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10th Anniversary of Fermentation: Feature Papers in the “Fermentation Process Design” Section

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A special issue of Fermentation (ISSN 2311-5637). This special issue belongs to the section "Fermentation Process Design".

Deadline for manuscript submissions: closed (31 December 2025) | Viewed by 23056

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Prof. Dr. Thaddeus Ezeji

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Departments of Animal Sciences and Food, Agricultural, and Biological Engineering, The Ohio State University, 305 Gerlaugh Hall, 1680 Madison Avenue, Wooster, OH 44691, USA
Interests: microbial physiology; biofuel (butanol, ethanol, methane) and biochemical (2,3-butanediol, acetone, isopropanol) production; downstream processing; biomass pretreatment technologies; lignocellulose-derived microbial inhibitory compounds and mitigations; metabolic engineering; bioreactor design; alcoholic fermentation and anaerobic digestion
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Prof. Dr. Miguel Ladero

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Department of Chemical Engineering and Materials, College of Chemical Sciences, Complutense University of Madrid, 28040 Madrid, Spain
Interests: glycerol; biodiesel; valorization; catalysts; carbonates; ketals; monomers; ethers; esters; lactic acid; hydrogen; diols; refining; oxidation; dehydration; biorefinery; biomaterials
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

As we celebrate the 10th anniversary of Fermentation, it is with great excitement that we announce the upcoming Special Issue titled “10th Anniversary of Fermentation: Feature Papers in the ‘Fermentation Process Design’ Section”. This Special Issue aims to publish high-quality original research and review articles spanning all aspects of fermentation process design. We invite researchers from related fields to contribute and highlight the latest developments in this area. Topics of interest for this Special Issue include, but are not limited to, novel bioreactor and bioprocess designs; the production of macromolecules (e.g., enzymes, proteins, antibodies, and lipids); the production of small molecules (e.g., amino acids, peptides, and vitamins); the bioremediation of pollutants; improved separation methods for the recovery of fermentation products; advanced tools for monitoring and controlling bioreactors; and analyses of bioreactor performance. We eagerly anticipate your innovative and impactful contributions to this special celebration of a decade of progress in fermentation science!

Prof. Dr. Thaddeus Ezeji
Prof. Dr. Miguel Ladero
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 250 words) can be sent to the Editorial Office for assessment.

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-anonymized 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

process design
bioreactor performance
scale-up
scale-down
microbial kinetics
fed-batch
purification methods
bioprocess monitoring

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Published Papers (10 papers)

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17 pages, 1110 KB

Open AccessArticle

Orange-Peel Waste Enzymatic Saccharification: Scaling-Up Under Diverse pH-Control Strategies

by Ramón J. Ceballos-Zúñiga and Miguel Ladero

Fermentation 2026, 12(6), 254; https://doi.org/10.3390/fermentation12060254 - 24 May 2026

Viewed by 687

Abstract

Waste from the fruit juice industry presents high sugar and phenolic contents, high humidity and biological activities and cumbersome disposal or low-added valorization. Orange-peel waste (OPW) represents 35–55% w/w of processed fruit, with oranges being the main citric crop. OPW saccharification leads to sugar-rich hydrolysates that can be further processed via fermentative and catalytic routes. In this work, OPW enzymatic hydrolysis was studied via batch and fed-batch processing using either a 50 mM citrate buffer or a 9 g/L NaCl solution with pH control by adding CaCO₃ to ensure high enzyme activity across the enzymatic process. Preliminary runs showed that particle size of 3.4 mm diameter and a 300 r.p.m. stirring speed, a six-blade Rushton turbine and wall baffles were adequate to reach high sugar yields in batch. Further scale-up in batch at medium solid loading (12.5% w/w) and fed-batch operation at high-solid loading (20% w/w) led to high yields and glucose and fermentable sugars (up to 74 and 136 g/L, respectively, when using the saline solution and CaCO₃ as pH-controlling agent, in only 50 h; notably shorter and higher than when using the citrate buffer). Fractal kinetic models have been shown to accurately represent the compositional change across all batch and fed-batch conditions, highlighting NaCl reaction medium and alkali-driven pH control as the most appropriate approach to achieve high yields at low process times, a promising result for further developments at demonstration and industrial scales using automatic pH control. Full article

(This article belongs to the Special Issue 10th Anniversary of Fermentation: Feature Papers in the “Fermentation Process Design” Section)

