Microbial Biotechnology and Agro-Industrial By-Products Fermentation

A special issue of Fermentation (ISSN 2311-5637). This special issue belongs to the section "Fermentation for Food and Beverages".

Deadline for manuscript submissions: closed (15 October 2023) | Viewed by 22839

Special Issue Editors


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Guest Editor
Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, 98168 Messina, Italy
Interests: microbial fermentation; by-product valorization; probiotics; gut microbiota; antimicrobial compounds; functional food
Special Issues, Collections and Topics in MDPI journals

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Guest Editor
Department of Chemical, Biological, Pharmaceutical and Environmental Science, University of Messina, 98168 Messina, Italy
Interests: antimicrobials; nutraceuticals; in vitro digestion; nutrients and phytochemicals release; gut health
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

In the “science of food”, the fermentation process is of greatest interest due to its multidisciplinary nature. Fermentation has been used since prehistoric times, well before the discovery of its scientific principles. Today, scientists investigate microbial fermentations from multiple points of view. The production of fermented food is greatly relevant to the food and nutraceutical industries, where fermentation not only extends products’ shelf life but also increases their nutritional quality. This is due to the health-stimulating effects of probiotic microorganisms and bioactive molecules derived from microbial metabolism. In addition, microbial biotechnology and fermentation are widely applied with the aim of finding innovative strategies promoting the sustainability of the agri-food industry through enhancing the valorisation of agro-food by-products.

This Special Issue welcomes comprehensive reviews, research articles, and short communications on novel findings focused on the use of microbial biotechnology and fermentation. In the food sector, and the agri-food industry in particular, microbial biotechnology and fermentative processes are the basis of many steps for certain foods’ production, favouring an increase in food product quality and promoting valorisation of agro-industrial by-products. This issue will contribute to the sustainability of the food chain and circular economy areas.

Dr. Teresa Gervasi
Dr. Giuseppina Mandalari
Guest Editors

Manuscript Submission Information

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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 2600 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

  • microbial biotechnology
  • fermentation process
  • food fermentation
  • product fortification
  • by-product fermentation
  • agro-food waste and by-product valorisation
  • probiotic microorganisms
  • food chain
  • agri-food industry sustainability
  • circular economy

Published Papers (9 papers)

