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Fermentation
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Feature Review Papers in Industrial Fermentation, 2nd Edition
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Feature Review Papers in Industrial Fermentation, 2nd Edition

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

Deadline for manuscript submissions: closed (31 December 2025) | Viewed by 45845

Special Issue Editors

Prof. Dr. Xiaoqing Lin

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Guest Editor
School of Chemical Engineering and Light Industry, Guangdong Provincial Key Laboratory of Plant Resources Biorefinery, Guangdong University of Technology, Guangzhou 510006, China
Interests: biofuels (ethanol and butanol); biomass pretreatment; downstream processing; lignocellulosic biorefineries; adsorption and separation; platform chemicals
Special Issues, Collections and Topics in MDPI journals
Dr. Konstantinos G. Kalogiannis

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Guest Editor
Department of Chemical Engineering, University of Western Macedonia (UOWM), Kozani, Greece
Interests: biorefineries; biofuels; delignification and fractionation technologies; biomass and wastes valorization; pyrolysis; heterogeneous catalysis; thermochemical conversion technologies
Special Issues, Collections and Topics in MDPI journals
Dr. Diomi Mamma

E-Mail Website
Guest Editor
Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
Interests: biochemical engineering; fermentation biotechnology; bioreactor design; valorization of agro-industrial wastes and food wastes for biofuels; kinetic modeling; halogenated hydrocarbons degradation; mass transfer phenomena; hydrolytic enzymes (purification, characterization); bio-scouring of cotton fabrics; growth of microalgae
Special Issues, Collections and Topics in MDPI journals
Dr. Alessio Siciliano

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Guest Editor
Department of Environmental Engineering, Università della Calabria, 87036 Cosenza, Italy
Interests: anaerobic digestion; biogas; bioreactors; organic waste pretreatment processes; water and wastewater treatment; soil reclamation
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue aims to collect high-quality review papers in all fields of industrial fermentation. We encourage researchers from related fields to contribute review papers highlighting the latest developments in industrial fermentation (including fermentation for the production of chemicals, materials, biofuels, and pharmaceuticals; environmental bioprocesses and the biodegradation of pollutants; and biorefinery), or to invite relevant experts and colleagues to do so. Full-length comprehensive reviews will be preferred.

This Special Issue aims to share these scientific findings as widely as possible.

Prof. Dr. Xiaoqing Lin
Dr. Konstantinos G. Kalogiannis
Dr. Diomi Mamma
Dr. Alessio Siciliano
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-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

  • fermentation for production of chemicals and materials
  • fermentation for production of biofuels
  • fermentation for production of pharmaceuticals
  • environmental bioprocesses
  • bioconversion and valorization of pollutants
  • bioprocesses for greenhouse gas mitigation
  • biodegradation of pollutants
  • bioreactor design and modeling
  • biorefinery processes

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  • Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
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Further information on MDPI's Special Issue policies can be found here.

Related Special Issue

Published Papers (6 papers)

