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Processes
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Recent Advances in Bioprocess Engineering and Fermentation Technology
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Recent Advances in Bioprocess Engineering and Fermentation Technology

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

Deadline for manuscript submissions: 10 September 2026 | Viewed by 11455

Special Issue Editors

Prof. Dr. José Manuel Pais-Chanfrau

E-Mail Website
Guest Editor
Agroindustrial Products from Residues Research Group, Universidad Técnica del Norte, Ibarra 100150, Ecuador
Interests: waste valorisation; biorefineries; fermentation; solid–liquid extraction
Prof. Dr. Ileana Pereda Reyes

E-Mail Website
Guest Editor
Center for Process Engineering Studies (CIPRO), Faculty of Chemical Engineering, José A. Echeverría Technological University of Havana (CUJAE), Calle 114 No 11901 between Cycle lane and Roundabout, Marianao, Havana, Cuba
Interests: waste management; biological process; anaerobic digestion; circular economy; resource recovery
Prof. Dr. Hortensia María Rodríguez Cabrera

E-Mail Website
Guest Editor
Yachay Tech Medicinal Chemistry Research Group (MedChem-YT), School of Chemical Science and Engineering, Yachay Tech, Yachay City of Knowledge, Urcuqui 100119, Ecuador
Interests: organic synthesis focused on solid-phase synthesis of small organic molecules and peptides; development of more sustainable synthetic approaches for biologically active chemical structures; study of selected organic systems; conjugation techniques; and antibody-drug conjugates (ADCs) as delivery systems
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Bioprocess engineering and fermentation technology are evolving rapidly, driven by the integration of artificial intelligence (AI), machine learning (ML), and advanced computational tools in order to address sustainability challenges.

Innovations such as genetic algorithms for process optimisation, metabolic flux analysis, and enhanced anaerobic digestion systems are transforming waste valorisation, bioenergy production, and circular economy frameworks.

Concurrently, advancements in submerged and solid-state fermentation techniques are enabling scalable, resource-efficient biomanufacturing. 

This Special Issue highlights pioneering research that bridges computational intelligence, metabolic engineering, and sustainable practices to unlock the potential of agricultural and agro-industrial waste streams.

Suitable topics for this Special Issue include, but are not limited to, the following:

  • AI/ML-driven optimisation: genetic algorithms for strain selection, neural networks for predicting fermentation dynamics, and digital twins for real-time bioprocess control.
  • Metabolic engineering: in silico flux analysis, CRISPR-enhanced pathways, and multi-omics integration for substrate conversion.
  • Anaerobic digestion: novel reactor designs, microbiome engineering, and process intensification for biomethaneand/or biohydrogen
  • Sustainable fermentation systems: innovations in solid-state and submerged fermentation for agro-waste valorisation into biofuels, enzymes, or bioplastics.
  • Circular biorefineries: hybrid systems combining enzymatic hydrolysis, microbial electrosynthesis, or electro-fermentation for multi-product cascades.
  • Waste-to-energy technologies: lifecycle assessments and techno-economic analyses of waste-derived bioenergy systems.

We welcome original research, reviews, and perspectives that address cross-disciplinary synergies, such as AI-guided metabolic modelling, ML-aided anaerobic co-digestion of mixed feedstocks, and policy frameworks for biorefinery scalability.

Contributions must align with global sustainability goals, emphasising carbon neutrality and resource efficiency.

Prof. Dr. José Manuel Pais-Chanfrau
Prof. Dr. Ileana Pereda Reyes
Prof. Dr. Hortensia María Rodríguez Cabrera
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. Processes is an international peer-reviewed open access semimonthly 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 2400 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

  • bioprocess engineering
  • fermentation technology
  • machine learning
  • genetic algorithms
  • metabolic flux analysis
  • anaerobic digestion
  • biohydrogen
  • biomethane
  • circular economy
  • agro-industrial waste

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Published Papers (4 papers)