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12 pages, 264 KB

Open AccessArticle

Effect of Variations in the Gas Outlet Location on an In Vitro Rumen Simulation Technique (RUSITEC^®) System

by Luiza N. C. Silva, Isabela F. Carrari, Ícaro R. R. Castro, Giulia B. C. Leite, Amanda M. Cezar, Eduardo M. Paula and Marcos I. Marcondes

Fermentation 2026, 12(4), 180; https://doi.org/10.3390/fermentation12040180 - 1 Apr 2026

Viewed by 1213

Abstract

The rumen simulation technique (RUSITEC^®) is a known model for research in rumen microbiology and fermentation. However, our research group observed inconsistencies in gas production across trials. This study investigated the effects of different gas outlet locations on digestibility, ruminal fermentation, gas production, and microbial protein synthesis. Fifteen fermenters tested three different gas outlet locations within the RUSITEC^® equipment: (1) gas outlet directly on the effluent vessel for output liquid (EV); (2) gas outlet directly on fermenter cap (F); and (3) gas outlet on both effluent vessel and fermenter cap (EVF). Data were analyzed using a completely randomized design in SAS (v. 9.4) with the MIXED procedure, and significance was set at p < 0.10. Results showed that altering the gas outlet location did not affect nutrient digestibility (p > 0.10), microbial protein synthesis (p > 0.10), and volatile fatty acid (VFA) production when expressed on a molar basis (p > 0.10). However, total gas production (p = 0.108) was higher in the EVF group and ammonia nitrogen produced in the fermenter was higher in group F (p = 0.081). Furthermore, methane (CH₄) production was underestimated when the gas outlet location was in just one of the locations when compared to the EVF group (p = 0.006). VFA proportion was also affected, with lower acetate (p = 0.005) and higher butyrate (p = 0.014) for group EV. These results indicate that the location of the gas outlet is an important methodological factor affecting fermentation measurements in the RUSITEC system, with outlets positioned in both the effluent and fermenter vessels enhancing gas recovery. Full article

(This article belongs to the Special Issue 10th Anniversary of Fermentation: Feature Papers in the “Fermentation Process Design” Section)

16 pages, 2295 KB

Open AccessArticle

Process Time Reduction in Lager Beer Fermentation Through Model-Based Control

by Elena Elsa Bricio-Barrios, Héctor Hernández-Escoto, Fernando López-Caamal, Santiago Arceo-Díaz and Salvador Hernández

Fermentation 2026, 12(2), 120; https://doi.org/10.3390/fermentation12020120 - 20 Feb 2026

Viewed by 1640

Abstract

This work aims to shorten the time of lager beer fermentation through a temperature profile determined by a model-based controller, as an exploratory proposal to reduce fermentation time while maintaining yeast viability and process performance, without compromising the fermentation dynamics or negatively affecting the yeast activity. This study was developed from an engineering perspective focused on the optimization of the beer fermentation process through model-based control, preserving the beer properties of the original process. This exploratory work was carried out in four stages: (1) performance of constant temperature fermentations of a lager-type beer where concentrations of yeast and ethanol were monitored along the process, (2) model parameters adjustment and validation of a beer fermentation mathematical model on the basis of data obtained from experiments, (3) outline of a temperature trajectory, in a simulation framework, from an ethanol controller of movable convergence rate constructed with a nonlinear technique and the mathematical model, (4) experimental implementation of the outlined temperature trajectory in the beer fermentation. Beer batches’ quality-control endpoints suggested by Mexican quality standards frameworks, such as fermentation time, alcoholic and caloric content, and fermentation efficiency, were analyzed. The lag stage was reduced when the temperature profile devised by the controller was employed, resulting in a reduction in the time required to reach the stationary stage. No significant final characteristic variations in bottled beers brewed at constant and variable temperatures were identified. The quality assessment of the analyzed variables was conducted in accordance with the measurement capabilities of the employed equipment and under the applicable Mexican quality standards framework. This proposal presents an alternative systematic strategy to reduce the fermentation time of lager beer, favoring the efficiency and profitability of craft beer production. Full article

(This article belongs to the Special Issue 10th Anniversary of Fermentation: Feature Papers in the “Fermentation Process Design” Section)

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16 pages, 3468 KB

Open AccessArticle

Study on Microbial Diversity and Product Quality of Corn Gluten Meal-Based Fermented Feed

by Nan Hu, Hongji Zhao, Jingyi Sun, Kerui Liu, Shuying Li, Yongping Xu and Shanzi Cong

Fermentation 2026, 12(2), 107; https://doi.org/10.3390/fermentation12020107 - 12 Feb 2026