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Review

24 pages, 2746 KB  
Review
Microbial Manufacturing of Recombinant Protein: Recent Advances, Challenges, and Strategies
by Yonghan Chen, Zhiyan Zhang, Chuan Wang, Qingjing Huang, Lixiu Yan, Chang Sun, Jun Kang, Jiamin Zhang and Jie Cheng
Fermentation 2026, 12(3), 132; https://doi.org/10.3390/fermentation12030132 - 4 Mar 2026
Viewed by 264
Abstract
Proteins are fundamental to life and indispensable for human physiological activities. However, traditional proteins derived from natural sources such as animals and plants face challenges including low extraction efficiency and limited availability. Therefore, recombinant proteins produced via microbial manufacturing have emerged as a [...] Read more.
Proteins are fundamental to life and indispensable for human physiological activities. However, traditional proteins derived from natural sources such as animals and plants face challenges including low extraction efficiency and limited availability. Therefore, recombinant proteins produced via microbial manufacturing have emerged as a promising alternative. This review specifically focuses on the production of recombinant protein with certain specific functional characteristics, using microorganisms. Owing to their unique functional attributes, such proteins are in increasing demand in diverse fields, including food, medicine, and agriculture. Firstly, this review outlines the definition of recombinant protein and summarizes the microbial manufacturing and applications of nine typical proteins with certain specific functional characteristics. Secondly, the strategies of utilizing microorganisms for the efficient production and purification of recombinant proteins was systematically reviewed. Full article
(This article belongs to the Special Issue Feature Review Papers in Industrial Fermentation, 2nd Edition)
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20 pages, 1299 KB  
Review
From Natural Defense to Synthetic Application: Emerging Bacterial Anti-Phage Mechanisms and Their Potential in Industrial Fermentation
by Hengwei Zhang, Jiajia You, Guomin Li, Zhiming Rao and Xian Zhang
Fermentation 2026, 12(1), 17; https://doi.org/10.3390/fermentation12010017 - 29 Dec 2025
Cited by 1 | Viewed by 935
Abstract
Bacteriophage contamination remains a persistent and costly challenge in industrial bio-manufacturing. Traditional control strategies rely heavily on physical exclusion and chemical disinfection, yet these passive measures often fail to address the rapid evolutionary adaptation of phages and their persistence in complex fermentation environments. [...] Read more.
Bacteriophage contamination remains a persistent and costly challenge in industrial bio-manufacturing. Traditional control strategies rely heavily on physical exclusion and chemical disinfection, yet these passive measures often fail to address the rapid evolutionary adaptation of phages and their persistence in complex fermentation environments. Recent genomic and biochemical discoveries have revealed a diverse arsenal of bacterial antiviral immune systems beyond the classical Restriction-Modification and CRISPR-Cas pathways, including cyclic oligonucleotide-based signaling systems and various abortive infection mechanisms. This review systematically summarizes the latest advances in bacterial anti-phage defense mechanisms, categorizing them into adsorption inhibition, replication interference, nucleic acid degradation, and population-level suicide defense. Furthermore, we discuss the application of synthetic biology in integrating these defense modules to construct broad-spectrum “pan-immune” microbial chassis. This active defense strategy offers a fundamental solution to phage predation and provides a theoretical basis for developing robust next-generation cell factories. Full article
(This article belongs to the Special Issue Feature Review Papers in Industrial Fermentation, 2nd Edition)
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20 pages, 3734 KB  
Review
Microbial Community and Metabolic Pathways in Anaerobic Digestion of Organic Solid Wastes: Progress, Challenges and Prospects
by Jiachang Cao, Chen Zhang, Xiang Li, Xueye Wang, Xiaohu Dai and Ying Xu
Fermentation 2025, 11(8), 457; https://doi.org/10.3390/fermentation11080457 - 7 Aug 2025
Cited by 10 | Viewed by 6031
Abstract
Anaerobic digestion (AD) is a sustainable and widely adopted technology for the treatment of organic solid wastes (OSWs). However, AD efficiency varies significantly across different substrates, primarily due to differences in the microbial community and metabolic pathways. This review provides a comprehensive summary [...] Read more.
Anaerobic digestion (AD) is a sustainable and widely adopted technology for the treatment of organic solid wastes (OSWs). However, AD efficiency varies significantly across different substrates, primarily due to differences in the microbial community and metabolic pathways. This review provides a comprehensive summary of the AD processes for four types of typical OSWs (i.e., sewage sludge, food waste, livestock manure, and straw), with an emphasis on their universal characteristics across global contexts, focusing mainly on the electron transfer mechanisms, essential microbial communities, and key metabolic pathways. Special attention was given to the mechanisms by which substrate-specific structural differences influence anaerobic digestion efficiency, with a focused analysis and discussion on how different components affect microbial communities and metabolic pathways. This study concluded that the hydrogenotrophic methanogenesis pathway, TCA cycle, and the Wood–Ljungdahl pathway serve as critical breakthrough points for enhancing methane production potential. This research not only provides a theoretical foundation for optimizing AD efficiency, but also offers crucial scientific insights for resource recovery and energy utilization of OSWs, making significant contributions to advancing sustainable waste management practices. Full article
(This article belongs to the Special Issue Feature Review Papers in Industrial Fermentation, 2nd Edition)
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27 pages, 1422 KB  
Review
Innovative Lactic Acid Production Techniques Driving Advances in Silage Fermentation
by Xiaorui Zhao, Yu Sun, Zhiyi Chang, Boqing Yao, Zixin Han, Tianyi Wang, Nan Shang and Ran Wang
Fermentation 2024, 10(10), 533; https://doi.org/10.3390/fermentation10100533 - 20 Oct 2024
Cited by 14 | Viewed by 6899
Abstract