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Research

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35 pages, 4903 KB  
Article
Production and Characterisation of Polyhydroxyalkanoates from Cocoa Mucilage Using a Wild-Type Priestia aryabhattai Strain
by Jimmy Núñez-Pérez, Osmar J. Cornejo-Lucero, Rosario C. Espin-Valladares, Pedro Barba, Hortensia M. Rodríguez Cabrera and José-Manuel Pais-Chanfrau
Processes 2026, 14(9), 1492; https://doi.org/10.3390/pr14091492 - 5 May 2026
Abstract
The accumulation of petroleum-based plastics demands sustainable alternatives such as polyhydroxyalkanoates (PHAs), biodegradable polyesters synthesised by numerous prokaryotes. However, high feedstock costs limit their commercialisation. This study evaluated cocoa mucilage, an underutilised by-product of the Ecuadorian cacao sector, as a low-cost carbon source [...] Read more.
The accumulation of petroleum-based plastics demands sustainable alternatives such as polyhydroxyalkanoates (PHAs), biodegradable polyesters synthesised by numerous prokaryotes. However, high feedstock costs limit their commercialisation. This study evaluated cocoa mucilage, an underutilised by-product of the Ecuadorian cacao sector, as a low-cost carbon source for PHA production by a wild-type strain isolated from cocoa fruit residues. Bacteria were recovered from cocoa mucilage and pod shell fractions and screened for PHA accumulation by Sudan Black B staining with UV–Vis spectrophotometric confirmation. A single PHA-positive isolate, designated Priestia aryabhattai strain NBP01-UTN (GenBank accession OR567321.1; 99.88% 16S rRNA gene sequence identity to the type strain B8W22T), was recovered from the cocoa shell surface—representing, to the best of our knowledge, the first report of a PHA-producing P. aryabhattai from cacao fruit residues. Fermentation conditions were optimised using the response surface methodology with a central composite design evaluating temperature, pH, and ammonium sulphate concentration. The fitted quadratic model was highly significant (R2 = 0.978, p < 0.0001), indicating that temperature and nitrogen limitation were the dominant factors. Optimal conditions (40 °C, pH 7.30, 0 g·L−1 (NH4)2SO4) yielded 0.496 g·L−1 PHA at 24 h (productivity ≈ 20.7 mg·L−1·h−1). Notably, no external nitrogen supplementation was required, as the endogenous nitrogen in cocoa mucilage sufficed to sustain growth whilst triggering the nutrient imbalance needed for PHA biosynthesis. FTIR and DSC analyses provided spectroscopic and thermal evidence consistent with poly(3-hydroxybutyrate) (PHB), although definitive monomer-level confirmation requires GC–MS or NMR spectroscopy. These results demonstrate the feasibility of coupling a locally isolated wild-type strain with cocoa mucilage to produce bioplastic within a circular bioeconomy framework. Full article
(This article belongs to the Special Issue Recent Advances in Bioprocess Engineering and Fermentation Technology)
17 pages, 5045 KB  
Article
Data-Driven Optimization of Cellulase-Assisted Extraction of Flavonoids and Chlorophyll from Silkworm Excrement
by Feng Qian, Jie-Juan Lu, De-Long Guan, Jing Song and Fuzhi Lu
Processes 2026, 14(3), 495; https://doi.org/10.3390/pr14030495 - 30 Jan 2026
Viewed by 487
Abstract
Guangxi, one of China’s dominant sericulture regions, generates substantial silkworm excrement (SE) annually, yet most remains underutilized. This study optimized cellulase-assisted ethanol extraction of flavonoids and chlorophyll from silkworm frass. Systematic experimentation (n = 31) revealed that extraction temperature exerted dominant influence [...] Read more.
Guangxi, one of China’s dominant sericulture regions, generates substantial silkworm excrement (SE) annually, yet most remains underutilized. This study optimized cellulase-assisted ethanol extraction of flavonoids and chlorophyll from silkworm frass. Systematic experimentation (n = 31) revealed that extraction temperature exerted dominant influence on both contents (r = 0.54 and 0.37 for chlorophyll and flavonoids, respectively), while the two contents exhibited near-zero correlation (r = 0.06). An XGBoost model achieved R2 = 0.9146 for flavonoid prediction; SHAP analysis identified a critical temperature threshold (~40 °C). Monte Carlo simulation (n = 10,000) constructed a Pareto frontier for multi-objective optimization. The optimized condition (9% enzyme, 50 °C) achieved chlorophyll and flavonoid contents of 1.13 and 6.42 mg/g, respectively. These findings demonstrate that sericulture waste can serve as a biorefinery feedstock and that interpretable machine learning can navigate multi-objective extraction challenges under data constraints. Full article
(This article belongs to the Special Issue Recent Advances in Bioprocess Engineering and Fermentation Technology)
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20 pages, 1051 KB  
Article
Synthetic Methods of Sugar Amino Acids and Their Application in the Development of Cyclic Peptide Therapeutics
by Chengcheng Bao and Dekai Wang
Processes 2025, 13(9), 2849; https://doi.org/10.3390/pr13092849 - 5 Sep 2025
Viewed by 2477
Abstract
Sugar amino acids (SAAs) represent a privileged class of molecular chimeras that uniquely merge the structural rigidity of carbohydrates with the functional display of amino acids. These hybrid molecules have garnered significant attention as programmable conformational constraints, offering a powerful strategy to overcome [...] Read more.
Sugar amino acids (SAAs) represent a privileged class of molecular chimeras that uniquely merge the structural rigidity of carbohydrates with the functional display of amino acids. These hybrid molecules have garnered significant attention as programmable conformational constraints, offering a powerful strategy to overcome the inherent limitations of peptide-based therapeutics, such as proteolytic instability and conformational ambiguity. The strategic incorporation of SAAs into peptide backbones, particularly within cyclic frameworks, allows for the rational design of peptidomimetics with pre-organized secondary structures, enhanced metabolic stability, and improved physicochemical properties. This review provides a comprehensive analysis of the synthetic methodologies developed to access the diverse structural landscape of SAAs, with a focus on modern, stereoselective strategies that yield versatile building blocks for peptide chemistry. A critical examination of the structural impact of SAA incorporation reveals their profound ability to induce and stabilize specific secondary structures, such as β- and γ-turns. Furthermore, a comparative analysis positions SAAs in the context of other widely used peptidomimetic scaffolds, highlighting their unique advantages in combining conformational control with tunable hydrophilicity. We surveyed the application of SAA-containing cyclic peptides as therapeutic agents, with a detailed case study on gramicidin S analogs that underscores the power of SAAs in elucidating complex structure–activity relationships. Finally, this review presents a forward-looking perspective on the challenges and future directions of the field, emphasizing the transformative potential of computational design, artificial intelligence, and advanced bioconjugation techniques to accelerate the development of next-generation SAA-based therapeutics. Full article
(This article belongs to the Special Issue Recent Advances in Bioprocess Engineering and Fermentation Technology)
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Review

