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A special issue of Processes (ISSN 2227-9717). This special issue belongs to the section "Biological Processes and Systems".

Deadline for manuscript submissions: closed (15 May 2024) | Viewed by 23975

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Special Issue Editors

Prof. Dr. Ali Demirci

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Guest Editor

Department of Agricultural and Biological Engineering, Pennsylvania State University, University Park, PA 16802, USA
Interests: fermentation; bioprocessing; value-added products; process optimization; reactor design; scale-up

Prof. Dr. Irfan Turhan

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Guest Editor

Department of Food Engineering, Akdeniz University, Antalya 07058, Turkey
Interests: enzymes; bioreactors; industrial microbiology, fermentation; biotransformation
Special Issues, Collections and Topics in MDPI journals

Dr. Ehsan Mahdinia

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Guest Editor

Stack Family Center for Biopharmaceutical Education & Training, Albany College of Pharmacy and Health Sciences, Albany, NY 12203, USA
Interests: biomanufacturing; recombinant biopharmaceuticals; fermentation; bioprocess optimization; upstream processing
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The fermentation process is an approach that promotes the growth of microorganisms for the production of value-added products such as organic acids, enzymes, vitamins, and biopharmaceuticals. Through fermentation, raw agricultural bioproducts or industrial wastes can be converted into value-added products. The production of value-added products from agricultural raw materials not only increases the value of farmers’ crops but can also improve the wellbeing of people. In most cases, the dependency on petroleum-based products can be minimized, owing to our ability to obtain the same products can obtained via microbial fermentation, utilizing renewable raw materials such as corn and potatoes. In terms of renewable energy production, biogas, ethanol, and bio-hydrogen are the most promising microbial products. With petroleum sources increasingly rendered unsustainable, this area alone is very exciting since with the ever greater need for new and cleaner energy sources. On the other hand, many compounds related to human health such as vaccines and prebiotics can be produced in bioreactors, making use of different microorganisms and fermentation techniques.

This Special Issue on “Fermentation and Bioprocess Engineering Processes” will not only provide the fundamentals for fermentation processes, but also provide some successful examples. We believe this will contribute significantly in this field and encourage for future research.

Prof. Dr. Ali Demirci
Prof. Dr. Irfan Turhan
Dr. Ehsan Mahdinia
Guest Editors

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Keywords

fermentation
bioprocessing
reactor design
process optimization
value-added products
industrial microbiology
biotechnology
microbial fermentation
cell culture
bioconversion

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Published Papers (9 papers)

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Research

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17 pages, 3682 KiB

Open AccessFeature PaperEditor’s ChoiceArticle

Characterizing Novel Acetogens for Production of C2–C6 Alcohols from Syngas

by Rahul Thunuguntla, Hasan K. Atiyeh, Raymond L. Huhnke and Ralph S. Tanner

Processes 2024, 12(1), 142; https://doi.org/10.3390/pr12010142 - 6 Jan 2024

Cited by 1 | Viewed by 1303

Abstract

Utilizing syngas components CO, CO_2, and H₂ to produce fatty acids and alcohols offers a sustainable approach for biofuels and chemicals, reducing the global carbon footprint. The development of robust strains, especially for higher alcohol titers in C4 and C6 compounds, and the creation of cost-effective media are crucial. This study compared syngas fermentation capabilities of three novel strains (Clostridium carboxidivorans P20, C. ljungdahlii P14, and C. muellerianum P21) with existing strains (C. ragsdalei P11 and C. carboxidivorans P7) in three medium formulations. Fermentations in 250-mL bottles were conducted at 37 °C using H₂:CO₂:CO (30:30:40) using P11, P7, and corn steep liquor (CSL) media. Results showed that P11 and CSL media facilitated higher cell mass, alcohol titer, and gas conversion compared to the P7 medium. Strains P7, P14, and P20 formed 1.4- to 4-fold more total alcohols in the CSL medium in comparison with the P7 medium. Further, strain P21 produced more butanol (0.9 g/L) and hexanol (0.7 g/L) in the medium with CSL, offering cost advantages over P7 and P11 media containing yeast extract. Enhancing strain activity and selectivity in converting syngas into C4 and C6 alcohols requires further development, medium formulation improvements, and characterization, particularly for the new strain P21. Full article