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Research

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14 pages, 9411 KiB  
Article
Discovery of a Novel β-xylosidase with Xylanase Activity and Its Application in the Production of Xylitol from Corncob Xylan
by Meng Liang, Yu Lin, Lixin Sun, Hao Pang, Hang Wei, Ribo Huang, Yutuo Wei and Liqin Du
Fermentation 2023, 9(7), 606; https://doi.org/10.3390/fermentation9070606 - 28 Jun 2023
Cited by 1 | Viewed by 1360
Abstract
Although β-xylosidases with xylanase activity are preferential for the hydrolysis of xylan and production of xylitol, reports on their use are scarce. In this study, a multifunctional β-xylosidase (XYL4) was identified. In addition to β-xylosidase activity, XYL4 also exhibited xylanase and low α-arabinosidase [...] Read more.
Although β-xylosidases with xylanase activity are preferential for the hydrolysis of xylan and production of xylitol, reports on their use are scarce. In this study, a multifunctional β-xylosidase (XYL4) was identified. In addition to β-xylosidase activity, XYL4 also exhibited xylanase and low α-arabinosidase activity. The enzyme was able to hydrolyze bagasse xylan, oat spelt xylan, birchwood xylan, beechwood xylan, and corncob xylan, and showed the highest hydrolysis activity for corncob xylan. Structural modeling analysis indicated that XYL4 had an additional PA14 domain, which may play a key role in binding xylan substrates. Moreover, XYL4 was used to hydrolyze corncob xylan to produce xylose. When enzymatic hydrolysis and whole-cell catalysis were used to hydrolyze 100 g/L of corncob xylan, the xylose yields were 60.26% and 35.85%, respectively. Then, the Candida tropicalis was inoculated with the above hydrolysates for fermentation to produce xylitol. Using enzymatic hydrolysis and whole-cell catalysis, xylitol yields of 77.56% and 73.67% were obtained by C. tropicalis after the optimization of fermentation, respectively. Full article
(This article belongs to the Special Issue Microbial Biotechnology and Agro-Industrial By-Products Fermentation)
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12 pages, 1027 KiB  
Article
Characterization of Bee Bread Produced with Defined Starter Cultures Mimicking the Natural Fermentation Process
by Fatmanur Poyraz, Dilara Yalmanci, Hümeyra İspirli and Enes Dertli
Fermentation 2023, 9(2), 174; https://doi.org/10.3390/fermentation9020174 - 15 Feb 2023
Cited by 7 | Viewed by 2859
Abstract
Bee bread is a product with unique properties for humans and bees that is produced through the fermentation of pollen in the honeycomb, mainly caused by lactic acid bacteria (LAB) and yeast strains present in the environment. It is a rich source of [...] Read more.
Bee bread is a product with unique properties for humans and bees that is produced through the fermentation of pollen in the honeycomb, mainly caused by lactic acid bacteria (LAB) and yeast strains present in the environment. It is a rich source of nutrients such as proteins, polyphenols and vitamins. Despite the potential nutritional value of bee bread, it is consumed at low levels, as harvesting bee bread from the hives is costly and difficult. This study aimed to produce a standard bee bread by using different strains of the fructophilic lactic acid bacteria (FLAB) Lactobacillus kunkeei and the yeasts Starmeralla magnolia MP-2 and Zygosaccharomyces siamensis MP-14, previously isolated from bee products. In this context, bee bread was produced from pollen by solid-state fermentation using selected FLAB and yeast species, which were then compared with spontaneously developed and commercially available bee bread in terms of microbial stability, physicochemical properties, total phenolic component amounts, in vitro digestibility and amino acid profiles. As a result, it was determined that bee bread made from bee pollen fermented with starter cultures showed improved characteristics than commercial bee bread and was more advantageous in terms of absorption as well as production processes. Full article
(This article belongs to the Special Issue Microbial Biotechnology and Agro-Industrial By-Products Fermentation)
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15 pages, 2061 KiB  
Article
Cellulose from Posidonia oceanica Sea Balls (Egagropili) as Substrate to Enhance Streptomyces roseochromogenes Cellulase Biosynthesis
by Odile Francesca Restaino, Sabrina Cuomo, Sergio D’Ambrosio, Valentina Vassallo, Seyedeh Fatemeh Mirpoor, Concetta Valeria L. Giosafatto, Raffaele Porta and Chiara Schiraldi
Fermentation 2023, 9(2), 98; https://doi.org/10.3390/fermentation9020098 - 21 Jan 2023
Cited by 3 | Viewed by 1304
Abstract
Enhancing Streptomyces cellulase production by supplying lignocellulose biomasses has been poorly investigated so far. In this research the biosynthesis of Streptomyces roseochromogenes ATCC13400 cellulases was increased for the first time by addition of a cellulose fraction (2.5 g·L−1) to the growth [...] Read more.
Enhancing Streptomyces cellulase production by supplying lignocellulose biomasses has been poorly investigated so far. In this research the biosynthesis of Streptomyces roseochromogenes ATCC13400 cellulases was increased for the first time by addition of a cellulose fraction (2.5 g·L−1) to the growth medium, isolated from the marine origin Posidonia oceanica sea balls, generally called egagropili.. In shake flasks the cellulase production increased of 4.3 folds, compared to the control, up to 268 U·L−1 in 72 h, with a productivity of 3.7 U·L−1·h−1, while in batch it was further enhanced up to 347 U·L−1 in 45 h with a doubled productivity of 7.7 U·L−1·h−1 A downstream protocol was set up by coupling two ultrafiltration steps on 10 and 3 kDa membranes to recover the enzymes from the supernatant. A pool of three cellulases, having molecular weights between 115 and 47 kDa, was recovered. The optimal conditions for their enzymatic activity were 60 °C and pH 5.0, and they showed CMCase, FPase and β-glucosidase action. In conclusion, S. roseochromogenes might be considered a new cell factory for cellulase biotechnological production that might be enhanced by using the cellulose from egagropili, a well-known marine origin plant waste, as the substrate. Full article
(This article belongs to the Special Issue Microbial Biotechnology and Agro-Industrial By-Products Fermentation)
