁺ ions had a positive effect on the activity of ChtCP, and an increase of 30 °C in the melting temperature was observed in the presence of Co²⁺. These features together with the structure of ChtCP at 1.2 Å highlight the relevance of ChtCP for further biotechnological applications. Full article

(This article belongs to the Special Issue Advanced Biotechnology of Microbial Enzymes)

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Review

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27 pages, 5460 KiB

Open AccessReview

Bacterial α-Glucan and Branching Sucrases from GH70 Family: Discovery, Structure–Function Relationship Studies and Engineering

by Manon Molina, Gianluca Cioci, Claire Moulis, Etienne Séverac and Magali Remaud-Siméon

Microorganisms 2021, 9(8), 1607; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9081607 - 28 Jul 2021

Cited by 18 | Viewed by 3527

Abstract

Glucansucrases and branching sucrases are classified in the family 70 of glycoside hydrolases. They are produced by lactic acid bacteria occupying very diverse ecological niches (soil, buccal cavity, sourdough, intestine, dairy products, etc.). Usually secreted by their producer organisms, they are involved in the synthesis of α-glucans from sucrose substrate. They contribute to cell protection while promoting adhesion and colonization of different biotopes. Dextran, an α-1,6 linked linear α-glucan, was the first microbial polysaccharide commercialized for medical applications. Advances in the discovery and characterization of these enzymes have remarkably enriched the available diversity with new catalysts. Research into their molecular mechanisms has highlighted important features governing their peculiarities thus opening up many opportunities for engineering these catalysts to provide new routes for the transformation of sucrose into value-added molecules. This article reviews these different aspects with the ambition to show how they constitute the basis for promising future developments. Full article

(This article belongs to the Special Issue Advanced Biotechnology of Microbial Enzymes)

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20 pages, 933 KiB

Open AccessReview

Consolidated Bioprocessing: Synthetic Biology Routes to Fuels and Fine Chemicals

by Alec Banner, Helen S. Toogood and Nigel S. Scrutton

Microorganisms 2021, 9(5), 1079; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9051079 - 18 May 2021

Cited by 17 | Viewed by 4241

Abstract

The long road from emerging biotechnologies to commercial “green” biosynthetic routes for chemical production relies in part on efficient microbial use of sustainable and renewable waste biomass feedstocks. One solution is to apply the consolidated bioprocessing approach, whereby microorganisms convert lignocellulose waste into advanced fuels and other chemicals. As lignocellulose is a highly complex network of polymers, enzymatic degradation or “saccharification” requires a range of cellulolytic enzymes acting synergistically to release the abundant sugars contained within. Complications arise from the need for extracellular localisation of cellulolytic enzymes, whether they be free or cell-associated. This review highlights the current progress in the consolidated bioprocessing approach, whereby microbial chassis are engineered to grow on lignocellulose as sole carbon sources whilst generating commercially useful chemicals. Future perspectives in the emerging biofoundry approach with bacterial hosts are discussed, where solutions to existing bottlenecks could potentially be overcome though the application of high throughput and iterative Design-Build-Test-Learn methodologies. These rapid automated pathway building infrastructures could be adapted for addressing the challenges of increasing cellulolytic capabilities of microorganisms to commercially viable levels. Full article

(This article belongs to the Special Issue Advanced Biotechnology of Microbial Enzymes)

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