(This article belongs to the Special Issue Fermentation and Bioprocess Engineering Processes)

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19 pages, 1905 KiB

Open AccessFeature PaperEditor’s ChoiceArticle

Yeast Lipids from Crude Glycerol Media and Utilization of Lipid Fermentation Wastewater as Maceration Water in Cultures of Edible and Medicinal Mushrooms

by Ilias Diamantis, Seraphim Papanikolaou, Savvoula Michou, Vassilios Anastasopoulos and Panagiota Diamantopoulou

Processes 2023, 11(11), 3178; https://doi.org/10.3390/pr11113178 - 7 Nov 2023

Cited by 2 | Viewed by 1696

Abstract

Four wild “red” yeast strains (Rhodosporidium kratochvilovae FMCC Y70, R. toruloides NRRL Y-27013, R. toruloides NRRL Y-17902 and R. toruloides NRRL Y-6985) were cultured in shake flasks on industrial glycerol at an initial substrate (Gly₀) concentration ≈ 50 g/L under nitrogen limitation. Strains NRRL Y-27013, NRRL Y-17902 and NRRL Y-6985 presented appreciable dry cell weight (DCW) and lipid synthesis (DCW up to 18–19 g/L containing lipids in quantities ≈ 47%, w/w). Strains NRRL Y-27013 and NRRL Y-6985 were further tested in higher Gly₀ concentrations (≈90 g/L and ≈110 g/L) with the same initial nitrogen quantity as in the first (“screening”) experiment. Both strains, despite the high Gly₀ concentrations and C/N ratios (up to 120 moles/moles) imposed, presented significant DCW production (up to c. 29.0–29.5 g/L). Yeast biomass contained significant lipid (42–43%, w/w) and endopolysaccharide (up to 42%, w/w) quantities. Both lipids and endopolysaccharide quantities (in % w/w) noticeably increased as a response to the imposed nitrogen limitation. Lipids containing mainly oleic and palmitic acids constituted ideal candidates for biodiesel synthesis. Thereafter, the wastewaters derived from the lipid production process (lipid fermentation wastewaters—LFWs) were used as maceration waters in cultivations of edible and medicinal fungi, where novel (non-conventional) substrates were used in the performed cultures. CW (coffee residue + wheat straw), CB (coffee residue + beech wood shavings), OW (olive crop + wheat straw), OB (olive crop + beech wood shavings), RW (rice husk + wheat straw) and RB (rice husk + beech wood shavings) were soaked/sprayed with LFWs or tap water and utilized in the cultivation of Pleurotus, Ganoderma and Lentinula mushrooms. The impact of LFWs on the mycelial growth rate (mm/d) and biomass production was evaluated. The results show that regardless of the wetting method, the highest growth rates (6.2–6.6 mm/d) were noticed on RW and RB for Pleurotus eryngii and Ganoderma resinaceum, on OW, OB and RW for Ganoderma applanatum and on RW, OW and OB for Lentinula edodes. Nevertheless, high biomass production was obtained on substrates soaked with LFWs for Pleurotus ostreatus (RW: 443 mg/g d.w.), L. edodes (RB: 238 mg/g d.w.) and Ganoderma lucidum (RW: 450 mg/g d.w.). Overall, this study demonstrates the possibility of the industrial conversion of low-value agro-waste to mycelial mass and eventually to important food products. Full article

(This article belongs to the Special Issue Fermentation and Bioprocess Engineering Processes)

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13 pages, 2812 KiB

Open AccessArticle

Screening of Microbial Strains Used to Ferment Dendrobium officinale to Produce Polysaccharides, and Investigation of These Polysaccharides’ Skin Care Effects

by Xin Tang, Bulei Wang, Bingyong Mao, Jianxin Zhao, Guangrong Liu, Kaiye Yang and Shumao Cui

