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Fermentation
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New Research on Strains Improvement and Microbial Biosynthesis
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New Research on Strains Improvement and Microbial Biosynthesis

A special issue of Fermentation (ISSN 2311-5637). This special issue belongs to the section "Microbial Metabolism, Physiology & Genetics".

Deadline for manuscript submissions: closed (30 June 2024) | Viewed by 18757

Special Issue Editors

Prof. Dr. Kaloyan Petrov

E-Mail Website
Guest Editor
Institute of Chemical Engineering, Bulgarian Academy of Sciences, Sofia, Bulgaria
Interests: biofuels; process optimization; waste substrates utilization
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Penka Petrova

E-Mail Website
Guest Editor
Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
Interests: gene expression; cloning; metagenomics; lactic acid fermentation; heterologous expression; glycoside hydrolase enzymes
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Microbial biosynthesis is the foundation of numerous biotechnological processes for the production of invaluable chemicals widely used as fuels, platform reagents, pharmaceuticals, and various ingredients in food and cosmetics everyday life. Biosynthetic pathways also provide a shortcut to the valorization of renewable natural resources and waste compounds, and a means for the development of a circular economy.

This special issue aims to bring together the latest research in the field of fermentation processes for the biosynthesis of primary and secondary metabolites by genetically improved microbial strains. The scope extends to low molecular weight compounds such as organic acids and alcohols, natural and recombinant enzymes, and biologically active molecules with a protein or lipopeptide nature. Despite the prevailing opinion that the most stable microbial strains applied in industrial biotechnologies are the wild-type isolates found after prolonged selection, modern approaches to genetic engineering offer vast horizons for improvement. In this way, new or enhanced biochemical pathways could be obtained, by-products could be marginalized, and the tolerance to the final biosynthetic product could be increased.

The present special issue provides a forum for cutting-edge research in genomics, mutagenesis, and metabolic/enzyme engineering whose purpose is to achieve enhanced biosynthesis of final metabolites. The development of biotechnologies for novel metabolites or highly optimized microbial processes for the overproduction of those already available, as well as their synthesis from renewable substrates or waste biomass, is also welcomed.

Prof. Dr. Kaloyan Petrov
Prof. Dr. Penka Petrova
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Fermentation is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2100 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • genetic improvement
  • biosynthetic pathways engineering
  • microbial biosynthesis of new metabolites
  • biofuels
  • enzymes production
  • bioactive molecules
  • process optimization

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Published Papers (10 papers)

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Editorial

Jump to: Research, Review

3 pages, 156 KiB  
Editorial
Strain Improvement and Microbial Biosynthesis
by Penka Petrova and Kaloyan Petrov
Fermentation 2024, 10(9), 443; https://doi.org/10.3390/fermentation10090443 - 23 Aug 2024
Viewed by 871
Abstract
Recent industrial biotechnology developments have revealed the enormous potential of microbial fermentation as an alternative to the chemical syntheses of many valuable compounds [...] Full article
(This article belongs to the Special Issue New Research on Strains Improvement and Microbial Biosynthesis)