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38 pages, 25214 KB  
Review
Advances and Challenges in Anaerobic Digestion for Biogas Production: Policy, Technological, and Microbial Perspectives
by Juan Carlos DelaVega-Quintero, Jimmy Nuñez-Pérez, Marco Lara-Fiallos, Pedro Barba, Jhomaira L. Burbano-García and Rosario Espín-Valladares
Processes 2025, 13(11), 3648; https://doi.org/10.3390/pr13113648 - 11 Nov 2025
Cited by 10 | Viewed by 7231
Abstract
This review comprehensively examines the advancements and challenges in anaerobic digestion (AD) for biogas production, emphasising technological, microbial, and policy perspectives. It highlights the AD significant potential for valorising diverse organic substrates, including manure, food waste, and microalgae, thereby contributing to renewable energy [...] Read more.
This review comprehensively examines the advancements and challenges in anaerobic digestion (AD) for biogas production, emphasising technological, microbial, and policy perspectives. It highlights the AD significant potential for valorising diverse organic substrates, including manure, food waste, and microalgae, thereby contributing to renewable energy generation and greenhouse gas mitigation. Key operational factors influencing biogas yield include substrate composition, temperature (preferably mesophilic conditions), pH (6.5–7.5), and the substrate-to-inoculum ratio (SIR), all of which significantly affect microbial activity and process stability. Co-digestion strategies and pretreatments are examined for their roles in enhancing biodegradability and methane yield, respectively. Microbial community dynamics, particularly responses to feedstock heterogeneity and operational parameters, are integral to process optimisation. Advances in metagenomics have provided insights into microbial resilience and adaptation to conditions such as high ammonium levels. This review also discusses various modelling approaches, including kinetic models and machine learning techniques, for predicting and optimising biogas production. Additionally, policy frameworks within regions such as the European Union and Brazil, along with economic incentives and regulatory hurdles, are also considered crucial for scaling up deployment. Challenges such as digestate management and high capital costs persist, underscoring the need for integrated strategies to enhance the sustainability and viability of AD-based biogas projects. Full article
(This article belongs to the Special Issue Recent Advances in Bioprocess Engineering and Fermentation Technology)
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