Processes 2023, 11(9), 2563; https://doi.org/10.3390/pr11092563 - 27 Aug 2023

Cited by 5 | Viewed by 1385

Abstract

The microbial fermentation of plants is a promising approach for enhancing the yield of polysaccharides with increased activity. In this study, ten microbial strains, Lactiplantibacillus plantarum CCFM8661, Limosilactobacillus reuteri CCFM8631, Lactobacillus helveticus M10, Lacticaseibacillus rhamnosus CCFM237, Lactilactobacillus sakei GD17-9, Lacticaseibacillus casei CCFM1073, Bacillus subtilis CCFM1162, Bacteroides cellulosilyticus FTJSI-E-2, Bacteroides stercoris FNMHLBEIK-4, and Saccharomyces cerevisiae HN7-A5, were used to ferment Dendrobium officinale. The skin care activity of the resulting polysaccharides (F-DOP) was evaluated in cultured HaCaT and RAW 264.7 cells, and a mouse model. The results indicated that D. officinale medium promoted strain proliferation, and fermentation significantly enhanced polysaccharide yield (up to 1.42 g/L) compared to that without fermentation (0.76 g/L). Moreover, F-DOPs, especially after CCFM8631 fermentation, exhibited an excellent ability to attenuate sodium dodecyl sulfate-induced HaCaT cell injury (from 69.04 to 94.86%) and decrease nitric oxide secretion (from 42.86 to 22.56 μM) in lipopolysaccharide-stimulated RAW 264.7 cells. In vivo, CCFM8631-FDOP reduced the transdermal water loss rate, skin epidermal thickness, and interleukin 6, and enhanced the expression of filaggrin, improving 2,4-dinitrofluorobenzene-induced skin damage. Therefore, considering viable cell counts, polysaccharide yields, and skin care efficacy in vitro and in vivo, CCFM8631 is the most suitable strain to enhance the skin care activity of DOPs and possesses promising potential for applications in the cosmetics industry. Full article

(This article belongs to the Special Issue Fermentation and Bioprocess Engineering Processes)

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16 pages, 1832 KiB

Open AccessFeature PaperArticle

Production and Characterization of Kombucha Tea from Different Sources of Tea and Its Kinetic Modeling

by Kubra Tarhan Kuzu, Gamze Aykut, Serap Tek, Ercan Yatmaz, Mustafa Germec, Ibrahim Yavuz and Irfan Turhan

Processes 2023, 11(7), 2100; https://doi.org/10.3390/pr11072100 - 14 Jul 2023

Cited by 4 | Viewed by 3285

Abstract

This study aimed to investigate the fermentation performance, sugar consumption, pH changes, total phenolic compounds, and antioxidant activity produced using different tea extracts and sugar concentrations and the kinetic characteristics of Kombucha fermentation. Three independent sugar concentrations (10 g/L, 40 g/L, and 70 g/L) were used in the fermentation process. The results showed that the Kombucha culture consumed all sugar in the fermentation medium when the sugar concentration was below a certain threshold, but when the sugar concentration was high, not all substrate was consumed. Sugar consumption values ranged from 48.39 to 55.40 g/L and affected biomass formation, with higher sugar consumption resulting in increased biomass production. The pH decreased during fermentation due to the production of organic acids and microbial by-products, while total acidity increased. Total phenolic compounds increased during fermentation, with the highest concentrations observed in herbal Kombucha teas. Antioxidant activity varied, with some samples showing a decrease in DPPH scavenging ability. Kinetic characterization revealed the relationship between substrate depletion, sugar consumption, total acidity, and phenolic compound production. The results showed that sugar concentration influenced the fermentation kinetics and end-product characteristics of Kombucha tea. Overall, this study provides valuable insights into the fermentation process of Kombucha tea and its impact on various parameters, contributing to the understanding of the factors affecting its quality and health benefits. Full article