Research

Jump to: Editorial, Review

32 pages, 4978 KiB  
Article
Optimization of Biodegradation of Common Bean Biomass for Fermentation Using Trichoderma asperellum WNZ-21 and Artificial Neural Networks
by Salma Saleh Alrdahe, Zeiad Moussa, Yasmene F. Alanazi, Haifa Alrdahi, WesamEldin I. A. Saber and Doaa Bahaa Eldin Darwish
Fermentation 2024, 10(7), 354; https://doi.org/10.3390/fermentation10070354 - 13 Jul 2024
Viewed by 913
Abstract
This study showcases a promising approach to sustainably unlocking plant biomass residues by combining biodegradation with artificial intelligence to optimize the process. Specifically, we utilized the definitive screening design (DSD) and artificial neural networks (ANNs) to optimize the degradation of common bean biomass [...] Read more.
This study showcases a promising approach to sustainably unlocking plant biomass residues by combining biodegradation with artificial intelligence to optimize the process. Specifically, we utilized the definitive screening design (DSD) and artificial neural networks (ANNs) to optimize the degradation of common bean biomass by the endophytic fungus Trichoderma asperellum WNZ-21. The optimized process yielded a fungal hydrolysate rich in 12 essential and non-essential amino acids, totaling 18,298.14 μg/g biomass. GC-MS analysis revealed four potential novel components not previously reported in microbial filtrates or plants and seven components exclusive to plant sources but not reported in microbial filtrates. The hydrolysate contained phenolic, flavonoid, and tannin compounds, as confirmed by FT-IR analysis. High-resolution transmission electron microscopy depicted structures resembling amino acid micelles and potential protein aggregates. The hydrolysate exhibited antioxidant, antibacterial, and anticancer properties and innovatively induced apoptotic modulation in the MCF7 cancer cell line. These findings underscore the potential of ANN-optimized fermentation for various applications, particularly in anticancer medicine due to its unique composition and bioactivities. The integration of the DSD and ANNs presents a novel technique for biomass biodegradation, warranting the valorization of plant biomass and suggesting a further exploration of the new components in the fungal hydrolysate. This approach represents the basic concept for exploring other biomass sources and in vivo studies. Full article
(This article belongs to the Special Issue New Research on Strains Improvement and Microbial Biosynthesis)
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16 pages, 4574 KiB  
Article
A Novel Extracellular Catalase Produced by the Antarctic Filamentous Fungus Penicillium Rubens III11-2
by Zdravka Koleva, Radoslav Abrashev, Maria Angelova, Galina Stoyancheva, Boryana Spassova, Lyudmila Yovchevska, Vladislava Dishliyska, Jeny Miteva-Staleva and Ekaterina Krumova
Fermentation 2024, 10(1), 58; https://doi.org/10.3390/fermentation10010058 - 15 Jan 2024
Viewed by 1722
Abstract
Catalase (CAT) is an enzyme involved in the first line of cellular antioxidant defense. It plays a key role in the protection of a wide range of Antarctic organisms against cold stress. Extracellular catalase is very rare and data on it are extremely [...] Read more.
Catalase (CAT) is an enzyme involved in the first line of cellular antioxidant defense. It plays a key role in the protection of a wide range of Antarctic organisms against cold stress. Extracellular catalase is very rare and data on it are extremely scarce. The aim of the present study was to select an efficient producer of extracellular catalase from amongst Antarctic filamentous fungi. Sixty-two Antarctic filamentous fungal strains were investigated for their potential ability to synthesize intracellular and extracellular CAT. The Antarctic strain Penicillium rubens III11-2 was selected as the best producer of extracellular catalase. New information on the involvement of the extracellular antioxidant enzymes superoxide dismutase and CAT in the response of filamentous fungi against low-temperature stress was obtained. An efficient scheme for the purification of CAT from culture fluid was developed. An enzyme preparation with high specific activity (513 U/mg protein) was obtained with a yield of 19.97% and a purification rate of 98.4-fold. The purified enzyme exhibited maximal enzymatic activity in the temperature range of 5–40 °C and temperature stability between 0 and 30 °C, therefore being characterized as temperature sensitive. To our knowledge, this is the first purified extracellular cold active catalase preparation from Antarctic filamentous fungi. Full article
(This article belongs to the Special Issue New Research on Strains Improvement and Microbial Biosynthesis)
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13 pages, 5788 KiB  
Article
A Physiogenomic Study of the Tolerance of Saccharomyces cerevisiae to Isoamyl Alcohol
by Jialin Song, Yu Wang, Hengyuan Xu, Jinshang Liu, Jianping Wang, Haojun Zhang and Cong Nie
Fermentation 2024, 10(1), 4; https://doi.org/10.3390/fermentation10010004 - 20 Dec 2023
Viewed by 1544
Abstract
Isoamyl alcohol is a clear, unpleasantly odorous, colorless liquid of higher alcohol that emits a fruity aroma when heavily diluted. It has received much attention in recent years as a new fuel with a high energy density. Isoamyl alcohol can be produced industrially [...] Read more.
Isoamyl alcohol is a clear, unpleasantly odorous, colorless liquid of higher alcohol that emits a fruity aroma when heavily diluted. It has received much attention in recent years as a new fuel with a high energy density. Isoamyl alcohol can be produced industrially by microbial fermentation. Still, its toxicity to host cells has limited its potential for industrial production, and the molecular mechanism of its toxic effects has not yet been elucidated. In this study, RNA-Seq technology was used to analyze the transcripts of Saccharomyces cerevisiae under normal conditions and in the presence of isoamyl alcohol (0.5 g/L and 2.5 g/L). The results showed that the expression of the cell wall (CCW12, BGL2, NCW2 and SUN4), cell membrane (ELO1, ERG2, FAA1, and OPI3), translation and other structural genes were significantly down-regulated. The expression of genes related to ATP biosynthesis, NADPH biosynthesis (ZWF1), and metal ion transport (PMC1) proteins were up-regulated. Strains with key genes knocked out were cultured without isoamyl alcohol. Combined results suggested that isoamyl alcohol may affect cell wall stability and cell membrane fluidity, and the expression of genes related to ion homeostasis and energy production may play a protective role against isoamyl alcohol stress. By maintaining cell wall stability/membrane fluidity under isoamyl alcohol pressure, improving certain ion homeostasis, and generating energy/NADPH, it is possible to overcome the toxicity of isoamyl alcohol in industrial fermentation processes to a certain extent. Full article
(This article belongs to the Special Issue New Research on Strains Improvement and Microbial Biosynthesis)