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22 pages, 6864 KiB  
Article
In Silico Prediction of Secondary Metabolites and Biosynthetic Gene Clusters Analysis of Streptomyces thinghirensis HM3 Isolated from Arid Soil
by Medhat Rehan, Abdellatif Gueddou, Abdulaziz Alharbi and Imen Ben Abdelmalek
Fermentation 2023, 9(1), 65; https://doi.org/10.3390/fermentation9010065 - 12 Jan 2023
Cited by 3 | Viewed by 3141
Abstract
Natural products produced by microorganisms are considered an important resource of bioactive secondary metabolites, such as anticancer, antifungal, antibiotic, and immunosuppressive molecules. Streptomyces are the richest source of bioactive natural products via possessing a wide number of secondary metabolite biosynthetic gene clusters (SM-BGCs). [...] Read more.
Natural products produced by microorganisms are considered an important resource of bioactive secondary metabolites, such as anticancer, antifungal, antibiotic, and immunosuppressive molecules. Streptomyces are the richest source of bioactive natural products via possessing a wide number of secondary metabolite biosynthetic gene clusters (SM-BGCs). Based on rapid development in sequencing technologies with advances in genome mining, exploring the newly isolated Streptomyces species for possible new secondary metabolites is mandatory to find novel natural products. The isolated Streptomyces thinghirensis strain HM3 from arid and sandy texture soil in Qassim, SA, exerted inhibition activity against tested animal pathogenic Gram-positive bacteria and pathogenic fungal species. In this study, we report the draft genome of S. thinghirensis strain HM3, which consists of 7,139,324 base pairs (bp), with an average G+C content of 71.49%, predicting 7949 open reading frames, 12 rRNA operons (5S, 16S, 23S) and 60 tRNAs. An in silico analysis of strain HM3 genome by the antiSMASH and PRISM 4 online software for SM-BGCs predicted 16 clusters, including four terpene, one lantipeptide, one siderophore, two polyketide synthase (PKS), two non-ribosomal peptide synthetase (NRPS) cluster)/NRPS-like fragment, two RiPP/RiPP-like (ribosomally synthesised and post-translationally modified peptide product), two butyrolactone, one CDPS (tRNA-dependent cyclodipeptide synthases), and one other (cluster containing a secondary metabolite-related protein that does not fit into any other category) BGC. The presented BGCs inside the genome, along with antibacterial and antifungal activity, indicate that HM3 may represent an invaluable source for new secondary metabolites. Full article
(This article belongs to the Special Issue Microbial Biotechnology and Agro-Industrial By-Products Fermentation)
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21 pages, 1417 KiB  
Article
Propionic Acid Fermentation—Study of Substrates, Strains, and Antimicrobial Properties
by Unigunde Antone, Inga Ciprovica, Maksims Zolovs, Rita Scerbaka and Janis Liepins
Fermentation 2023, 9(1), 26; https://doi.org/10.3390/fermentation9010026 - 28 Dec 2022
Cited by 7 | Viewed by 5817
Abstract
Since milk whey is an abundant dairy by-product and a significant threat to the environment, its utilization is of great interest. The study compares valorization of lactose and lactates—the main carbon sources of whey—by fermentation—an environmentally friendly process. Antimicrobials released during fermentation by [...] Read more.
Since milk whey is an abundant dairy by-product and a significant threat to the environment, its utilization is of great interest. The study compares valorization of lactose and lactates—the main carbon sources of whey—by fermentation—an environmentally friendly process. Antimicrobials released during fermentation by food-grade bacteria can help increase the microbiological safety of food. Propionic acid—a strong antimicrobial—is obtained mainly by the petrochemical route, yet there is increasing interest in its synthesis in biotechnological pathway. Five strains of propionic acid bacteria (Acidipropionibacterium acidipropionici, Propionibacterium cyclohexanicum, Propionibacterium freudenreichii, Acidipropionibacterium jensenii and Acidipropionibacterium thoenii) were investigated for their ability to produce organic acids and biomass using Na lactate or lactose as carbon sources. Selected fermentates were investigated for their antimicrobial efficacy during in vitro studies with foodborne pathogens: Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Bacillus subtilis and Staphylococcus aureus. Results confirm that the production of acids and biomass is considerably influenced by the added carbon source. The tested fermentates have strong and specific antimicrobial activity against Pseudomonas aeruginosa, Bacillus subtilis and Staphylococcus aureus. In addition, inhibition of Staphylococcus aureus and Klebsiella pneumonia depends on the activity of produced bacteriocins. The article also discusses the possibility of increasing the antimicrobial activity of fermentates by acidification. Full article
(This article belongs to the Special Issue Microbial Biotechnology and Agro-Industrial By-Products Fermentation)
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18 pages, 2398 KiB  
Article
Biological Potential of Alternative Kombucha Beverages Fermented on Essential Oil Distillation By-Products
by Aleksandra Ranitović, Olja Šovljanski, Milica Aćimović, Lato Pezo, Ana Tomić, Vanja Travičić, Anja Saveljić, Dragoljub Cvetković, Gordana Ćetković, Jelena Vulić and Siniša Markov
Fermentation 2022, 8(11), 625; https://doi.org/10.3390/fermentation8110625 - 10 Nov 2022
Cited by 4 | Viewed by 1934
Abstract
The complete waste streams (solid waste residue, wastewater, and hydrolate) from the essential oil production of basil, chamomile, lavender, rosemary, and hyssop plants were used as a cultivation media for fermentations of a health-beneficial beverage called kombucha. Considering that these waste streams have [...] Read more.