(This article belongs to the Special Issue Fermentation and Bioprocess Engineering Processes)

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16 pages, 2340 KiB

Open AccessArticle

Fermentation of Menaquinone-7: The Influence of Environmental Factors and Storage Conditions on the Isomer Profile

by Neha Lal, Mostafa Seifan and Aydin Berenjian

Processes 2023, 11(6), 1816; https://doi.org/10.3390/pr11061816 - 15 Jun 2023

Cited by 2 | Viewed by 2622

Abstract

Menaquinone-7 (MK-7) provides significant health gains due to its excellent pharmacokinetic properties. However, MK-7 occurs at low concentrations in mainstream foods, heightening the demand for nutritional supplements. MK-7 exists as geometric isomers, and only all-trans MK-7 is bioactive. Exposure to certain environments impacts the isomer profile. Knowledge of these factors and their influence on the isomer composition is important, as the efficacy of fermented MK-7 end products is solely determined by the all-trans isomer. This investigation aimed to evaluate the short- and long-term effect of atmospheric oxygen, common temperatures, and light on the isomer profile. From the short-term study, it was ascertained that MK-7 is moderately heat-stable but extremely light-sensitive. The stability of all-trans MK-7 was then examined during 8 weeks of storage at a low temperature with minimal oxygen exposure in the absence of light. Negligible change in the all-trans MK-7 concentration occurred, suggesting it is reasonably stable during prolonged storage in this environment. These findings will aid the development of optimal storage conditions to preserve bioactive MK-7 in fermented nutritional supplements, the large-scale availability and consumption of which will help compensate for the dietary deficit of this essential vitamin and provide consumers with better health outcomes. Full article

(This article belongs to the Special Issue Fermentation and Bioprocess Engineering Processes)

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13 pages, 2888 KiB

Open AccessFeature PaperEditor’s ChoiceArticle

Synergistic Ball Milling–Enzymatic Pretreatment of Brewer’s Spent Grains to Improve Volatile Fatty Acid Production through Thermophilic Anaerobic Fermentation

by Can Liu, Ahamed Ullah, Xin Gao and Jian Shi

Processes 2023, 11(6), 1648; https://doi.org/10.3390/pr11061648 - 28 May 2023

Cited by 3 | Viewed by 1484

Abstract

Brewer’s spent grain (BSG) as the major byproduct in the brewing industry is a promising feedstock to produce value-added products such as volatile fatty acids (VFAs). Synergistic ball mill–enzymatic hydrolysis (BM-EH) process is an environmentally friendly pretreatment method for lignocellulosic materials before bioprocessing. This study investigated the potential of raw and BM-EH pretreated BSG feedstocks to produce VFAs through a direct thermophilic anaerobic fermentation process without introducing a methanogen inhibitor. The highest VFA concentration of over 30 g/L was achieved under the high-solid loading fermentation (HS) of raw BSG. The synergistic BM-EH pretreatment helps to increase the cellulose conversion to 70%. Under conventional low TS fermentation conditions, compared to the controlled sample, prolonged pretreatment of the BSG substrate resulted in increased VFA yields from 0.25 to 0.33 g/g_VS, and butyric acid became dominant instead of acetic acid. Full article

(This article belongs to the Special Issue Fermentation and Bioprocess Engineering Processes)

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27 pages, 2494 KiB

Open AccessFeature PaperReview

Physical Cell Disruption Technologies for Intracellular Compound Extraction from Microorganisms