Viewed by 1233

Abstract

This study aimed to evaluate the effects of mixed strain fermentation on the microbial diversity, fermentation quality, and flavor of corn gluten meal-based fermented feed (CGMFF). High-throughput sequencing techniques (16S rDNA and ITS) and GC-MS technology were used to determine microbial community succession and flavor changes during the fermentation and storage stages of CGMFF and to explore their correlations. The results showed that Xeromyces and Lactobacillus became the dominant genera at the end of storage, with a relative abundance exceeding 96%. During fermentation and storage, the contents of soluble protein and ammonia nitrogen increased while the crude protein content decreased. The protein molecular weight was concentrated in the range of 75–1100 Da (96.98%), and the free amino acid (FAA) content increased by 1.42 times. This reduction in the proportion of bitter amino acids enhanced the palatability of CGMFF. The aroma gradually developed characteristics dominated by esters and alkanes. This study is intended to provide a theoretical basis for the application of corn gluten meal as a protein-rich raw material in fermented feed. Full article

(This article belongs to the Special Issue 10th Anniversary of Fermentation: Feature Papers in the “Fermentation Process Design” Section)

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17 pages, 3143 KB

Open AccessArticle

High Cell Density Fermentation Strategy for High-Level Soluble Expression of Glucagon-like Peptide-1 Analogue in Escherichia coli

by Sushmita R. Kumar, Esha Shukla and Gaurav Pandey

Fermentation 2026, 12(1), 53; https://doi.org/10.3390/fermentation12010053 - 16 Jan 2026

Cited by 1 | Viewed by 2954

Abstract

Glucagon-like peptide-1 (GLP-1) is an incretin hormone and therapeutic agent for Type II diabetes mellitus. However, recombinant production in E. coli yields insufficient quantities, increasing manufacturing costs and limiting patient access. Improving yield and productivity is crucial to make GLP-1 treatments more affordable. An optimized bioprocess was developed to enhance the yield of recombinant GLP-1 (rGLP-1) analogues. Expression constructs encoding monomeric and concatemeric GLP-1 fused to GST were designed. Batch fermentations of these clones at varying pre-induction specific growth rates guided the fed-batch strategy for yield enhancement. The specific yield of monomer construct exhibited higher yields than the concatemer. Process optimization achieved a specific yield (Yp/x) of 116.7 mg/g, a dry cell weight of 88.9 g/L, and a volumetric yield of 10.3 g/L. The specific productivity of soluble rGLP-1 reached 0.4 g/L/h. Purification via affinity chromatography and enterokinase cleavage yielded authentic GLP-1 peptide confirmed by Western blot and mass spectrometry. The developed high-yield fermentation process significantly enhances rGLP-1 productivity in E. coli, potentially reducing upstream production costs by 20–30% and enabling wider accessibility to affordable GLP-1 therapies. Full article

(This article belongs to the Special Issue 10th Anniversary of Fermentation: Feature Papers in the “Fermentation Process Design” Section)

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14 pages, 2814 KB

Open AccessArticle

Optimizing Caproic Acid Biosynthesis in Anaerobic Fermentation of Ethanol and Butanoic Acid: The Effects of C/N Ratio

by Longlong Liu, Yingmeng Shen, Sen Yang, Zhengang Chen, Xiaofeng Ji and Jiying Zhu

Fermentation 2025, 11(6), 316; https://doi.org/10.3390/fermentation11060316 - 2 Jun 2025

Cited by 2 | Viewed by 3015

Abstract

The carbon-to-nitrogen (C/N) ratio is a critical player in microbial growth and metabolism. This study explored the effects of this ratio on caproic acid yield, electron efficiency, and microbial community composition in an anaerobic fermentation system wherein ethanol and butanoic acid were used as electron donors and acceptors, respectively. With a C/N ratio of 3–25, the system maintained a reducing environment conducive to carbon chain elongation, which led to a high caproic acid yield. The highest caproic acid concentration of 6175.9 mg/L was attained at a C/N ratio of 3, with an electron efficiency of 72.9% and a selectivity of 60.8%. At C/N ratios of 58, 75, and 100, the highest concentration of caproic acid decreased by 26.2%, 35.4%, and 39.4%, respectively, compared to that at a C/N ratio of 3. At a C/N ratio of 1, acetic acid-producing bacteria were enriched, severe excessive ethanol oxidation occurred, and the caproic acid concentration was only 31% of that at a C/N ratio of 3. Caproic acid biosynthesis was attributed to the cooperative activity of Clostridium_sensu_stricto_12, DMER64, Para clostridium, Thermovirga, and Sporanaerobacter. Full article