The complete waste streams (solid waste residue, wastewater, and hydrolate) from the essential oil production of basil, chamomile, lavender, rosemary, and hyssop plants were used as a cultivation media for fermentations of a health-beneficial beverage called kombucha. Considering that these waste streams have not been used as a medium for obtaining kombucha, the main focus of this study was on the biological profiling and sensory analysis of newly-obtained kombucha beverages. According to fermentation parameters and advanced mathematical modelling, it can be concluded that kombucha made from chamomile essential oil by-products achieved the fastest successful kombucha fermentation, with a maximal titratable acidity of 7.2 g/L and a minimal pH value of 2.8. The results of other kombucha fermentations varied between the chosen plant and the waste stream used for beverage production. The obtained phenol and flavonoid contents were in the range of 12.4–56.46 mg GA/100 mL and 0.25–5.07 mg RU/100 mL, respectively. Higher antioxidant capacity as well as anti-inflammatory and antihyperglycemic activities of all kombucha beverages were observed compared to controls. Briefly, achieved DPPH, ABTS, and reducing power values were in the range 30.28–73.70, 192.25–683.29, and 19.37–82.76 mmol TE/100 mL, respectively. According to sensory analysis, the best performance or complete acceptability was noted for kombucha beverages made from lavender and hyssops (in the case of solid waste stream mixed with hydrolate) as well as basil (in the case of concentrated wastewater and hydrolate). Full article
(This article belongs to the Special Issue Microbial Biotechnology and Agro-Industrial By-Products Fermentation)
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10 pages, 648 KiB  
Communication
Fermentative Production of Volatile Metabolites Using Brettanomyces bruxellensis from Fruit and Vegetable By-Products
by Melodie A. Lindsay, Ninna Granucci, David R. Greenwood and Silas G. Villas-Boas
Fermentation 2022, 8(9), 457; https://doi.org/10.3390/fermentation8090457 - 12 Sep 2022
Cited by 3 | Viewed by 1970
Abstract
Natural sources of flavour and aroma compounds are highly sought by the modern consumer; however, traditional sources are often low-yielding, and global supply is often outstripped by consumer demand. Fermentation is a favourable route by which natural flavours and fragrances can be produced. [...] Read more.
Natural sources of flavour and aroma compounds are highly sought by the modern consumer; however, traditional sources are often low-yielding, and global supply is often outstripped by consumer demand. Fermentation is a favourable route by which natural flavours and fragrances can be produced. A non-Saccharomyces yeast, Brettanomyces bruxellensis, was investigated for its fermentative potential for the production of flavour and aroma metabolites from juice industry by-products: apple pomace, carrot pomace, and orange pomace. Submerged solid-substrate fermentations were carried out using sterile by-products without nutrient supplementation. Gas chromatography–mass spectrometry was used for volatile metabolite profiling of fermented substrates. One compound of interest, phenylethyl alcohol (rose fragrance), was extracted and quantified using GC-MS at a yield of 2.68 g/kg wet carrot pomace weight. This represents a novel, natural production strategy for phenylethyl alcohol compared to the traditional steam distillation of Rosa domascus sp. petals. Full article
(This article belongs to the Special Issue Microbial Biotechnology and Agro-Industrial By-Products Fermentation)
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18 pages, 2287 KiB  
Article
Production of Polyhydroxyalkanoates through Soybean Hull and Waste Glycerol Valorization: Subsequent Alkaline Pretreatment and Enzymatic Hydrolysis
by Zulma Sarmiento-Vásquez, Luciana Porto de Souza Vandenberghe, Susan Grace Karp and Carlos Ricardo Soccol
Fermentation 2022, 8(9), 433; https://doi.org/10.3390/fermentation8090433 - 1 Sep 2022
Cited by 7 | Viewed by 2039
Abstract
Alkaline pretreatment and sequential enzymatic hydrolysis of soybean hull were investigated to obtain fermentable sugars for polyhydroxyalkanoates production along with residual glycerol as low-cost carbon sources. Soybean hull is composed of approximately 32% cellulose, 12% hemicellulose, 6% lignin, and 11% protein. Alkaline pretreatment [...] Read more.
Alkaline pretreatment and sequential enzymatic hydrolysis of soybean hull were investigated to obtain fermentable sugars for polyhydroxyalkanoates production along with residual glycerol as low-cost carbon sources. Soybean hull is composed of approximately 32% cellulose, 12% hemicellulose, 6% lignin, and 11% protein. Alkaline pretreatment was carried out with 2% NaOH concentration, 10% (w/v) biomass loading, and 60 min incubation time in an autoclave at 120 °C. The response surface methodology (RSM) based on the central composite design (CCD) tool was employed to optimize the enzymatic hydrolysis process, where the variables of biomass loading, enzymes’ concentration, and time were considered. The maximum total reducing sugars concentration obtained was 115.9 g∙L−1 with an enzyme concentration of 11.5 mg protein/g dry substrate for enzyme preparation B1, 2.88 mg protein/g dry substrate for XylA, and 57.6 U/g dry substrate for β-glucosidase, after 42 h at 45 °C, and pH was 4.5. Subsequently, the saccharification step was conducted by increasing the processing scale, using a 1 L tank with stirring with a controlled temperature. Implementing the same enzyme concentrations at pH 4.5, temperature of 45 °C, 260 mL working volume, and incubation time of 42 h, under fed-batch operation with substrate feeding after 14 h and 22 h, a hydrolysate with a concentration of 185.7 g∙L−1 was obtained. Initially, to verify the influence of different carbon sources on Cupriavidus necator DSMz 545 in biomass production, batch fermentations were developed, testing laboratory-grade glucose, soybean hull hydrolysate, and waste glycerol (a by-product of biodiesel processing available in large quantities) as carbon sources in one-factor-at-a-time assays, and the mixture of soybean hull hydrolysate and waste glycerol. Then, the hydrolysate and waste glycerol were consumed by C. necator, producing 12.1 g∙L−1 of biomass and achieving 39% of polyhydroxyalkanoate (PHB) accumulation. To the best of our knowledge, this is the first time that soybean hull hydrolysate has been used as a carbon source to produce polyhydroxyalkanoates, and the results suggest that this agro-industrial by-product is a viable alternative feedstock to produce value-added components. Full article
(This article belongs to the Special Issue Microbial Biotechnology and Agro-Industrial By-Products Fermentation)
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Review