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25 pages, 2502 KiB  
Article
Screening Bacterial Strains Capable of Producing 2,3-Butanediol: Process Optimization and High Diol Production by Klebsiella oxytoca FMCC-197
by Anastasia Marina Palaiogeorgou, Ermis Ioannis Michail Delopoulos, Apostolis A. Koutinas and Seraphim Papanikolaou
Fermentation 2023, 9(12), 1014; https://doi.org/10.3390/fermentation9121014 - 12 Dec 2023
Cited by 3 | Viewed by 1651
Abstract
In the present investigation, the potential of various newly isolated strains which belong to the Enterobacteriaceae family to produce 2,3-butanediol (BDO), an important bio-based compound, was studied. The most interesting strain, namely Klebsiella oxytoca FMCC-197, was selected for further investigation. Commercial (raw) sucrose [...] Read more.
In the present investigation, the potential of various newly isolated strains which belong to the Enterobacteriaceae family to produce 2,3-butanediol (BDO), an important bio-based compound, was studied. The most interesting strain, namely Klebsiella oxytoca FMCC-197, was selected for further investigation. Commercial (raw) sucrose or molasses, which are important agro-industrial surpluses, were employed as carbon sources for most of the trials performed. Different fermentation parameters (viz. incubation te4mperature, utilization of different carbon sources, substrate inhibition, aeration) were tested to optimize the process. Fermentations under non-aseptic conditions were also conducted to investigate the potential of growth of the strain K. oxytoca FMCC-197 to surpass the growth of other microorganisms in the culture medium and produce BDO. Besides BDO production, in trials in which molasses was employed as the sole carbon source, significant color removal was observed simultaneously with the production of microbial metabolites. The very high BDO concentration ≈115 g L−1 was reported in approximately 64 h during a fed-batch bioreactor experiment, using sucrose and molasses as carbon sources at 30 °C, reaching a conversion yield (YBDO) of 0.40 g g−1 and a productivity rate (PBDO) of 1.80 g L−1 h−1, while similar results were also obtained at 37 °C. The strain demonstrated remarkable results in non-previously sterilized media, as it produced 58.0 g L−1 in 62 h during a fed-batch bioreactor experiment, while the potential to decolorize molasses-based substrates over 40% was also recorded. From the results obtained it is shown that this wild-type strain can be used in large-scale microbial BDO production using various raw materials as fermentative substrates. The wastewater derived after BDO fermentation by K. oxytoca FMCC-197 can be disposed relatively safely into the environment. Full article
(This article belongs to the Special Issue New Research on Strains Improvement and Microbial Biosynthesis)
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15 pages, 7839 KiB  
Article
Whole-Genome Analysis of Novacetimonas cocois and the Effects of Carbon Sources on Synthesis of Bacterial Cellulose
by Yujuan Zheng, Min Chen, Jiaxin Li, Shuangwen Fei, Shuai Shang, Sixin Liu, Longxiang Liu and Congfa Li
Fermentation 2023, 9(11), 972; https://doi.org/10.3390/fermentation9110972 - 14 Nov 2023
Cited by 2 | Viewed by 1507
Abstract
Novacetimonas cocois WE7 (formally named Komagataeibacter cocois WE7) is a strain isolated from contaminated coconut milk, capable of producing bacterial cellulose (BC). We sequenced its genome to investigate why WE7 cannot synthesize BC from glucose efficiently. It contains about 3.5 Mb and six [...] Read more.
Novacetimonas cocois WE7 (formally named Komagataeibacter cocois WE7) is a strain isolated from contaminated coconut milk, capable of producing bacterial cellulose (BC). We sequenced its genome to investigate why WE7 cannot synthesize BC from glucose efficiently. It contains about 3.5 Mb and six plasmid DNAs. N. cocois WE7 contains two bcs operons (bacterial cellulose operon, bcs I and bcs II); the absence of bcs III operons may lead to reduced BC production. From genome predictions, glucose, sucrose, fructose, maltose, and glycerol can be utilized to generate BC, with WE7 unable to metabolize carbohydrate carbon sources through the Embden–Meyerhof–Parnas (EMP) pathway, but rather through the Hexose Monophosphate Pathway (HMP) and tricarboxylic acid (TCA) pathways. It has a complete gluconic acid production pathway, suggesting that BC yield might be very low when glucose, maltose, and trehalose are used as carbon sources. This study represents the first genome analysis of N. cocois. This information is crucial for understanding BC production and regulation mechanisms in N. cocois and lays a foundation for constructing engineered strains tailored for diverse BC application purposes. Full article
(This article belongs to the Special Issue New Research on Strains Improvement and Microbial Biosynthesis)
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15 pages, 6846 KiB  
Article
Effects of Aromatic Compounds Degradation on Bacterial Cell Morphology
by Maria Gerginova, Gulzhan Spankulova, Tsvetelina Paunova-Krasteva, Nadejda Peneva, Stoyanka Stoitsova and Zlatka Alexieva
Fermentation 2023, 9(11), 957; https://doi.org/10.3390/fermentation9110957 - 8 Nov 2023
Cited by 1 | Viewed by 1652
Abstract
The aim of the present study was to evaluate in parallel the capacity of three bacterial strains originating from oil-polluted soils to degrade monoaromatic compounds and the alterations in the bacterial cell morphology as a result of the biodegradation. The strain Gordonia sp. [...] Read more.
The aim of the present study was to evaluate in parallel the capacity of three bacterial strains originating from oil-polluted soils to degrade monoaromatic compounds and the alterations in the bacterial cell morphology as a result of the biodegradation. The strain Gordonia sp. 12/5 can grow well in media containing catechol, o-, m-, and p-cresol without significant morphological changes in the cells, as shown by scanning electron microscopy. This implies good adaptation of the strain for growth in hydrocarbon-containing media and indicates it is a proper candidate strain for further development of purification methodologies applicable to ecosystems contaminated with such compounds. The growth of the two Rhodococcus strains in the presence of the above carbon sources is accompanied by changes in cell size characteristic of stress conditions. Nevertheless, their hydrocarbon-degrading capacity should not be neglected for future applications. In summary, the established ability to degrade monoaromatic compounds, in parallel with the morphological changes of the bacterial cells, can be used as a valuable indicator of the strain’s vitality in the presence of tested aromatic compounds and, accordingly, of its applicability for bioremediation purposes. Full article
(This article belongs to the Special Issue New Research on Strains Improvement and Microbial Biosynthesis)
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Review