by Fujunzhu Zhao, Zhiwu Wang and Haibo Huang

Processes 2024, 12(10), 2059; https://doi.org/10.3390/pr12102059 - 24 Sep 2024

Viewed by 2103

Abstract

This review focuses on the physical disruption techniques in extracting intracellular compounds, a critical step that significantly impacts yield and purity. Traditional chemical extraction methods, though long-established, face challenges related to cost and environmental sustainability. In response to these limitations, this paper highlights the growing shift towards physical disruption methods—high-pressure homogenization, ultrasonication, milling, and pulsed electric fields—as promising alternatives. These methods are applicable across various cell types, including bacteria, yeast, and algae. Physical disruption techniques achieve relatively high yields without degrading the bioactivity of the compounds. These techniques, utilizing physical forces to break cell membranes, offer promising extraction efficiency, with reduced environmental impacts, making them attractive options for sustainable and effective intracellular compound extraction. High-pressure homogenization is particularly effective for large-scale extracting of bioactive compounds from cultivated microbial cells. Ultrasonication is well-suited for small to medium-scale applications, especially for extracting heat-sensitive compounds. Milling is advantageous for tough-walled cells, while pulsed electric field offers gentle, non-thermal, and highly selective extraction. This review compares the advantages and limitations of each method, emphasizing its potential for recovering various intracellular compounds. Additionally, it identifies key research challenges that need to be addressed to advance the field of physical extractions. Full article

(This article belongs to the Special Issue Fermentation and Bioprocess Engineering Processes)

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18 pages, 466 KiB

Open AccessFeature PaperReview

Hybrid Modeling for On-Line Fermentation Optimization and Scale-Up: A Review

by Mariana Albino, Carina L. Gargalo, Gisela Nadal-Rey, Mads O. Albæk, Ulrich Krühne and Krist V. Gernaey

Processes 2024, 12(8), 1635; https://doi.org/10.3390/pr12081635 - 3 Aug 2024

Cited by 1 | Viewed by 2684

Abstract

Modeling is a crucial tool in the biomanufacturing industry, namely in fermentation processes. This work discusses both mechanistic and data-driven models, each with unique benefits and application potential. It discusses semi-parametric hybrid modeling, a growing field that combines these two types of models for more accurate and easy result extrapolation. The characteristics and structure of such hybrid models will be examined. Moreover, its versatility will be highlighted, showing its usefulness in various stages of process development, including real-time monitoring and optimization. Scale-up remains one of the most relevant topics in fermentation processes, as it is important to have reproducible critical quality attributes, such as titer and yield, on larger scales. Furthermore, the process still relies on empirical correlations and iterative optimization. For these reasons, it is important to improve scale-up predictions, through e.g., the use of digital tools. Perspectives will be presented on the potential that hybrid modeling has by predicting performance across different process scales. This could provide more efficient and reliable biomanufacturing processes that require less resource consumption through experimentation. Full article

(This article belongs to the Special Issue Fermentation and Bioprocess Engineering Processes)

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27 pages, 847 KiB

Open AccessFeature PaperReview

Production of Value-Added Products as Food Ingredients via Microbial Fermentation

by Attia Iram, Ali Ozcan, Irfan Turhan and Ali Demirci

Processes 2023, 11(6), 1715; https://doi.org/10.3390/pr11061715 - 3 Jun 2023

Cited by 5 | Viewed by 5652

Abstract

Humankind has been unknowingly utilizing food fermentations since the first creation of bread, cheese, and other basic foods. Since the beginning of the last century, microbial fermentation has been extensively utilized for production of commodity chemicals. It has also gained substantial interest in recent decades due to its underlying applications in the preparation of natural and safe food ingredients including enzymes, antimicrobial agents, vitamins, organic acids, sweeteners, stabilizers, emulsifiers, oligosaccharides, amino acids, and thickening agents. In addition, some novel food ingredients that were conventionally made from some other sources such as plant tissue cultures or animals are now being introduced in the industry as ‘fermentation products.’ Some examples of such novel fermentation food ingredients include flavonoids, cultured meat products, food colorants, antioxidants, lipids, and fatty acids. This review summarizes some of the most prominent food ingredients and novel fermentation food products currently being produced via microbial fermentation as well as the strategies to enhance such fermentation processes. Additionally, economical feedstocks are discussed with their potential to be converted into value-added products with the help of microbial fermentations. Full article

(This article belongs to the Special Issue Fermentation and Bioprocess Engineering Processes)

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