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17 pages, 1530 KiB  
Review
Valorization of Agro-Industrial Orange Peel By-Products through Fermentation Strategies
by Teresa Gervasi and Giuseppina Mandalari
Fermentation 2024, 10(5), 224; https://doi.org/10.3390/fermentation10050224 - 23 Apr 2024
Viewed by 1147
Abstract
The use of whole-cell biocatalysts in microbial cell factories is of great interest to produce added-value compounds. Through large-scale fermentative processes, which use secondary raw materials as substrates, it is possible to recycle and upgrade agro-industrial by-products. This review addresses the main fermentative [...] Read more.
The use of whole-cell biocatalysts in microbial cell factories is of great interest to produce added-value compounds. Through large-scale fermentative processes, which use secondary raw materials as substrates, it is possible to recycle and upgrade agro-industrial by-products. This review addresses the main fermentative processes and bioreactors currently used for the valorization of orange peel, a by-product of the Citrus processing industry. Among the main added-value products, bioethanol, organic acids, enzymes, single cell proteins (SCPs), dyes and aromatic compounds have been industrially produced using orange peel via solid state fermentation and submerged fermentation. This approach fits within the circular economy goals in terms of clean technology and renewable energy, valorization and recycling, upgrade of industrial by-products and sustainability. Full article
(This article belongs to the Special Issue Microbial Biotechnology and Agro-Industrial By-Products Fermentation)
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