Lactic acid (LA) plays a crucial role in the silage process, which occurs through LA fermentation. Consequently, there is a strong correlation between lactic acid production and the efficiency of the silage. However, traditional methods face challenges like long fermentation times, low acid [...] Read more.
Lactic acid (LA) plays a crucial role in the silage process, which occurs through LA fermentation. Consequently, there is a strong correlation between lactic acid production and the efficiency of the silage. However, traditional methods face challenges like long fermentation times, low acid production, and unstable quality, limiting agricultural preservation. This paper aims to explore innovations in lactic acid production technologies and show how these technologies have driven the development of silage fermentation for agricultural conservation. First, the important role of LA in agricultural preservation and the limitations of traditional silage techniques are presented. Next, advancements in LA production methods are thoroughly examined, covering the selection of microbial strains and the substitution of fermentation substrates. Following this, new technologies for silage fermentation are explored, drawing from innovations in LA production. These include the selection of LA strains, optimization of fermentation conditions, and improvements in fermentation techniques. These innovations have proven effective in increasing LA production, improving feed quality, extending shelf life, and providing new solutions to enhance agricultural production and sustainability. Full article
(This article belongs to the Special Issue Feature Review Papers in Industrial Fermentation, 2nd Edition)
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21 pages, 2365 KB  
Review
Progress and Trends in Forage Cactus Silage Research: A Bibliometric Perspective
by Stéfani A. Santos, Hortência E. P. Santana, Meirielly S. Jesus, Iran Alves Torquato, Joana Santos, Preciosa Pires, Denise Santos Ruzene and Daniel Pereira Silva
Fermentation 2024, 10(10), 531; https://doi.org/10.3390/fermentation10100531 - 19 Oct 2024
Cited by 3 | Viewed by 3083
Abstract
Opuntia spp. (forage cactus or spineless cactus) is a plant native to Mexico that is commonly used as alternative nutrient-rich fodder in semi-arid regions. Due to its resistance to drought, forage cactus has become an important least-cost ingredient for formulating balanced rations for [...] Read more.
Opuntia spp. (forage cactus or spineless cactus) is a plant native to Mexico that is commonly used as alternative nutrient-rich fodder in semi-arid regions. Due to its resistance to drought, forage cactus has become an important least-cost ingredient for formulating balanced rations for ruminants during times of scarcity. In addition, ensiling, an anaerobic fermentation process, is also a strategy used to allow a supply of bulky food all year round, since it conserves forage and maintains its nutritional value. In this sense, using the Scopus database and the visualization tool VOSviewer, the present work proposes a bibliometric analysis of forage cactus silage to track and map the evolution and main issues in the research field, current trends, and future directions. The results revealed that the first publication was in 2013; and since 2020, the number of publications has been growing. Brazil was highlighted, by far, as the most relevant country on the topic, and the top institutions were from northeast Brazil, which has been working on co-authored articles. The current hot research topics are focusing on the mixed silage of forage cactus and other forages such as gliricidia, maniçoba, and sorghum biomass, as well as evaluating the fermentative performance and chemical characteristics for improving ruminal diets, especially for goats and sheep. This study provides important information for researchers to identify gaps and direct their studies to better use the whole potential of forage cactus as an alternative roughage source. Full article
(This article belongs to the Special Issue Feature Review Papers in Industrial Fermentation, 2nd Edition)
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13 pages, 3407 KB  
Review
Microbial Degradation of (Micro)plastics: Mechanisms, Enhancements, and Future Directions
by Wei Gao, Mingxuan Xu, Wanqi Zhao, Xiaorui Yang, Fengxue Xin, Weiliang Dong, Honghua Jia and Xiayuan Wu
Fermentation 2024, 10(9), 441; https://doi.org/10.3390/fermentation10090441 - 23 Aug 2024
Cited by 51 | Viewed by 27299
Abstract
Plastic wastes, widely distributed in the environment, can be transformed into microplastics, posing a huge threat to ecosystems and human health due to their stability and adsorbability to other toxic pollutants (e.g., heavy metals and antibiotics). Recently, microbial degradation of (micro)plastics has gained [...] Read more.
Plastic wastes, widely distributed in the environment, can be transformed into microplastics, posing a huge threat to ecosystems and human health due to their stability and adsorbability to other toxic pollutants (e.g., heavy metals and antibiotics). Recently, microbial degradation of (micro)plastics has gained widespread attention because of its green and sustainable properties. Microbial degradation of (micro)plastics is based on the cascade effects of various enzymes secreted by microorganisms, which can convert (micro)plastics into oligomers and monomers, or even mineralize them into CO2 and H2O. The microbial degradation of (micro)plastics is affected by multiple factors, such as microbial species, plastic properties, and environmental conditions. Currently, limited efficient plastic-degrading microorganisms have been discovered, and their degradation mechanisms are still unclear. Furthermore, the efficiency of microbial degradation needs to be improved for future application. Therefore, this review systematically summarizes the sources and properties of existing plastics, identifies pure cultures and mixed cultures for plastic degradation, and examines their influencing factors. In particular, the microbial degradation behaviors of (micro)plastics, including relevant enzymes, degradation efficiency, and degradation mechanisms, were thoroughly discussed. Additionally, the augmentation technologies coupling with microbial degradation, such as advanced oxidation, electrochemical, and genetic engineering technologies, were introduced and highlighted for their potential prospects. This review provides a reference for future research and development of (micro)plastic biodegradation technology. Full article
(This article belongs to the Special Issue Feature Review Papers in Industrial Fermentation, 2nd Edition)
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