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18 pages, 811 KiB  
Review
An Update on Microbial Biosynthesis of β-Caryophyllene, a Sesquiterpene with Multi-Pharmacological Properties
by Lidia Tsigoriyna, Chakarvati Sango and Daniela Batovska
Fermentation 2024, 10(1), 60; https://doi.org/10.3390/fermentation10010060 - 15 Jan 2024
Viewed by 2061
Abstract
The sesquiterpene β-caryophyllene (BCP) is a major component of various plant essential oils, to which it confers a unique spicy aroma. It is mainly used as a fragrance additive in the food, cosmetic and perfume industries, with an annual consumption ranging between 100 [...] Read more.
The sesquiterpene β-caryophyllene (BCP) is a major component of various plant essential oils, to which it confers a unique spicy aroma. It is mainly used as a fragrance additive in the food, cosmetic and perfume industries, with an annual consumption ranging between 100 and 1000 metric tons worldwide. Recently, BCP has attracted attention as a promising precursor for the production of high-density fuels and for its various biological activities and pharmacological effects. These include antioxidant, anti-inflammatory, anticancer, immune–modulatory, and many other activities. Due to its underlying mechanisms, β-caryophyllene interacts with various human receptors, including CB2 of the endocannabinoid system, which defines it as a phytocannabinoid with therapeutic potential for certain serious conditions. Due to β-caryophyllene’s high utility, various green and sustainable strategies for its production in microorganisms have been developed. This article provides an update on the state-of-the-art in this field to identify directions for further development to extend the compound’s potential. Full article
(This article belongs to the Special Issue New Research on Strains Improvement and Microbial Biosynthesis)
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Graphical abstract