(This article belongs to the Special Issue 10th Anniversary of Fermentation: Feature Papers in the “Fermentation Process Design” Section)

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18 pages, 2970 KB

Open AccessArticle

Synthetic Biofilm Reactor with Independent Supply of Gas and Liquid Phase for Studying Chain Elongation with Immobilized Clostridium kluyveri at Defined Reaction Conditions

by Josha Herzog, Karlis Blums, Simon Gregg, Lukas Gröninger, Johannes Poppe, Verena Uhlig, Qifei Wang and Dirk Weuster-Botz

Fermentation 2025, 11(4), 200; https://doi.org/10.3390/fermentation11040200 - 9 Apr 2025

Cited by 3 | Viewed by 2554

Abstract

In this study, we explore the use of C. kluyveri in synthetic biofilms for the production of 1-butyrate and 1-hexanoate, investigating the impact of inoculation temperature during biofilm formation and the presence of yeast extract. Therefore, a novel synthetic biofilm reactor has been designed and constructed. Prior to investigating synthetic biofilms in this reactor, we carried out preliminary batch experiments in anaerobic flasks containing an inoculated agar hydrogel fixed at the bottom and overlaid medium. For the operation of the novel synthetic biofilm reactor, specific volumes of inoculated agar hydrogel were dispensed into a cylindrical mold with a diameter of 102 mm, forming the synthetic biofilm with a height of 4 mm, which was then transferred into the biofilm reaction chamber onto the support grid. The biofilm support grid separates the gas phase (CO₂, N₂) above the synthetic biofilm from the aqueous phase (medium) below. Our results show that C. kluyveri remains metabolically active at biofilm preparation temperatures of up to 45 °C, with extended lag phases observed at 70 °C. The synthetic biofilm demonstrated efficient chain elongation in batch processes, converting ethanol and acetate into 1-butyrate and 1-hexanoate, with final concentrations of 2.7 g L⁻¹ and 10.1 g L⁻¹, respectively, with yeast extract in the circulating liquid medium of the synthetic biofilm reactor setup. The maximum estimated space-time yields for 1-butyrate and 1-hexanoate, referenced to the biofilm volume, were 1.331 g L⁻¹ h⁻¹ and 4.947 g L⁻¹ h⁻¹, respectively. Experiments without yeast extract lead to final concentrations of 2.0 g L⁻¹ 1-butyrate, and 7.3 g L⁻¹ 1-hexanoate and maximum estimated space-time yields, referenced to the biofilm volume, were 0.332 g L⁻¹ h⁻¹ and 1.123 g L⁻¹ h⁻¹, respectively. The use of synthetic biofilms, even without yeast extract, eliminates the need for significant cell growth during chain elongation. However, product concentrations were lower without yeast extract. Full article

(This article belongs to the Special Issue 10th Anniversary of Fermentation: Feature Papers in the “Fermentation Process Design” Section)

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20 pages, 1971 KB

Open AccessArticle

Enhanced Sugar Yield from Enzymatic Hydrolysis of Cellulignin from Sugarcane Bagasse Using a Biosurfactant and Soybean Protein in Powdered and Cavitated Forms

by Alain Monsalve Mera, Salvador Sánchez Muñoz, Felipe A. Fernandes Antunes, Júlio C. dos Santos and Silvio Silvério da Silva

Fermentation 2025, 11(3), 114; https://doi.org/10.3390/fermentation11030114 - 28 Feb 2025

Cited by 2 | Viewed by 2467

Abstract

The enzymatic hydrolysis of lignocellulosic biomass is often hindered by lignin, which acts as a physical barrier and promotes non-productive enzyme adsorption. This study evaluated the potential of soybean protein in powdered and cavitated forms, along with lactonic sophorolipid biosurfactant (LSLB), to enhance sugar yields from cellulignin derived from sugarcane bagasse, a residue with a high lignin content. A Box–Behnken design was used to investigate the effects of enzyme loading (10–20 FPU/g cellulignin), soybean protein powder (10–30% w/w of dried cellulignin), and LSLB concentration (25–250 mg/L) on glucose and xylose yields. Hydrodynamic cavitation was employed to produce soluble soybean protein, achieving a solubility yield of 44.4% w/w in 10 min. The cavitated protein was compared with powdered protein to assess its impact on enzymatic hydrolysis efficiency. The results showed that hydrodynamic cavitation reduced the required SBP dosage while maintaining sugar yields, allowing 10% w/w of dried cellulignin cavitated SBP to achieve glucose and xylose yields comparable to 25% w/w of dried cellulignin non-cavitated SBP. Specifically, glucose yield increased by 24.92% (from 34.1% ± 1.01 to 42.6% ± 1.4), and xylose yield by 30.86% (from 32.4% ± 0.53 to 42.4% ± 2.21) compared to the no-additive condition. These improvements were linked to enhanced solubility, increased surface area, and reduced particle size in the cavitated protein. This study highlights hydrodynamic cavitation as a novel approach for modifying soybean protein structure to optimize enzymatic hydrolysis in lignocellulosic bioconversion. Full article