34 pages, 1136 KiB  
Review
Cloning Systems in Bacillus: Bioengineering of Metabolic Pathways for Valuable Recombinant Products
by Alexander Arsov, Nadya Armenova, Emanoel Gergov, Kaloyan Petrov and Penka Petrova
Fermentation 2024, 10(1), 50; https://doi.org/10.3390/fermentation10010050 - 9 Jan 2024
Viewed by 3502
Abstract
Representatives of the genus Bacillus have been established as one of the most important industrial microorganisms in the last few decades. Genetically modified B. subtilis and, to a lesser extent, B. licheniformis, B. amyloliquefaciens, and B. megaterium have been used for [...] Read more.
Representatives of the genus Bacillus have been established as one of the most important industrial microorganisms in the last few decades. Genetically modified B. subtilis and, to a lesser extent, B. licheniformis, B. amyloliquefaciens, and B. megaterium have been used for the heterologous expression of numerous proteins (enzymes, vaccine components, growth factors), platform chemicals, and other organic compounds of industrial importance. Vectors designed to work in Bacillus spp. have dramatically increased in number and complexity. Today, they provide opportunities for genetic manipulation on every level, from point mutations to systems biology, that were impossible even ten years ago. The present review aims to describe concisely the latest developments in the shuttle, integrative, and CRISPR-Cas9 vectors in Bacillus spp. as well as their application for large-scale bioengineering with the prospect of producing valuable compounds on an industrial scale. Genetic manipulations of promoters and vectors, together with their impact on secretory and metabolic pathways, are discussed in detail. Full article
(This article belongs to the Special Issue New Research on Strains Improvement and Microbial Biosynthesis)
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14 pages, 1164 KiB  
Review
Symbiosis Mechanism of Associated Bacteria on 2-keto-L-gulonic Acid Production via Mixed Fermentation: A Review
by Wenhu Chen, Qian Liu, Meng Liu, Hongling Liu, Di Huang, Yi Jiang, Tengfei Wang and Haibo Yuan
Fermentation 2023, 9(12), 1000; https://doi.org/10.3390/fermentation9121000 - 25 Nov 2023
Viewed by 1823
Abstract
Vitamin C, a water-soluble vitamin with strong reducing power, cannot be synthesized by the human body and participates in a variety of important biochemical reactions. Vitamin C is widely used in the pharmaceutical, food, health care, beverage, cosmetics, and feed industries, with a [...] Read more.
Vitamin C, a water-soluble vitamin with strong reducing power, cannot be synthesized by the human body and participates in a variety of important biochemical reactions. Vitamin C is widely used in the pharmaceutical, food, health care, beverage, cosmetics, and feed industries, with a huge market demand. The classical two-step fermentation method is the mainstream technology for vitamin C production. D-sorbitol is transformed into L-sorbose by Gluconobacter oxydans in the first step of fermentation; then, L-sorbose is transformed into 2-keto-L-gulonic acid (2-KGA) by a coculture system composed of Ketogulonicigenium vulgare and associated bacteria; and finally, 2-KGA is transformed into vitamin C through chemical transformation. The conversion of L-sorbose into 2-KGA in the second fermentation step is performed by K. vulgare. However, considering the slow growth and low 2-KGA production of K. vulgare when cultured alone, it is necessary to add an associated bacteria to stimulate K. vulgare growth and 2-KGA production. Although the mechanism by which the associated bacteria promote K. vulgare growth and 2-KGA production has extensively been studied, this remains a hot topic in related fields. Based on the latest achievements and research, this review summarizes the metabolic characteristics of K. vulgare and associated bacteria and elucidates the mechanism by which the associated bacteria promote the growth and 2-KGA production of K. vulgare. Full article
(This article belongs to the Special Issue New Research on Strains Improvement and Microbial Biosynthesis)
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