(This article belongs to the Special Issue 10th Anniversary of Fermentation: Feature Papers in the “Fermentation Process Design” Section)

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18 pages, 4037 KB

Open AccessArticle

Bioenergetic Modeling of the Relationship Between Voltage and Electroactive Microbial Biomass Yield for Bioelectrochemical Carbon Dioxide Reduction to Methane

by Vafa Ahmadi and Nabin Aryal

Fermentation 2025, 11(1), 40; https://doi.org/10.3390/fermentation11010040 - 17 Jan 2025

Cited by 3 | Viewed by 2533

Abstract

Optimal product synthesis in bioelectrochemical systems (BESs) requires a comprehensive understanding of the relationship between external voltage and microbial yield. While most studies assume constant growth yields or rely on empirical estimates, this study presents a novel thermodynamic model, linking anodic oxidation and [...] Read more.

{C O}_{2}

) reduction to methane (

{C H}_{4}

) by growing microbial biofilm. Through integrating theoretical Gibbs free energy calculations, the model predicts electron and proton transfers for autotrophic methanogen and anode-respiring bacteria (ARB) growth, accounting for varying applied voltages and substrate concentrations. The findings identify an optimal applied cathodic potential of −0.3 V vs. the standard hydrogen electrode (SHE) for maximizing

{C H}_{4}

production under standard conditions (pH 7, 25 °C, 1 atm) regardless of ohmic losses. The model bridges the stoichiometry of anodic and cathodic biofilms, addressing research gaps in simulating anodic and cathodic biofilm growth simultaneously. Additionally, sensitivity analyses reveal that lower substrate concentrations require more negative voltages than standard condition to stimulate microbial growth. The model was validated using experimental data, demonstrating reasonable predictions of biomass growth and

{C H}_{4}

yield under different operating voltages in a multi substrate system. The results show that higher voltage inputs increase biomass yield while reducing

{C H}_{4}

output due to non-optimal voltage. This validated model provides a tool for optimizing BES performance to enhance

{C H}_{4}

recovery and biofilm stability. These insights contribute to finding optimum voltage for the highest

{C H}_{4}

production for energy efficient

{C O}_{2}

reduction for scaling up BES technology. Full article

(This article belongs to the Special Issue 10th Anniversary of Fermentation: Feature Papers in the “Fermentation Process Design” Section)

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23 pages, 2711 KB

Open AccessSystematic Review

Electro-Composting: An Emerging Technology

by Ahmad Shabir Hozad and Christian Abendroth

Fermentation 2025, 11(7), 401; https://doi.org/10.3390/fermentation11070401 - 14 Jul 2025

Cited by 1 | Viewed by 3689

Abstract

This study focuses on electrical stimulation for composting. Using the PSALSAR method, a comprehensive systematic review analysis identified 22 relevant articles. The examined studies fall into four main systems: electric field-assisted aerobic composting (EAAC), electrolytic oxygen aerobic composting (EOAC), microbial fuel cells (MFCs), and thermoelectric generators (TEGs). Apart from the main systems highlighted above, bioelectrochemically assisted anaerobic composting (AnC_{BE, III}) is discussed as an underexplored system with the potential to improve the efficiency of anaerobic degradation. Each system is described in terms of key materials, composter design, operating conditions, temperature evolution, compost maturity, microbial community, and environmental outcomes. EAAC and EOAC systems accelerate organic matter decomposition by improving oxygen distribution and microbial activity, whereas MFC and TEG systems have dual functioning due to the energy generated alongside waste degradation. These innovative systems not only significantly improve composting efficiency by speeding up organic matter breakdown and increasing oxygen supply but also support sustainable waste management by reducing greenhouse gas emissions and generating bioelectricity or heat. Together, these systems overcome the drawbacks of conventional composting systems and promote future environmental sustainability solutions. Full article

(This article belongs to the Special Issue 10th Anniversary of Fermentation: Feature Papers in the “Fermentation Process Design” Section)

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